Our last weekly summary of July 2024, summarizing what caught our eye in the field of microbiome research, microbial genomics/ecology, and others. Comments in blue are personal and hopefully useful! Just as a reminder: you can subscribe to this weekly list via WordPress (bottom right of the screen) or the RSS feed.

In this post, I’m introducing some tags and topic keywords, as I realised there is quite a varied breadth of topics presented. Hopefully this is clearer and will allow the reader to focus on what’s relevant. Always open to suggestions on how to improve clarity and readability, if you have ideas!

I also post these pages on Twitter, BlueSky and LinkedIn, but feel free to share them wherever. Hopefully this is interesting to some, let us know! 🙂

(a) Microbiome

• PREPRINT: Early life microbial succession in the gut follows common patterns in humans across the globe
  Guilherme Fahur Bottino et al. 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!
  Topics: early-life microbiome; multiple human cohorts, prediction

• STUDY: Gut microbial features and circulating metabolomic signatures of frailty in older adults
  Yanni Pu, Zhonghan Sun, Hui Zhang, Qingxia Huang et al. 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 metabolites with altered abundances correlating with frailty severity, consistently associating F. prausnitzii. Sex-specific differences were also observed, with more dramatic microbial 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.
  Topics: aging microbiome; links with frailty and mortality; human cohort

• STUDY: Enhancing recovery from gut microbiome dysbiosis and alleviating DSS-induced colitis in mice with a consortium of rare short-chain fatty acid-producing bacteria
  Achuthan Ambat et al. 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 indica 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.
  Topics: functional microbiome; importance of low-abundance taxa; mouse model

• REVIEW: The oral–gut microbiome axis in health and disease
  Benoit J. Kunath et al. 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.
  Topics: oral-gut axis, impact of oral microbes on health

• STUDY: Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics
  Sophie M. Leech et al. 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.
  Topics: early-life microbiome; human cohort

• STUDY: Gut microbiota signatures of vulnerability to food addiction in mice and humans
  Solveiga Samulėnaitė, Alejandra García-Blanco, Jordi Mayneris-Perxachs et al. 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.
  Topics: links with diet; functional microbiome; mouse and human study

• REVIEW: The interplay between diet and the gut microbiome: implications for health and disease
  Fiona C. Ross et al. 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, polyunsaturated fatty acids, SCFAs, etc. Very exhaustive and actually quite an authoritative review to recommend for anyone interested in the human microbiome.
  Topics: links with diet; impact of different types of fibre

• STUDY: Maternal Diet and Gut Microbiota Influence Predisposition to Cardiovascular Disease in Offspring
  Hamdi A. Jama et al. 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.
  Topics: mouse model; early-life microbiome; links with diet

• STUDY: Diet at birth is critical for healthy growth, independent of effects on the gut microbiota
  Lieke J. W. van den Elsen et al. 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.
  Topics: early-life microbiome; breastfeeding; mouse model

• STUDY: Gut microbial factors predict disease severity in a mouse model of multiple sclerosis
  Alex Steimle, Mareike Neumann et al. 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 important 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!
  Topics: functional microbiome; multiple sclerosis

• STUDY: Dietary fiber monosaccharide content alters gut microbiome composition and fermentation
  Nick Jensen, Maria Maldonado-Gomez et al. 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 compositions 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.
  Topics: effect of different types of fibre; functional microbiome

(b) Microbial and pathogen genetics, ecology, evolution and AMR

• STUDY: CRISPRi–TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria
  Bimal Jana et al. 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 interference 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 repressed 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).
  Topics: pathogen genomics; functional gene interactions; epistasis; gene essentiality

• STUDY: Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease
  Wei-Chen Wu et al. 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 diseased pets observed to have a higher load than healthy ones.
  Topics: viral/bacterial zoonotic pathogen surveillance; companion animals

• STUDY: Genomic insights into the 2022–2023 Vibrio cholerae outbreak in Malawi
  Chrispin Chaguza, Innocent Chibwe et al. 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 countries). 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.
  Topics: pathogen genomics; surveillance; epidemiology; Africa

(c) Other general interest

• PREPRINT: Effect of disclosing a polygenic risk score for coronary heart disease on adverse cardiovascular events: 10-year follow-up of the MI-GENES randomized clinical trial
  Mohammadreza Naderian et al. 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.
  Topics: clinical translation; polygenic score; cardiovascular health

• PREPRINT: Haplotype Analysis Reveals Pleiotropic Disease Associations in the HLA Region
  Courtney Smith et al. 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.
  Topics: human genetics; HLA links to diseases