Our weekly summary of some interesting microbiome, microbial genomics/ecology studies and others, shorter this week somehow! Comments in blue are personal and hopefully useful! Just as a reminder: you can subscribe to this weekly list via WordPress (bottom right of the screen) or the RSS feed. I also post these pages on Twitter, BlueSky and LinkedIn, but feel free to share them wherever. Hopefully this is interesting to some, let us know, feedback is always appreciated! 🙂

Noteworthy publications

(a) Microbiome

• PREPRINT: In utero human intestine contains maternally derived bacterial metabolites.
  Wenjia Wang et al. bioRxiv — 8 August 2024.
  Comment: In this preprint, authors used untargeted metabolomics on 49 fetal and maternal tissue samples to highlight bacterial metabolites in the fetal intestine. They SCFA and secondary bile acids that are likely vertically transmitted from the maternal microbiota and may be biologically active in the fetal gut. They also show using scRNAseq that bile acid and SCFA transport/signaling genes are expressed in fetal intestinal cells, which altogether would suggest a potential biological function for these metabolites in utero. Nice work, it would be nice to see which of the maternal taxa could contribute to this!
  Topics: infant microbiome, in utero, pregnancy, microbiome

• REVIEW: Game of microbes: the battle within – gut microbiota and multiple sclerosis.
  Ti-Ara Turner et al. Gut Microbes — 8 August 2024.
  Comment: Interesting review highlighting that despite the robust established links between EBV and MS, examining the impact of gut microbiome is also important as it offers an accessible therapeutic target. For instance, microbial metabolites like SCFA and tryptophan derivatives can exert anti-inflammatory effects and support gut barrier integrity, which are essential in managing MS beyond the existing focus on viral triggers, and potentially altering disease progression.
  Topics: multiple sclerosis, gut microbiota, EBV

• STUDY: Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.
  Luisa W. Hugerth, Maria Christine Krog et al. Microbiome — 19 August 2024.
  Comment: An extremely clear and well-presented study, with excellent figures and execution, focusing on the individual variations in the vaginal microbiome and examining the impact of menstruation and sexual intercourse on microbial dynamics. The results are very interestingly quite heterogenous, with women showing an extremely stable community and others displaying a lot of variation.
  Topics: vaginal microbiome, microbial dynamics, community succession

• STUDY: Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.
  Suet-Ying Kwan et al. mSystems — 21 August 2024.
  Comment: The gut microbiota varies according to many factors, but one strong ecological one is predation by bacteriophages, which present in the ecosystem or excised from the very bacteria inhabiting it upon various stimuli. Phages have broad or narrow host range, which makes them good factors influencing variation in gut microbial populations. And when features of the gut microbiota are associated with health outcomes, it becomes interesting to study how phages could contribute to this or even just vary themselves. In this study, authors look at the gut phageomes of 340 Mexican-Americans and associate their variation (and an enrichment in Inoviridae) with diabetes and liver steatosis. Diabetes correlated with an abundance of E. coli phages and liver steatosis with a depletion of Lactococcus phages and increase in Crassvirales phages associated with Prevotella copri. Phage-bacterial interactions could contribute to these conditions.
  Topics: bacteriophages, disease association, phage-bacteria ecology

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

• STUDY: Identification of pathways to high-level vancomycin resistance in Clostridioides difficile that incur high fitness costs in key pathogenicity traits.
  Jessica E. Buddle et al. Plos Biology — 15 August 2024.
  Comment: Interesting experimental evolution study in which authors compare 10 replicate populations of C. difficile under increasing vancomycin selection, and observe that fast high-level resistance appears within ~250 generations. They identify 2 distinct genetic pathways affected: mutations in a new target: two-component system regulating a D,D-carboxypeptidase (dacJRS), and alterations in the vanG cluster, with mutations in dacS and vanT frequently observed across the evolved populations. Interestingly, mutated strains had reduced fitness (lower growth) in rich media, sporulation defects and other which raises the question of whether such mutants would outcompete wild types in the gut.
  Topics: experimental evolution, C. difficile, AMR

• STUDY: Adaptive evolution of carbapenem-resistant hypervirulent Klebsiella pneumoniae in the urinary tract of a single patient.
  Shikai Song, Shixin Yang, Ruicheng Zheng et al. PNAS — 16 August 2024.
  Comment: Studying pathogen populations brings a lot of knowledge on how different virulent lineages emerge, but it is equally interesting to look at within-patient evolution to understand mechanisms of pathogenicity. This study focused on resistant and hypervirulent K. pneumoniae from a single patient with UTI in a Chinese hospital, and identified a phenotypic switch from hypermucoviscosity to hypomucoviscosity linked to mutations in rmpADC and wcaJ genes, mediated by IS insertions/deletions, and which significantly altered the bacteria’s virulence and persistence in the urinary tract.
  Topics: Klebsiella pneumoniae, UTI, AMR

• STUDY: Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study.
  Harry A. Thorpe et al. The Lancet Microbe — 20 August 2024.
  Comment: In a prospective cohort study of 256 patients in an Italian hospital during the first wave of COVID-19, a multi-pathogen sequencing survey was done to analyze 2418 clinical samples cultured on selective media. This 7 key pathogen species with extensive genetic diversity and high antimicrobial resistance gene prevalence in the patients. Authors inferred accurate hospital transmission events and detect co-colonisation of highly similar bacterial strains in different patients, which is a good example of pathogen surveillance and infection control in healthcare settings using genomics.
  Topics: AMR, pathogen surveillance, nosocomial infections

• REVIEW: Nature should be the model for microbial sciences.
  Brett J. Baker et al. Journal of Bacteriology — 19 August 2024.
  Comment: This very short opinion piece is actually an editor’s pick for published papers but it raises a very original and interesting idea in microbiology, arguing that the current model organisms used for many discoveries, applications, therapeutics, bioengineering, etc, (main target there is E. coli and the coli-centric view of biology) should be replaced by bacterial and archaeal organisms that are actually most abundant in nature and successful colonizers of our planet, namely members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others. An interesting suggestion, especially as these organisms are currently very understudied compared to current model organisms.
  Topics: microbial models, coli-centric view of microbiology, ecological relevance