Noteworthy things — Week 28 (08/07/2024)

Another 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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Noteworthy studies and publications

(a) Microbiome

  • Emerging tools and best practices for studying gut microbial community metabolism
    Cecilia Noecker & Peter J. Turnbaugh Nature Metabolism — 3 July 2024.
    Comment: The inclusion of strain-level metabolic functions is an increasingly valuable addition to microbiome studies. In this review, authors give a good comprehensive view on the tools available to annotate metabolic genes, curate genome-scale metabolic reconstructions, perform high-throughput microbial phenotyping, identify possible sources of metabolites in samples or even model metabolic functions in microbial communities.

  • Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries
    Elisa Piperni, Long H. Nguyen et al. Cell— 8 July 2024.
    Comment (Camila): The contribution of gut bacteria to human health is well-established, but much less is known about other organisms such as archaea or micro-eukaryotes. Blastocystis, commonly present in the gut, was the subject of this study, which analyzed data from approximately 57K individuals across 32 countries. The findings suggest an association of this micro-eukaryote with a healthier cardiometabolic profile, decreased body mass, and healthier diets. This study is an impressive effort and we hope that future studies will also be conducted to directly assess causality.

  • Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring
    Shilan Wang et al. Cell Host & Microbe — 10 July 2024.
    Comment: In this study using a cohort from Hong Kong, authors find that gestational diabetes mellitus can shape the maternal and infant gut microbiome, as well as intriguingly affect the development and gut-brain axis in the male offspring. They used large-scale longitudinal metagenomic sequencing to analyze the gut microbiome of 264 mother-infant pairs, tracking changes throughout pregnancy and the first year of the infant’s life. Mothers with GDM exhibited altered gut microbiome diversity and composition, with these changes persisting into the third trimester. Infants of GDM mothers, particularly males, showed higher gut microbial richness and diversity, as well as increased head circumference growth, indicating a potential sex-specific impact of GDM on offspring development.

  • In situ targeted base editing of bacteria in the mouse gut
    Andreas K. Brödel, Loïc H. Charpenay et al. Nature — 10 July 2024.
    Comment: In this impressive methodology paper, authors describe the ability to manipulate the gut microbiome through CRISPR base editing, delivered through phage particles. The proof-of-principle shows editing of a beta-lactamase gene in E. coli directly in the mouse gut, with an efficiency of 93% (of the target population with a single dose). Authors also edit curli genes from E. coli and Klebsiella. This potentially opens some doors in microbiome engineering, in addition to FMT and probiotics!

  • Non-SCFA microbial metabolites associated with fiber fermentation and host health
    Erica T. Grant, Hélène De Franco et al. Trends in Endocrinology & Metabolism — 10 July 2024.
    Comment: SCFA production has been associated with a myriad of health outcomes and is currently one of the main avenues for microbiome health and translation. In this recent review, authors explain that diverse gut microbial metabolites are influenced by dietary fiber, impacting host health through mechanisms that are sometimes beyond SCFA production. Authors describe a multi-faceted research topic, including human and animal studies, to link specific fiber-associated metabolites with immune and neurological effects. Maternal fiber intake for offspring is particularly significant and influential on the microbiota and authors even (re)introduce the concept of ‘celobiotics’ (defined as a “bioactive compounds that are released after microbial degradation of fibre”) as a factor in personalized fiber responses.

  • Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke
    Muhammed Manzoor et al. ISME Communications — 20 June 2024.
    Comment: The study used shotgun metagenomic sequencing from the SECRETO Oral study to identify significant differences in the oral microbiome’s composition and functional capacity between young patients with cryptogenic ischemic stroke (CIS; which is IS without a clear recognised cause) and stroke-free controls. Results identified 51 microbial species associated with CIS across multiple interacting kingdoms, as well as 5 pathways found to be differentially abundant between CIS patients and controls. This study suggests a role for the oral microbiome in metabolic processes that could influence stroke risk and recovery, especially in cases that have a cryptic aetiology.

(b) Microbial genetics, ecology, evolution and AMR

  • Unveiling the critical roles of cellular metabolism suppression in antibiotic tolerance
    Sayed Golam Mohiuddin et al. npj antimicrobials and resistance — 24 June 2024.
    Comment: Metabolic inhibitors are known to exhibit complex interactions with antibiotics in bacteria, potentially acting as antagonists by inducing cell dormancy and promoting cell survival and persistance (defined here as the reversible survival in the presence of antibiotics). In this paper, authors looked at the synergistic interactions of metabolic inhibitors (i.e. chloramphenicol, a translation inhibitor, rifampicin, a transcription inhibitor, arsenate, an ATP production inhibitor, and thioridazine, a proton motive force inhibitor, all in combination with the antibiotic ofloxacin. The highest synergy was observed with thiridazine. This shows that there is potential utility in combining certain metabolic inhibitors with antibiotics for more anti-persistance effects in pathogens.

  • Evolution and host-specific adaptation of Pseudomonas aeruginosa
    Aaron Weimann et al. Science — 5 July 2024.
    Comment: This very impressive phylogenomics study highlights that a few environmental P. aeruginosa strains have become dominant, host-adapted epidemic clones, with a preference for either CF or non-CF hosts, via HGT over 200 years. Analyses of ~10,000 isolates find some genetic signatures and phenotypic traits underlying host adaptation, including DksA1’s role in CF infection. These pathoadaptive mutations, often causing loss of function, drive P. aeruginosa evolution, leading to specialized host infection and reduced cross-infection between different patient groups. Very cool and impactful!

  • microGWAS: a computational pipeline to perform large scale bacterial genome-wide association studies
    Judit Burgaya et al. bioRxiv — 10 July 2024.
    Comment: As an early contributor and adopter, I can agree that running microbial GWAS can look a bit daunting at first, given the number of approaches and lack of best practices. In this preprint, authors attempt to solve this, by providing with a pipeline to perform bacterial GWAS from a set of assemblies and annotations, with 1 or multiple phenotypes as groups. Definitely something to test and happy to hear what others think.

  • Patient characteristics and antimicrobial susceptibility profiles of Escherichia coli and Klebsiella pneumoniae infections in international travellers: a GeoSentinel analysis
    Sarah L McGuinness et al. Journal of Travel Medicine — 2 July 2024.
    Comment: This work, from Australian researchers in Melbourne, identified a significant prevalence of MDR resistance in 655 international travellers with E. coli and K. pneumoniae infections, with 37% of E. coli and 28% of K. pneumoniae isolates exhibiting resistance to at least three drug classes. Travellers to South-Central Asia were found to have the highest rates of non-susceptibility to key antibiotics, including third-generation cephalosporins, fluoroquinolones, and carbapenems, indicating regional variation in AMR profiles too. Data from the GeoSentinel Network over an 8y-period shows an increased trend in phenotypic ESBL and carbapenem resistance among the isolates.

(c) Other general interest

  • Longitudinal analysis of the lung proteome reveals persistent repair months after mild to moderate COVID-19
    Shreya M. Kanth et al. Cell Reports Medicine — 8 July 2024.
    Comment: Interesting results from this “long COVID” prospective study of the lung proteome with bronchoalveolar lavage vs. healthy controls. Results show that even after mild to moderate COVID infection, the inflamed lung undergoes prolonged repair for more than a year, even though chest X-ray and clinical symptoms may have seemingly resolved. This could be related to the long COVID symptoms that are starting to be very robustly shown all around the world. Given how many of us have been infected in the recent past, this is concerning, to say the least, but also gives a good insight to what can happen in our bodies once pathogens are seemingly cleared.

  • Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study
    George Taiaroa et al. The Lancet Regional Health: Western Pacific — 6 June 2024.
    Comment: This molecular epidemiology study focused on HIV-1 transmission in Victoria, Australia, and shows that 70% of cases are part of identifiable transmission groups, with certain demographics (e.g., males born in Australia) being more prevalent within these groups. Using a genetic distance threshold approach, some specific transmission groups had high effective reproductive numbers (Re), indicating significant potential for HIV spread, and also detected transmitted drug resistance mutations (SDRMs) in 10.7% of cases.