Hello folks! Long time no write. At least on here! I’ve realised that it was a lot of work to do a single weekly blog update on interesting noteworthy publications, but that it was much less taxing to share publication updates on social media! This is what I mostly do over at BlueSky now (check and follow my account if interested).

However, maybe because of age or just general clogging, I’ve often found myself in need of a static page to easily search for previously mentioned articles or papers, and this website is quite useful for this, as opposed to social media. I thought that I might then periodically just summarize my BlueSky updates here, mainly for myself but also for whoever would be interested and not have/want to have BlueSky.

A few disclaimers: this first list is going to be LONG given how long it has been I hadn’t posted anything. Subsequently, I’ll try to do this more often, perhaps monthly. The post format will change a bit from the previous blog entries, but I’ll try to keep it simple by simply copy/pasting (and editing a bit for format) the brief 300-char descriptions I already made on BlueSky, so you know what’s what. Importantly, I do what I want. Comments are my own, and reflect nothing else than my own appreciation, from my own context. If you disagree, post your own comment. I might not have read the article fully or in depth, nor I endorse its content as I am just bringing them to the attention of the community. Finally, the timing of my posts does not relate necessarily to the publication date of the study, but more when I became aware of it and decided to make the post.

Last thing, I will roughly separate them (emphasis on roughly) into the various fields I’m interested in:

• Microbiome
• Microbial and pathogen genomics, ecology, evolution and AMR
• Other general interest (host genetics, metabolomics, nutrition, etc.)

All right, let me know if this is of any interest! It’s always nice to hear that these things are useful!

(a) Microbiome

Title: Rare taxa in the core microbiome
Journal: Trends in Microbiology
Comment: Dominant taxa in microbiomes are obviously important but here’s a discussion on low abundance taxa that are highly persisting/prevalent. We can see a lot of these in metagenomics, often obscured by a high false negative rate.

Title: Deep culturing the fecal microbiota of healthy laying hens
Journal: Animal Microbiome
Comment: Impressive amount of work! Culturing 1240 bacterial isolates from the healthy chicken microbiota under 76 different conditions. Interesting considerations on strain diversity (Escherichia coli) and on some taxa only retrieved by culture (vs. sequencing)🤔🐓.

Title: Why do babies cry? Exploring the role of the gut microbiota in infantile colic, constipation, and cramps in the KOALA birth cohort study
Journal: Gut Microbes
Comment: With no obvious causes and consequences, infantile colics can still be very distressing for parents. Here, authors suggest a gut microbiota contribution to colic in >1000 infants in KOALA cohort + higher levels of milk HMOs linked to less early constipation.

Title: Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism
Journal: Nature Chemistry
Comment: Morganella and gut-brain axis again! New insights here on how gut commensals can metabolise drugs and affect efficiency. It seems to be structure-dep & from specific taxa, e.g. Morganella morganii metabolizing an antipsychotic drug into a novel active metabolite!

Title: Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics
Journal: bioRxiv
Comment: In this preprint, authors phenotyped effects of 39 sweeteners on growth of 25 gut bacteria (+omics & in vitro human cell cultures etc). ~3/4 of tested sweeteners altered growth of >1 gut bacterium (ex of isosteviol altering metabolism and reducing butyrate levels).

Title: Gut microbiome evolution from infancy to 8 years of age
Journal: Nature Medicine
Comment: Impressive longitudinal work show infant gut microbiota dev is individual, rapid & shaped by pre-weaning diet enterotypes; ~4k MAGs show over 1/4 strains persisting up to 8y of age with many horizontally transferred within families. Weaning leads to major changes.

Title: Microbiome–metabolome dynamics associated with impaired glucose control and responses to lifestyle changes
Journal: Nature Medicine
Comment: Using cross-sectional metabolomics from 2 Swedish cohorts (IGT & SCAPIS subset; n=1167), authors ID ~150 blood metabolites linked to gut microbiota disruption & impaired glucose control; with Hominifimenecus microfluidus🤔 & Blautia wexlerae linked to hippurate metabolism.

Title: Exploring the causal role of the human gut microbiome in endometrial cancer: a Mendelian randomization approach
Journal: Scientific Reports
Comment: Everyone thinking of using MR for microbiome studies should read this! So many microbiome MR work is published w/o any validation😠 Here, Kaitlin Wade et al. explain (very well!) that a good MR result can be inconclusive after appropriate subsequent sensitivity checks.

Title: Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome
Journal: Nature Microbiology
Comment: Intriguing robust association between Collinsella and central-veinal subtypes of liver hepatocytes, & cholesterol metabolism. I might be trying too hard to conceptually link this with our 2022 microbiome GWAS linking Collinsella & ABO variation!😅 Still v. interesting!

Title: Associations of 2923 plasma proteins with incident inflammatory bowel disease in a prospective cohort study and genetic analysis
Journal: Nature Communications
Comment: Interesting new computational study on the host genetics of incident (future) IBD using Olink data from UKB as discovery (n=48k, 336 incident IBD cases). Promising targets include IL12B, IL18, CD6, CXCL9, which are also microbiota-influenced (not explored here).

Title: Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact
Journal: Cell Host & Microbe
Comment: CRC tumor location influences greatly diagnosis and prognosis but is not often included in CRC microbiome studies. Here, authors suggest that tumor location associates with different microbial fecal signatures, with F. nucleatum being enriched in all CRC types.

Title: Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation
Journal: bioRxiv
Comment: What happens to microbial genomic evolution in highly stable, closed ecosystems? In this preprint, authors look at 111 MAGs from a Romanian cave isolated from external influences for 5.5My(!) and see more pseudogenisation of core genes & limited HGT. Unsurprising?

Title: Wild house mice have a more dynamic and aerotolerant gut microbiota than laboratory mice
Journal: BMC Microbiology
Comment: Does host diversity correlate with microbiota diversity? In this 16S study, 7 wild house mice populations are compared to 6 lab colonies to show wild hosts harbour more diverse and dynamic microbiota, and esp. more aerotolerant bacteria 🐀🐁.

Title: Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts
Journal: Gut Microbes
Comment: New 16S retrospective (FFPE tissue-based) study on n=72 (w/ 24 CAC, 24 sporadic CRC, and 24 non-neoplastic IBD controls) shows colitis-associated colorectal carcinoma to be associated with distinct microbiota profiles enriched in colibactin+ E. coli (qPCR).

Title: Clade-specific extracellular vesicles from Akkermansia muciniphila mediate competitive colonization via direct inhibition and immune stimulation
Journal: Nature Communications
Comment: Impressive! Authors analyse 92 A. muciniphila genomes &global microbiome samples (890 novel Korean) to show that people typically harbour 1 dominant Am clade (AmI/AmII) & then show that EVs from AmII can unilaterally inhibit AmI in vitro & induce specific IgA in mice.

Title: Bacterial membrane vesicles restore gut anaerobiosis
Journal: npj Biofilms and Microbiomes
Comment: Intriguing! In this study, authors suggest that E. coli-derived membrane vesicles (MVs) can reduce gut oxygen levels, mitigate colitis symptoms, and shift the microbiome from pro-inflammatory to more beneficial profiles by promoting more anaerobic species.

Title: Prevalence of Oxalotrophy in the Human Microbiome
Journal: bioRxiv
Comment: Oxalate is a dietary compound found in plants & also produced endogenously in the liver. In this preprint screening ~5k genomes/MAGs from various human sites: microbial oxalotrophy (with frc, oxc, oxlT co-harboured) seems rare & to occur exclusively in gut species.

Title: SCFA biotherapy delays diabetes in humanized gnotobiotic mice by remodeling mucosal homeostasis and metabolome
Journal: Nature Communications
Comment: Nice study showing that 6-wk HAMSAB intervention in adults with T1D impacts gut mucosal immunity & host-microbiome metabolism. Some participants (2 responders/2 non-resp) then used as FMT donors in NOD mice to identify SCFA producers linked to anti-inflam + IgA prod.

Title: Archaeal diversity in the microbiomes of four wild bird species
Journal: mSpectrum
Comment: This is a small study with limited interpretation but I do love birds, and I really like archaea. Do I like them both at the same time? (I do!👌).

Title: Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice
Journal: Nature Microbiology
Comment: Impressive integrated fecal metagenomics+metabolomics, genome-scale metab reconstruction & multi-organ transcriptomics on 50+ mice from 5 age groups to showing an aging-associated decline in microbiome metabolic activity and reduced metabolic interactions w/ host.

Title: Carbohydrate consumption drives adaptive mutations in Escherichia coli associated with increased risk for systemic infection
Journal: bioRxiv
Comment: Authors suggest lactulose-treated cirrhotic patients may have 15–21% increased E. coli infection risk (VOCAL cohort). Lactulose appears to select for lac⁺ E. coli, enhancing gut colonization; in mice, raffinose seems to mitigate this by inhibiting lactulose uptake.

Title: nf-core/detaxizer: A Benchmarking Study for Decontamination from Human Sequences
Journal: bioRxiv
Comment: New method to remove human-read contaminants from metagenomes, critical before sharing clinical samples publicly. I wonder how it compares to Michael Hall’s (University of Melbourne) very good “NoHuman” pangenome-based approach (which we use in our lab and seems to work perfectly!)? 🤔.

Title: Global Metagenomics Reveals Hidden Protist Diversity
Journal: bioRxiv
Comment: Very cool new preprint uncovering eukaryotic/protist diversity in >27k metagenomes from various environments and geographical locations. 13 new eukaryotic lineages identified & co-occurrence analysis to predict predator–prey relationships between protists & bacteria. Nice!

Title: Functional modulation of the human gut microbiome by bacteria vehicled by cheese
Journal: AEM
Comment: How to not click on a paper title like that! 😀 Yes please 🧀.

Title: The host susceptibility/resistance-related genes and gut microbial characteristics in Salmonella pullorum-infected chickens
Journal: mSpectrum
Comment: Are there host genetic factors involved in infection susceptibility? In this GWAS in chicken, using susceptibility to Salmonella serovar Pullorum as an examined trait, authors identify genotypes of interest + examine impact of Salmonella infection on microbiota 🐔🦠.

Title: Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer
Journal: Nature Microbiology
Comment: In this work, authors show that dietary fibre can mitigate the known CRC oncogenic potential of pks+ AIEC (strain NC101) in IL10-deficient mice by ↘️ mucosal inflammation, ↗️ PPAR-γ signaling, and ↘️ luminal nitrate levels that promote DNA damage and tumour growth.

Title: Microbiome-emitted scents activate olfactory neuron-independent airway-gut-brain axis to promote host growth in Drosophila
Journal: Nature Microbiology
Comment: Drosophila microbiome studies are something else sometimes! 🪰 Here, authors suggest that microbial volatile factors (‘scents’) could activate host growth and response in an airborne, contact-independent and OLFACTORY-INDEPENDENT(!) way. 🤔🤨.

Title: Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice
Journal: Nature Communications
Comment: Lab mice (domesticated for >100y) have kept gut bacterial strains that codiversified w/ rodents for >25My. Here, authors show genetic drift occured in the lab, leading to loss of microb diversity+more deleterious mutations, impacting microbial fitness in lab vs wt mice.

Title: Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle
Journal: Animal Microbiome
Comment: Archaea are often thought to live in syntrophy with bacteria in the gut. Here, authors link 16S (😐) rumen microbiota networks with methane emission measures in 750 cows & identify a Prevotella/Methanobrevibacter module linked to methane production.

Title: Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities
Journal: PNAS
Comment: How many external bacteria are needed to establish in another colonized environment? Here, authors show that initial population size + metabolic similarity to already resident community can predict successful establishment in vitro, w/ some species variation observed.

Title: Principles of gut microbiota assembly
Journal: Trends in Microbiology
Comment: Very interesting review: how does a host-associated microbiota ecologically assemble? Good discussions on niche availability, priority effects, host interactions, microbiota resilience & homeostasis.

Title: Human gut microbial aromatic amino acid and related metabolites prevent obesity through intestinal immune control
Journal: Nature Metabolism
Comment: Nice human cohort+mice follow-up work highlights specific gut microbial aromatic AAs metabolites [4-hydroxyphenylacetic acid (4-HPAA) & analogs] to prevent obesity by modulating intestinal immune resp. & controlling lipid uptake+reducing chronic inflammation.

Title: Fiber- and acetate-mediated modulation of MHC-II expression on intestinal epithelium protects from Clostridioides difficile infection
Journal: Cell Host & Microbe
Comment: Interesting immunology study looking at the central role of MHC-II in exarcerbating/alleviating C. difficile infection after low/high fibre diet (and SCFA), with indications that fibre-derived acetate in particular inhibits MHC-II through promotion of IL-22.

Title: Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences
Journal: npj Biofilms and Microbiomes
Comment: How did toothbrushing impact oral bacterial evolution in humans? Here, ancient human dental calculus and modern oral non-human primate microbiomes are compared: ubiquity of Streptococcus sanguinis and S. mitis & non-human primates show more diversity (ie, S. sinensis) 🦷.

Title: Salmonella virulence factors induce amino acid malabsorption in the ileum to promote ecosystem invasion of the large intestine
Journal: PNAS
Comment: Great work on how Salmonella can colonize a (stable and resistant to colonization) SCFA-producer rich large intestine: it first triggers malabsorption of dietary AAs in the small intestine leading to downstream changes in nutrient availability in the large intestine.

Title: The Lost Kingdom: commensal protists in the gut microbiota
Journal: Trends in Microbiology
Comment: We’re starting to better understand that the gut microbiota isn’t only bacterial. This review highlights the role of commensal protists (particularly from the Parabasalia phylum) in modulating immune responses and influencing general gut microbial ecology.

Title: Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health
Journal: Microbiome
Comment: This interesting work identifies globally prevalent A. muciniphila variants with specific mutations following penicillin exposure, which show in vivo reduced capacity to mitigate diet-induced obesity in C57BL/6N mice compared to WT strain.

Title: A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability
Journal: Cell Host & Microbe
Comment: This work highlights Bte1, a contact-dependent effector found to be widespread in human gut metagenomes and which seems to target gut Bacteroides periplasmic chaperones and protein folding, in what authors suggest to be a new antagonistic interaction mechanism.

Title: Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study
Journal: Phenomics
Comment: Interesting work on how DNA extraction methods impact metagenomics quality. Importance of mechanical lysis is highlighted and good to see measures of DNA integrity too. It would have been nice to see more exploration of impact on long-read sequencing quality.

Title: Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo
Journal: Nature Communications
Comment: Nice to see good methods being developped for long-reads metagenomic sequencing analyses. This one focuses on attempting to use coverage of long reads to assign AMR genes to host microbial species, something that’s pretty hard to do with Illumina atm. Looks promising!

Title: Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism
Journal: npj Biofilms and Microbiomes
Comment: That’s an interesting change from clinical studies looking at CVD and microbiome in humans! Authors compare gut microbiota of gorillas in captivity/wild & see differences in diversity and taxa composition which seem to correlate with negative CVD outcomes in zoo apes.

Title: Bifidobacterium longum increases serum vitamin D metabolite levels and modulates intestinal flora to alleviate osteoporosis in mice
Journal: mSphere
Comment: In this work, authors identify a gut Bifidobacterium longum strain (FSHHK13M1) enhancing serum vitamin D metabolite levels in mice (n=32) + significantly improved bone structure, with possible suggested potential for osteoporosis outcomes & human therapy.

Title: Flagellin in the human gut microbiome is a diet-adjustable adjuvant for vaccination
Journal: bioRxiv
Comment: The gut microbiota is thought to modulate immune responses to vaccines. This super cool preprint from the lab of Ruth Ley suggests that gut microbial flagellin in particular can stimulate innate immunity & vaccine reactogenicity, which can be influenced by diet.

Title: Microbial succession at weaning is guided by microbial metabolism of host glycans
Journal: bioRxiv
Comment: The transition from milk-based to solid-based foods has been observed to correlate with very important changes in the gut microbiota. This preprinted work (on mice) suggests that host-derived glycans are important factors involved in the observed microbial successions.

Title: Sucrose-preferring gut microbes prevent host obesity by producing exopolysaccharides
Journal: Nature Communications
Comment: Intriguing paper identifying abundance of EPS-producing Streptococcus salivarius in human donors being inversely correlated with BMI. In glucose-fed mice, Ss(+) microbiota produced more fecal EPS+SCFAs than Ss(-) microbiota & significantly linked to less weight gain.

Title: Blanking on blanks: few insect microbiota studies control for contaminants
Journal: mBio
Comment: On the importance of negative controls in microbiota research (this one with a focus on insect microbiota)...

Title: Bridging data gaps: African reference genomes advancing inclusive microbiome research
Journal: Trends in Microbiology
Comment: There is an urgent need to diversify microbiome science for more applicable outcomes. Great discussion piece on inclusive microbiome research, its challenges and how African-led microbiome research can benefit the entire field & precision medicine in general.

Title: Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment
Journal: mSpectrum
Comment: Another interesting work from the wonderful archaeal lab in Graz, Austria! They observed that gut archaeal methanogens don’t associate with MS onset or progression in a case-control cohort, but vary in treated patients vs. untreated which could reflect microbiome health during treatment.

Title: Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients
Journal: mSystems
Comment: Interesting preliminary observation of Campylobacter jejuni enrichment in the colon mucosa-associated microbiota from colon cancer patients, which also correlates with bile secretion. 16S study only but would be interesting to see which C. jejuni strains are involved.

Title: A gut Eggerthella lenta–derived metabolite impairs neutrophil function to aggravate bacterial lung infection
Journal: Science Translational Medicine
Comment: New study on the gut-lung axis 🫁 Authors show that gut Eggerthella lenta can produce taurine ursodeoxycholic acid (TUDCA) which impairs neutrophil function by reducing AMPK phosphorylation & exacerbating bacterial lung infections, esp. in bronchiectasis patients.

Title: Individual leaf microbiota tunes a genetic regulatory network to promote leaf growth
Journal: Cell Host and Microbe
Comment: Not everyday we see phyllosphere microbiota in Cell Host & Microbe! 🥬 Specific bacteria within the maize leaf microbiota seem to promote individual leaf growth by repressing defense genetic regulatory network & modulating leaf growth-defense tradeoff.

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

Title: Trace elements increase replicability of microbial growth
Journal: Open Biology
Comment: All microbiologists have fond memories of spending hours in lab kitchens preparing synthetic media. In this work, authors show that by adding trace elements to the mix greatly reduces technical variability in microbial growth experiments. Cool stuff!

Title: microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies
Journal: Microbial Genomics
Comment: Potentially interesting? New tool to perform bacterial GWAS just published in MGen. Happy to hear feedback if you’ve tried it!

Title: Antibiotic killing of drug-induced bacteriostatic cells
Journal: AAC
Comment: There’s an idea that bacteriostatic ABs impede the use of bacteriocidal ones (need cell growth to be efficient). In this small E. coli & MRSA in vitro study, authors rather show synergistic effects of bacteriostatic ABs pre-exposure, esp w/ gentamicin/ampicillin.

Title: Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex
Journal: Nature Reviews Microbiology
Comment: Very nice recent review on the ecology and diversity of the MDR Mycobacterium tuberculosis complex genotypes circulating worldwide.

Title: Interactions and evolutionary relationships among bacterial mobile genetic elements
Journal: Nature Reviews Microbiology
Comment: Impressive, recent and very complete review on microbial mobile genetic elements diversity and their evolutionary impact of horizontal gene transfer.

Title: Revealing the clinical relevance of Staphylococcus borealis
Journal: mSpectrum
Comment: Apparently, Staphylococcus borealis are often misidentified as S. haemolyticus. Here, 129 clinical Sb isolates from Norwegian hospitals show link with UTI/skin infections, mainly in elderly males. Also low MDR, low methicillin res. & good biofilm formation 🇳🇴🦠.

Title: Dissecting apicoplast functions through continuous cultivation of Toxoplasma gondii devoid of the organelle
Journal: Nature Communications
Comment: Wow! Authors here find conditions in which the apicoplast is non-essential in Toxoplasma, and further engineer an apicoplast-free T. gondii strain that can be maintained indefinitely in culture, potentially useful for drug research etc. Pretty cool!

Title: Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics
Journal: mSystems
Comment: Unlike bacteria (except mycoplasma), archaea don’t ubiquitously have a peptidoglycan equivalent at all. However, some lineages have pseudomurein. This study characterises its biosynthesis, contributing genes and evolutionary links with bacterial counterparts.

Title: Antibiotics change the population growth rate heterogeneity and morphology of bacteria
Journal: Plos Pathogens
Comment: Intriguing results suggest AB treatment influences bacterial population growth rate heterogeneity (PGRH) which positively correlates with functional distance of AB target to protein synthesis.

Title: Helicobacter pylori, microbiota and gastric cancer — principles of microorganism-driven carcinogenesis
Journal: Nature Reviews Gastroenterology & Hepatology
Comment: Interesting review updating the state of research on Helicobacter pylori and gastric cancer. Good section on the links with other microbiota members contributing to the outcomes (Fig 4), highlighting Streptococcus sp. and others.

Title: Footprints of Human Migration in the Population Structure of Wild Baker’s Yeast
Journal: Molecular Ecology
Comment: I had no idea that ancestral S. cerevisiae which gave rise to all domesticated strains came from trees! Here, authors compare 300 wild Sc genomes from trees to recreate population evolutionary history with respect to human migrations. Fascinating stuff!

Title: Macrogenetic atlas of prokaryotes
Journal: bioRxiv
Comment: Very interesting new preprint from the Daniel Falush lab in Shanghai, describing an effort to parameterize a large number of microbial and population (phylo)genetic traits for >15k species, then examining their interactions. Loads to dig up & possibly quite impactful!

Title: Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution
Journal: Nature Communications
Comment: Interesting in vivo exp. evolution paper on Bordetella hinzii, an emerging zoonotic pathogen affecting immunocompromised patients, highlighting the remarkable plasticity of niche-specific modifications allowing the pathogen to adapt to colonizing various compartments.

Title: Bacterial galvanotaxis: a neglected biological process
Journal: Trends in Microbiology
Comment: Did you know bacteria could apparently migrate following electric fields? ⚡ Me neither, but Trends in Microbiol has a new piece on it & it’s called “galvanotaxis”, with details on how this could help Salmonella enter epithelial cells 🤔 (I am somehow skeptical).

Title: The evolution of antibiotic resistance in Europe, 1998–2019
Journal: Plos Pathogens
Comment: Here, authors applied models to ECDC data (30 countries, 8 species, 36 ABs) to classify AMR evolution between 1998-2019 in Europe🇪🇺 as stable/stabilising (E. coli), increasing (Klebs,Acineto) or decreasing (MRSA,S. pneumo). Trends also varied by country & AB class.

Title: Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection
Journal: Nature Microbiology
Comment: Interesting observation of coordinated division of labour from subpop of P. syringae during plant infection🌱. Both T3SS/flagella are required to suppress immunity & most bacterial cells seem to segregate into distinct expression states of either one or the other.

Title: Progressive evolution of Streptococcus equi from Streptococcus equi subsp. zooepidemicus and adaption to equine hosts
Journal: Microbial Genomics
Comment: Interesting story capturing the microbial genetics of adaptation and pathogenicity evolution in Streptococcus equi a globally disseminated equine pathogen 🐴.

Title: Genome-wide analysis of fitness determinants of Staphylococcus aureus during growth in milk
Journal: Plos Pathogens
Comment: Good CRISPRi-seq screens in microbes are often very interesting! Here, authors identify 282 essential genes for S. aureus fitness in milk. Purine & folate metab were so critical that inhibition by TMP-SMX (targeting folate) was more effective in milk than BHI medium.

(c) Other general interests

Title: Gathering No Moss
Journal: Annual Reviews of Microbiology
Comment: [post from 5th February] The passing of Julian Davies is truly sad news! Aside from a fantastic microbiology career (his 2003 editorial in Annual Revs below was a great read👇), I fondly remember Julian Davies’ later and fascinating research on various effects sub-MIC of antibiotics, which inspired my MSc research greatly!

Title: Moroccan genome project: genomic insight into a North African population
Journal: Communications Biology
Comment: New study presenting the Moroccan Genome Project (MGP), sequencing and analysing 109 Moroccan genomes and adding on to the overall human genomic diversity with more North African representatives.

Title: The burden of β-lactam allergy labels in health care: a systematic review and meta-analysis
Journal: The Lancet Infectious Diseases
Comment: Interesting read! When patients self-report β-lactam allergy, it often is recorded but not verified. In this meta-analysis of 63 studies, authors look at possible health impacts of unnecessary use of broad-spectrum antibiotics instead of 1st-line β-lactams.

Title: Existing food processing classifications overlook the phytochemical composition of processed plant-based protein-rich foods
Journal: Nature Foods
Comment: Interesting LC–MS analyses on 168 plant-based protein-rich foods highlight that beneficial phytochemicals are rarely mentioned, but could benefit general public health and nutrition. E.g., isoflavonoid content in soy-based foods is found to vary a lot with processing.

Title: Tracing the Spread of Celtic Languages using Ancient Genomics
Journal: bioRxiv
Comment: Methods a bit complicated for me to follow, but this preprinted work uses genomic data from Bronze/Iron age to reconstruct the spread of Celtic languages, suggesting Eastern Central rather than West European origin for Irish, Scottsh Gaelic, Welsh & Breton languages.

Title: Iguanas rafted more than 8,000 km from North America to Fiji
Journal: PNAS
Comment: Just leaving this here. Very cool 😀🦎.

Title: A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome
Journal: Nature
Comment: Recent identification of lariocidin and lariocidin B, a new broad spectrum “lasso peptide” antibiotic targeting the 16S ribosome in a unique new site, and unaffected by current resistance mechanisms.

Title: Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement
Journal: Nature Genetics
Comment: Tea lovers! 🍵 New genomics study on 1325 Camellia accessions from 14 major tea-producing countries incl. 1251 cultivated C. sinensis + 74 related species➡️new insights on pop structure, domestication history & introgression; GWAS➡️new SNP assoc w/ key agronomic traits.

Title: New fish migrations into the Panama Canal increase likelihood of interoceanic invasions in the Americas
Journal: Current Biology
Comment: Obviously, not only boats cross the Panama canal! Here, authors look at how fish can also migrate through it, and how it can increase chances of interoceanic migrations in the Americas.

Title: Maternal circadian rhythms during pregnancy dictate metabolic plasticity in offspring
Journal: Cell Metabolism
Comment: This work shows how maternal circadian rhythms in mice can have a long-lasting impacts on offspring health, with disturbances linked to more diet-induced obesity, altered feeding behaviours & impaired metabolic regulation in progeny.

Title: Bioaccumulation of microplastics in decedent human brains
Journal: Nature Medicine
Comment: Not a fun read but interesting: authors looked here at micro- and nanoplastics (MNP) occurence in various tissues during autopsies and saw more accumulation in the brain than prev reported for liver/kidneys + more accumulation in brains with dementia diagnosis.