In June 2026, I have migrated my previous (horrendous) Wordpress-fueled blog (as I said, horrendous) into a more manageable one (this one). However, I had quite a lot of these reading list entries on the previous blog, and they are sometimes useful as a delocalized memory for my aging brain (read: “damn I know I’ve read about this one day! Let me check the reading list!”).
That being said, it’s a bit tedious to migrate every blog entry. I’ve done it (semi)manually for those before 2024 but I couldn’t really bring myself to do it for the entire 2024 year (when I started doing this). I will just do one big post with all of them here (extracted with a very ad-hoc parsing script I’ve done), hoping that there aren’t many errors and it will still be useful to some, let alone me.
Noteworthy things — Week 35 (26/08/2024)
Cell Host & Microbe, 27 August 2024
Comment: Authors looked at >2.5k stool samples from 236 preterm infants in 3 NICUs to characterize gut microbiome development. Key findings included the identifica- tion of shared strains of Clostridioides difficile and Staphylococcus epidermidis (!) among infants, the fact that both AB and non-AB medications impact the infant gut mi- crobiota composition and that there waas a persistant fraction of the low-diversity microbiome that could be associated with necrotizing enterocolitis after 40d of life.
Pediatric Cardiology, 22 August 2024
Comment: This 16S rRNA work from Ireland shows that infants with congenital CHD (GuMiBear study, with INFANTMET cohort as healthy controls) have an altered gut mi- crobiome when compared with healthy controls and there might be a possible link between an abundance of virulent species and necrotising enterocolitis.
mSystems, 27 August 2024
Comment: Parasitic infection, although low in developped countries with increased hygiene, has been an infectious burden for the entirety of humanity and still is in various parts of the world. It is quite fascinating to try and understand how the gut microbiome adapted to this pressure. Using a zebrafish model here and a joint gut 16S + untar- geted metabolomics approach, authors identify a significant association between composition and infection burden by Pseudocapillaria tomentosa, as well as a role for sal- icylaldehyde, a metabolite inversely related to worm burden and potentially produced by Pelomonas, completely inhibited P. tomentosa egg larvation in vitro and, which showed anthelmintic activity in vivo.
mBio, 28 August 2024
Comment: In cases of chronic constipation, bacteria are observed to overgrow in parts of the GI tract abnormally, something sometimes called “SIBO” for “small intestine bacterial overgrowth” and which is quantifiable with breath tests. In this work, 218 patients with chronic constipation are categorized as SIBO/non-SIBO to investigate the impact of FMT on symptoms and the gut microbiota (16S-based). Post-FMT, patients with SIBO experienced better outcomes, including increased bowel movement fre- quency and enhanced quality of life. The small intestinal microbiota showed more significant shifts than the colonic microbiota after treatment, with baseline differences in microbial composition, such as varying abundances of Veillonella, Escherichia-Shigella, and Acinetobacter, potentially impacting the effectiveness of FMT.
medRxiv, 8 August 2024
Comment: In this preprint, authors show a significant correlation between the composition of the gut microbiota and the volatile organic compounds (VOCs) in breath, both using a clever gnotobiotic mouse model with a tracheostomy step bypassing the potential effects of the oral microbiota, and a small sample of 27 healthy children. Gut mi- crobes accounted for 40% of the variance in breath VOCs in humans.
Plos Pathogens, 12 August 2024
Comment: Here, authors look at the diet-immunity-infection dynamics using the Drosophila model. They show that adult flies fed a high-sugar diet exhibit increased sus- ceptibility to Gram-negative bacterial infections, specifically Providencia rettgeri and Serratia marcescens. High sugar intake led to hyperglycemia and elevated pathogen burden, with S. marcescens capitalizing on the host’s increased glucose levels functionally. Also, high-sugar diet impaired the immune response by reducing the production of antimicrobial peptides at the translational level, despite normal gene expression.
Applied and Environmental Microbiology, 31 July 2024
Comment: Interesting US survey from a couple of months ago, describing ETEC isolated from livestock over a 53-year period (since the 1970s). More precisely, authors look at the evolution of AMR gene acquisition over time, and identify key genetic and virulence elements differentiating pig from cattle ETEC.
Microbiology, 27 August 2024
Comment: It is sometimes a bit unclear how various food components act on microbial physiology, and a lot of studies are often underpowered or unclear. In this interest- ing small-scale attempt, authors use a fluorescence-based flow cytometry-based approach to suggest that extracts from black pepper, ginger, and kamala, as well as the compounds 6-gingerol, capsaicin, and rottlerin, can reduce plasmid conjugation frequency in Escherichia coli and Klebsiella pneumoniae. Rottlerin, in particular, seemed to be effective in both bacterial species. It is unclear how this fits into the broad aspect of things, but a good reminder that the complexity of foods does interact with the complexity of microbes!
Molecular Systems Biology, 22 August 2024
Comment: Harnessing evolution to control wine production and taste? This work shows the outcome of experimental evolution of 10,000 wine yeast strains, selecting for variants that can tolerate higher alcohol levels, produce various aromatic compounds while maintaining their growth rate.
Noteworthy things — Week 34 (19/08/2024)
bioRxiv, 8 August 2024
Comment: In this preprint, authors used untargeted metabolomics on 49 fetal and maternal tissue samples to highlight bacterial metabolites in the fetal intestine. They SCFA and secondary bile acids that are likely vertically transmitted from the maternal microbiota and may be biologically active in the fetal gut. They also show using scRNAseq that bile acid and SCFA transport/signaling genes are expressed in fetal intestinal cells, which altogether would suggest a potential biological function for these metabolites in utero. Nice work, it would be nice to see which of the maternal taxa could contribute to this!
Gut Microbes, 8 August 2024
Comment: Interesting review highlighting that despite the robust established links between EBV and MS, examining the impact of gut microbiome is also important as it offers an accessible therapeutic target. For instance, microbial metabolites like SCFA and tryptophan derivatives can exert anti-inflammatory effects and support gut bar- rier integrity, which are essential in managing MS beyond the existing focus on viral triggers, and potentially altering disease progression.
Microbiome, 19 August 2024
Comment: An extremely clear and well-presented study, with excellent figures and execution, focusing on the individual variations in the vaginal microbiome and examin- ing the impact of menstruation and sexual intercourse on microbial dynamics. The results are very interestingly quite heterogenous, with women showing an extremely stable community and others displaying a lot of variation.
mSystems, 21 August 2024
Comment: The gut microbiota varies according to many factors, but one strong ecological one is predation by bacteriophages, which present in the ecosystem or excised from the very bacteria inhabiting it upon various stimuli. Phages have broad or narrow host range, which makes them good factors influencing variation in gut microbial populations. And when features of the gut microbiota are associated with health outcomes, it becomes interesting to study how phages could contribute to this or even just vary themselves. In this study, authors look at the gut phageomes of 340 Mexican-Americans and associate their variation (and an enrichment in Inoviridae) with dia- betes and liver steatosis. Diabetes correlated with an abundance of E. coli phages and liver steatosis with a depletion of Lactococcus phages and increase in Crassvirales phages associated with Prevotella copri. Phage-bacterial interactions could contribute to these conditions.
Plos Biology, 15 August 2024
Comment: Interesting experimental evolution study in which authors compare 10 replicate populations of C. difficile under increasing vancomycin selection, and observe that fast high-level resistance appears within ~250 generations. They identify 2 distinct genetic pathways affected: mutations in a new target: two-component system reg- ulating a D,D-carboxypeptidase (dacJRS), and alterations in the vanG cluster, with mutations in dacS and vanT frequently observed across the evolved populations. Interestingly, mutated strains had reduced fitness (lower growth) in rich media, sporulation defects and other which raises the question of whether such mutants would outcompete wild types in the gut.
PNAS, 16 August 2024
Comment: Studying pathogen populations brings a lot of knowledge on how different virulent lineages emerge, but it is equally interesting to look at within-patient evolu- tion to understand mechanisms of pathogenicity. This study focused on resistant and hypervirulent K. pneumoniae from a single patient with UTI in a Chinese hospital, and identified a phenotypic switch from hypermucoviscosity to hypomucoviscosity linked to mutations in rmpADC and wcaJ genes, mediated by IS insertions/deletions, and which significantly altered the bacteria’s virulence and persistence in the urinary tract.
The Lancet Microbe, 20 August 2024
Comment: In a prospective cohort study of 256 patients in an Italian hospital during the first wave of COVID-19, a multi-pathogen sequencing survey was done to analyze 2418 clinical samples cultured on selective media. This 7 key pathogen species with extensive genetic diversity and high antimicrobial resistance gene prevalence in the patients. Authors inferred accurate hospital transmission events and detect co-colonisation of highly similar bacterial strains in different patients, which is a good example of pathogen surveillance and infection control in healthcare settings using genomics.
Journal of Bacteriology, 19 August 2024
Comment: This very short opinion piece is actually an editor’s pick for published papers but it raises a very original and interesting idea in microbiology, arguing that the current model organisms used for many discoveries, applications, therapeutics, bioengineering, etc, (main target there is E. coli and the coli-centric view of biology) should be replaced by bacterial and archaeal organisms that are actually most abundant in nature and successful colonizers of our planet, namely members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others. An interesting suggestion, especially as these organisms are currently very understudied compared to current model organisms.
Noteworthy things — Week 33 (12/08/2024)
Cell, 8 August 2024
Comment: Quite an impressive functional gut-brain axis study in mice showing that mucin-secreting glands in the small intestine have GLP-1 receptors that can connect to the brain via the vagal nerve, and influence Lactobacillus levels in the gut as well as host immunity.
Cell Host & Microbe, 5 August 2024
Comment: The links between infection, gut microbiota and CRC are extensively studied and some trends are starting to slowly emerge. In this human clinical and animal model study, authors followed patients with a progression of symptoms from healthy to colorectal adenoma (CA) to colorectal cancer (CRC), and observed that Clostridium symbiosum levels increased significantly. Following this with animal (mice) model experiments, they highlight the role of microbial branched-chain amino acids (BCAAs) in activating signaling leading to tumorigenesis, in a process that is linked to cholesterol metabolism and can be influenced by statin intake.
Nature Communications, 13 August 2024
Comment: Quite an extensive study (with great figures) characterizing plasmids in the infant gut (using their Rep groups), predicted hosts and host ranges. Interesting find- ings suggesting that plasmid dynamics reflects environmental changes faster/better than their hosts. The phylum Bacteroidota seems to act as a major hub for plasmid transfer and reservoir in the gut.
Trends in Microbiology, 1 August 2024
Comment: Interesting short review on the importance of considering how external factors might influence metabolic gene regulation in gut microbiota members, with im- portant functional impact going beyond the mere presence/absence of the taxa (currently an all-too-common shortcut taken by many observational microbiome studies, including some of ours…!)
Gut Microbes, 2 August 2024
Comment: This work involving our collaborators Katariina and Leo, looks at the dynamics of ARGs in the gut microbiota of infants during their first 2 years of life, with an in- teresting focus on early life exposures and familial transmission. They use the HELMi cohort (Finland, n=475 infants with 305 maternal and 123 paternal samples) and high- light the role of Bacteroides and Bifidobacterium genera as potential reservoirs of ARGs in the infant gut. They show within-family transmissions of ARGs but mostly be- tween the infant-mother, as the paternal effect appears negligeable.
PNAS, 5 August 2024
Comment: A very interesting real-life successful example of phage therapy! Livestock is sensitive to MAP, causing Johne’s disease in cattle, an often fatal gastric illness. In this study, authors gave dairy calves a cocktail of mycobacteriophages aiming to line up their GI tract and measured a significantly high reduction in faecal shedding and tis- sue infection in controlled pathogen infection experiments. Good discussion included on MAP transmission, and the possibility to influence animal immunity with phages.
npj Biofilms and Microbiomes, 14 August 2024
Comment: Short study involving our FR02 collaborators led by a Swedish group showing a potential link between gut microbiota members and incident (future) bone frac- tures. Seems intriguing at first but the microbiota has been linked to bone mineral density in several other studies before this one. Using our favourite FINRISK cohort, au- thors attempt to predict the influence of specific taxonomic groups for fracture risk, whether positive or negative, and Gammaproteobacteria are highlighted.
Gut Microbes, 12 August 2024
Comment: In this work, prophages were analysed in the HpGP genomes (n=1,011), showing that most of them seem to be co-evolving and diversifying within their specific Hp lineages, while a few others show signatures of recombination, specifically between the Hp SWEurope and NEurope lineages.
Nature Communications, 7 August 2024
Comment: Using proteomics and Tn-Seq (150k genome-wide insertions), authors show that limiting arginine inhibits protein synthesis, thereby increasing tolerance to an- tibiotics in Staphylococcus aureus biofilms; and this effect is counteracted by citrulline supplementation, which restores arginine levels via ArgGH enzymes. Using homog- enized biofilms in mice, they confirm that arginine availability directly influences antibiotic efficacy in vivo.
The Lancet Infectious Diseases, 13 August 2024
Comment: Impressively large dataset from USA veterans (~1M records, ~0.5M individuals followed over 15 years) highlighting interesting observations: 15y reduction of fluoroquinolone (FQ) use correlates with decline in FQ resistance; targeted efforts seem to have specifically reduced MRSA and VR-E. faecium infections over 15y. Important comments too about the effect of COVID-19 on these results too.
Nature Reviews Immunology, 9 August 2024
Comment: Why are we observing so much inter-individual variation in illness severity? Why is this also the case for infectious diseases (ID) from the same aethiological agent having the same infectious dose? In this extensive review, authors describe the various ways that the varying presence of antibodies in people could affect infec- tious disease severity, potentially explaining why it is heterogenous in populations. Fascinating stuff and really at the heart of precision ID medicine.
Nature, 7 August 2024
Comment: In this work, authors used the UK 100,000 Genomes Project to analyze 2,023 CRC samples to identify >250 putative driver genes in CRC, including many novel ones, and suggest 4 new common subgroups of CRC with distinct genomic features. More interesting for the microbiologists that we are, a mutational signature called SBS88 (i.e. a reproducible pattern of somatic mutations) was associated with colibactin-producing E. coli, and was found to be more prevalent in distal CRCs which sug- gests that E. coli might contribute to CRC in specific locations of the bowel.
Nature Communications, 31 July 2024
Comment: Perhaps as expected after a few large studies of this kind, this work from the UK supports the cardiovascular safety of COVID-19 vaccines, with the benefits of reducing common cardiovascular events outweighing the risks of rare complications. Authors see similar associations irrespectively of demographic and clinical sub- groups in the population cohort, adjusting for a wide range of factors and disease histories.
Noteworthy things — Week 31 (29/07/2024)
bioRxiv, 26 July 2024
Comment: In this interesting preprint, authors present a model that predicts infant age from gut microbiota features relatively accurately, and suggest a global pattern of microbial succession with key taxa changes worldwide. These include a decrease in Bifidobacterium and an increase in F. prausnitzii and Lachnospiraceae within 12 months. Potentially another interesting way to look at “progression” from cross-sectional samples!
Nature Aging, 25 July 2024
Comment: In this very nice study from China, authors use a cohort from the Rugao Longitudinal Ageing Study (RLAS) with 1,821 participants aged 62–96 to link gut metagenomic and plasma metabolomic (NMR) features with assessments of frailty in elderly individuals. They identify 18 gut microbial species and 17 circulating metabo- lites with altered abundances correlating with frailty severity, consistently associating F. prausnitzii. Sex-specific differences were also observed, with more dramatic mi- crobial shifts linked to frailty than males. Finally, authors build a microbial composite score from frailty indices to predict 2-year mortality, outperforming traditional frailty assessments and suggesting future incorporation in geriatric care.
Gut Microbes, 29 July 2024
Comment: The distribution of species from human faecal microbiota is often quite skewed, with a few very abundant species and lots of low-abundance species. But is this translating to function and importance? Does this reflect a technical bias (faecal vs. “gut”)? In this rather interesting study, authors induce colitis in a mouse model, observe the associated dysbiosis but aim to aid recovery using a consortium of low-abundance SCFA producers (Coprococcus comes, Butyricimonas paravirosa, Megasphaera in- dica and Agathobaculum butyriciproducens), with success. Many thoughts come to mind, from functional redundancy to spatial distribution of species in the gut. In any case, an original study.
Nature Reviews Microbiology, 22 July 2024
Comment: A lot of focus is placed on the links between the gut microbiota and clinical traits, and it has been now obvious that the oral microbiota and oral health can be linked a myriad of proximal effects on health and disease too. In this clear review, authors present the recent advances in the field of the oral-gut axis.
Microbial Genomics, 12 July 2024
Comment: Interesting observation from the longitudinal Queensland Family Cohort Study in Australia. Authors looked at stool metagenomes from 25 mother-infants pairs and observe more microbiota differences according to delivery mode at 6 weeks post-partum (lower Bacteroidetes, altered beta-diversity) than with antibiotic exposure around birth. It would be nice to see a larger sample size being examined, but in any case, good to see work on an Australian microbiome cohort.
Gut, 26 June 2024
Comment: The mechanisms of food addiction, defined as patterns of compulsive eating behaviors, are largely unclear besides the complex psychological and behavioural links. In this interesting study, authors suggest that the gut microbiota plays a crucial role in these mechanisms both in mice and humans, with specific bacterial markers identified (only 16S profiles unfortunately): protective effect from Blautia (the study includes functional validation in mice using B. wexlerae) and Actinobacteria, while members of the Proteobacteria phyla seem to be having detrimental effects. This paper is one of the first robust suggestion that dietary interventions, especially with non- digestible carbohydrates, could prevent food addiction.
Nature Reviews Microbiology, 15 July 2024
Comment: A very broad and ambitious review (and therefore a pretty good read), attempting to shed some clarity and light on the links between various diets (Mediterranean, high-fibre, plant-based, etc) on the gut microbiota, with subsequent effects and links to health. Interesting summaries of the effects of fibre, polyunsatu- rated fatty acids, SCFAs, etc. Very exhaustive and actually quite an authoritative review to recommend for anyone interested in the human microbiome.
Circulation Research, 17 July 2024
Comment: This work from the Marques Lab and collaborators shows that maternal high-fibre intake during pregnancy in a mouse model can improve offspring’s cardiac health through gut microbiota modulation. Make sure to check the thread from Francine Marques on Twitter.
Microbiome, 27 July 2024
Comment: This study (from researchers in Perth) uses mice models to show that very early diet, especially colostrum, has an important impact on shaping the offspring gut microbiota, and promoting healthy growth. Under their experimental conditions, newborn mice fed with mature milk instead of colostrum showed growth retardation, metabolic disturbances and symptoms similar to undernutrition. Authors discuss the practice of feeding preterm infants with mature donor milk instead of the mother’s own colostrum and suggest more studies and re-evaluations.
Nature Microbiology, 15 July 2024
Comment: Here, authors suggest that microbial functions, unsurprisingly, are much better predictors of microbially-influenced disease than just the detection of microbial abundances. This is somehow expected given strain-specific pangenomic diversity and the spread of various functions within and across bacterial species in the gut. Authors use mice models of multiple sclerosis in very comprehensive experiments to identify the IgA coating index of specific gut bacteria before disease onset as an im- portant risk factor for MS, highlighting the role of pre-onset microbiota (and what they call “reporter species”) on disease development, which raises the need for better longitudinal sampling and experimental design to capture these early events. Much more is included in the study!
Applied and Environmental Microbiology, 15 July 2024
Comment: The last decades have probably brought us that “fiber” is beneficial for health and the gut microbiota. But what kind of fiber are we talking about? Recently a few studies are characterizing this further, and this one is one of them. High-throughput glycomics of 55(!) dietary fibers sources with varying monosaccharide composi- tions were fermented by a real-life (feline) faecal inoculum in an in vitro bioreactor to measure various different factors and outcomes. The main finding is that yes, different monosaccharide compositions in fiber sources do influence the microbiome structure differently.
Nature Microbiology, 19 July 2024
Comment: This is a good one for the mechanistic study of bacterial epistasis! In this work, authors cleverly introduce a new method simultaneously combining CRISPR in- terference with transposon insertion sequencing (“CRISPRi-TnSeq”) which basically allows to study interactions between essential and non-essential genes by affecting them both in a controlled way. Authors pick a few previously identified essential genes, create corresponding CRISPRi strains in which essential gene expression is re- pressed without completely eliminating the gene product (and preserving essentiality). Then in these strains with “knocked-down” essential genes, they use genome-wide TnSeq to identify and knock down interacting non-essential genes. Using this approach to make 13 CRISPRi strains of Streptococcus pneumoniae, authors then identify 1,334 genetic interactions (754 positive, 580 negative).
mSphere, 16 July 2024
Comment: In this work, authors focus on the role of pets as reservoirs for potentially zoonotic pathogen transmission. Sampling 571 diseased and healthy cats and dogs across 4 provinces of China, followed by metatranscriptomics (to capture RNA viruses) analyses, they detect 27 potentially zoonotic pathogens, mostly bacterial, with dis- eased pets observed to have a higher load than healthy ones.
Nature Communications, 26 July 2024
Comment: In 2022-2023, Malawi experienced its deadliest cholera outbreak to date, with >59,000 cases and 1,771 deaths (CFR of 3%, higher than neighbouring coun- tries). In this pathogen genomic surveillance/epidemiology study, authors show that the outbreak was primarily caused by the 7th pandemic El Tor (7PET) lineage O1 Ogawa serotype of Vibrio cholerae, suggesting an importation from Asia. Authors also mention that outbreak severity was also probably made worse with topical cyclones at that time.
medRxiv, 19 July 2024
Comment: This is pretty cool! In this preprint, authors describe a long-term follow-up of the MI-GENES trial to show that telling people (n=103/203) their genetic risk for heart disease, along with their usual risk factors (also what the control group was told), helps lower their chances of having serious heart problems over a 10 years period. Enhanced risk perception, earlier and longer statin therapy, better reduction of LDL cholesterol and other modifiable risk factors could explain this difference.
medRxiv, 31 July 2024
Comment: Human genetics has a problem when it comes to human leukocyte antigen (HLA): the region has extensive linkage desequilibrium, high gene density (100s of genes, not just a “locus”) and very high polymorphism and so many studies just exclude it from their statistical models. In this extensive statistical genetics preprint, authors use a new method to investigate pleiotropy in the HLA region linked to 1000s of diseases. They find 7,649 HLA associations across 647 traits. Quite interestingly, some haplotypes seem to mitigate disease in a trade-off manner, while some are consistently associated with increased risk. Make sure to check out the first author’s thread on Twitter too.
Noteworthy things — Week 30 (22/07/2024)
Gut Microbes, 21 July 2024
Comment: Using the Estonian Microbiome (EstMB) cohort, this study shows that repeated antibiotic use leads to long-term alterations in gut microbiota composition, which in turns can resulting in impaired colonic mucus barrier function in mice following FMT from affected humans to mice. Elegant and very clever way to study function- ality in microbiome studies!
Microbiome, 18 July 2024
Comment: IBD is notoriously progressive and complicated to study, and finding microbial markers is not always straightforward. In this study, authors looked at the gut vi- rome of 71 Chinese IBD patients (15 with Crohn’s disease and 56 with ulcerative colitis) and 77 healthy individuals, and interestingly not only looked for phages but also eu- karyotic viruses. They identified 139 viral signatures with significant abundance changes in IBD, including an increase in Retroviridae and Genomoviridae in IBD patients, as well as alterations in the abundance of various bacteriophage families like Siphoviridae, Myoviridae, and Microviridae.
Nature Communications, 23 July 2024
Comment: Human cytomegalovirus (CMV) is highly prevalent herpesvirus that is known to transmit to neonates via breast milk, with known negative effects on immuno- compromised and preterm infants. However, the effect on health infants is still unclear. Here, authors analyse the MILK cohort (n=276 mother-infant pairs) to report that CMV presence in breast milk can affect milk composition and metabolic profile but also the infant gut microbiome (reduction in Bifidobacterium!), and full-term infant growth patterns in possible negative ways too.
bioRxiv, 24 July 2024
Comment: What a beast of a study, from colleagues over at Graz in Austria! In this preprint, authors conducted a longitudinal study on both the oral and gastrointestinal tract of 30 healthy infants during their 1st year of life, with a particularly great focus on understudied taxonomic groups such as archaea and anaerobic organisms. Important results highlight the influence of breastfeeding on microbiome transitions in infants, particularly the oral microbiome. Interestingly, the archaeome in infants seems to be transient and not stable in the first year of life. Very interesting investigations on the oral/gut transfer too. Really great work, and go check Christine Moissl- Eichinger’s thread on Twitter about it.
Scientific Reports, 22 July 2024
Comment: These short methodological benchmarking studies are sometimes useful to the field! In this one, authors compare various ways to collect human stool samples for microbiota analyses and recommend the use of PSP buffer and/or RNALater, followed by immediate freezing at -80C to retain an optimal microbial diversity in the sam- ple, according to their parameters.
bioRxiv, 25 July 2024
Comment: What is “health”? How do we assess it? The question is more complicated than it seems. In this preprint, authors identify significant intra-individual variability in gut “health” markers in 10 “healthy” adults. These markers are quite exhaustively defined and include stool consistency, water content, pH, total short-chain fatty acids (SCFAs), total branched-chain fatty acids (BCFAs), total bacteria and fungi copies, calprotectin, myeloperoxidase, and untargeted metabolites, as well as microbiota compo- sition and diversity. Interestingly, authors propose that “mill-homogenisation” (the grinding of frozen faecal samples into a fine powder) can enhance sample homogeneity and the reliable measurement of these gut health markers. (b) Microbial and pathogen genetics, ecology, evolution and AMR
Nature, 24 July 2024
Comment: Very likely to be impactful for the treatment of patients with sepsis. Authors present here a novel ultra-rapid antimicrobial susceptibility testing method (called “uRAST”), developed to bypass traditional blood culture and significantly reducing the time for reporting drug susceptibility profiles and potentially improving patient out- comes in sepsis treatment. Results can be obtained in less than 8h for some cases, bypassing entirely the existing lengthy culturing step.
Microbial Genomics, 19 July 2024
Comment: Campylobacter jejuni ST353 is a major zoonotic lineage infecting humans from chicken, worldwide. In this interesting paper, authors analyse the genomes of 221 C. jejuni from Brazil and find ST353 to be the most prevalent. Using Bayesian dating methods, they managed to propose an evolutionary history of C. jejuni ST353 in Brazil, estimating its origins to the late 1500s, which coincides with Portuguese colonization (and presumably the transfer of novel chicken-associated bacteria). A fun read, which reminded me of our similar Campylobacter ST-61 cattle study!
mBio, 7 May 2024
Comment: In this study from a couple of months ago, authors managed to cultivate an endosymbiont in vitro without its host. No biggie! They focused their efforts on Candidatus Fukatsuia symbiotica, an essential bacterial endosymbiont of the pea aphid, managed to reinfect the host subsequently, observed transgenerational transmis- sion of the reinfected endosymbiont. The trick was apparently very careful synthetic media preparation, homogenization of the host cells onto the culture medium followed by 2 weeks of incubation. This is a nice step forward for endosymbiont research, although it remains to be seen whether this approach would work for all other endosym- bionts. There is a nice commentary in mBio on it too.
bioRxiv, 19 July 2024
Comment: When I was in PhD working on E. coli, weird cryptic Escherichia clade had just come out and they were being undersampled, underdescribed, completely misun- derstood. Now, people know far more about them! In this preprint, authors describe genomic features specific to environmental Escherichia cryptic clade IV strains (44 di- verse genomes including the first South American isolate), with a notable absence of AMR genes and a distinct set of virulence factors, supporting the environmental hy- pothesis of niche adaptation.
Microbiome, 23 July 2024
Comment: In the context of zoonotic foodborne pathogens, a lot of the chicken side of things is often studied and inferred from agricultural chicken, often from intensive agriculture. It is always refreshing to see alternative models. Here, authors compare the microbiota from 243 indigenous Ethiopian chickens and show a significant impact of altitude-dependent agro-ecologies (i.e. variations in agricultural practices that are influenced by changes in altitude) on the diversity of their gut microbiota. They further identify 3 distinct enterotypes and assemble ~10,000 novel MAGs. An additional interesting point for me was the presence in these MAGs of 3 known species of Campylobacter and 2 new ones! Also strikingly very little E. coli, which happens to be quite a problem in industrial chicken.
bioRxiv, 25 July 2024
Comment: Multiple strains from the same species can co-exist in particular environments, but why is that the case? In this exhaustive genome-scale metabolic modelling study, Ben Vezina and Kelly Wyres across the road from our lab observe evidence of lineage-specific metabolism in >7,800 genomes from Klebsiella pneumoniae species complex, which supports the co-existence of diverse lineages in the same environment, through metabolic differentiation/complementation and possible commensal in- teractions.
Charles Coluzzi & Eduardo Rocha bioRxiv, 24 July 2024
Comment: Understanding the evolutionary dynamics of plasmids is essential for understanding antimicrobial resistance spread. In this preprint, authors analyse 37,061 plasmid sequences and show that the acquisition of antibiotic resistance genes by bacteria is largely due to the horizontal transfer of some specific plasmids only. They in- troduce a novel approach using Plasmid Taxonomic Units (PTUs) to classify plasmids, revealing that those encoding AMR are inherently more plastic and evolvable, with these traits persisting even when resistance genes are excluded from the analysis. Nice thread from Eduardo Rocha on Twitter. (c) Other general interest
Cell Reports, 24 July 2024
Comment: Intriguing study (for profanes like me I suppose). In this work, authors analysed data from a cohort of 217 Ghanaian individuals, including 62 asymptomatic and 155 symptomatic COVID-19 patients, to evaluate the impact of malaria exposure on the cellular immune response to SARS-CoV-2, and found that asymptomatic individu- als showed reduced T cell activation, higher P. falciparum antibody levels, and a more polyfunctional T cell response, which seems to suggest a potential protective role of malaria exposure against severe COVID-19 in Africa!
Editorial comment The Lancet Microbe, 18 July 2024
Comment: This was a brilliant read, not often seen in editorial comments of a prestigious journal. Excerpt: “The sheer hubris needed to underpin alternative hypotheses was an early signal of their tenuousness, when we are intensely aware that the natural processes needed to bring about this sort of pandemic are constantly churning and testing the boundaries between animal and human populations. The most remarkable thing about the whole COVID-19 origin saga is the confected controversy over some- thing that should not be controversial at all. The thing that should be controversial is how little of the energy expended over this discussion has been directed towards ac- tual beneficial outcomes.”
Discover Food, 12 July 2024
Comment: In this almost parodic article, authors use very serious phylogenetic and biogeographic methods to classify filled pasta and related foods in Europe. Excerpt from the abstract: “Based on the proposed evolutionary hypothesis, the Italian pasta are divided into two main clades: a ravioli clade mainly characterized by a more or less flat shape, and a tortellini clade mainly characterized by a three-dimensional shape. The implications of these findings are further discussed.”
Noteworthy things — Week 29 (15/07/2024)
Cell Reports Medicine, 16 July 2024
Comment: This new study addresses a very important topic in microbiome science: the influence of (self-reported) bowel movement frequency (BMF) on the microbiota structure and links with disease. Authors leverage a large human cohort of ~2,000 individuals with good phenotyping, with matching 16S rRNA microbial data. They find that abnormal BMF can associate with microbial toxins in blood and with inflammation, as well as kidney function. Additionally and interestingly, diet, lifestyle but also cog- nitive factors seem to be associated with BMF variation. See this nice thread by senior author Sean Gibbons on Twitter about it!
Circulation Research, 17 July 2024
Comment: This study from our great collaborators at the Marques Lab and others at the Baker Institute, used scRNA-seq on cardiac tissue of mice offspring (n=8 per group) to show a reduced inflammation and fibrosis linked to maternal high-fiber intake. This link is possibly through increased SCFA and beneficial shifts in gut microbiota composition, with predicted lasting effects into adulthood.
bioRxiv, 9 July 2024
Comment: Despite having seen it a few times now, I am always amazed when large-scale human metagenomic assembly projects identify novel bacterial species. In this preprint, authors assemble a population-specific reference of ~85k MAGs from ~1,900 individuals in the Estonian Microbiome (EstMB) cohort, to identify 353 potentially novel bacterial species and linking 44 bacterial species to 15 prevalent diseases, including associations with new species not previously identified. As more and more popu- lations will be examined in the future, it will be fascinating to see how much novel (and population-specific!) diversity is linked to global human health. Also see the thread from lead author on Twitter!
bioRxiv, 15 July 2024
Comment: Original and probably quite impactful for any wet-lab microbiologist! In this preprint, authors look at soil samples to demonstrate that storage at -80°C, even af- ter a complete thaw, preserves microbial diversity better than storage of extracted DNA at -20°C for extended periods (unsurprising perhaps). They also show that fungal richness and the overall composition of bacterial and fungal communities in soil samples are highly resilient to both short-term thawing events and long-term frozen stor- age.
bioRxiv, 15 July 2024
Comment: A billion-dollar question (no, really) in microbiome science is to understand well how colonizing bacteria (probiotics, opportunistic pathogens, etc) establish, in- teract, integrate or not complex microbial communities and microbiomes. In this preprint, authors compare how E. coli or Bacteroides ovatus differ in their colonization strategies on a synthetic microbial community (complemented by co-culture growth experiments). Bacteroides tends to replace existing bacteria while E. coli tends to inte- grate into the microbiome. It is a simplified model, but still interesting to contextualise in a broader context.
Nature Microbiology, 15 July 2024
Comment: Some very interesting approaches in this mice/microbiome study! Authors first used both gnotobiotic mice with defined synthetic microbiota and SPF mice with complex microbiotas, to look at the role of specific microbial strains and their interactions within the gut on the experimental autoimmune encephalomyelitis (EAE) model (most widely used animal model for human MS and mimics key pathological and clinical features). They find that the impact of a single commensal like A. muciniphila (previously associated with the disease) on disease development is significantly influenced by the broader microbial community and cannot be assessed in isolation. More interestingly, they also see that IgA coating index of gut bacteria, particularly Bacteroides ovatus, is a potent predictor of individual disease severity, as opposed to the presence of the bacteria alone, which shows the power of looking at co-abundance networks and at function when associating microbial features to diseases.
Nature Reviews Immunology, 15 July 2024
Comment: Quite authoritative review updating the knowledge on the intricate interactions between bile acids, the gut microbiota, and host immunity. It includes examples on the continued identification of microbially conjugated bile acids (MCBAs) and their modulatory immune effects. An interesting highlight for me was also that MCBAs can have a stronger effect after binding receptors like FXR and TGR5 than primary bile acids (produced by the host), highlighting their key importance. Some interesting links with IBD are also presented.
bioRxiv, 17 July 2024
Comment: For anyone doing MAGs out there and who has used CompareM before, here’s the new version of it, with some useful benchmarks from authors. This version in- tegrates several analyses such as QC, annotation, function and species calling as well as comparative analyses like computation of core/pan genomes and phylogenetics. Link to the CompareM2 Github.
bioRxiv, 11 July 2024
Comment: On the importance of the gut microbiome in aging and in population-dependent effects in microbiome research! In this nice preprint, authors analyse metage- nomic data from 234 healthy community-living octogenarians from Singapore (enrolled in the SG90 cohort) to identify gut microbial hallmarks of healthy aging. They iden- tify reduced species richness and a metabolic potential expansion towards alternative butyrate synthesis pathways, with key species like Alistipes shahii and Bacteroides xylanisolvens becoming more abundant. Interestingly, they find novel associations involving Parabacteroides goldsteinii (a potential probiotic) and Klebsiella pneumoniae (a pathobiont). By comparing results to other Asian cohorts (SPMM, CPE, T2D), they interestingly find some that are only consistently seen in Asian and not European cohorts. (b) Microbial and pathogen genetics, ecology, evolution and AMR
Nature Communications, 12 July 2024
Comment: Plasmids constitute an interesting ecological cost/benefit balance for their microbial hosts and there’s been considerable research trying to understand this be- yond modeling and theoretical arguments. Here, authors use a novel scRNA-seq approach in Pseudomonas putida to show that plasmid-encoded genes are differentially expressed among bacterial cells, with key plasmid functions correlating with host cell activity. They uncover a distinct bacterial subpopulation that particularly does not transcribe conjugation-related genes, implying a potential bet-hedging strategy for plasmid persistence within bacterial communities.
PNAS, 11 July 2024
Comment: Intriguing and original study looking at the genetic basis of microbial pigmentation and the reflective colouring of colonies observed on synthetic media! Similar to green bird feathers, authors show the presence of “structural colour” in microbial colonies that are vividly iridescent and compare their genomes to other types of coloured colonies using a bacterial GWAS approach, to uncover a set of genes linked to biosynthesis of pigments (uroporphyrin and pterins, also found in butterfly wings) but also carbohydrate metabolism. They go on to build a classifier to predict structural colouring directly from sequences. I am not sure I know what practical translatable finding will be derived from this yet, but this is clearly very cool!
bioRxiv, 2 July 2024
Comment: This ecology paper is an enormous effort (>100 authors on the preprint) attempting to link wild animal density to interaction networks, using data from all around the world from 55k individual animals across 34 wildlife systems. I did not really understand every single aspect of the work (which is very ecological), but I take some findings from it regarding pathogen transmission, in the context of One Health perhaps: as the number of animals in a given area increases (higher population den- sity), the chances of those animals coming into contact with each other also increases. The study found that as density increases, animals are more likely to share the same space, which could lead to the spread of diseases that are transmitted indirectly, such as through the environment (e.g., contaminated water or soil). However, the increase in social interactions, like touching or grooming, does not increase at the same rate. This means that while animals might be closer together in space, they may not neces- sarily be interacting socially more often, which could affect how diseases that require direct contact spread. Authors suggest that animals might change their behavior at high densities to avoid too much contact, possibly to reduce the risk of disease transmission or to cope with limited resources or space. Interesting to see such big data analyses in the field of ecology and pathogen transmission! (c) Other general interest
Lloyd-Smith PNAS, 16 July 2024
Comment: In this work, authors use historical data (including ship passenger lists and manifests, ship population data, journey times, ship types, points of origin for ships arriving to multiple locations, etc) along with pathogen natural history parameters (incubation time, infectiousness, R0 numbers) to build mathematical models quantifying the historical risks of shipborne pathogen introduction during the 15th-19th centuries. Authors challenges longstanding narratives that suggested a rapid and inevitable spread of pathogens across the globe following European exploration, highlighting the complexity and variability of historical pathogen transfer. Furthermore, they show the importance of ship size and population density in facilitating sustained pathogen circulation on long voyages, with larger and more crowded ships presenting greater risks of pathogen introduction, and suggesting that the advent of steam over sail (unsurprisingly) accelerated the risk of pathogen transfer. It remains a modelling study, but it is an interesting take!
Cell, 11 July 2024
Comment: Ridiculously fun developments in ancient DNA studies with this one. Authors used a novel approach (PaleoHi-C) on a single preserved skin sample of a 52,000- year-old woolly mammoth, successfully reconstructing its 3D genome architecture, including chromosomal territories, loops, and compartments. It revealed a distinct tetradic inactive X chromosome structure in elephantids. Authors suggest that it is the particular dehydration conditions that led to the exceptional preservation of tissue structure in this sample, arresting molecular movement. Those two (one – two) pieces in popular press are also well-written and explain more.
Noteworthy things — Week 28 (08/07/2024)
Turnbaugh Nature Metabolism, 3 July 2024
Comment: The inclusion of strain-level metabolic functions is an increasingly valuable addition to microbiome studies. In this review, authors give a good comprehensive view on the tools available to annotate metabolic genes, curate genome-scale metabolic reconstructions, perform high-throughput microbial phenotyping, identify possi- ble sources of metabolites in samples or even model metabolic functions in microbial communities.
bioRxiv, 6 July 2024
Comment: Emulsifiers that are added in foods (to prevent the separation of oil/water) have been shown to have a detrimental effect on the gut microbiota, driving chronic inflammation. In this preprint focusing on mice models, authors suggest that a maternal diet enriched in these emulsifiers can have profound and long-lasting effects on the microbiota and health of the offspring. Make sure to check the Twitter thread from Benoit Chassaing, the senior author of the study.
Cell Host & Microbe, 10 July 2024
Comment: In this study using a cohort from Hong Kong, authors find that gestational diabetes mellitus can shape the maternal and infant gut microbiome, as well as in- triguingly affect the development and gut-brain axis in the male offspring. They used large-scale longitudinal metagenomic sequencing to analyze the gut microbiome of 264 mother-infant pairs, tracking changes throughout pregnancy and the first year of the infant’s life. Mothers with GDM exhibited altered gut microbiome diversity and composition, with these changes persisting into the third trimester. Infants of GDM mothers, particularly males, showed higher gut microbial richness and diversity, as well as increased head circumference growth, indicating a potential sex-specific impact of GDM on offspring development.
Nature, 10 July 2024
Comment: In this impressive methodology paper, authors describe the ability to manipulate the gut microbiome through CRISPR base editing, delivered through phage particles. The proof-of-principle shows editing of a beta-lactamase gene in E. coli directly in the mouse gut, with an efficiency of 93% (of the target population with a single dose). Authors also edit curli genes from E. coli and Klebsiella. This potentially opens some doors in microbiome engineering, in addition to FMT and probiotics!
Trends in Endocrinology & Metabolism, 10 July 2024
Comment: SCFA production has been associated with a myriad of health outcomes and is currently one of the main avenues for microbiome health and translation. In this recent review, authors explain that diverse gut microbial metabolites are influenced by dietary fiber, impacting host health through mechanisms that are sometimes be- yond SCFA production. Authors describe a multi-faceted research topic, including human and animal studies, to link specific fiber-associated metabolites with immune and neurological effects. Maternal fiber intake for offspring is particularly significant and influential on the microbiota and authors even (re)introduce the concept of ‘celobi- otics’ (defined as a “bioactive compounds that are released after microbial degradation of fibre”) as a factor in personalized fiber responses.
ISME Communications, 20 June 2024
Comment: The study used shotgun metagenomic sequencing from the SECRETO Oral study to identify significant differences in the oral microbiome’s composition and functional capacity between young patients with cryptogenic ischemic stroke (CIS; which is IS without a clear recognised cause) and stroke-free controls. Results identi- fied 51 microbial species associated with CIS across multiple interacting kingdoms, as well as 5 pathways found to be differentially abundant between CIS patients and controls. This study suggests a role for the oral microbiome in metabolic processes that could influence stroke risk and recovery, especially in cases that have a cryptic ae- tiology. (b) Microbial genetics, ecology, evolution and AMR
npj antimicrobials and resistance, 24 June 2024
Comment: Metabolic inhibitors are known to exhibit complex interactions with antibiotics in bacteria, potentially acting as antagonists by inducing cell dormancy and pro- moting cell survival and persistance (defined here as the reversible survival in the presence of antibiotics). In this paper, authors looked at the synergistic interactions of metabolic inhibitors (i.e. chloramphenicol, a translation inhibitor, rifampicin, a transcription inhibitor, arsenate, an ATP production inhibitor, and thioridazine, a proton motive force inhibitor, all in combination with the antibiotic ofloxacin. The highest synergy was observed with thiridazine. This shows that there is potential utility in combining cer- tain metabolic inhibitors with antibiotics for more anti-persistance effects in pathogens.
Science, 5 July 2024
Comment: This very impressive phylogenomics study highlights that a few environmental P. aeruginosa strains have become dominant, host-adapted epidemic clones, with a preference for either CF or non-CF hosts, via HGT over 200 years. Analyses of ~10,000 isolates find some genetic signatures and phenotypic traits underlying host adaptation, including DksA1’s role in CF infection. These pathoadaptive mutations, often causing loss of function, drive P. aeruginosa evolution, leading to specialized host infection and reduced cross-infection between different patient groups. Very cool and impactful!
microGWAS: a computational pipeline to perform large scale bacterial genome-wide association studies
bioRxiv, 10 July 2024
Comment: As an early contributor and adopter, I can agree that running microbial GWAS can look a bit daunting at first, given the number of approaches and lack of best practices. In this preprint, authors attempt to solve this, by providing with a pipeline to perform bacterial GWAS from a set of assemblies and annotations, with 1 or multiple phenotypes as groups. Definitely something to test and happy to hear what others think.
The Lancet Microbe, 9 July 2024
Comment: Enteric fever is still a major burden, particularly in LMICs. In this study, stemming from the STRATAA surveillance programme, authors estimate that 98% of drug-resistant enteric fever cases from urban sites in Bangladesh, Nepal and Malawi result from local circulation of resistant variants. They show genetically indistinguish- able variants (either resistant or susceptible) persisting for up to 2·3 years and causing infections across all age groups (<5 years, 5 to <15 years, and ≥15 years).
Journal of Travel Medicine, 2 July 2024
Comment: This work, from Australian researchers in Melbourne, identified a significant prevalence of MDR resistance in 655 international travellers with E. coli and K. pneumoniae infections, with 37% of E. coli and 28% of K. pneumoniae isolates exhibiting resistance to at least three drug classes. Travellers to South-Central Asia were found to have the highest rates of non-susceptibility to key antibiotics, including third-generation cephalosporins, fluoroquinolones, and carbapenems, indicating regional variation in AMR profiles too. Data from the GeoSentinel Network over an 8y-period shows an increased trend in phenotypic ESBL and carbapenem resistance among the isolates. (c) Other general interest
Cell Reports Medicine, 8 July 2024
Comment: Interesting results from this “long COVID” prospective study of the lung proteome with bronchoalveolar lavage vs. healthy controls. Results show that even af- ter mild to moderate COVID infection, the inflamed lung undergoes prolonged repair for more than a year, even though chest X-ray and clinical symptoms may have seem- ingly resolved. This could be related to the long COVID symptoms that are starting to be very robustly shown all around the world. Given how many of us have been infected in the recent past, this is concerning, to say the least, but also gives a good insight to what can happen in our bodies once pathogens are seemingly cleared.
The Lancet Regional Health: Western Pacific, 6 June 2024
Comment: This molecular epidemiology study focused on HIV-1 transmission in Victoria, Australia, and shows that 70% of cases are part of identifiable transmission groups, with certain demographics (e.g., males born in Australia) being more prevalent within these groups. Using a genetic distance threshold approach, some specific transmission groups had high effective reproductive numbers (Re), indicating significant potential for HIV spread, and also detected transmitted drug resistance mutations (SDRMs) in 10.7% of cases.
bioRxiv, 10 July 2024
Comment: A new recent study shows that COVID-19 pandemic caused a 70.35% rise in Guillain-Barre Syndrome (GBS) cases globally, affecting more women, younger in- dividuals (15-29yo) and low-income regions (especially in the first 2 years of the pandemic). SARS-CoV-2 vaccination is key to reduce the GBS sequelae burden worldwide.
Noteworthy things — Week 27 (01/07/2024)
Trends in Microbiology, 20 January 2024 (July Issue)
Comment: Our review on leveraging the gut microbiome for predicting disease risk and outcome that have a (known or unknown) microbial component has finally been as- signed to the July issue of TiM. Have a look if you haven’t already! Noteworthy studies and publications (a) Microbiome
Gut, 6 June 2024
Comment: Long-term proton pump inhibitor (PPI) usage has been linked to various medical conditions and alteration of the microbiota. A safer alternative are histamine-2 receptor antagonists (H2RAs) but not much has been done on their effects on the microbiota, until this study. Authors show that H2RAs impact less the gut microbiota than PPIs and who that (very intriguingly) PPIs seem to induce more oral-to-gut transmission of Fusobacterium nucleatum and Streptococcus anginosus, which have also been linked to a range of other diseases! Very interesting!
Immunology & Cell Biology, 11 June 2024
Comment: Another very interesting paper form the Milieu Intérieur consortium, this time looking at the impact of socioeconomic status on human immune response, using an Elo-based ranking system (like in chess) to stratify individuals from the MI cohort according to SES. A very good thread from one of the main senior authors here!
Nature Metabolism, 1 July 2024
Comment: This 16S rRNA-based study on fecal samples from 16 male mice found that the time of sample collection within a 4-hour window significantly affected the gut microbiome’s diversity and composition, more so than dietary changes, suggesting the necessity for standardized sampling times (accounting for diurnal variations in mi- crobiota) to maximise data accuracy in microbiome studies.
Nature Microbiology, 25 June 2024
Comment: Great study and figures! Here, authors use a novel high-resolution imaging method combining DNA FISH with rRNA-FISH to visualize mobile genetic elements and their bacterial hosts in oral biofilms, no less! This revealed spatial clusters of AMR genes and bacteriophages, indicating heterogeneous distribution and potential barri- ers to their spread within biofilms. Very impressive! Also check the thread on Twitter from the lead author.
Nature Microbiology, 25 June 2024
Comment: Fibre-rich diets are thought to have the potential to beneficially modulate the gut microbial metabolic output. In this in vitro/in vivo study, authors show that di- etary fibre alters gut microbial tryptophan metabolism by suppressing indole production in favour of beneficial indolelactic acid (ILA) and indolepropionic acid (IPA). This shift occurs as fibre-degrading bacteria inhibit indole-producing E. coli via catabolite repression, thereby increasing tryptophan availability for other taxa to generate me- tabolites.
Microbiology Spectrum, 25 June 2024
Comment: In this study, authors show that the maternal microbiome undergoes substantial changes after birth that may be long-lasting. They tracked 30 women from their pregnancy to 1-mo after birth, profiling oral, urinary, and vaginal microbiomes, including archaeome, mycobiome, and urinary metabolome. The oral microbiome seem to stabilize quickly after birth, but the urogenital microbiome is depleted from Lactobacillus after birth, which suggests the potential use of probiotic interventions to opti- mize postpartum recovery. See comment from our collaborator Prof. Moissl-Eichinger.
Cell Host & Microbe, 12 June 2024
Comment: In this small mother-infant cohort, authors compare hospital versus at-home delivery on infant microbiota transmission and show an impact. They show that hu- man milk is a key modulator of infant microbiota during the first year, with a variation across delivery modes and locations, except for Bifidobacteria, with B. longum persist- ing and diversifying more according to breastfeeding duration.
The Lancet Microbe, 20 June 2024
Comment: Very interesting study from collaborators, investigating the relationship between gut microbiota and infectious disease risk in 10,699 participants from the HELIUS (Netherlands) and FINRISK (Finland) cohorts. Over a 5-7 year follow-up, it was observed that individuals with a higher abundance of butyrate-producing bacteria had a lower risk of hospitalisation for infections. Results show a 25% and 14% risk reduction for every 10% increase in butyrate producers in the HELIUS and FINRISK co- horts respectively.
The ISME Journal, 21 June 2024
Comment: Do taller people have more diverse gut microbiomes? Yes! says Sean Gibbons and colleagues (link to Twitter thread). A well rounded and exhaustive read, com- paring vertebrate microbiomes and suggesting mechanisms.
Gut, 12 May 2024
Comment: A few years ago, a collaboration between us and Finnish colleagues found that Enterobacteriaceae could be associated with incident mortality in the FINRISK 2002 cohort, but it has been quite difficult to conduct similar studies with such important follow-up in large cohorts. Until now! Here, authors use faecal metagenomes from a cohort of solid organ transplantation recipients (n=1,337) and the general population (n=8,208) from the northern Netherlands, with 6.5 years of follow up. Findings include the observation that gut dysbiosis is partly driven by the use of immunosuppressive drugs which prevent organ rejection, coupled with a frequent use of antibiotics, which suggests that their life-saving nature could come at a cost. Check the Twitter thread about it from Johannes Bjork, a senior author on the study. (b) Microbial genetics, ecology, evolution and AMR
Nature Communications, 1 July 2024
Comment: The CC398 lineage of Staphylococcus aureus is an important zoonotic one, shown to colonize livestock, pets and humans and is a very interesting model for studying host adaptation in S. aureus. Here, authors analyzed >3000 global S. aureus CC398 genomes, constructing a time-calibrated phylogeny that reveals distinct evo- lutionary lineages, with a notable focus on the equine-associated EP5-Leq lineage. They also identify interesting key MGEs driving adaptation and AMR in CC398.
Nature Communications, 13 June 2024
Comment: Pretty innovative study in which authors used imaging and ML to predict ciprofloxacin susceptibility in Salmonella. They analyzed 16 clinical isolates and 4 lab strains and captured detailed morphological data from bacterial cells exposed to various ciprofloxacin concentrations over 24 hours. ML classifiers were trained on key imaging features to distinguish susceptible from resistant isolates, even without direct antimicrobial exposure. Not sure how this could be scaled-up and translated in prac- tice but this is quite original and interesting! (c) Other general interest
A lipidomic based metabolic age score captures cardiometabolic risk independent of chronological age
eBioMedicine, 20 June 2024
Comment: This nice study from colleagues at the Baker Institute finds that a lipidomic-based metabolic age can be associated with an increased risk of CVD, diabetes & all-cause mortality that is independent of chronological age. This “mAge score” has the potential to identify those at elevated risk of metabolic diseases.
Noteworthy things — Week 24 & 25 (10-17/08/2024)
Nature Metabolism, 19 June 2024
Comment: Fascinating review with an original angle, summarizing knowledge on bacterial translocation in metabolically active organs, something they term “tissue- resident bacteria”. Various body sites are well known to have a high biomass of microbes and active functional microbiota, but less is known about microbial colonization of other sites (e.g. liver, adipose tissue, pancreas, kidney) and its impact on metabolic health. Very interesting read., especially with an ecological consideration of holobionts etc.
npj Biofilms and microbiomes, 19 June 2024
Comment: I found the angle of this review very interesting and somehow original. The role of Bifidobacterium in health, particularly infant health, is very described and studied, which means that it becomes possible to look at cross-feeding and metabolic interactions between various different species and strains within this genus. A clear summary of what is known!
Gut Microbes, 11 June 2024
Comment: This interesting study investigates the association between gut microbiota, specifically the enrichment of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae, and the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). A few hundred samples from colorectal adenocarci- noma tumors and adjacent normal tissue were analysed which led authors to suggest a potential influence of bacteria on DNA methylation patterns in CRC.
Nature Microbiology, 11 June 2024
Comment: These studies always seem at first to feel as is we are looking too hard for anything meaningful, just because the samples are extremely original and difficult to obtain. Are there really particularities in human-microbes interactions during spaceflight and prolonged life in absence of gravity? If there is anything, this study is the most comprehensive I’ve seen so far (without really following the field). Authors look at time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. They mostly find transient alterations of the skin and oral microbiota and immune cell expression. Very in- tresting study, most probably impactful for spaceflight management.
Nature Microbiology, 12 June 2024
Comment: Quite an impressive study, using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional het- erogeneity of the rumen microbiome. The resulting atlas encompasses 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters, allowing to study the microbiome at unprecedented resolution. On the biological side of things, authors highlight a new potential key role for Basfia suc- ciniciproducens in the carbohydrate metabolic niche of the rumen microbiome, as well as its biofilm abilities.
Cell Host & Microbe, 12 June 2024
Comment: The role of the gut microbiota in early life is of course extensively studied, but this particular study focuses on analysing the HELMi and SECFLOR cohorts and look at the impact of maternal fecal microbiota transplantation (FMT) on cesarean-born infants (something that has been studied and “semi” debated over the years). Authors show that maternal FMT can enhance microbial richness, increase strain sharing with infants, and reduce pathogen colonization. Interestingly, they also under- score the importance of both parents (including paternal) in shaping the infant gut microbiome and suggest that maternal FMT could potentially restore disrupted micro- biota transmission in cesarean-born infants. (b) Microbial genetics, ecology, evolution and AMR
bioRxiv, 13 June 2024
Comment: I hadn’t come across such a study before, this is very cool! In this preprint, authors fluorescently tagged bacteriophages to follow their transmission and infec- tion routes. Extremely cleverly, they designed a tagging system consisting of multiple fluorescent proteins called “SpyCatcher” which tags the virion differently after each infection of a new bacterial host. The combination of colours can then help visualise the succession of infections. They test their method with in vitro communities of multi- ple species, as well as in vivo in the gut of zebrafish! Using this tool, they observe that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and can quickly disseminate to extraintestinal sites, including the liver and brain. Additionally, antibiotics can trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Very elegant and impressive!
bioRxiv, 18 June 2024
Comment: On the importance of sanity checks and careful validation when designing vectors and plasmids in the lab! This will not surprise a lot of “wet lab” plasmid- cloning scientists, I’m sure. This preprint presents a large survey of plasmids from hundreds of academic and industrial labs worldwide and shows that nearly half of them contain design and/or sequence errors. More usefully, authors report what type of errors they encounters, hopefully helpful information for future engineering.
bioRxiv, 12 June 2024
Comment: New preprint from Zamin Iqbal’s group that will appeal to everyone who has ever worked with plasmid sequences and epidemiology. Plasmids evolve very rapidly and can restructure their genome quite substentially, adding and removing genes and sequences extremely rapidly. Given that, how can we call two plasmids the “same” epidemiologically speaking? This was a central (and tricky) question during our 2018 Bacillus cereus plasmid diversity study, and the fact that this genus harbours “megaplasmids” combining multiple other ones. Here, authors tackle the problem far more elegantly, by incorporating genetic distance, and precise accounting of the pos- sible changes that can occur in plasmid sequences. Their proposed tool (called “pling”, not to be confused with plink!) builds sequence similarity networks (i.e. connect 2 plasmids if 50% of their sequences is alignable). More details on Zamin’s great and clear Twitter thread about it!
The ISME Journal, 31 May 2024
Comment: In this modelling (only) study, authors challenge the assumption that one phage strategy (lytic vs. lysogenic) is universally superior, proposing instead that the coexistence of lytic and temperate phages is a natural outcome of complex population dynamics.
bioRxiv, 28 May 2024
Comment: In this preprint, authors examine the evolution of anaerobic methanotrophic archaea in the genus Methanovorans. Their analyses of genomes from 10 isolates from various locations suggest an importance of key metabolic genes for methane oxidation and energy conservation, with a role of HGT in local adaptation. They interest- ingly characterize a gradual loss of genes involved in methylotrophic methanogenesis during the transition to methanotrophy.
Nature Microbiology, 19 June 2024
Comment: Rhodosporidiobolus fluvialis is a human fungal pathogen, from a genus that is highly resistant to antifungals. In this paper, authors demonstrate that the species can undergo a yeast-to-pseudohyphal transition in, which is considered a key determinant of its increased virulence. Interestingly, human body temperature-induced muta- genesis is highlighted as a driving force behind the development of drug resistance (notably except to polymyxin B) and hypervirulence, also in fungal pathogens in general.
Nature Biomedical Engineering, 11 June 2024
Comment: A bit of a hyped title for something actually very cool. This study presents an interesting approach combining ML models to predict antimicrobial activity from predicted peptides, and identified a large number of those in extinct organisms! Notably, they found that mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk had some anti-infective activity in a mouse model of infectious skin absess. (c) Other general interest
Nature Reviews Microbiology, 29 May 2024
Comment: This very nice review presents geobiological, geochemical, and genomic perspectives on how early microbial life co-evolved with Earth’s environments, particu- larly focusing on the transition from an anoxic to an oxygen-rich atmosphere (really like the figures!). It presents an interesting angle on the distinction between the emer- gence of early metabolic processes and their subsequent proliferation, highlighting how these metabolisms were not only a product of environmental conditions but also a driving force in shaping the chemical properties of the oceans, continents, and atmosphere. There are also some cool astrobiological implications, suggesting that similar biosignatures could be used to detect life on other planets, and that understanding Earth’s past could inform the search for extraterrestrial life. A bit wild, I know, but fun!
Cell Genomics, 29 May 2024
Comment: If you had to guess, which gene might have the most described alleles? Pathogen effectors are probably up in this list, and in this paper, authors describe HYP effectors with potentially 1000s alleles from cyst nematodes that are necessary for their parasitism in potato plants. Alleles are due to particularly variable domains termed hyper-variable domains (HVD). Authors suggest a mechanism of programmed, locus-specific, somatic genome editing for these peculiar and very diverse genes.
Noteworthy things — Week 22 & 23 (27/05 & 03/06/2024)
Cell Host & Microbe, 24 May 2024
Comment: Very interesting methodological study, using MALDI mass spectrometry method to colocalize host and bacterial lipids. In this study on mice, authors identify 103 lipids from Bacteroides thetaiotaomicron which were mapped across various regions of the colon. Among the interesting results, mice colonized with B. thetaiotaomi- cron lacking sphingolipids have increased bacterial lipid uptake, and microbial phosphatidic acid was identified as the greatest signal for host lipid transfer.
eClinicalMedicine, 26 April 2024
Comment: How are UTIs linked to gut microbiome composition? No groundbreaking new knowledge on the matter from this recent study but it is well executed and a good, clear read. In this multi-centre (USA) longitudinal (2016 to 2019) cohort study, 125 patients with UTI caused by an antibiotic-resistant bacteria were recruited and had matching samples collected (644 stool samples, 895 UPEC isolates for AMR gene characterisation and phenotyping). They find that the gut microbiome is implicated in re- current UTI and serves as an AMR gene reservoir for UPEC, which can asymptomatically colonize the gut and the urinary tract. The recurrence of UTI involves post- antimicrobial blooms of gut E. coli among urinary tract-colonized patients, which unsurprisingly suggests that cross-habitat migration of UPEC is an important mechanism of recurrent UTI.
Nature Medicine, 23 May 2024
Comment: Medicine in general and microbiome science in particular are still very biased towards Western countries and their populations and there is a crucial need to in- clude more human diversity in research data and studies, but it should be done with considerations of equity, empowerment and representativity. Authors present here an implementation framework for African microbiome research, which includes local research leadership, ethical and equitable partnerships but also standardized micro- biome protocols and governmental involvement. I have been impressed by the quality of seminars from the H3Africa Microbiome Task Force in the past, so this is really a great addition now.
Cell, 24 May 2024
Comment: It has been observed in the past that microbes are able to interact with host-produced steroids but the mechanisms are unclear. Here, authors show that gut mi- crobes from the Gordonibacter and Eggerthella genera are able to convert corticoids from the bile into progestins, a form of the sex hormone progesterone, in an enzy- matic step called 21-dehydroxylation that requires microbially-produced gaseous hydrogen. Progestin levels and the presence of gut microbial gene clusters involved in 21- dehydroxylation were found to be significantly more abundant during pregnancy, which suggests that gut microbes can importantly affect physiology and hormone bal- ance during that phase of life.
Trends in Microbiology, 25 May 2024
Comment: Nice microbiome ecology opinion piece on the need for more individual longitudinal variation in microbiome science. Authors use example animal hosts to sum- marize what is known, possible mechanisms and associated methodology and challenges.
bioRxiv, 27 May 2024
Comment: It is always interesting to have meaningful comparators between individual microbiomes, but oh my, how challenging can this be. What do you choose, how do you do it? Is it even possible to reduce the microbiota’s complexity to a single index score? an interesting way could be to look at the “core microbiome” (a tricky concept) and how much individuals vary from it. As debatable as this is, it’s interesting to see what people are trying when the answers are not clear sometimes. In this recent effort, authors suggest that their “HACK-index” can provide a more reliable framework for identifying and comparing gut microbiome markers of health across various demo- graphics and disease states. Maybe worth looking at? And check out the thread from senior author Tarini Shankar Ghosh.
Gut Microbes, 26 May 2024
Comment: In this recent study, authors venture in the field of colonization resistance and exhaustively test the supernatants of 74 commensal gut microbial species cul- tured in vitro for their interaction with Salmonella, aiming for protective effects affecting pathogenic growth. It remains to be seen how these actually mean in complex real-life systems, but the analysis is nonetheless interesting to read.
Gut Microbes, 26 May 2024
Comment: Gestational diabetes (GDM) is quite common in pregnant women, but its impact on the infant’s subsequent microbiota is not well known. This study compares pairs of mothers (16 of which who experienced maternal GDM and 14 without) and their infants 1 year after birth. Authors observe that the mode of delivery is the biggest contributor, irrespective of GDM, and that any possible mild effects from GDM are not persisting in infants after 12 months of life.
Cell Host & Microbe, 27 May 2024
Comment: This paper adds to the considerable list of studies looking at how gastrointestinal pathogens like Salmonella invade and thrive in the inflamed (mouse) gut. It is quite ecologically interesting to understand how introduced, virulent microbes can hijack functional communities and their metabolic products for their benefit. Here, au- thors show that Salmonella can use aspartate from the gut microbiota for growth in mice with colitis, enabling anaerobic fumarate respiration in the pathogen and allowing it to expand in the gut. In turn, ROS produced by the host in response to inflammation has the effect to lyse gut commensals and increase aspartate availability to Salmonella. A tight tale of adaptation and co-evolution!
Nature, 29 May 2024
Comment: A lot of hype has already been made on this paper, including a descriptive commentary here. I am a bit on the fence, honestly. Briefly, in this study, authors find and engineer a molecule, called “lolamicin”, which specifically targets an essential system (encoded by 5 genes from the lol operon) responsible for lipoprotein transport between the inner and outer membranes in Gram-negative bacteria. Because of this, authors claim that the action of lolamicin spares Gram-positive bacteria and “non- pathogenic Gram-negative bacteria” (this is the bit I have some conceptual issue with, as pathogen vs. commensal is more than a hot debate when you consider things that broadly). Nonetheless, it is obviously a very interesting effort for when obvious Gram-negative pathogens are infecting, such as C. difficile (tested in the paper). Interesting to imagine how bacteria could evolve resistance to this.
Scientific Reports, 30 May 2024
Comment: Differential abundance methods are themselves quite abundant in the literature, and each are having their pros and cons (check out this very nice recent com- parison from our collaborator Leo Lahti as well as this very well-explained benchmarking in the ZicoSeq paper). This recent manuscript presents a new DAA approach which claims to address the specificities of microbiome data better (including inflated zero counts, overdispersion, and non-normality). Perhaps worth considering, and in- teresting to see what people think.
Nature Communications, 29 May 2024
Comment: Somehow I find mucin-degrading bacteria fascinating. I know, this is a bit of a weird ice-breaker in parties, but such nice microbial biochemistry research is done to understand how the gut microbiome as a dynamic whole juggles between using dietary nutrients vs. mucin. In this new study, authors characterise even further the mucin-binding abilities of a big suspect in gut health (and mucin degradation, as its name suggests), Akkermansia muciniphila. They show that it is able to selectively recog- nize the unsialylated LacNAc on O-glycans from mucin. (b) Microbial genetics, ecology, evolution and AMR
medRxiv, 17 May 2024
Comment: There is a large effort in trying to predict antimicrobial resistance phenotypes in bacterial pathogens from minimum inhibitory concentration (MIC) in vitro tests. There are arguments as to how relevant and realistically those MIC tests are performed, but in this preprint from Nicole Stoesser’s lab in Oxford, authors use a collection of ~2.9k phenotyped and sequenced E. coli to look at another problem: what happens to the MIC measurement when pathogens acquire new resistance genes? They find evi- dence of various effects, additive or not, and suggest a way to predict outcomes of AMR gene acquisition.
Gut Microbes, 5 May 2024
Comment: This study shows that human gut-associated Bifidobacterium can convert exogenous indole into tryptophan and then indole-3-lactic acid (ILA), an im- munomodulatory compound, using tryptophan synthase β subunit (TrpB) and aromatic lactate dehydrogenase (ALDH). Exogenous indole is known to contribute to the pro- gression of kidney dysfunction after absorption by the intestine and sulfation in the liver, so any potential way to reduce its concentrations in the gut could be an interesting candidate probiotic activity.
Víctor Mateo-Cáceres & Modesto Redrejo-Rodríguez bioRxiv, 22 May 2024
Comment: Bacteria have evolved various systems to protect themselves against viral infections and other genetic mobile elements. In this preprint, authors present a new category of integrated defense system based on primer-independent DNA polymerase B, which they term “pipolins”. They find them to be common in Gammaproteobacteria, but also on plasmids in other taxa.
PNAS, 25 May 2024
Comment: Another interesting effort showing how pathogens adapt and co-evolve with their hosts when it comes to infecting them. This study identifies a novel ʟ- arabinose uptake system called Aau in EHEC and Citrobacter that enhances virulence and fitness by linking the arabinose metabolism to the regulation of a type 3 secre- tion system (T3SS), independently from its role as a nutrient source. It interestingly challenges the traditional view of nutrient sensing, by showing that the metabolism of ʟ-arabinose, rather than its mere presence, is a key regulator of virulence factor expression in EHEC.
Nature Reviews Microbiology, 24 May 2024
Comment: Interesting review on pathogen control in the food chain using genome-based approaches. An interesting part of this review focuses on external factors like cli- mate change and consumer preferences and how they shape the ecology of foodborne pathogens.
bioRxiv, 24 May 2024
Comment: It is fascinating to imagine that protist predation is actually one of the biggest (if not the main) selective pressure on bacteria in the wild. As such, some believe that host-association in general could have evolved from bacteria surviving predation by living inside protists. More practically, this means that some pathogens are able to do it, and it might confer them additional protection and transmission potential. In this preprint, authors describe the interaction between a zoonotic pathogen Campylobacter jejuni and the amoeba A. castellanii in various ways. Very interesting links with lactate production are suggested.
Microbial Genomics, 4 June 2024
Comment: New interesting one from our collaborator and friend Ryan Wick and colleague George Bouras (and others) nicely looking at assembly polishing, and how to pro- duce highly accurate microbial genome assemblies. They present a new approach, named Pypolca (github here) and suggest best practice in combination with Ryan’s Polypolish tool (github here).
Plos One, 31 May 2024
Comment: My Campylobacter past is always haunting me (in a good way) (I hope). In this interesting brief paper, authors show how to selectively culture C. hepaticus, the aetiological agent of spotty liver disease in chicken. This will hopefully help boosting research on this pathogen that causes lots of animal mortality and welfare/economical concerns.
bioRxiv, 27 May 2024
Comment: One of my failings is probably that I am generally less interested in the absolute latest fungal research, but this one caught my eye as authors sought to study Candida albicans, a clinical fungal pathogen, using an interesting set of in vitro conditions carefully picked to mimic the human environment. These included 48 environ- mental conditions, including combinations of glucose/nitrogen concentrations, pH and temperature. Such a panel would be great for lots of human microbiology research.
The ISME Journal, 28 May 2024
Comment: Microbes are present in the air. They are part of the water cycle, through aerosolisation from plant evaporation and subsequent precipitation. This is a very cool perspective from Rachael Lappan and Chris Greening (Monash University, Melbourne, Aus.) presenting arguments on whether the atmosphere is only there for microbial transport or could constitute an ecosystem of its own. This piece also comes after the Greening lab showed last year that some bacteria could perform “aerotrophy” and use atmospheric hydrogen as a source of energy, so this is a really cool topic. (c) Other general interest
The Lancet, 25 May 2024
Comment: Human T-cell leukaemia virus 1 (HTLV-1)-1 is an oncovirus, the largest incidence of which is in Australia, particularly in indigenous populations (it also dispropor- tionately affects First Nations elsewhere in the world). People living with HTLV-1 infection have a 57% increase in mortality rate, with 5–10% of them developing life- threatening diseases, such as aggressive blood cancer, adult T-cell leukaemia or lymphoma, and HTLV-1 associated myelopathy, a progressive, painful walking disability. There is a lot to do in public awareness of HTLV-1, as well as steps to ensure its eradication, as explained in this important opinion piece.
Scientometrics, 19 May 2024
Comment: Another grain of salt for a frustrating problem. Submitting and assessing grants is a frustrating process for both parties involved, and it has been suggested (and calculated) a while ago that the amount of salary-hours spent by publicly-funded researchers writing lengthy unsuccessful grants often outweighs the amount of pub- lic money awarded by governments. This is, at worst, a fundamental financial issue in how our governments fund research, and it really not helped when funding bodies ask for extremely unnecessarily lengthy proposals (looking at you ERC). In this paper, the Dutch Research Council (NWO) did a field experiment in which they asked a grant- reviewing panel to assess proposals. They randomly split the panel according to whether the applicant submitted (1) a CV and a one-paragraph summary of the proposed research or, (2) a CV and a full detailed proposal of many pages (taking considerably more time to prepare for researchers). They found that withholding proposal texts from reviewers did not detectibly impact their proposal rankings. This raises a lot of questions on how grant proposals are currently asked to be made. There probably isn’t an easy answer to this, but hopefully a much-needed change will come, soon. Other things:
Noteworthy things — Week 21 (20/05/2024)
bioRxiv, 17 May 2024
Comment: It is important to know how much microbial DNA is in the metagenome for downstream abundance analyses, etc. This is a very interesting preprint if you are cu- rious about how much eukaryotic DNA is present in microbial metagenomes, when reference databases are incomplete or inexistent. Authors present a new approach called SingleM microbial fraction (SMF) and run it on 250k metagenomes as a proof-of-principle. Very good thread explaining it all on Twitter from the lead author.
Lynch Nature Reviews Microbiology, 22 May 2024
Comment: We are starting to understand a bit better the dynamics between oral, airway and gastrointestinal microbial communities and their role in respiratory diseases. This review is a great resource and has very nice figures about it. Make sure to check our 2023 JACI study led by Dr Yang Liu, on the use of gut microbes to predict incident respiratory diseases.
Nature Metabolism, 22 May 2024
Comment: From a very nice accompanying piece: “In an attempt to investigate the role of enteroendocrine cells in the colon using elegant, targeted depletion tools, au- thors highlight the orexigenic role of a bacterial metabolite in the intestinal lumen, l-glutamate.” This suggests, using mice work, the presence of a bidirectional enteroendocrine–microbiota axis in the large intestine, which regulates host metabolism.
Jaebeom Kim & Martin Steinegger Nature Methods, 20 May 2024
Comment: This is a new metagenomic classifier, based on the joint analysis of DNA and translated AA sequences. Happy to hear what people think, especially in terms of reference database customization, sensitivity to low-abundance/understudied taxa and overall computation speed (so far it seems very long and hard to scale-up). Very nice thread explaining it from the lead author here.
Nature Communications, 16 May 2024
Comment: One of my favourites this week. Some enterobacteria can produce self-aggregating amyloid fibers (such as curlis in E. coli) that are critical during early attach- ment to surfaces and subsequent biofilm formation. The similarity with how amyloid fibers self-aggregate in some age-related neurodegenerative diseases has not gone unnoticed and a few studies have tried to link the two already. This new one is quite impactful in the matter; authors show that the abundance of certain biofilm-related genes in the gut microbiome can be correlated with Parkinson’s disease incidence, and go further by proving using C. elegans and mice models that bacterial biofilm- derived amyloids can induce α-synuclein aggregation, and promote key pathological features of PD in mice when injected in their brains.
bioRxiv, 16 May 2024
Comment: Archaea are notoriously hard to grow in vitro. This is a great effort straight out of the experts’ lab with Christine Moissl-Eichinger in Graz (Austria), showing how to culture new critically important methanogen species (including Methanobrevibacter intestini, a novel one) from human faeces. This will allow phenotyping and a much better study of the role of archaea in humans.
bioRxiv, 21 May 2024
Comment: An original preprint from the EMBL at Heidelberg! The fate of known carcinogenic products in our bodies is not well known (apart from the end outcome) and this study shows that 34 bacterial species representative of the human lower intestine are able to biotransform 41/68 known carcinogen products in vitro. Those included cigarette smoke, industrial reagents or clinical drugs (picked from their toxicity on the Ames test and presence on the EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database). Authors go on to test how this interacts with the host response to carcinogens and suggest an interplay between host/microbiome for exposome- induced tumorigenesis.
bioRxiv, 20 May 2024
Comment: Combining comparative microbial genomics can critically enhance our understanding of the microbiome, and shed light on strain variation, whether within- individuals or between. This preprint does that on Segatella copri (formerly from the ill-defined Prevotella copri complex and now aptly renamed in honour of Nicola Segata). Authors isolated and cultured and sequenced 63 S. copri strains from a single participant with S. copri abundances at ~75% of all detected gut taxa) from a Fijian cohort and compared them. This added knowledge on variation in metabolic capabilities, cellular morphologies, SCFA production yield, and translated to the observation that only some S. copri isolates induced strong transcriptional responses from Caco-2 epithelial cells. Good discussion too on the limitations of metagenomics to distin- guish clades (vs. culturing + sequencing/typing).
mSystems, 16 May 2024
Comment: In the same spirit, authors looked here at within- and between-individual strain variation in Gardnerella sp. from vaginal microbiomes. They show that that single microbiomes can contain all currently known species of Gardnerella and that multiple similar species can exist within the same environment, prompting more questions on how these strains interact in individuals. Looking at cohort data suggests that some species appear more commonly in certain populations, highlighting the need for large surveys to capture the whole genus diversity. (b) Microbial genetics, ecology, evolution and AMR
bioRxiv, 17 May 2024
Comment: Always been a bit bugged when MIC tests are performed at the bench (in full aerobic conditions) in contrast with the microaerophilic or even anaerobic environ- ment that bacteria would actually encounter in a patient (wounds, gut, etc). In this preprint, authors looked at whether different atmospheric oxygen conditions could influ- ence resistance in E. coli and K. pneumoniae. Guess what, it does! shocked This suggests that anaerobiosis conditions should really be taken into consideration when try- ing to predict resistance levels in bacterial pathogens. Nice work!
mSphere, 22 May 2024
Comment: Good descriptive study on prophages in Salmonella. Authors characterized prophage regions from 303 Salmonella spp. genomes (254 unique serovars) to as- sess their distribution and genetic content, which was found to harbour a large range of functions having to do with metabolic, virulence, and resistance traits.
PNAS, 6 May 2024
Comment: I did not follow all the mathematical and modelling details but I quite enjoyed the central idea and concept presented here. It stems from the observation that statistic models can predict the effect of a species on a community-level function, akin to epistasis reported in genetics. This “ecological global epistasis” stems from widespread species-by-species interactions, and can potentially be interacted with to modulate functions from microbial communities. Tweet thread from the lead author here!
Chong & Lucy Shapiro mBio, 21 May 2024
Comment: Very interesting microbial ecology minireview on the various ways bacteria act as multi-cellular organisms within functional communities, structures etc. This includes biofilms, swarming and fruiting bodies as well as some pathogenicity processes. “Obligate” differentiation (the case of Caulobacter crescentus) is also discussed.
bioRxiv, 21 May 2024
Comment: Tn-seq is a very proven and popular microbial mutagenesis technique, whereby you deactivate genes using transposons that are randomly (or not) inserted throughout the microbial genome. There are some drawbacks to it, mainly that sometimes Tn insertion is inefficient, and it is also easy to deactivate essential genes and therefore not be able to study the resulting non-viable mutants. In this preprint, authors present a new method called InducTn-seq, which allows for the induction of muta- genesis and a temporal control of transposon insertion. One of the major outcomes suggested is the possibility to move beyond a binary outcome of gene essentiality to a more quantitative measure of fitness. As a proof-of-concept, authors use a mouse model of colitis to identify more functions involved in infection.
Manlu Zhu & Xiongfeng Dai Nature Communications, 18 May 2024
Comment: Very exhaustive review on how trade-offs (at various levels) shape microbial biology, ecology and evolution. Authors talk about trade-offs between growth and adaptability, growth and survival, generalist and specialists (the most interesting to me). A long but good read. (c) Other general interest
Maag F1000 Research, 20 November 2018
Comment: Old tool but came across it recently again. Everything is in the name! If you need to draw some anatomical or organelle diagrams in R, this is your library!
Plos Biology, 20 May 2024
Comment: Synteny (the order of genes) has been an interesting addition to the reconstruction of various species phylogenetic trees, in particular for deep branches with uncertainty. In this critical essay, authors discuss the state of using synteny for phylogenetics, with very interesting examples (humans/apes, sponges/ctenophores, fishes, etc).
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
Annual Review of Genomics and Human Genetics, 25 April 2024
Comment: A few years ago (surprisingly recently), the concept of human pangenomes came a bit more into light (it’s been decades we study this in microbes), facilitated by advances in whole genome sequencing of humans. This review summarizes very well the state of this field including the resolution of centromeres in human genomics, and what are the benefits of including non-reference sequences for maximizing human diversity and representativity. New reference pangenomes are discussed too. To our microbiome-minded minds, considering the human pangenome is useful when wanting a more efficient human read filtering, incorporating pangenomic sequences and not just the artificial hg38 reference (check the nice method from Michael Hall to do this; we’ve used it and it works relatively well; adds ~1000s of additional human reads to filter per sample out vs. hg38 even on European samples).
Nature Genetics, 15 April 2024
Comment: Coffee genomics and evolutionary biology! Who possibly couldn’t like coffee genomics and evolutionary biology?! Very nice commentary about it here.
bioRxiv, 22 May 2024
Comment: Happy to hear the thoughts of others using this, if any; we will certainly give it a go. This is a tool aiming to facilitate sequence recovery from repositories from the command line. A few others exist, but this one seems promising (?).
medRxiv, 22 May 2024
Comment: Likely a very impactful preprint in the field of pandemic preparedness and the causes of zoonotic spillovers. Using outbreak reporting data, authors look at which factors affect the risk of zoonotic outbreak worldwide for major pathogens. Living in mosaic landscapes (at the border of forests or fragmented environments) is found to be a factor, exacerbated by regular decreases in precipitations (and climate change). Outbreak reporting is mostly affected by socio-economic aspects and geog- raphy, such as time and distance to healthcare facility. Good data analysis study, with a lot to unpack!
Xiaofei Ge & Jiawei Wang Nature Communications, 17 May 2024
Comment: These studies are always fascinating for microbiologists (I assume… at least they are for me! ). In this structural biology paper, authors use cryo-EM to show how a bacteriophage docks itself into a receptor protein on the outer membrane of a bacterium. So cool!
Noteworthy things — Week 20 (13/05/2024)
Gut Microbes, 8 January 2024
Comment: I had missed this one from a few months ago, but it is a good one for those interested in precision microbiome engineering! In this study, authors use a synbiotic mix of bacteria and nutrients to control a microbial influence in infants. They looked at what happens after co-delivering Bifidobacterium infantis (an important species in infant microbiomes) with human milk oligosaccharides. As is the goal for synbiotics, they observe that the HMO favours the creation of a stable ecological niche for B. in- fantis to colonize, and together, they impact gut metabolites in the host.
MicrobiologyOpen, June 2022
Comment: From a few years ago, everything you have always wanted to know about metagenome-assembly and MAGs but were too afraid to ask at this point! Very clear and informative.
mSystems, 14 May 2024
Comment: Interesting read of this review re-analyzing 16S rRNA studies from 21 dietary fiber interventions from 12 studies in humans (n=2,564 samples from 538 sub- jects) and showing that the effects of increased fiber consumption seem to be comparable across studies, with the identification of particular genera with consistant re- sponses (increased/decreased abundances after treatment).
Nature Microbiology, 13 May 2024
Comment: Interesting comment on soil microbiology (but also applicable to human microbiomes) and the presence of non-bacterial DNA linked to function. Authors jazzily coin this as “microbial dark matter” but it is now an exciting time (and also high time) to be working on other domains of life present in ecosystems, such as archaea and others.
medRxiv, 1 May 2024
Comment: Really likely to be another very impactful study from the Milieu Interieur consortium in France. In this preprint, authors looked at co-abundance networks in the gut microbiome and described their various aspects exhaustively to find factors linked to variation in these networks. These sort of studies really touch on to the ecology of microbiomes and how dynamic of a system they are. Looking forward to seeing the paper published. (b) Microbial genetics, ecology, evolution and AMR
bioRxiv, 7 May 2024
Comment: As a Staphylococcus enthusiast myself (it is a weird thing to say out of context), how to not be thrilled when seeing a new strain ecology study drop from the Tami Lieberman lab in Boston! In this new preprint, authors profiled ~15,000 pairwise interactions between different skin S. epidermidis strains from 18 individuals and 6 families and found a lot of within-species antagonism linked to strains fitness success, with various mechanistic reasons and linked to horizontal gene transfer. Wonderful job.
Environmental Microbiology Reports, 10 May 2024
Comment: Examples of syntrophy between bacteria and archaea are starting to be studied in detail. Examples include some acetogenic bacteria, which convert fatty acids (butyrate, propionate) with the requirement of H consumption from methanogenic archaea. This recent work from the Netherlands goes a bit further in the characteriza- tion of this functional interaction by examining co-cultures of Syntrophomonas wolfei (bacterium) and Methanospirillum hungatei (methanogenic archaeon) with and with- out addition of the acetate-scavenger archaeon Methanothrix soehngenii using transcriptomics evidence, highlighting the importance of acetate scavengers in the syn- trophic functional community degrading fatty acids.
npj Antimicrobials and Resistance, 7 May 2024
Comment: Very nice longitudinal study characterizing circulating lineages of Staphylococcus aureus causing bloodstream infections in a single hospital (New Hampshire, USA) along a 12-years period. Authors look at the dynamics of lineages and AMR over time, and observe that ST5 and ST8 were more prevalent, with 24 distinct AMR genes conferring susceptibility to 9 classes of antibiotics. Both ST5/8 seemed to have independent acquisitions of beta-lactam resistance. Nice use of time-calibrated phylogenies too with such a collection of strains.
Nature Communications, 10 May 2024
Comment: There is what the sequence analysis tells you, and then there is real life. In real clinical settings, transient resistance to antibiotics is observed. This heteroresis- tance has very biological and ecological reasons and is described as a “medically relevant phenotype where small antibiotic-resistant subpopulations coexist within sus- ceptible bacterial population“. In this study using Klebsiella pneumoniae in mice models, authors investigate 3 mechanisms of gene copy number variation that lead to het- eroresistance, whether by tandem amplification, plasmid copy number increase or transposition of AMR genes onto cryptic plasmids. And when checking real life samples, all three of these also seem to happen in bloodstream E. coli isolates. 2
ISME Communications, 13 May 2024
Comment: Great study working on the hypothesis that spatial ecological proximity between plant-associated bacteria and their hosts could promote cross-kingdom hori- zontal gene transfer, a rare but not unseen phenomenon. Using the highly-sequenced plant model Arabidopsis and its myriad of associated metagenomic datasets, authors look for events of HGT and suggest that 75 unique genes seem to have been transferred, including DET2 involved in phytohormones biosynthesis.
bioRxiv, 12 May 2024
Comment: Vibrio parahaemolyticus is a marine bacterium that can cause seafood-borne illness in humans. This preprint suggests a mechanism for this virulence and host invasion, by identifying a secretion system (T6SS) used to translocate toxins across membranes and activated by human secondary bile acids.
bioRxiv, 5 May 2024
Comment: Sometimes it’s interesting to be able to test how various different species or strains interact together in synthetic medium, but can be cumbersome to design if you have more than a few. In this preprint, authors share their method to design and implement 96-well plate-based experiments to inoculate various synthetic microbial consortia together for future phenotyping, and also cleverly demonstrate feasibility using colorants in the cultures and light spectra analysis. My first thoughts would be to pay particular attention to technical replicates, as wall-specific batch effect and well cross-contamination are not uncommon with 96-well plates (especially if not using a robotic liquid handler). But very cool! (c) Other general interest
bioRxiv, 14 May 2024
Comment: No less! Some similar indexing efforts were done in the microbial field, but in this preprint from ETH Zurich, authors found a clever way to index petabases of DNA from most large sequencing public repositories and make it searchable on this website. Could be useful to generate hypotheses somehow! Happy to hear more about interesting possible uses.
Science, 10 May 2024
Comment: I am absolutely not qualified enough to look at this in detail, but it looks promising enough to be noteworthy? Science has a recent article presenting a new and much cheaper alternative for MRI scanning, which uses a magnet of far less magnetic flux density (0.05T vs 1.5-3T in current MRI), and importantly operates much faster (<10mins) with far less noise, and is much cheaper. I suspect this could have a great impact on medicine in places where current MRI scanners are definitely unaffordable.
Nature Communications, 14 May 2024
Comment: Cool effort in this environmental metagenomic assembly of 2,949 archaeal MAGs from 12 phyla and comprising 392 newly identified species. Authors look at predicted functions in the genomes and provide new insights into the metabolism and ecology of these organisms in geothermal springs. Always amazed to see these eff- fforts describing new uncultured, unknown diversity. What a great time to be a microbiologist!
The Lancet Public Health, May 2024
Comment: There is an urgent need for gender-responsive approaches to health for better equity in the future. In this paper, based on the Global Burden of Disease Study 2021 data, authors look at differences in major causes of disease burden between females and males, across regions of the world and their evolutions since 1990. A trove of very useful information!
Noteworthy things — Week 19 (06/05/2024)
PNAS, 6 May 2024
Comment: Authors show that a high fat diet acts on the gut microbiome and promotes breast cancer/melanoma progression, describing a “gut–bone marrow–tumor” axis. Microbes produce leucine, which activating polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) production. Desulfovibrio seems to be implicated, and is de- tected in cancer patients with worse outcomes.
Cell Host & Microbe, 1 April 2024
Comment: Paper from a month ago, looking at the extent of insertion sequences (IS) in the human microbiota. They provide with a new IS database and observe that gut bacteria have diverse IS maintained over long timescales, but is sensitive to perturbation by nutrients and/or bacteriophages. Interestingly, IS insertions are enriched in “hot spots” in the accessory genomes of bacteria, particularly in susCD/tonB transporters, which encode high-affinity substrate-uptake receptors for carbohydrates and cofactors. All in all, this seems to highlight IS as being an interesting evolutionary and adaptive mechanism to perturbations in the microbiota.
Advances in Therapy, 30 January 2024
Comment: I’ve been told at University 15 years ago that it is a good idea to take probiotics after antibiotics, to promote “good bacteria” after AB-induced dysbiosis (quotes are to insist on the vagueness of this statement). I had missed this interesting study from a few months ago, in which authors suggest that the administration of specific probiotic strains of interest (a yeast, Saccharomyces boulardii CNCM I-745 and a bacterium, Lactobacillus rhamnosus GG) within 48h of starting antibiotics can promote a return to the pre-antibiotic state faster than without.
Cell Host & Microbe, 8 May 2024
Comment: A much needed high-quality review on this topic. Most of microbiome research is performed in high-income country, but in low-income countries (LMICs), a lot of children who are infected by pathogens are co-infected with helminths, which have been proven to induce and add considerable changes on the microbiome and a very important impact on morbidity. This echoes in my mind with the 2011 study from Fumagalli et al. showing that pathogen (helminth) pressure was probably one of the main selective pressure throughout human evolution.
Nature Communications, 3 April 2024
Comment: In the same week showing that APOE4 homozygotes have nearly 100% penetrance for a distinct form of AD, I was reminded of this month-old study on the contribution of the microbiome in AD’s pathogenesis, by suppressing immune mediated amyloid clearance by microglia in mice, and seems to be mediated by members of the Bacteroidota phylum. A very complex multi-factorial disease indeed. (b) Microbial genetics, ecology, evolution and AMR
eLife, 2 May 2024
Comment: A very promising looking method to predict metabolic pathways and interactions in genomes with a focus on incompleteness, which is quite an important addi- tion compared to other approaches like METABOLIC. We’ll definitely give it a try.
The Journal of Wildlife Management, 24 April 2024
Comment: The fight against worldwide AMR takes multiple OneHealth approaches, as the spread can be clinical, enviornmental and affect many hosts beyond humans. In this interesting review, authors highlight wild birds as important sentinel and carriers for AMR, but there are many challenges and outstanding questions regarding trans- mission. Sensible recommendations included for surveillance standardization.
Plos Biology, 7 May 2024
Comment: It is almost unbelievable (and puzzling — personal opinion) that the LTEE has stayed relevant to some for so long, but it seems to be! In this paper, Jeff Barrick, Howard Ochman and colleagues look at where new E. coli genes come from. They suggest that within the very controlled and in vitro environment of the LTEE, promoters can arise from transposable elements to create “new” genes. Interesting! (c) Other general interest
BMJ, 8 May 2024
Comment: An impactful exhaustive study from USA with >30 years of follow up of more than 115,000 people, highlighting outcomes from consuming ultra-processed foods (UPFs). Higher intake of UPFs was associated with slightly higher all cause mortality, not just caused by cancer and CVD. Associations varied but ready-to-eat meat/ poultry/seafood-based UPFs showed particularly strong associations with mortality. In a meta-analysis, UPFs were shown to be linked to 40% higher risk of T2D, 35% higher risk of CVD, 23% higher risk of hypertension, 55% higher risk of obesity, 81% higher risk of metabolic syndrome and 50% higher risk of CVD mortality. Article about it in the New York Times.
Egan — New England Journal of Medicine, 9 May 2024
Comment: The mini-abstract of this review is very short and speaks for itself: “Much of what we learned in school about how we taste is wrong. Progress in understanding how taste works is providing insights that may help in the management of obesity, diabetes, and other illnesses“. A great and enlightening read, with very nice figures.
Environmental Microbiome, 7 May 2024
Comment: An environmental microbiology paper, but the approach was quite interesting and innovative. Authors wanted to look at what changes occur in the soil microbial communities when crops grow and rotate in the same field. To do so, they created ‘soil sentinels’, which are permeable bags of autoclaved soil acting as a substrate for wild microbes to colonize, buried those and looked at their microbial composition at different intervals. They show that the approach work, and seems to capture microbial taxa that actually differentiate crops much better than if whole soil communities would be compared. Noteworthy preprints:
bioRxiv, 2 May 2024
Comment: Promising tool to explore pangenomic co-occurrence (and “co-avoidance”) in microbial genomes, with a particular care on distinguishing linkage due to shared ancestry from traces of actual co-selection. We’re definitely going to check this out but let us know if you are too.
bioRxiv, 5 May 2024
Comment: The skin microbiome (as all the other microbiomes) is not just composed of bacteria, and yet, the non-bacterial parts are routinely plainly ignored by many stud- ies. In this study, authors show that a fungal species, Malassezia sympodialis reduces skin colonization by Staphylococcus aureus through bactericidal activity. Some S. au- reus strains with mutations in the GTP pyrophosphokinase Rel can resist this antagonism, which seems to coincide with multidrug emergence in the same strains.
medRxiv, 8 May 2024
Comment: This study from Phil Ashton and international colleagues describes tuberculosis isolates in a poorly-studied region. They show that a majority of Papuan M. tu- berculosis (71.4%) are from the L1.2.1.2.1 sublineage. Genomic analysis suggests frequent introductions and a long-standing presence of MTB L1 in the region, widespread transmission across different districts and ethnic groups in Papua and very little drug resistance (11.9%), attributed to limited healthcare infrastructure and ineffective treatment programs in the region. Other noteworthy things:
Noteworthy things — Week 18 (29/04/2024)
Nature, 1 May 2024
Comment: Quite an impressive find this week in Nature, in which authors report that altering the community of gut bacteria in male mice can have negative consequences for the health and lifespan of their offspring. Male mice given antibiotics targeting gut microbes showed RNA changes to their testes and sperm, which led to their off- spring having a higher probability of growth issues. Authors even go to the extent of naming this a potential regulatory ‘gut–germline axis’ in males. It’s quite unclear whether this could be found in humans, but I suspect social and other external confounders would overwhelm that germline effect quite strongly. Still very interesting and puzzling. Well written “News & Views” associated article in Nature too.
Nature Microbiology, 2 May 2024
Comment: Interesting hypothesis-driven framing of this study. Authors investigate the increased relative abundance of oral bacteria in faeces in mice, and examine two competing interpretations: the ‘expansion’ hypothesis, where oral bacteria invade the gut ecosystem and expand, and the ‘marker’ hypothesis, where oral bacteria transit through the gut and their relative increase marks the depletion of other gut bacteria. The latter seems to prevail, which is (I believe) very impactful for microbiome studies in general. A lot is still unknown on the role and function of bacteria that transit in the gut vs. those that are established residents, and these results contribute to under- standing this better.
Nature Ecology & Evolution, 1 May 2024
Comment: One of these very cool stories that is perhaps not surprising in hindsight, but that somebody had to look up. We know that microbes transmit between individu- als, and observe individuals within families or households with more of the same microbes, for instance. In this article combining wild radio-tagged wood mice (to infer their social interactions) and 16S rRNA gut microbiota profiling, authors show that different sets of gut microbes spread through different groups: social contacts tend to spread more anaerobes whereas shared environments (without close contact) spread more aerophilic taxa. Seems intuitive, but implications are very interesting and it’s a very cool study!
npj Antimicrobials and Resistance, 22 April 2024
Comment: Interesting new paper from the OUCRU team in Vietnam. The study investigates the impact of antibiotics on the gut microbiota of children recovering from wa- tery diarrhoea from a longitudinal cohort of a recent randomised control probiotic trial in Vietnam. Interestingly, it shows that when antibiotics were administered (~40% of these kids were treated with ciprofloxacin/cephalosporins), recovery was slower, as alpha and beta diversity remained lower for longer, with a transient overabundance of Enterococcus and depletion of Bifidobacterium pseudocatenulatum.
Nutrition & Hypertension, 12 April 2024
Comment: New review on the topic of gut health and hypertension by collaborators at Monash University. This one interestingly summarises what is known about the ob- servation that hypertension increases gut permeability, with subsequent microbiome/health impacts. There is a scarcity of human studies while this is starting to be well observed in humans.
Cell Host & Microbe, 22 April 2024
Comment: We all know there is a world of phages in the gut and other microbial envionments, but they are quite difficult to study in their entirety for various technical and biological reasons. This very interesting work starts from the observation that bacterial colonies isolated from faeces are heavily depleted in virulent phages, as they are not amplified on synthetic media. From there, authors reintroduce virulent phages into synthetic strain communities (up to 73 strains) to show which ones can impact which susceptible microbes and their prophages.
Nature Methods, 30 April 2024
Comment: Long-read sequencing applied to metagenomics is a very promising alternative but has been lagging due to scale-up costs and lack of specific tools. This is changing and this review is a good overview on this.
Cell Host & Microbe, 23 April 2024
Comment: In the brain, serotonin acts as a neurotransmitter, but most serotonin is produced by the gut microbiota, and helps control bowel function and nutrient absorp- tion. In this study, authors look at how the gut microbiota can deplete amino acids and affect AA homeostasis. They find that depletion of branched-chain AA and trypto- phan regulates glucose tolerance via peripheral serotonin production, which has quite interesting implications linking diet and nutrient absorption.
Schizophrenia, 8 April 2024
Comment: Functional causal studies on the gut-brain axis are complicated to realise, low-powered and sometimes quite difficult to interpret. This is an interesting attempt in which authors transplanted the gut microbiota from schizophrenic patients into mice, and observed schizophrenia-like symptoms in social behaviour, as well as modifica- tions in the brain transcriptomes.
Nature Reviews Gastroenterology & Hepatology, 10 November 2023
Comment: I had missed this review on characterizing the various different stages of IBD, which is a very difficult spectrum to carefully diagnose and understand. Defining better diagnostics points will allow a better understanding of its progression. This review is very exhaustive on the matter, if you’re interested. (b) Microbial genetics, ecology, evolution and AMR
Nature Microbiology, 29 April 2024
Comment: Using microbes to engineer universal blood type has been a story in the making for a few years now. This led to the identification of carbohydrate-active en- zymes able to convert of A and B blood group erythrocytes to blood group O (which was of prime importance for our interpretation of ABO-microbiota links in our 2022 mi- crobiome GWAS work in which we found more of these CAZymes in taxa associated with ABO variation in humans). This study pushes the boundaries further, with the identification of exoglycosidases from the well-described mucin-degrading Akkermansia muciniphila. This strongly suggests that mucin-degrading bacteria could be valu- able sources of enzymes for production of universal blood for transfusions. Exciting prospect!
The ISME Journal, 22 April 2024
Comment: I really enjoyed reading this one. Bacteria (unsurprisingly) move towards food! Authors screened ~26,000 bacterial genomes across 12 phyla for flagellar genes as a proxy to predict flagellar motility. They observed that predicted motility seemed to be associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates. Then, in 4 independent soil experiments collecting the microbiome and measuring gradients in soil carbon availability, they ob- served a positive relationship between flagellar motility and soil carbon availability in all datasets, validated by an in vitro soil incubation experiment.
Ecology Letters, 11 April 2024
Comment: As more and more longitudinal microbiome samples are being generated, it becomes possible to model how species interact with each other. From a simplistic point of view, looking at variations in levels of co-abundant taxa (or how that co-abundance metric varies in time) can help us infer what are the growth/depletion dynamics of said taxa, and potentially how they interact ecologically. Until now, the best approaches for this were summarized well by models based on Lotka–Volterra equations, which were initially developed to model predator-prey competition interactions. In this paper, which I am not skilled enough to understand in precise detail, authors develop a way to introduce a third species into what has been traditionally a two-species model. Potentially very cool if applied to longitudinal microbiome datasets, I think!
The Lancet Gastroenterology, May 2024
Comment: This review focuses on very promising new applications of microbial bioengineering with health outcomes. Examples include the delivery of engineered Lactococcus lactis to deliver proinsulin and IL-10, to promote immune tolerance to proinsulin and suppress autoimmunity in type 1 diabetes patients. Another example is the delivery of cancer antigens as live attenuated vaccines for cervical, prostate, or pancreatic cancer via engineered Listeria monocytogenes. Finally some mention of en- gineered E. coli strains to degrade phenylalanine that detrimentally accumulates in patients with phenylketonuria. (c) Other general interest
iMeta, 4 July 2022
Comment: An old publication that I had missed, and haven’t tried yet. From having done Circos plots in the past the hard way, this could help make them a bit more easily. Let us know if anyone has tried!
(Segata/Ceresto groups) Nature Communications, 24 April 2024
Comment: The CRISPR-Cas9 revolutionary genome editing tools that are based on microbial enzymes. In this study, authors screen a repository of MAGs from micro- biomes and uncover a large variety of new Cas9 enzymes (n=17,173). They highlight a particular one, CoCas9, from Collinsella sp. which is highly active and high-fidelity, and can expand the current toolbox for genome editing.
Science, 26 April 2024
Comment: A great effort in yeast genomics and ecology this week in Science. Based on sequences, metabolic diversity and phenotypes of 1,154 new yeasts, authors sug- gest a surprising lack of trade-off in growth rate between specialists and generalists. In other words, on particular substrates, specialists of that substrate don’t always seem to grow faster than generalists, which sometimes outcompete them. Puzzling and interesting! Noteworthy preprints:
bioRxiv, 21 April 2024
Comment: Authors found here that Lactobacillus gasseri and the Lachnospiraceae family are associated with enhanced resistance to SHIV infection in a pediatric nonhu- man primate cohort. Two Lachnospiraceae in particular, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo via tryptophan metab- olism into 3-indolelactic acid, which agonizes the aryl hydrocarbon receptor (AhR). Metagenomic analysis of individuals at risk for HIV showed a lower fecal abundance of the bacterial ArAT gene in those who acquired HIV compared to those who did not, indicating a protective role of ArAT-expressing bacteria in humans.
bioRxiv, 29 April 2024
Comment: In this work, authors identify and characterize pMMCAT, a large conjugative plasmid, frequently transferred among Bacteroidales species and ubiquitous in di- verse human populations (as profiled in 4,467 human faecal metagenomes from healthy adults in 26 countries). pMMCAT encodes both an extracellular polysaccharide and fimbriae and promotes multispecies biofilm formation in vitro and in the mammalian gut, which could explain its persistance and distribution.
bioRxiv, 19 April 2024
Comment: Very interesting and this is likely going to be an impactful paper! Fasting causes extensive remodelling of the gut microbiome at species level, affecting ~2/3 of examined species in this study. CAZyme profiling alone can reveal that a metabolic switch occurs during long-term fasting, from dietary fibers to host glycans, which does not seem to involve the main suspected species Akkermansia muciniphila. When looking at the serum metabolomes, they saw changes in ~52% metabolites after fasting, including microbiome-derived metabolites such as indole-3-propionic acid, suspected here to be produced by Oscillibacter with potential links to cardiometabolic health. Other results can be seen in this exhaustive paper, and on Robin Mesnage’s (senior author) tweet thread. Other noteworthy things:
Noteworthy things — Week 17 (22/04/2024)
Nature Biotechnology, 15 April 2024
Comment: Quite a unique proof-of-principle effort of combining microbiome science with citizen science, this time by crowdsourcing a multiple alignment task of 1 million 16S ribosomal RNA sequences obtained from human microbiome studies into a minigame inside the video game Borderlands 3. An interesting news article about it can be found here. Actual real-life benefits from it are still a bit nebulous to me, but it definitely is a cool project!
Cellular and Molecular Gastroenterology and Hepatology, 18 April 2024
Comment: Irritable bowel syndrome (IBS) is a complex disease which can present with various diverse symptoms, which means that the few different ways to diagnose it will impact how we research it. This interesting study from colleagues at Monash University in Melbourne (and others) uses the UK Biobank and the LifeLines cohorts to highlight new genetic links between IBS and cardiovascular diseases when diagnosis follows the Rome III criteria.
iScience, 18 April 2024
Comment: It’s often very valuable to have an intermediate in vitro validation model between in silico and in vivo investigations of host-microbes interactions. In this new in- teresting study from the lab of Susana Fuentes (RIVM, Netherlands), authors present a new in vitro model system to study host-commensal-pathogen interaction and im- mune responses, using cell cultures and human intestinal enteroids. It seems to respond well to co-cultures too!
American Journal of Clinical Nutrition, 29 February 2024
Comment: From a few months ago, this is from the interesting (PREDIMED)-Plus RCT from Spain investigating the effects of a 1 year of intensive intervention (Mediterranean diet and exercise regime) on fecal metabolites, gut microbiome and CVD risk factors in overweight people, to measure impacts and changes of lifestyle changes on health. Results highlight notable differences in patient following by dieticians vs. self-imposed on weight reduction and general health. Fecal metabolites and the gut microbiome are impacted, with Eubacterium and Dorea being highlighted. One of our collaborative 2021 FINRISK study on microbiome association with healthy food choices led by Kari Koponen (in the same journal) had also highlighted Eubacterium to be linked with healthier food choices, so there might be something there!
Nature Reviews Gastroenterology & Hepatology, 22 February 2024
Comment: Also from a few months ago, this very timely review from Benoit Chassaing’s lab on how ultra-processed foods impact the gut microbiome and health. Very good nutrition and immunology examples, a quite exhaustive review!
Nature Communications, 20 April 2024
Comment: Promising new tool to improve MAG recovery when assembling metagenomes. I particularly like the integrative approach; maybe could be one to test? Happy for comments if you already have. (b) Microbial ecology, evolution and AMR
npj Antimicrobials and Resistance, 15 April 2024
Comment: There is an interesting (and complex) debate on whether microbial adaptation to compounds that are not thought to be antimicrobial could actually be and drive antimicrobial resistance or cross-resistance. In this brief but interesting study, authors observed toxicity (inferred through reduced optical density of in vitro cultures) of ac- etaminophen (paracetamol), ibuprofen, propranolol (beta-blockers) and metformin on the lab strain E. coli K-12 MG1655. Interestingly, a 30-day exposure experiment did not show an increased cross-resistance with antibiotics. (c) Other general interest
Zuntini et al, 24 April 2024
Comment: If like me you like to see “new things having their genome sequenced”, this is for you. A major genomics study has been published in the field of plant biology, wit a new phylogeny being presented for angiosperms, inbluding ~60% of all genera (n=8000), a 15-fold increase in numbers compared to previous efforts. Figure 1 is a beautiful poster-worthy tree, and other results include attempts at timing the phylogeny and insights into diversification of angiosperms in the Mesozoic and Cenozoic Eras.
Noteworthy things — Week 16 (15/04/2024)
Cell, 11 April 2024
Comment: The FHS cohort was used to identify microbes and metabolites associated with CVD, and highlighted Oscillibacter sp. as being associated with decreased blood and stool cholesterol. Subsequently, Oscillibacter sp. were found to encode for conserved cholesterol-metabolizing enzymes, which could causally explain the observation!
Cell Host & Microbe, 10 April 2024
Comment: Very good longitudinal, multi-body site study on the human microbiome! Highlights are that the stability of the microbiome seems to vary among individuals and body sites (not unexpected), but interestingly, more “individualized” microbial genera look like they are more stable over time. Also, disease induces coordinated microbial dynamics at each body site, which suggests a systemic response from disease impacting microbes, and finally, authors show that microbiome stability and skin microbial composition are altered with insulin resistance.
Nature Reviews Microbiology, 18 December 2023
Comment: Very thorough review from a group in Israel, formalising the various knowledge and approaches enabling the use of microbiome modification in precision medicine. Very useful ref for many in the field, I’m sure!
Cell Host & Microbe, 10 April 2024
Comment: As multi-omics and/or extensively phenotyped datasets become larger and more body sites in the same individuals become more “matched”, the importance of the oral microbiome in general health starts to be confirmed (it always had kind of been hypothesized). This paper highlights that the human dental plaque and oral ab- scesses can harbor multiple types of oral fusobacteria, that F. nucleatum subspecies prevalence stratifies by ecological niches and that subsp. animalis seems to dominate in absesses. Interestingly too, authors suggest that F. nucleatum should be reclassified, as it clearly seems to harbour ecologically and taxonomically distinct (currently called) subspecies. Very nice “Preview” article in the same issue too.
Cell Reports, 15 April 2024
Comment: Interesting further links between the gut-brain axis and tryptophan metabolism. Chronic stress affects tryptophan metabolism in the gut in such a very sensi- tive manner that it is observable as diurnal oscillations in this mice study. Authors used metabolomics to see that Trp metabolism was one of the most affected pathway af- ter stress, and Trp-producing gut bacteria are the most affected by diurnal rhythmicity.
Cell Host & Microbe, 10 April 2024
Comment: Interesting new IBD study in mice, highlighting the importance of mucus-degrading microbiota in the disease. In this integrative approach, authors show that a combination of genetics, reduced dietary fiber & mucolytic bacteria can trigger IBD in mice. More specifically, mucus loss can promote type 1 T helper (Th1) cells (which produce interferon-gamma, IL-2, and TNF-beta), which drives colitis. Interestingly a fiber-free exclusive enteral nutrition seems to promote bacterial isobutyrate and pre- vent colitis.
The Lancet Gastroenterology & Hepatology, 12 April 2024
Comment: Interesting review summarizing the current state of all methods available to engineer microbiomes, such as probiotics, prebiotics and FMT as well as their cur- rent limitations and future prospects.
Xiaowen Feng & Heng Li, Genome Biology, 11 April 2024
Comment: New promising metagenome-assembly tool? Authors present a novel “reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs” after observing that “even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs.” (b) Microbial ecology, evolution and AMR
Nature Metabolism, 12 April 2024
Comment: Streptomyces sp. are notoriously very abundant in biosynthetic gene clusters (BGCs), and their metabolic flexibility and are used in bioengineering for creating mutants with particular metabolic abilities, for example for industrial production of particular compounds. Aside from this strategy, not much else is done to enhance the efficiency of these cloned BGCs but in this study, authors examined whether you could identify other genes that have co-evolved with the BCGs, and whether they im- proved biosynthetic abilities if you cloned them along with the BCGs. And they did!
Wright BMC Genomics, 15 April 2024
Comment: This is somehow not a surprising fact, as often are all bioinformatics-driven “dogma” in biology. This paper explores how much of the genes that are annotated as pseudogenes may be wrongly so due to technical limitations. The conclusions of the paper: “many pseudogenes in microbial genome assemblies are actually genes; high read coverage is required for correct assembly and indicate an inflated number of pseudogenes due to internal stops is indicative of poor overall assembly quality.”
Scientific Reports, 22 March 2024
Comment: Authors use fluorescent reporters to measure how exactly antibiotics can cause translation errors in bacteria. From the abstract: “Bactericidal amikacin induced preferably stop-codon readthrough at a moderate level. Bacteriostatic azithromycin on the other hand induced both frameshifting and stop-codon readthrough at much higher level. Single cell analysis revealed that fluorescent reporter-protein signal can be lost due to leakage from a fraction of bacteria in the presence of antibiotics, demonstrating the complexity of the antimicrobial activity”
Antimicrobial Agents and Chemotherapy, 8 April 2024
Comment: A pretty interesting study in my book! This study looks at transcriptomic response to 17 antibiotics in M. tuberculosis. Authors focus on the response speed of M. tuberculosis to antibiotics, but I am kind of fascinated at the amount of genes responding to antibiotics, and wondering about individuality in AB response in bacteria and whether it could explain differences in MICs or other. (c) Other general interest
New England Journal of Medicine, 10 April 2024
Comment: Very interesting review on the history of “recommended dietary requirements”, energy from diet and macronutrients.
Letunic & Bork Nucleic Acids Research, 13 April 2024
Comment: New version of the useful iTOL platform to visualise phylogenetic trees.
Nature Communications, 17 April 2024
Comment: What happens to bacteria when environmental conditions fluctuates and become unfavourable? We assume most of them are going dormant? Some of them die? Do functional communities survive somehow? I love these “real life” microbiology investigations like this one, where authors simulated rain on biocrust microbial com- munities from a desert and looked at microbial survival and resuscitation. Conclusions: desert communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity at the community level. Other noteworthy things:
Noteworthy things — Week 15 (08/04/2024)
Cell, 9 April 2024
Comment: Quite impressive integrative study of matched datasets (metagenomics, genomics, transcriptomics, and clinical data) for 4,160 metastatic tumor biopsies from the Hartwig pan-cancer metastasis cohort (on 26 cancer types). In the light of previous “debate” on the topic, tumor-resident bacteria DNA could be detected, and assem- bled into species-level MAGs, revealing that bacterial diversity is associated with specific cellular and molecular tumor immunity features. Interesting, the main culprit seems to still be a main culprit: Fusobacterium DNA abundance associated with poor immunotherapy response in a non-small cell lung cancer (NSCLC) validation cohort. Aside from this comment, there is already controversy on the methods (link on Twitter), as cancer/fetal microbiomes are quite (rightfully) debated subjects.
Cell Host & Microbe, 2 April 2024
Comment: In this interesting intervention RCT, authors fed n=210 infants with breastmilk or various formula compositions to show that the global microbiota assembly in infants is affected more by age than diet. Interestingly, bacterial rhythmicity was observed to be present in the infant gut and increased with age. Even more interestingly, circadian control of bacterial rhythms could be reproduced ex vivo in continuous cultures in chemostats.
Nature Reviews Gastroenterology & Hepatology, 4 April 2024
Comment: Very seminal and timely review from Peter Dorrestein’s and Rob Knight’s labs which details latest knowledge on the essential role of bile acids in human biology and suggests novel pathways to target them.
Nature Communications, 8 April 2024
Comment: The study provides direct evidence of a skin-gut axis by showing that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut mi- crobiome (in mice), including increased expression of host defense genes in the colon (Muc2 and Reg3) and changes the composition and behavior of intestinal bacteria, some of which are seen to penetrate the intestinal epithelium and enhance colitis from DSS.
Cell, 29 February 2024
Comment: Sorbitol intolerance is generally believed to be caused by malabsorption, but the actual underlying mechanism remains unknown. Through observation and complementation with sorbitol dehydrogenase-expressing probiotic strains, this study gives very interesting evidence in mice pointing to microbial sorbitol catabolism as a key player in overall sorbitol intolerance.
Cell Reports Medicine, 5 April 2024
Comment: There’s been an increasing realisation over the years that circulating blood could contain quite a lot of microbiome-derived features like DNA (and probably transiently some actual microbes), and this nice report shows that circulating microbiome DNA can be used as a (predictive) biomarker of incident lung cancer (using a moderately small cohort of 416 participants before splitting into training/validation groups).
Cell Metabolism, 5 April 2024
Comment: Another interesting gut-brain axis study coming up, this time on the role of homovanillic acid (HVA), a neurotransmitter linked to depression when depleted. Authors have found that gut Roseburia intestinalis promotes the abundance of Bifidobacterium longum for HVA production, and that complementation with HVA, or B. longum, or R. intestinalis alleviated depression in mice. Proposed mechanism is that HVA restores synaptic function by inhibiting autophagic death. Very cool!
Molecular Neurodegeneration, 1 April 2024
Comment: Interesting commentary on the possible infectious aethiolgy of Alzheimer’s Disease. AD patients have higher than normal levels of LPS endotoxin in their blood and there is a current hypothesis that LPS from gut, lungs or gums may increase blood LPS, which may directly or indirectly increase the pathology of Aβ, TAU and mi- croglia, to exacerbate Alzheimer’s disease. This adds to some earlier hypotheses that HSV-1 could also contribute. Would be interesting to see how this conflates with APOE ε4 status.
Hypertension, 8 April 2024
Comment: This new paper from the Marques Lab (Melbourne, Aus.) builds on previous work showing evidence that fibre intake can lower blood pressure via an increase in microbial production of short-chain fatty acids. This new publication interestingly formalises suggested recommendations for this.
Science Translational Medicine, 10 April 2024
Comment: Likely quite an impactful study, showing that many pathogens that cause surgical site infections during spine surgery come from the patient’s own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols. Also a very good commentary from Jack Gilbert & John Alverdy in the same issue.
The Lancet Microbe, 9 April 2024
Comment: Very interesting ecological perspective on pathogens/commensals in humans, and how to better integrate research in infectious disease.
npj antimicrobials and resistance, 1 April 2024
Comment: Very interesting review from the University of Exeter (UK) summarizing what is known about the influence of micropollutants on AMR spread in the environ- ment, including metals, non-antibiotic drugs (ibuprofen or even the antidepressant fluoxetine!) or even fungicides (like mancozeb).
ISME Communications, 27 March 2024
Comment: It is a very important challenge in microbiology to experimentally functionally study complex assembled community of microbes interacting with each other. This study provides with interesting considerations derived from in vitro monocultures and supernatant analyses.
mSphere, 5 April 2024
Comment: A lot has been described for the pathogen Acinetobacter baumannii but far less comparatively for another species in the genus, A. lwoffii. Authors present one of the first comprehensive study on this species, which has emerging pathogenic potential and has thus remained more antibiotic-sensitive than A. baumannii.
Nature Microbiology, 18 January 2024
Comment: From a few months ago, this study “demonstrate[s] that a specialized subset of [Yersinia entomophaga] produces a complex toxin cocktail […] which is subse- quently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS)”. (c) Other general interest
Science, 10 April 2024
Comment: Not every day you see the discovery of a new organelle in a eukaryotic species!! Meet the “nitroplast”, nitrogen-fixing organelle identified in the green alga Candidatus Atelocyanobacterium thalassa.
New England Journal of Medicine, 7 April 2024
Comment: The early clinical trials for routinely prescribing beta-blockers after heart attacks were performed decades ago, and we now have better tools to assess their efficacy. A new randomized trial in people with preserved ejection fraction (EF>50%) shows they’re not helpful or necessary.
Nature Medicine, 7 April 2024
Comment: Hopeful results in a clinical trial using personalized therapeutic cancer vaccines (PTCV) to induce antitumor T cells which, in combination with pembrolizumab (anti-cancer antibody) is showing clinical activity in advanced liver cancer.
Psychological Medicine, 4 September 2023
Comment: If you sometimes wonder (like me, as a microbiologist) why the gut-brain axis is so hard to study robustly in humans, this could be one of the reasons to keep in mind. In this study (summarized very well by Nicholas Fabiano on Twitter here) authors map the repetition among the 1419 symptoms described in 202 diagnoses of adult psychopathology in section II of the DSM-5 and finds that although ~65% of distinct symptoms are unique to a single diagnosis, ~70% of the diagnoses also have at least one symptom repeated in another diagnosis and/or “chapters” (categories). Symptoms of major depressive disorder (MDD) seem to also repeat the most frequently. This shows how tricky it can be to categorise invididuals with mental health symptoms for downstream analyses.
PNAS, 10 April 2024
Comment: Fascinating findings suggesting that the vertebrate IRBP gene (for interphotoreceptor retinoid-binding protein) has a bacterial origin. Commentary here. Noteworthy preprints:
bioRxiv, 18 April 2023
Comment: Preprinted a while ago but still a very interesting new technique (“phylogenetic compression”) to search (and align) a large amount of sequence data with much greater speed. Michael Baym had done a good Twitter thread detailing it. Other noteworthy things:
Noteworthy things — Week 14 (01/04/2024)
Cell, 2 April 2024
Comment: Multi-omic profiling in the US-based Framingham Heart Study identifies microbes/metabolites associated with CVD. Oscillibacter sp. are associated with de- creased blood and stool cholesterol, and are found to encode for conserved cholesterol-metabolizing enzymes.
Cell, 3 April 2024
Comment: Very exhaustive and impressive study! Using the All Babies in Southeast Sweden (ABIS) cohort, a birth cohort with 20 years follow-up (n=16,440; with n=1,197 developing an ND), these authors show that microbes and associated metabolites in infants contribute to future neurodevelopmental disorders (NDs) (other contributors to higher ND risk are preterm birth, infection, stress, parental smoking and a specific HLA variant). Other results include early-life otitus lowering Coprococcus sp. and increas- ing Citrobacter sp. in future NDs, potentially once again highlighting the role of early infection in incident disease risk/development.
Microbiome, 26 March 2024
Comment: “Pre-term birth, the leading cause of neonatal mortality, has been associated with maternal periodontal disease and the presence of oral pathogens in the pla- centa.” This study finds evidence to suggest that oral bacteria might translocate to the placenta via serum and trigger immune signaling pathways capable of inducing pla- cental vascular pathology
npj Biofilms and Microbiomes, 30 March 2024
Comment: Intriguing observation! Authors examined biliary stents from pancreatic cancer patients and found that 17 of 36 prevalent stent species are also common oral microbiome members, associate with disease conditions when present in the gut, and include dozens of biofilm- and AMR-related genes. Not a lot is hypothesised yet on the origin of these microbes or the infection route…
Environmental Microbiome (19), 28 March 2024
Comment: Interesting benchmarking study looking at various different conditions and classifiers with mock soil metagenomic datasets, with the conclusion: “Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.“. It somehow mirrors what we have been using (among other things) in our group for metagenomics classi- fication, with the tweaking of confidence parameters for Kraken2.
Cell Host & Microbes, 01 April 2024
Comment: New catalogue and tool to detect IS insertions. Intestinal bacteria have diverse IS insertions maintained over long timescales, which are enriched in accessory genes, such as susCD/tonB transporters. IS insertion activity seems to be affected by perturbations like nutrients and phage.
Nature Review in Microbiology, 4 April 2024
Comment: Microbiologists often think of sepsis and entry of pathogens through wounds or epidermis disruption of some kind. This recent review is a good summary of what we know on what happens in wounds re: microbial diversity and immune responses.
Microbial Cell Factories, 30 March 2024
Comment: Interesting review summarizing what is likely to happen in a bacterial cell when a protein is overexpressed. Authors focus on bioengineering and synthetic biol- ogy applications, but I think this could be generally speaking something quite fundamental to understand when thinking of bacterial evolution, horizontal gene transfer and adaptation.
mSystems, 26 March 2024
Comment: Interesting new improved genus-wide dataset from the zoonotic pathogen Campylobacter. This paper provides with a good new addition from our previous genus-wide study in eLife (link) led by Evangelos Mourkas (now Uppsala University).
The Lancet Infectious Diseases, 26 March 2024
Comment: A very concerning prospect: “Major priorities at present are the expansion of genomic surveillance for ART-R mutations across the continent, more frequent testing of the efficacies of artemisinin-based regimens against uncomplicated and severe malaria in trials, more regular assessment of ex-vivo antimalarial drug suscepti- bilities, consideration of changes in treatment policy to deter the spread of ART-R, and accelerated development of new antimalarial regimens to overcome the impacts of ART-R.“
Journal of Bacteriology, 23 February 2024
Comment: Interesting minireview (with absolutely stunning figures) if you are also puzzled about the variability and prevalence of actin-like proteins in microbes (over 40 classes found in bacterial genomes and plasmids, remarkably divergent compared to eukaryotes). The current hypothesis supported by this review is for an engulfment model for eukaryogenesis, where archaeal membrane protrusions encircling a bacterial partner eventually fused to produce an archaeal host cell with a stably engulfed bacterial endosymbiont. Cool stuff!
Nature, 1 April 2024
Comment: Very important paper for those with an interest in birds (like I do)! The approach is something quite nice that we had somehow also done for bacteria in some early studies (but not on that scale at all!): in this study, authors reconstructed local phylogenies at 150,000 loci from 363 avian species, building thousands of species trees and test the impact of data quantity and taxon sampling. They found many incongruences of these local trees with the species trees (great examples here from a second paper from some of the authors published in PNAS on the same day), suggesting gene dynamics at the family-level. Not entirely surprising when you know bird, ring species and how promiscuous bird ecology can be sometimes. Very cool stuff!
Scientific Reports 14:7003, 25 March 2024
Comment: Just because how cool is that!! Findings are as expected, finding usual suspects and possible new taxa to consider for the field of historical artefact conserva- tion.
Nature Communications, 12 March 2024
Comment: Authors suggests that biases in scientific literature might have led to the common belief that males are generally larger than females, while the opposite is true for most mammal species.
Neurology, 21 March 2024
Comment: Caffeine consumption (mainly through 2 metabolites, paraxanthine and theophylline) has been indicated to play a significant role in reducing risk of PD, as well as mitigating PD symptoms in animal models. In this study, authors looked at a population-based 20y-long longitudinal cohort across 6 European countries (EPIC4PD study) to show that coffee consumption inversely correlated with risk of developing PD. Those who consumed the highest amounts of coffee exhibited ~40% lower risk of PD compared to coffee non-consumers.
Juho Pelto, Kari Auranen, Janne Kujala, Leo Lahti aRxiv, 3 April 2024
Comment: Very comprehensive and nice assessment of differential abundance methods (DAA) in microbiome science.