A weekly summary of what caught our eye in the field of microbiome research, microbial genomics and ecology, and others. Comments in blue are personal and hopefully useful!

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From our lab

• Harnessing human microbiomes for disease prediction
  Yang Liu et al. Trends in Microbiology — 20 January 2024 (July Issue)
  Comment: Our review on leveraging the gut microbiome for predicting disease risk and outcome that have a (known or unknown) microbial component has finally been assigned to the July issue of TiM. Have a look if you haven’t already! 🙂

Noteworthy studies and publications

(a) Microbiome

• Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial
  Jiaying Zhu et al. Gut — 6 June 2024.
  Comment: Long-term proton pump inhibitor (PPI) usage has been linked to various medical conditions and alteration of the microbiota. A safer alternative are histamine-2 receptor antagonists (H2RAs) but not much has been done on their effects on the microbiota, until this study. Authors show that H2RAs impact less the gut microbiota than PPIs and who that (very intriguingly) PPIs seem to induce more oral-to-gut transmission of Fusobacterium nucleatum and Streptococcus anginosus, which have also been linked to a range of other diseases! Very interesting!

• Impact of socioeconomic status on healthy immune responses in humans
  Anthony Bertrand et al. Immunology & Cell Biology — 11 June 2024.
  Comment: Another very interesting paper form the Milieu Intérieur consortium, this time looking at the impact of socioeconomic status on human immune response, using an Elo-based ranking system (like in chess) to stratify individuals from the MI cohort according to SES. A very good thread from one of the main senior authors here!

• Time of sample collection is critical for the replicability of microbiome analyses
  Celeste Allaband et al. Nature Metabolism — 1 July 2024.
  Comment: This 16S rRNA-based study on fecal samples from 16 male mice found that the time of sample collection within a 4-hour window significantly affected the gut microbiome’s diversity and composition, more so than dietary changes, suggesting the necessity for standardized sampling times (accounting for diurnal variations in microbiota) to maximise data accuracy in microbiome studies.

• Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes
  Benjamin Grodner et al. Nature Microbiology — 25 June 2024.
  Comment: Great study and figures! Here, authors use a novel high-resolution imaging method combining DNA FISH with rRNA-FISH to visualize mobile genetic elements and their bacterial hosts in oral biofilms, no less! This revealed spatial clusters of AMR genes and bacteriophages, indicating heterogeneous distribution and potential barriers to their spread within biofilms. Very impressive! Also check the thread on Twitter from the lead author.

• Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota
  Anurag K. Sinha, Martin F. Laursen et al. Nature Microbiology — 25 June 2024.
  Comment: Fibre-rich diets are thought to have the potential to beneficially modulate the gut microbial metabolic output. In this in vitro/in vivo study, authors show that dietary fibre alters gut microbial tryptophan metabolism by suppressing indole production in favour of beneficial indolelactic acid (ILA) and indolepropionic acid (IPA). This shift occurs as fibre-degrading bacteria inhibit indole-producing E. coli via catabolite repression, thereby increasing tryptophan availability for other taxa to generate metabolites.

• The dynamics of the female microbiome: unveiling abrupt changes of microbial domains across body sites from prepartum to postpartum phases
  Charlotte J. Neumann et al. Microbiology Spectrum — 25 June 2024.
  Comment: In this study, authors show that the maternal microbiome undergoes substantial changes after birth that may be long-lasting. They tracked 30 women from their pregnancy to 1-mo after birth, profiling oral, urinary, and vaginal microbiomes, including archaeome, mycobiome, and urinary metabolome. The oral microbiome seem to stabilize quickly after birth, but the urogenital microbiome is depleted from Lactobacillus after birth, which suggests the potential use of probiotic interventions to optimize postpartum recovery. See comment from our collaborator Prof. Moissl-Eichinger.

• Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
  Marta Selma-Royo, Léonard Dubois, Serena Manara et al. Cell Host & Microbe — 12 June 2024.
  Comment: In this small mother-infant cohort, authors compare hospital versus at-home delivery on infant microbiota transmission and show an impact. They show that human milk is a key modulator of infant microbiota during the first year, with a variation across delivery modes and locations, except for Bifidobacteria, with B. longum persisting and diversifying more according to breastfeeding duration.

• Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies
  Robert FJ Kullberg, Irina Wikki et al. The Lancet Microbe — 20 June 2024.
  Comment: Very interesting study from collaborators, investigating the relationship between gut microbiota and infectious disease risk in 10,699 participants from the HELIUS (Netherlands) and FINRISK (Finland) cohorts. Over a 5-7 year follow-up, it was observed that individuals with a higher abundance of butyrate-producing bacteria had a lower risk of hospitalisation for infections. Results show a 25% and 14% risk reduction for every 10% increase in butyrate producers in the HELIUS and FINRISK cohorts respectively.

• Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes
  Katherine Ramos Sarmiento et al. The ISME Journal — 21 June 2024.
  Comment: Do taller people have more diverse gut microbiomes? Yes! says Sean Gibbons and colleagues (link to Twitter thread). A well rounded and exhaustive read, comparing vertebrate microbiomes and suggesting mechanisms.

• Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients
  J Casper Swarte et al. Gut — 12 May 2024.
  Comment: A few years ago, a collaboration between us and Finnish colleagues found that Enterobacteriaceae could be associated with incident mortality in the FINRISK 2002 cohort, but it has been quite difficult to conduct similar studies with such important follow-up in large cohorts. Until now! Here, authors use faecal metagenomes from a cohort of solid organ transplantation recipients (n=1,337) and the general population (n=8,208) from the northern Netherlands, with 6.5 years of follow up. Findings include the observation that gut dysbiosis is partly driven by the use of immunosuppressive drugs which prevent organ rejection, coupled with a frequent use of antibiotics, which suggests that their life-saving nature could come at a cost. Check the Twitter thread about it from Johannes Bjork, a senior author on the study.

(b) Microbial genetics, ecology, evolution and AMR

• Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution
  Javier Eduardo Fernandez et al. Nature Communications — 1 July 2024.
  Comment: The CC398 lineage of Staphylococcus aureus is an important zoonotic one, shown to colonize livestock, pets and humans and is a very interesting model for studying host adaptation in S. aureus. Here, authors analyzed >3000 global S. aureus CC398 genomes, constructing a time-calibrated phylogeny that reveals distinct evolutionary lineages, with a notable focus on the equine-associated EP5-Leq lineage. They also identify interesting key MGEs driving adaptation and AMR in CC398.

• Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium
  Tuan-Anh Tran et al. Nature Communications — 13 June 2024.
  Comment: Pretty innovative study in which authors used imaging and ML to predict ciprofloxacin susceptibility in Salmonella. They analyzed 16 clinical isolates and 4 lab strains and captured detailed morphological data from bacterial cells exposed to various ciprofloxacin concentrations over 24 hours. ML classifiers were trained on key imaging features to distinguish susceptible from resistant isolates, even without direct antimicrobial exposure. Not sure how this could be scaled-up and translated in practice but this is quite original and interesting!

(c) Other general interest

• A lipidomic based metabolic age score captures cardiometabolic risk independent of chronological age
  Tingting Wang et al. eBioMedicine — 20 June 2024.
  Comment: This nice study from colleagues at the Baker Institute finds that a lipidomic-based metabolic age can be associated with an increased risk of CVD, diabetes & all-cause mortality that is independent of chronological age. This “mAge score” has the potential to identify those at elevated risk of metabolic diseases.