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! Just as a reminder: you can subscribe to this weekly list via WordPress (bottom right of the screen) or the RSS feed.

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Noteworthy studies and publications

(a) Microbiome

• A history of repeated antibiotic usage leads to microbiota-dependent mucus defects
  Kertu Liis Krigul et al. Gut Microbes — 21 July 2024.
  Comment: Using the Estonian Microbiome (EstMB) cohort, this study shows that repeated antibiotic use leads to long-term alterations in gut microbiota composition, which in turns can resulting in impaired colonic mucus barrier function in mice following FMT from affected humans to mice. Elegant and very clever way to study functionality in microbiome studies!

• Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease
  Xiangge Tian et al. Microbiome — 18 July 2024.
  Comment: IBD is notoriously progressive and complicated to study, and finding microbial markers is not always straightforward. In this study, authors looked at the gut virome of 71 Chinese IBD patients (15 with Crohn’s disease and 56 with ulcerative colitis) and 77 healthy individuals, and interestingly not only looked for phages but also eukaryotic viruses. They identified 139 viral signatures with significant abundance changes in IBD, including an increase in Retroviridae and Genomoviridae in IBD patients, as well as alterations in the abundance of various bacteriophage families like Siphoviridae, Myoviridae, and Microviridae.

• Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth
  Kelsey E. Johnson et al. Nature Communications — 23 July 2024.
  Comment: Human cytomegalovirus (CMV) is highly prevalent herpesvirus that is known to transmit to neonates via breast milk, with known negative effects on immunocompromised and preterm infants. However, the effect on health infants is still unclear. Here, authors analyse the MILK cohort (n=276 mother-infant pairs) to report that CMV presence in breast milk can affect milk composition and metabolic profile but also the infant gut microbiome (reduction in Bifidobacterium!), and full-term infant growth patterns in possible negative ways too.

• First-Year Dynamics of the Anaerobic Microbiome and Archaeome in Infants Oral and Gastrointestinal Systems
  Charlotte Julia Neumann et al. bioRxiv— 24 July 2024.
  Comment: What a beast of a study, from colleagues over at Graz in Austria! In this preprint, authors conducted a longitudinal study on both the oral and gastrointestinal tract of 30 healthy infants during their 1st year of life, with a particularly great focus on understudied taxonomic groups such as archaea and anaerobic organisms. Important results highlight the influence of breastfeeding on microbiome transitions in infants, particularly the oral microbiome. Interestingly, the archaeome in infants seems to be transient and not stable in the first year of life. Very interesting investigations on the oral/gut transfer too. Really great work, and go check Christine Moissl-Eichinger’s thread on Twitter about it.

• Optimised human stool sample collection for multi-omic microbiota analysis
  Metthew R. Gemmell et al. Scientific Reports — 22 July 2024.
  Comment: These short methodological benchmarking studies are sometimes useful to the field! In this one, authors compare various ways to collect human stool samples for microbiota analyses and recommend the use of PSP buffer and/or RNALater, followed by immediate freezing at -80C to retain an optimal microbial diversity in the sample, according to their parameters.

• An optimised approach to evaluate variability in gut health markers in healthy adults
  Kirsten Krüger et al. bioRxiv — 25 July 2024.
  Comment: What is “health”? How do we assess it? The question is more complicated than it seems. In this preprint, authors identify significant intra-individual variability in gut “health” markers in 10 “healthy” adults. These markers are quite exhaustively defined and include stool consistency, water content, pH, total short-chain fatty acids (SCFAs), total branched-chain fatty acids (BCFAs), total bacteria and fungi copies, calprotectin, myeloperoxidase, and untargeted metabolites, as well as microbiota composition and diversity. Interestingly, authors propose that “mill-homogenisation” (the grinding of frozen faecal samples into a fine powder) can enhance sample homogeneity and the reliable measurement of these gut health markers.

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

• Blood culture-free ultra-rapid antimicrobial susceptibility testing
  Tae Hyun Kim, Junwon Kang, Haewook Jang et al. Nature — 24 July 2024.
  Comment: Very likely to be impactful for the treatment of patients with sepsis. Authors present here a novel ultra-rapid antimicrobial susceptibility testing method (called “uRAST”), developed to bypass traditional blood culture and significantly reducing the time for reporting drug susceptibility profiles and potentially improving patient outcomes in sepsis treatment. Results can be obtained in less than 8h for some cases, bypassing entirely the existing lengthy culturing step.

• Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil
  Ana Beatriz Garcez Buiatte et al. Microbial Genomics — 19 July 2024.
  Comment: Campylobacter jejuni ST353 is a major zoonotic lineage infecting humans from chicken, worldwide. In this interesting paper, authors analyse the genomes of 221 C. jejuni from Brazil and find ST353 to be the most prevalent. Using Bayesian dating methods, they managed to propose an evolutionary history of C. jejuni ST353 in Brazil, estimating its origins to the late 1500s, which coincides with Portuguese colonization (and presumably the transfer of novel chicken-associated bacteria). A fun read, which reminded me of our similar Campylobacter ST-61 cattle study!

• Intracellular defensive symbiont is culturable and capable of transovarial, vertical transmission
  Gerald P. Maeda et al. mBio — 7 May 2024.
  Comment: In this study from a couple of months ago, authors managed to cultivate an endosymbiont in vitro without its host. No biggie! They focused their efforts on Candidatus Fukatsuia symbiotica, an essential bacterial endosymbiont of the pea aphid, managed to reinfect the host subsequently, observed transgenerational transmission of the reinfected endosymbiont. The trick was apparently very careful synthetic media preparation, homogenization of the host cells onto the culture medium followed by 2 weeks of incubation. This is a nice step forward for endosymbiont research, although it remains to be seen whether this approach would work for all other endosymbionts. There is a nice commentary in mBio on it too.

• Ecotype-specific genomic features within the Escherichia cryptic clade IV
  Martin Saraceno et al. bioRxiv— 19 July 2024.
  Comment: When I was in PhD working on E. coli, weird cryptic Escherichia clade had just come out and they were being undersampled, underdescribed, completely misunderstood. Now, people know far more about them! In this preprint, authors describe genomic features specific to environmental Escherichia cryptic clade IV strains (44 diverse genomes including the first South American isolate), with a notable absence of AMR genes and a distinct set of virulence factors, supporting the environmental hypothesis of niche adaptation.

• Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia
  Laura Glendinning et al. Microbiome — 23 July 2024.
  Comment: In the context of zoonotic foodborne pathogens, a lot of the chicken side of things is often studied and inferred from agricultural chicken, often from intensive agriculture. It is always refreshing to see alternative models. Here, authors compare the microbiota from 243 indigenous Ethiopian chickens and show a significant impact of altitude-dependent agro-ecologies (i.e. variations in agricultural practices that are influenced by changes in altitude) on the diversity of their gut microbiota. They further identify 3 distinct enterotypes and assemble ~10,000 novel MAGs. An additional interesting point for me was the presence in these MAGs of 3 known species of Campylobacter and 2 new ones! Also strikingly very little E. coli, which happens to be quite a problem in industrial chicken.

• A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports persistent co-existence of diverse lineages
  Ben Vezina et al. bioRxiv— 25 July 2024.
  Comment: Multiple strains from the same species can co-exist in particular environments, but why is that the case? In this exhaustive genome-scale metabolic modelling study, Ben Vezina and Kelly Wyres across the road from our lab observe evidence of lineage-specific metabolism in >7,800 genomes from Klebsiella pneumoniae species complex, which supports the co-existence of diverse lineages in the same environment, through metabolic differentiation/complementation and possible commensal interactions.

• The spread of antibiotic resistance is driven by plasmids amongst the fastest evolving and of broadest host range
  Charles Coluzzi & Eduardo Rocha bioRxiv — 24 July 2024.
  Comment: Understanding the evolutionary dynamics of plasmids is essential for understanding antimicrobial resistance spread. In this preprint, authors analyse 37,061 plasmid sequences and show that the acquisition of antibiotic resistance genes by bacteria is largely due to the horizontal transfer of some specific plasmids only. They introduce a novel approach using Plasmid Taxonomic Units (PTUs) to classify plasmids, revealing that those encoding AMR are inherently more plastic and evolvable, with these traits persisting even when resistance genes are excluded from the analysis. Nice thread from Eduardo Rocha on Twitter.

(c) Other general interest

• Cellular immune response to SARS-CoV-2 and clinical presentation in individuals exposed to endemic malaria
  Kesego Tapela et al. Cell Reports — 24 July 2024.
  Comment: Intriguing study (for profanes like me I suppose). In this work, authors analysed data from a cohort of 217 Ghanaian individuals, including 62 asymptomatic and 155 symptomatic COVID-19 patients, to evaluate the impact of malaria exposure on the cellular immune response to SARS-CoV-2, and found that asymptomatic individuals showed reduced T cell activation, higher P. falciparum antibody levels, and a more polyfunctional T cell response, which seems to suggest a potential protective role of malaria exposure against severe COVID-19 in Africa!

• COVID-19 origins: plain speaking is overdue
  Editorial comment The Lancet Microbe — 18 July 2024.
  Comment: This was a brilliant read, not often seen in editorial comments of a prestigious journal. Excerpt: “The sheer hubris needed to underpin alternative hypotheses was an early signal of their tenuousness, when we are intensely aware that the natural processes needed to bring about this sort of pandemic are constantly churning and testing the boundaries between animal and human populations. The most remarkable thing about the whole COVID-19 origin saga is the confected controversy over something that should not be controversial at all. The thing that should be controversial is how little of the energy expended over this discussion has been directed towards actual beneficial outcomes.”

• Evolution of the Italian pasta ripiena: the first steps toward a scientific classification
  Vazrick Nazari et al. Discover Food — 12 July 2024.
  Comment: In this almost parodic article, authors use very serious phylogenetic and biogeographic methods to classify filled pasta and related foods in Europe. Excerpt from the abstract: “Based on the proposed evolutionary hypothesis, the Italian pasta are divided into two main clades: a ravioli clade mainly characterized by a more or less flat shape, and a tortellini clade mainly characterized by a three-dimensional shape. The implications of these findings are further discussed.” 🙂