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.

(a) Microbiome and population health

Title: Microbiome signature of Parkinson’s disease in healthy and genetically at-risk individuals
Journal: Nature Medicine, April 2026
Comment: Microbiota signatures could perhaps be used as part of earlier Parkinson disease diagnosis? In this metagenomics study, authors found 176 altered microbial species in PD cases, incl. 142 already altered in asymptomatic GBA1 carriers. Clever use of Cliff’s δ after DAA too (I think!).

Title: Lung microbiome predictors of epigenetic aging and potential associations with smoking and electronic cigarette use
Journal: Clinical Epigenetics, April 2026
Comment: Intersting contribution to the microbiome-exposure-aging theme. Here, metatranscriptomics + lung DNAm clocks in (small number of) healthy individuals identifies live bacterial species predicting faster/slower lung aging (AUC 0.78-0.91).

Title: Paradigms for microbiome analysis in infectious and non-communicable diseases
Journal: Trends in Microbiology, May 2026
Comment: Interesting read on the challenges and paradigms for analysing the microbiome in infectious and NCDs.

Title: Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition
Journal: Nature Comms, April 2026
Comment: Longitudinal shotgun metagenomics+fecal/urine metabolomics show habitual coffee intake shifts specific gut taxa and neuroactive metabolites, with abstinence partly reversing this. Decaf still rapidly changes the microbiome, interestingly (so not driven by caffeine?).

Title: The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms
Journal: Cell Host & Microbe, April 2026
Comment: Very complete review, including good sections on probiotics/applications.

Title: Gut microbiome predicts personalized responses to dietary fiber in prediabetes: a randomized, open-label trial
Journal: Nature Comms, December 2025
Comment: That’s cool. Randomized multicenter trial (n=802) shows baseline gut microbiome profiles can predict fiber response in prediabetes. Authors also identify and characterise 4 different responder clusters with improved glycemic control.

Title: The island biology of the host microbiome
Journal: Trends in Microbiology, May 2026
Comment: Really enjoyed this essay/review on the host microbiome through the lens of island biology. Great explanations, and a very good read throughout. The debate is open on how pervasive of an island the microbiome really is (is anything evolving as an island except islands under some very specific island-specific conditions? hmm.)

Title: Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires
Journal: Nature Microbiology, April 2026
Comment: Finally something like this was developped. For all of us who have painfully tried to work with CAZymes and the clonky inflexible CAZyme encyclopedia online, this is extremely promising. This new too, Cayman, enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires. Happy to hear feedback from those who tried it!

Title: Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
Journal: Cell Host & Microbe, May 2026
Comment: Wow, very complete & cool study using ancient coprolite metagenomes + modern human sampling (+ in vivo/vitro exp) showing that Segatella copri has evolved has evolved higher oxygen tolerance in industrialised populations via HGT of an oxyR stress response operon.

Title: The impact of artificial sweeteners on bacterial physiology and the microbiome
Journal: Trends in Microbiology, May 2026
Comment: Very complete summary of studies on artificial sweeteners vs. gut microbiota, showing impacts on growth, pathogen resistance, bacterial conjugation and natural transformation.

Title: Studying low-dose antibiotic effects on the gut microbiome
Journal: Trends in Microbiology, May 2026
Comment: Something I always wanted to see more on (perhaps I have nostalgic flashbacks to my MSc project on E. coli biofilm regulation by sub-MIC antibiotics back in… phew… the beginning of the century). Very nice review on why it can be interesting to look at the effect of low-doses of antibiotics on the gut microbiota.

Title: Genetic predictors of GLP1 receptor agonist weight loss and side effects
Journal: Nature, April 2026
Comment: Not technically about the microbiome but this was still interesting. Here’s a new GWAS in Nature to investigate why people respond differently to GLP-1 weight loss drugs. Authors find different alleles for GLP1R (targeted by semaglutide drugs) and GPIR (semaglutide and tirzepatide) linked to both, incl. to side effects of nausea/vomiting.

(b) Microbial ecology and genomics, AMR, etc.

Title: Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes
Journal: mSystems, April 2026
Comment: This study curated optimal growth temperature (OGT) and genomic data for ~2.8k bacterial species and built a new OGT prediction model. Interesting focus on bacteria vs. archaea too.

Title: IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Journal: MBE, May 2026
Comment: The latest version of this great phylogenetic tree inferrence method is out.

Title: First genome sequence and functional profiling of Psychrobacter SC65A.3 preserved in 5,000-year-old cave ice: insights into ancient resistome, antimicrobial potential, and enzymatic activities
Journal: Frontiers in Microbiology, Feb 2026
Comment: “Whole-genome analysis identified >100 AMR-associated genes, including clinically relevant determinants (e.g., ampC, gyrA, gyrB, parC, parE, dfrA, rpoB, tetA, tetC, and mcr-1), as well as multiple heavy-metal resistance and multidrug efflux genes” This excerpt wouldn’t be as cool to report if you didn’t know that it comes from a Psychrobacter strain isolated from 5,000-year-old ice.

Title: Interspecies interaction alters the trajectory of antibiotic resistance evolution by amplifying negative fitness epistasis
Journal: The ISME Journal, May 2026
Comment: Interesting study suggesting that interspecies competition (S. enterica + E. coli) results in “the selection of resistance mutations with higher levels of resistance and greater growth trade-offs”. There’s also a good spotlight of this in Trends in Microbiology here.

Title: The selfish ribosome
Journal: Plos Biology, April 2026
Comment: An interesting essay considering the ribosome as a selfish complex symbiont element, and the evolutionary consequences of this perspective.

(b) Other general interests (mostly human health related but not only)

Title: Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence
Journal: Nature Aging, April 2026
Comment: Here, authors ask whether male & female immune systems age differently at single-cell level across adulthood. Answer is yes: looking at PBMCs in 982 adults, they find immune aging is sex-biased with stronger female remodeling + some male-specific shifts too.

Title: Prevalence of liver fibrosis in the general population (the LiverScreen project): a multinational European cohort study
Journal: The Lancet, April 2026
Comment: Study on 30,199 individuals from 9 EU countries finds that undiagnosed liver fibrosis is common in the general population and primarily driven by metabolic factors and alcohol consumption. Early detection is key to avoid cirrhosis progression and complications.

Title: Emergency Department Opt-Out Testing for Hepatitis B: A Two-Year UK Multicentre Evaluation of Outcomes Across Seven Sites
Journal: Liver International, April 2026
Comment: Routine opt-out HepB testing in 7 UK emergency departments led to >2x assessments, found many undiagnosed or disengaged patients & linked most needing follow-up to specialist care. This works. 👏👏👏.

Title: Eight vaccines linked to a lower risk of dementia
Journal: GAVI Article (not peer-reviewed), Apr 2026
Comment: Not a scientific article but a great report to read, summarizing that we are now starting to have extremely good data on the reduction of dementia risk associated with vaccination (shingles, flu, COVID, etc). The decrease in risk is phenomenal in these studies. Have a look, and get vaccinated people.

Title: Multinational validation of the PREVENT and SCORE2 cardiovascular risk equations across 6.4 million individuals
Journal: Nature Medicine, May 2026
Comment: Largest external validation of the 2 major CVD risk scores: PREVENT (AHA) & SCORE2 (used in Europe) across ~6.4M people worldwide. Both scores showed similar overall performance across regions + adding albuminuria as variable improved PREVENT discrimination.

Title: Once-weekly semaglutide versus placebo in patients with alcohol use disorder and comorbid obesity: a randomised, double-blind, placebo-controlled trial
Journal: The Lancet, May 2026
Comment: New trial in Lancet suggests that semaglutide may also help reduce heavy drinking in treatment-seeking patients with alcohol use disorder and obesity.