Last week was full blown grant writing time so not a lot of time to peruse the literature! But here is the weekly summary of some interesting microbiome, microbial genomics/ecology studies and others.

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Recent from the lab/collaborators

• PREPRINT: Population variation and prognostic potential of gut antibiotic resistome.
  Katariina Pärnänen et al. medRxiv — 8 August 2024.
  Topics: AMR, gut resistome, large-scale population cohorts

Noteworthy publications

(a) Microbiome

• STUDY: Stress-sensitive neural circuits change the gut microbiome via duodenal glands
  Hao Chang et al. Cell— 8 August 2024.
  Comment: Quite an impressive functional gut-brain axis study in mice showing that mucin-secreting glands in the small intestine have GLP-1 receptors that can connect to the brain via the vagal nerve, and influence Lactobacillus levels in the gut as well as host immunity.
  Topics: gut-brain axis, gut microbiota, animal model, Lactobacillus

• STUDY: BCAA-producing Clostridium symbiosum promotes colorectal tumorigenesis through the modulation of host cholesterol metabolism
  Yi-Meng Ren, Zi-Yan Zhuang, Yuan-Hong Xie, Peng-Jie Yang et al. Cell Host & Microbe — 5 August 2024.
  Comment: The links between infection, gut microbiota and CRC are extensively studied and some trends are starting to slowly emerge. In this human clinical and animal model study, authors followed patients with a progression of symptoms from healthy to colorectal adenoma (CA) to colorectal cancer (CRC), and observed that Clostridium symbiosum levels increased significantly. Following this with animal (mice) model experiments, they highlight the role of microbial branched-chain amino acids (BCAAs) in activating signaling leading to tumorigenesis, in a process that is linked to cholesterol metabolism and can be influenced by statin intake.
  Topics: cancer microbiota, CRC, animal model, Clostridium

• STUDY: Insights into the ecology of the infant gut plasmidome
  Wanli He et al. Nature Communications — 13 August 2024.
  Comment: Quite an extensive study (with great figures) characterizing plasmids in the infant gut (using their Rep groups), predicted hosts and host ranges. Interesting findings suggesting that plasmid dynamics reflects environmental changes faster/better than their hosts. The phylum Bacteroidota seems to act as a major hub for plasmid transfer and reservoir in the gut.
  Topics: plasmids, HGT, MGEs, gut microbiome, infant microbiome

• REVIEW: Regulation of microbial gene expression: the key to understanding our gut microbiome
  Anurag Kumar Sinha, Martin Frederik Laursen et al. Trends in Microbiology — 1 August 2024.
  Comment: Interesting short review on the importance of considering how external factors might influence metabolic gene regulation in gut microbiota members, with important functional impact going beyond the mere presence/absence of the taxa (currently an all-too-common shortcut taken by many observational microbiome studies, including some of ours…!)
  Topics: functional microbiome, microbial gene regulation, secondary metabolite production

• STUDY: A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life
  Roosa Jokela et al. Gut Microbes — 2 August 2024.
  Comment: This work involving our collaborators Katariina and Leo, looks at the dynamics of ARGs in the gut microbiota of infants during their first 2 years of life, with an interesting focus on early life exposures and familial transmission. They use the HELMi cohort (Finland, n=475 infants with 305 maternal and 123 paternal samples) and highlight the role of Bacteroides and Bifidobacterium genera as potential reservoirs of ARGs in the infant gut. They show within-family transmissions of ARGs but mostly between the infant-mother, as the paternal effect appears negligeable.
  Topics: AMR, resistome, infant microbiota, familial transmission

• STUDY: Lining the small intestine with mycobacteriophages protects from Mycobacterium avium subsp. paratuberculosis and eliminates fecal shedding
  Victoria K. Harman-McKenna et al. PNAS — 5 August 2024.
  Comment: A very interesting real-life successful example of phage therapy! Livestock is sensitive to MAP, causing Johne’s disease in cattle, an often fatal gastric illness. In this study, authors gave dairy calves a cocktail of mycobacteriophages aiming to line up their GI tract and measured a significantly high reduction in faecal shedding and tissue infection in controlled pathogen infection experiments. Good discussion included on MAP transmission, and the possibility to influence animal immunity with phages.
  Topics: phage therapy, in vivo, animal microbiome

• STUDY: Associations between gut microbiota and incident fractures in the FINRISK cohort
  Louise Grahnemo, Oleg Kambur et al. npj Biofilms and Microbiomes — 14 August 2024.
  Comment: Short study involving our FR02 collaborators led by a Swedish group showing a potential link between gut microbiota members and incident (future) bone fractures. Seems intriguing at first but the microbiota has been linked to bone mineral density in several other studies before this one. Using our favourite FINRISK cohort, authors attempt to predict the influence of specific taxonomic groups for fracture risk, whether positive or negative, and Gammaproteobacteria are highlighted.
  Topics: bone mineral density, prospective cohort, incident disease, gut microbiota

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

• STUDY: Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project
  Filipa F. Vale et al. Gut Microbes — 12 August 2024.
  Comment: In this work, prophages were analysed in the HpGP genomes (n=1,011), showing that most of them seem to be co-evolving and diversifying within their specific Hp lineages, while a few others show signatures of recombination, specifically between the Hp SWEurope and NEurope lineages.
  Topics: prophages, comparative genomics, Helicobacter pylori

• STUDY: Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus
  Jeffrey A. Freiberg et al. Nature Communications — 7 August 2024.
  Comment: Using proteomics and Tn-Seq (150k genome-wide insertions), authors show that limiting arginine inhibits protein synthesis, thereby increasing tolerance to antibiotics in Staphylococcus aureus biofilms; and this effect is counteracted by citrulline supplementation, which restores arginine levels via ArgGH enzymes. Using homogenized biofilms in mice, they confirm that arginine availability directly influences antibiotic efficacy in vivo.
  Topics: antibiotic tolerance, stringent response, MRSA

• STUDY: Trends in infection incidence and antimicrobial resistance in the US Veterans Affairs Healthcare System: a nationwide retrospective cohort study (2007–22)
  Thi Mui Pham et al. The Lancet Infectious Diseases — 13 August 2024.
  Comment: Impressively large dataset from USA veterans (~1M records, ~0.5M individuals followed over 15 years) highlighting interesting observations: 15y reduction of fluoroquinolone (FQ) use correlates with decline in FQ resistance; targeted efforts seem to have specifically reduced MRSA and VR-E. faecium infections over 15y. Important comments too about the effect of COVID-19 on these results too.
  Topics: follow-up large cohort, AMR trends, link between use and resistance

• REVIEW: Mechanisms of antibody-dependent enhancement of infectious disease
  Timothy J. Wells et al. Nature Reviews Immunology — 9 August 2024.
  Comment: Why are we observing so much inter-individual variation in illness severity? Why is this also the case for infectious diseases (ID) from the same aethiological agent having the same infectious dose? In this extensive review, authors describe the various ways that the varying presence of antibodies in people could affect infectious disease severity, potentially explaining why it is heterogenous in populations. Fascinating stuff and really at the heart of precision ID medicine.
  Topics: infectious disease, antibody-dependent enhancement (ADE), disease severity

(c) Other general interest

• STUDY: The genomic landscape of 2,023 colorectal cancers
  Alex J. Cornish [and 10(!) other co-first authors] et al. Nature — 7 August 2024.
  Comment: In this work, authors used the UK 100,000 Genomes Project to analyze 2,023 CRC samples to identify >250 putative driver genes in CRC, including many novel ones, and suggest 4 new common subgroups of CRC with distinct genomic features. More interesting for the microbiologists that we are, a mutational signature called SBS88 (i.e. a reproducible pattern of somatic mutations) was associated with colibactin-producing E. coli, and was found to be more prevalent in distal CRCs which suggests that E. coli might contribute to CRC in specific locations of the bowel.
  Topics: colorectal cancer, colibactin, E. coli, human genomics

• STUDY: Cohort study of cardiovascular safety of different COVID-19 vaccination doses among 46 million adults in England
  Samantha Ip et al. Nature Communications — 31 July 2024.
  Comment: Perhaps as expected after a few large studies of this kind, this work from the UK supports the cardiovascular safety of COVID-19 vaccines, with the benefits of reducing common cardiovascular events outweighing the risks of rare complications. Authors see similar associations irrespectively of demographic and clinical subgroups in the population cohort, adjusting for a wide range of factors and disease histories.
  Topics: COVID-19, vaccination, cardiovascular disease