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).
(a) Microbiome and population health
Nature, Jan 2026
Comment: Very impactful study of dense strain-resolved shotgun metagenomics in a nursery cohort (43 babies; 1,013 stools; 3 sites). Authors show rapid baby-baby gut strain transmission (within ~3 months). Regarding origin of strains, nursery strains contribute as much or more than family strains; siblings can buffer acquisition and antibiotics amplify strain turnover/influx.
Nature, Jan 2026
Comment: Re-analysis of saliva WGS from 12,519 people (SPARK) turns “human-genome” sequencing into the largest oral microbiome GWAS yet: 11 host loci (esp. FUT2 and AMY1 CNV) shape oral community composition and even bacterial genome content. Signals colocalize with dentures/tooth-loss risk in UK Biobank (AMY1/FUT2/PITX1), suggesting specific host–microbe genetic interactions in cariogenesis.
bioRxiv (preprint), Jan 2026
Comment: I love these studies starting to link the human archaeome with health outcomes (positive or not). Here, gnotobiotic/Abx mice colonized with human gut methanogens (M. smithii or M. stadtmanae) show thicker colonic mucus, more goblet cells, more Foxp3+ Tregs, and protection from DSS colitis vs controls. Mechanistically, M. smithii seems to retains partial benefit in Rag2-/- mice, while M. stadtmanae needs adaptive immunity, which leads to the author’s argument that archaea can be causal mucosal protectors (cautious but plausible!)
Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk
Nature Communications, November 2025
Comment: Microbiota from 195 healthy breastfeeding mother-infant pairs identifies shared strains and ARGs between mother’s milk and infant stool, involving commensals (B. longum, B. bifidum) but also pathobionts like Klebsiella.
Communications Biology, Nov 2025
Comment: Gut microbes can synthesize essential amino acids (EAAs), but how much these actually contribute to host EAA pools is unclear. Here, authors find no detectable microbial EAA across all organs examined, after analysing marked δ¹³C-EAA given to GF/conventionalized mice.
Nature Reviews Microbiology, Jan 2026
Comment: Interesting review on microbiome & cancer risk + treatment response. Addressing multiple topics in there, with also an interesting part on microbiome disruption being linked to ↓ drug efficacy across multiple cancer therapies (chemo/immuno) + tumour types.
Cell Host and Microbe, Jan 2026
Comment: Interesting! 152 mother-infant dyads from rural Burkina Faso; MISAME-III subset) with longitudinal metagenomics+milk 16S+HMOs/nutrients/metabolomics. Infant gut <2mo = 3 clusters (“Escherichia”/”Bifidobacterium”/diverse+pathogen-prevalent) + links with milk HMOs.
Trends in Microbiology, Dec 2025
Comment: Interesting review on sub-MIC antibiotic exposures from food/environment on the gut microbiome/resistome with suggested mechanisms impacting it. Interesting comments on methods/approaches + current regulatory framework to .
Nature Communications, Dec 2025
Comment: Anelloviruses are considered to be “commensal” viruses with no obvious disease links. Here, authors describe an ubiquitous & diverse anellovirome in infants with FUT2 secretors having ↑ viral abundance but no associations w/ atopic disease (minor w/ allergic rhinitis).
Nature Microbiology, Jan 2026
Comment: Autobrewery syndrome is a rare disorder of alcohol intoxication due to gut microbial ethanol production. Using an observational ABS cohort (n=22), authors suggest mechanism/therapy signals, with an FMT attempt on 1 patient showing symptom improvement.
The Lancet Microbe, Dec 2025
Comment: Interesting new meta-analysis in the Lancet Microbe, outlining phages as signatures or drivers of microbiome dysbiosis.
Nature Comms, Jan 2026
Comment: Cool work! Mining 7 ancient (1-2ky) human coprolite metagenomes for ORFs with AMP potential: 160 peptide candidates > 40 synthesised > 36 active at <100 µM in vitro with ~2/3 being Segatella copri–derived.
Respiratory Research, Dec 2025
Comment: Nice work from Finnish colleagues, looking at gut microbial associations from 685 pneumonia cases in 17.8y of FINRISK registry follow-up. Some limitations but butyrate-producers seem to associate with lower pneumonia risk & Clostridium_AQ innocuum with higher risk.
npj Biofilms and Microbiomes, Jan 2026
Comment: New review on role of microbiota in prostate cancer, expliciting the “gut–prostate axis”. Interesting examples of FMT/commensals modulating ADT response (therapy used to slow PC growth). Good caution+criticism on studies w/ potential caveats on low biomass/risk of FP.
Gut Microbes, Jan 2026
Comment: Nice review from Alex Almeida’s group on gut microbiome & enteric infection susceptibility/severity, including focus on some recurring susceptibility associations: decrease of α-diversity+butyrate producers & Proteobacteria/Enterobacteriaceae blooms.
(b) Microbial ecology and genomics, AMR, etc.
AEM, Nov 2025
Comment: Pretty cool! Engineered periplasmic binding proteins+fluorophore sensors (for sugars+AAs) are used to report real-time extracellular metabolite dynamics in E. coli + many others species after 24h in plate readers, showing hierarchical substrate use.
Environmental Microbiology Reports, Jan 2026
Comment: Reading about bacteria in the atmospheric water cycle is always fun. In this review, authors think about the possible selective pressures on bacteria in the atmosphere after aerosolization.
Plos Pathogens, Dec 2025
Comment: Interesting phage host-range network between 23 apricot-orchard phages & 44 P. syringae strains w/ varying disease outcome. Findings include strong nestedness for phage susceptibility (i.e bacterial phylogroup>ecological origin) + interesting genomic links.
(c) Other general interests
The Lancet Haematology, Jan 2026
Comment: Very large RCT (STRIDES Trial, 73 UK blood donation sites; 1.3M donors; >4M donations) shows no meaningful impact of additional strategies to prevent vasovagal syncope during whole-blood donation. A good way to assess whether “standard practice” actually works!
The Lancet Microbe, Jan 2026
Comment: Interesting commentary on the elimiation of viral hepatitis in England: HBV/HCV mortality targets exceeded, HBV vertical transmission elimination achieved. However still many chronic HBV cases, no national registry & disinvestment in harm-reduction approaches.
eClinicalMedicine, Jan 2026
Comment: Interesting new study analysing data from wearables from subset of UKBiobank participants. Optimal combo (+9.45y lifespan vs worst tertiles) was sleep 7.2–8.0 h/d, min exercise >42 min/d, good diet quality score. Minimal changes “added” several years of life.