Health

Some new articles in the reading list. I’ll probably do a little break for those during the summer holidays. Have a good one! (a) Microbiome and population health Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin Nature Genetics, June 2026 Comment: Microbiome GWAS studies have historically started with the gut (and we’ve been part of this effort here, and more recently here). Other body sites have been looked too, starting with the oral microbiota last January. Here, authors present the first (metagenomics-based) vaginal microbiome GWAS study, but with much more than this, by also building a major genome catalog/resource (GVMG) of >65k genomes from public data (prokaryotic, eukaryotic and viral), which almost doubles the previous cataloguing efforts. They find that many vaginal microbes were missing from previous databases (and identify M. smithii as an archaeon there, which perhaps is worthy of some further study). They also refine the Gardnerella/Bifidobacterium links by looking at how species cluster together. The vaginal virome is also better characterised, with some interesting phage-bacterial dynamics depending on health state. Regarding the host association part, 7 loci reach study-wide significance and replicate in >1 cohort, with the strongest signal being OPRK1 with Ureaplasma urealyticum. Other signals include: ADAP1 with Lactobacillus mulieris, PRAMEF-region with B. piotii, MIR548AB with Ezakiella coagulans, STON1–GTF2A1L/LHCGR/FSHR with Prevotella sp000758925, MAN1A2P1/UQCRFS1 with B. swidsinskii and CHIC2/PDGFRA with Lactobacillus u861. Very cool stuff! Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro Molecular Systems Biology, June 2026 Comment: For those of you who put artificial sweeteners in your coffee (nobody is perfect), this very interesting work looks at what happens when sweeteners meet the other xenobiotics we consume alongside them (here, advantame, caffeine, vanillin or duloxetine). In a large in vitro screen, they found that isosteviol and duloxetine together were interacting to suppress selected gut bacteria, reduce diversity in a synthetic community (very cool passage experiment there), changed metabolite output (incl. lower SCFA/butyrate) and altered host cell responses. All in vitro so far so no need to worry. Well, besides the nastiness of artificial sweeteners in general. Regional organization of nutrient absorption across the small intestine Nature Reviews Gastroenterology & Hepatology, July 2026 Comment: Very interesting review on the spatial organisation of nutrient absorption in the small intestine (duodenum, jejunum, ileum until the ileocaecal valve) and how these function in different ways to absorb different nutrients in various “metabolic domains”. Very good food for thoughts when thinking of the gut microbiota! Bifidobacterial genes upregulated by resistant starch investigated using multi-omics have orthologs in infant gut isolates ISME Communications, Jan 2026 Comment: Interesting study including some of our friends on this, and a very “microbial systems-biology” mechanistic Bifidobacterium paper on resistant starch degradation. Authors highlight an interesting CAZyme CBM74-containing amylase cluster in Bifidobacterium globosum linked to high-amylose resistant starch. The link to infant B. pseudocatenulatum isolates is interesting when thinking about weaning, strain-level metabolism, and what starch-related CAZyme detections in metagenomes may actually mean. Applying Artificial Intelligence and machine learning in precision nutrition Nature Communications, July 2026 Comment: Not entirely on the microbiota but very interesting Perspective on the topic of ML/AI and precision nutrition. Interesting discussion on how AI/ML should be selected, implemented, validated and reported for precision nutrition research, given the distinctive problems posed by dietary, microbiome, multi-omic, behavioural and longitudinal data. Authors suggest the AI-PNUTRI checklist, a practical framework that could be implemented to existing standards. Effects of probiotic supplementation on faecal short-chain fatty acid concentrations in healthy individuals: a systematic review and meta-analysis of randomized controlled trials Nutrition Journal, July 2026 Comment: Do probiotics work? We hear this so much all the time as microbiome researchers and not many people can give a straight answer with confidence. Here, authors present a very interesting metaanalysis of RCTs testing whether probiotic supplementation actually does changes faecal SCFA concentrations in generally healthy people. For this work, the results are… negative! No statistically significant differences were detected in the faecal butyrate, acetate and propionate levels between individuals taking and not taking probiotics. I guess we’ll have to stick to eating a lot of fibre then? :) (More could probably be done, with more participants and not looking at fecal SCFA, but this is a start!) (b) Microbial genomics, ecology, evolution AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics bioRxiv, July 2026 Comment: The preprint for a great resource led by the otherwise great Zamin Iqbal at the University of Bath along with many other talented collaborators. AllTheBacteria is an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. It gathers more than 2.4M bacterial/archaeal genomes from >11k species with all possible annotations you can think of. Really a great effort and I should use it more! The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study The Lancet Infectious Diseases, July 2026 Comment: Important genomic epidemiology paper on sexually-transmissible Shigella sonnei infections in the UK (15 health regions) between 2004-2020. Authors found about a third of infections coming from MSM, another third from non-MSM and the rest from high-risk travel. The phylogenomic analysis showed that sexually transmitted S. sonnei were spreading faster and more intensely than domestically acquired infections. They also observed a decline of azithromycin resistant in some isolates consistent with policy changes on treatments for gonorrhoea. Nicely done phylogenomic epidemiology paper. Glucagon-like peptide-1 receptor agonist prevents pulmonary fibrosis following acute COVID-19 infection associated with type 2 diabetes Journal of Virology, July 2026 Comment: From the importance statement: Some COVID-19 patients develop pulmonary post-acute sequelae of COVID-19 (PASC) with clinical symptoms lasting for years. Critically, the incidence of pulmonary PASC in PWT2D is four times higher than that in those without T2D. GLP1 drugs are really found to be positively acting on a lot of things, either (most of the time) indirectly through weight-loss-related better health but more interestingly sometimes through more direct effects. Here, in this virology paper, authors show that GLP-1R agonist drugs directly acted on the pulmonary fibrosis symptoms that are typically seen in T2D patients after SARS-CoV-2 infection. Mechanisms are investigated in mice model. (c) Other pop health, AI & other topics Analysis of 173,303 exomes and genomes in the Pakistan Genome Resource Nature, June 2026 Comment: Impressive new resource adding onto the non-European reference genomic resources. Around 30% of coding variants found in this resource were absent even from all gnomAD, including South Asian samples there. Authors identify homozygous LoF variants in >6k genes (1/3rd of all protein-coding genes), with ~20% participants carrying at least one of these LoF gene variant. Very good example that under-represented populations can reveal biological findings that are missed by larger but less diverse other resources, and overall potentially improve genomic research representativity. The expanding landscape of GLP-1 medicines Nature Medicine, January 2026 Comment: Already from last January, so potentially outdated when you see all the overwhelming advances made just in the first half of 2026 on additional treatments and new molecules targeting GLP1/GIPR going into clinical trials but still a very interesting review detailing the multiple reported benefits of these weight loss drugs already. Extreme heat and cause-specific risk of hospital admission in the adult population in England: a case time series analysis BMJ Open, June 2026 Comment: There is a heatwave in Europe as this paper is being published, which is an interesting coincidence. Here, authors look at heat-related risks for unscheduled hospital admissions. They analyse >4M records between 2008-2019 and find increases for a range of conditions like acute renal failure (Relative Risk of 1.37), metabolic disorders (1.28) and also marginally infectious and parasitic diseases (1.06), pneumonia (1.07) and COPD (1.08). Interestingly the associations were less clear and even negative for a range of cardiovascular outcomes. These events will only increase in frequency, this study helps to inform for a better planning. Whole-population trends in obesity across dimensions of inequality in England, 2019–25: a retrospective, longitudinal cohort study of 54 million adults The Lancet, June 2026 Comment: Impressive retrospective longitudinal cohort of the whole population in England (n>54M individuals with NHS records), looking at trends in obesity across many variables, including age, sex, ethnicity, geography and SES factors. Obesity now affects ~1 in 3 adults in England (30.3% in April 2025, up from 26.3% before 2020). The fastest increases in new cases is observed in younger adults: +16% in 20–29yo and +19% in 30–39yo. People in the most deprived areas were 35% more likely to develop obesity than those in the least deprived. The gap was wider for women, and widest for Asian women, where the rate was nearly double. Finally, geographically, rates varied almost 6-fold across the country, and the steepest increases happened in the poorest areas (source: one of the authors). Diagnoses earlier in life are quite worrying, given that obesity associates with increased risks of many other illnesses. Citizen science platforms must mitigate against the threat of generative AI Nature Ecology & Evolution, July 2026 Comment: Interesting and alarming letter highlighting the rise of AI-generated and AI-enhanced pictures on citizen science projects like eBird or any other wildlife resource, which obviously (duh) is of major impairment to identification, conservation and many other things. Rethinking bioinformatics expertise in the era of artificial intelligence npj Digital Medicine, May 2026 Comment: A very interesting read for bioinformaticians who have been wondering about the value of their knowledge, expertise and skills with the tsunami wave of ever-so-competent LLM coding agents. Fear not, we will still need human brains to make good science. Sure, AI does accelerate technical execution but it will always remain very poor at designing studies scientifically decisively, curating data, validating and interpreting things in a biologically meaningful way.

Not many entries today (just 6!), as times are busy with other things! Just a few new interesting papers that came to my attention on the human microbiome and some other population health studies. (a) Microbiome and population health Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals Cell Press Blue, June 2026 Comment: Another very interesting paper from the Segata lab in Italy, looking at microbiome transmission within households of cohabiting individuals. They find that cohabitation strongly predicts strain sharing, with an average sharing between cohabitants of 19% of gut strains and 26% of oral strains (compared to 6% gut and 0% oral sharing among non-cohabitants), with a highest value (44%) of oral sharing amongst romantic partners (unsurprisingly 😘). On that, they observed that oral strains appeared to be more dynamic/more transmissible than gut strains, and have a highest “replacement” rate. Oral-to-gut movement seemed to be observed and real, but quite selective which is an interesting observation. They found ~4% of species overlap between oral/fecal samples. Interestingly, when one strain was found at both sites in the same person, it was found in 3/4 of the cases, which supports the hypothesis of saliva-mediated oral-to-gut transmission, which is that abundant oral bacteria that are swallowed have more chances to survive the gut. Generally speaking though, they observed that when a species was found in both oral/gut of the same person, it was another strain, suggesting a body site-specific longer-term adaptation happening. Finally, these transmissible microbes weren’t always “beneficial”, with some associated with T2D and CRC biomarkers, suggesting that disease-associated microbes might also have traits allowing them to transmit more easily. Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics Nature Microbiology, June 2026 Comment: Very interesting applied microbiome research, in my opinion! Here, authors looked at 352 OTC probiotic products from US pharmacy websites. They found 36 unique “probiotic” species across 70 brands but no clear clustering of species composition by the proposed use by the manufacturer, such as gut vs vaginal health, reinforcing the point that the “probiotics industry is selling us certainty it hasn’t earned” (yet). Authors go on to build a genome-scale metabolic mode from public genomes, called HaPaPro and which contains ~1k probiotics and other host-associated bacteria. They focus on vaginal health in this paper, and test 11 species found to inhibit (through their modelling) the in vitro growth of Gardnerella vaginalis, a pathogen. Identification of the complete pathway for conversion of bilirubin to urobilinogen by human gut bacteria bioRxiv, June 2026 Comment: Bilirubin is a major product of mammalian heme catabolism and enters the intestine via the bile, after liver conjugation, and then can be metabolized by gut microbes through mechanisms that are largely unclear. In this preprint, authors ask which specific bacteria (and enzymes) convert bilirubin into urobilinogen. They identify enzymes BilR and BilV and characterise their activities, before screening for them in a broader collection of 1200 GTDB reference genomes encoding putative BilV. They identify Collinsella genomes to have quite a lot of these genes. (d) Other pop health & other topics Distinct metabolic signatures of Alzheimer's and Parkinson's disease revealed through genetic overlap eBioMedicine, May 2026 Comment: Interesting paper on >300,000 people from UKB and Estonian Biobank using 249 of their circulating metabolites + proglucagon, along with summary statistics for AD, PD and cardiometabolic traits. Authors find that AD and PD have very different and distinct metabolic and genetic signatures, with AD being more liked to metabolic states influenced by BMI, T2D, CAD and stroke, while PD has very opposing patterns. Neurodegeneration, unsurprisingly, isn’t a one-size-fits-all box and this works informs better on targeted metabolic approaches. Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging Cell Genomics, June 2026 Comment: Very interesting new review from the Inouye Lab in Cambridge, summarizing how GWAS findings are being translated into biological/clinical insight at molecular, cellular and organ-levels scales. Among other things, it addresses how genetics can help for drug target reprioritisation. More generally, it argues that GWAS translation should not happen at one level only but after integrating genetics, molecular QTLs and proteomics, single-cell omics, imaging and MR/colocalisation/PRS. Plasma proteomic signatures of cellular aging predict human disease Nature Medicine, June 2026 Comment: Very important study on aging, at the cellular level this time. Here authors looked at plasma proteomics from >60,000 individuals across 3 cohorts (GNPC incl. healthy + AD/PD/ALS, UKB participants with Olink plasma proteomics and follow-up, and NSHD 1946 birth cohort). They built those interesting cell type-specific aging models and looked at the “cell age gap” between cell-type age and expected age for someone of the same chronological age. They found that in healthy participants, there was a mix of people with no extreme cell age gaps, some with accelerated aging in 1 cell type and some with accelerated aging in >10 cell types. They linked lifestyle (smoking, obesity) and genetics (APOE) showing cell specific effects on aging. The strongest associations they found were for neurodegenerative diseases, especially ALS, linked to skeletal myocyte/cardiomyocyte aging. Alzheimer disease was strongly linked to astrocyte aging in UKB, and lung cancer also had links with alveolar cells aging. A lot to unpack, but cool study.

A lot of interesting things were published lately in multiple fields, and it’s been a bit hard to keep up! But this is hopefully helpful to some. In other news, you’ll perhaps notice that this website has changed and migrated to another server, much better than @£!# Wordpress. The only issue of this migration was to lose the email mailing list for those who were subscribed to it. I can only encourage people to follow this blog through RSS syndication, on this link. ...

Again this blog post is not happening as I would like, but that’s how it is! This is the latest update of interesting additions to my reading list, gathering some noteworthy recent publications in the field of microbiome science and other! I hope this will be helpful, please subscribe below the post if you’d like to be kept in the loop of future posts by email. Also feel free to see these posts more regularly on BlueSky. ...

Not as often as I would like and fewer entries this time than in the last post, but this is the latest update of my reading list gathering some noteworthy recent publications in the field of microbiome science and other! I hope this will be helpful, please subscribe below the post if you’d like to be kept in the loop of future posts by email. Also feel free to see these posts more regularly on BlueSky. ...

Two in a row! It’s been a while. I hope this list of interesting recent papers (at least to me!) in the field of microbiome science, microbial ecology and other stuff will be useful to you! As always, feel free to subscribe to get this list by email and/or follow on bluesky where I generally also post something. This time, we also start with a great achievement from our collaborators, published in Nature Genetics. We’re delighted to have been part of this (and more is to come!). ...

Well, despite being marginally more active on BlueSky, my last blog post summarizing the papers I come across has been almost a year ago now. Shocking news, I know. Since then, I’ve moved across hemispheres, got a new job (now associate prof at the University of Bath, yay!) and it’s taken a while to update this but, hey! a warm hello to the handful of hopefuls that will find this useful! 🙂 (Do you find this useful? I promise I’ll try my best to keep at it for 2026). ...

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. ...

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. ...