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!).

🚨New publication from the lab!🚨

Title: Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation
Journal: Nature Genetics, Feb 2026
Comment: Delighted to have contributed with Camila to this great effort from Prof Tove Fall lab in Uppsala University (Sweden). The work is focusing on human microbiome GWAS in Swedish cohorts (~16,000 individuals + 12,000 validation) and published back to back with similar efforts in another Nordic cohort, HUNT from Norway (link here). Thanks to an increased sample size, findings expand what we previously understood of the human genetic factors associated with gut microbiota variation, and add particular candidate mechanisms from gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition. Great!

(a) Microbiome and health

Title: Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease
Journal: Nature Microbiology, Dec 2025
Comment: Very cool study. Paired saliva+stool shotgun metagenomes in an advanced chronic liver disease (ACLD) cohort (n=86 patients + 2 control groups) show oral to gut strain translocation increases with disease severity (Veillonella/Streptococcus). Very interestingly, translocators share a prtC collagenase-like gene whose fecal abundance is a strong ACLD biomarker and tracks higher stool collagenase activity. Moreover, prtC+ strains isolated from patient are seen to exacerbate gut barrier disruption and liver fibrosis in a CCl4 mouse model, which suggests a mechanistic link, not just association

Title: The fate of dietary protein in the gastrointestinal tract and implications for colonic disease
Journal: Nature Reviews Gastroenterology & Hepatology, Jan 2026
Comment: Very interesting review on how modern high-protein/processed diets + low fibre can lead to more colonic protein fermentation (H2S, ammonia, phenols) vs protective SCFAs, with some implications stated on UC/CRC risk and outcomes.

Title: GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome
Journal: bioRxiv, Jan 2026
Comment: Not a lot of these still, but this is an interesting long-read gut metagenomics preprint (n=109 samples) using Hi-C which uncovers globally prevalent, Firmicutes-host “GuFi” phage families that have been missed by short reads. It seems to have broad host range + active replication.

Title: Distinct trajectories of urbanization shape the human gut microbiome across South Asia
Journal: bioRxiv, Jan 26
Comment: We need more non-European microbiome studies! This is an interesting new preprint on the SAMBAR cohort of 16S gut microbiomes from 575 adults across 10 South Asian communities (India + Sri Lanka) with matched rural vs urban sampling + detailed diet/health metadata (lifestyle/diet survey (36 questions) + BMI/BP/glucose). Authors find that microbiomes are shaped more by geography/community than a single urbanisation axis, yet urbanisation still links to disease-associated taxa, with community-specific shifts like a wheat/yogurt-associated Bifidobacterium–Ligilactobacillus–Megasphaera module and urban Megamonas tied to metabolic markers.

Title:Longitudinal Dynamics and Site-Specific Recovery of the Human Respiratory Microbiome Following Smoking Cessation
Journal: bioRxiv, Feb 2026
Comment: What is the impact of smoking cessation on the respiratory microbiome? In this unreviewed preprint, authors present a longitudinal 16S profiling study across nose, oropharynx and BAL in smokers who have quit (LuMEn subcohort, Germany, n=25). Smoking shows opposite diversity shifts by site (increase of nasal richness, decrease of lung richness/core) and increased individualisation of signatures. After quitting, recovery is partial and site-specific: early oropharynx–lung convergence; even after 1y, lung richness rebounds but composition/network features remain altered.

Title: Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function
Journal: Nature Microbiology, Feb 2026
Comment: On the importance of validating clinical microbiome associations and performing a robust covariates analysis. Here, quantitative faecal metagenomics study (n=130) + covariate modelling + 11-study benchmarking to disentangle chronic kidney disease (CKD) microbiome signals from host covariates and link to eGFR (i.e. kidney function) + 4y progression. Authors see that intestinal transit time (stool moisture) and medication explain microbiome variation in CKD patients more than kidney function (measured by eGFR). Advanced CKD shows a proteolytic functional tilt (increase in p-cresol/indole potential + plant:animal CAZyme ratio decreasing). Patients on dialysis show a distinct dysbiosis/inflammation pattern but no robust microbiome predictors of 4y CKD progression.

Title: Gut inflammation promotes adverse food reactions by disrupting the microbial metabolism of food triggers
Journal: bioRxiv, Feb 2026
Comment: New preprint tests whether gut inflammation in mice drives “food intolerance” by disrupting microbial digestion of trigger foods (dairy/gluten). The logic is: inflammation can deplete microbes that normally metabolise food leading to increased antigen exposure at inflamed mucosa & IgE/mast-cell sensitisation. Later re-exposure triggers mast-cell–mediated pain/inflammation and can amplify colitis.

Titles:
* Fecal microbiota transplantation plus immunotherapy in metastatic renal cell carcinoma: the phase 1 PERFORM trial
* Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial
* Fecal microbiota transplantation plus pembrolizumab and axitinib in metastatic renal cell carcinoma: the randomized phase 2 TACITO trial
Journal: Nature Medicine, Jan 2026
Comment: Publication of 3 recent trials in Nature Medicine (2 Canadian, 1 Italian) which show results on using FMT as an ICI add-on (renal+lung cancers). Early efficacy signals + mechanistic hints that taxa/function shifts may matter more than donor similarity + toxicity effects mixed. Promising, but prob need larger trials and more standardisation.

Title: Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health
Journal: Cell Host & Microbes, Feb 2026
Comment: Great work again from the lab of Alex Almeida in Cambridge, highlighting an uncultured genus CAG-170 (Oscillospiraceae) to be central node in healthy co-abundance networks in >11k gut metagenomes, with predicted B12 biosynthesis/cross-feeding functions possibly involved.

Title: Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
Journal: Cell Host & Microbe, April 2024
Comment: Interesting older paper that I stumbled upon: the analysis of a large 16S dataset (6 years longitudinal profiling across stool/skin/oral/nasal in 86 adults+plasma multi-omics) shows that stool/oral microbiomes are most stable, with insulin resistance linking to less stable stool/skin, less gut butyrate-producers, more skin opportunists and generally rewired host-microbe networks.

Title: Escherichia coli promotes colorectal cancer metastasis by maintaining enhancer-promoter loops through releasing neutrophil extracellular traps
Journal: Nature Communications, Feb 2026
Comment: Gut E. coli (especially pks+/colibactin+ strains) have long been thought to be a link between CRC and liver metastasis, possibly by translocating via the portal vein. This work is the first to explore in-depth causal molecular mechanisms of liver metastasis by E. coli strains enriched in CRC patients. As far as I could tell, E. coli seems to activate neutrophils so they release neutrophil extracellular traps (NETs, or “sticky DNA webs“). Those NETs then act like an external signal that makes cancer cells take in more calcium, which turns on a STAT3-based gene-control program that boosts pro-metastasis genes (like TNS1), helping tumors seed and grow in the liver.

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

Title: Safety and immunogenicity of a conjugate vaccine candidate against Salmonella enterica serovars Typhi and Paratyphi A in healthy adults in Europe: a phase 1 randomised controlled trial
Journal: The Lancet Infectious Diseases, Jan 2026
Comment: Results from a phase 1 RCT looking at safety + immunogenicity of a bivalent Typhi + Paratyphi A conjugate vaccine (Vi-CRM197 + O:2-CRM197) in healthy European adults (n=96). Authors see that one dose induced strong anti-Vi/O:2 IgG and Paratyphi A bactericidal activity, with no boost after dose 2, and support moving into endemic/paediatric studies.

Title:Climate change and antimicrobial resistance
Journal: Nature Reviews Microbiology, Feb 2026
Comment: Interesting review in Nat Rev Microbiol links climate change to AMR via multiple suggested routes: warming/extreme weather can raise infection incidence and thereby antibiotic demand, while heat may also affect AMR more directly (HGT/mutation; ARG reservoirs; sanitation disruption). All in all, evidence is growing but causality remains hard and we need better individual-level, multi-context epidemiology studies.

Title: Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut
Journal: AEM, Feb 2026
Comment: Comparative genomics of Bifidobacterium adolescentis (n=1.6k genomes, mostly MAGs from 44 countries) for adult-gut adaptation signatures: 203 soft-core host-interaction genes (incl adhesion/pili) +7 clades w/ some geographic structure + co-occur w/ butyrate producers.

(c) Other general interests

Title: Reliability of LLMs as medical assistants for the general public: a randomized preregistered study
Journal: Nature Medicine, Feb 2026
Comment: Randomized study (n=1,298) tested LLMs as medical assistants and found that users didn’t make better care-seeking decisions and got worse at naming likely conditions vs. control group that could use any resources. Bottleneck was not medical knowledge but the interaction with the user itself (inacuracy, missing details, unclear advice, etc).

Title: Inequalities in cancer mortality between people with and without disability: A nationwide data linkage study of 10 million adults in Australia
Journal: Plos Medicine, Jan 2026
Comment: This new large Australian data linkage study of 10.4M adults followed 9+ years shows an important cancer mortality gap for people with disability, who die from cancer at nearly 2x the rate of those without. Lung cancer drives largest absolute inequality, with breast, prostate, and colorectal cancers also major causes. Authors estimate that 18-83% of excess deaths are linked to preventable lifestyle-related cancers (smoking, obesity, alcohol). Strong suggestion to get more accessible cancer screening and prevention programs tailored for disabled people.

Title: Genetic dissection of stool frequency implicates vitamin B1 metabolism and other actionable pathways in the modulation of gut motility
Journal: Gut, Dec 2025
Comment: New multiancestry GWAS meta-analysis (n=268,606) identifies 21 loci for stool frequency, which is a proxy for gut motility. Fine-mapping converges on vitamin B1 (thiamine) metabolism via SLC35F3 and XPR1, a previously unrecognised pathway. In ~98K UK Biobank participants, dietary thiamine intake correlates with stool frequency, modulated by genotype at these loci. Mendelian randomisation supports causal effects on IBS.

Title: Integrating natural and engineered genetic variations to decode regulatory influence on blood traits
Journal: Cell Reports, Feb 2026
Comment: New integrative framework combines MPRA + RNA-seq to functionally validate 94 rare non-coding variants from blood trait GWAS. Identified 22 with direct regulatory effects. In-depth validation shows CUX1 enhancer variant alters megakaryocyte maturation and platelet size. Great work showing an example of what can be done from association work to functional validation!