This is 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

• Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function
  Johannes P. Johnson-Martínez et al. Cell Reports Medicine — 16 July 2024.
  Comment: This new study addresses a very important topic in microbiome science: the influence of (self-reported) bowel movement frequency (BMF) on the microbiota structure and links with disease. Authors leverage a large human cohort of ~2,000 individuals with good phenotyping, with matching 16S rRNA microbial data. They find that abnormal BMF can associate with microbial toxins in blood and with inflammation, as well as kidney function. Additionally and interestingly, diet, lifestyle but also cognitive factors seem to be associated with BMF variation. See this nice thread by senior author Sean Gibbons on Twitter about it!

• Maternal Diet and Gut Microbiota Influence Predisposition to Cardiovascular Disease in Offspring
  Hamdi A. Jama et al. Circulation Research — 17 July 2024.
  Comment: This study from our great collaborators at the Marques Lab and others at the Baker Institute, used scRNA-seq on cardiac tissue of mice offspring (n=8 per group) to show a reduced inflammation and fibrosis linked to maternal high-fiber intake. This link is possibly through increased SCFA and beneficial shifts in gut microbiota composition, with predicted lasting effects into adulthood.

• Metagenome-assembled genomes of Estonian Microbiome cohort reveal novel species and their links with prevalent diseases
  Kateryna Pantiukh et al. bioRxiv — 9 July 2024.
  Comment: Despite having seen it a few times now, I am always amazed when large-scale human metagenomic assembly projects identify novel bacterial species. In this preprint, authors assemble a population-specific reference of ~85k MAGs from ~1,900 individuals in the Estonian Microbiome (EstMB) cohort, to identify 353 potentially novel bacterial species and linking 44 bacterial species to 15 prevalent diseases, including associations with new species not previously identified. As more and more populations will be examined in the future, it will be fascinating to see how much novel (and population-specific!) diversity is linked to global human health. Also see the thread from lead author on Twitter!

• Not All Is Lost: Resilience of Microbiome Samples to Freezer Failures and Long-term Storage
  M. Fabiola Pulido-Chavez et al. bioRxiv — 15 July 2024.
  Comment: Original and probably quite impactful for any wet-lab microbiologist! In this preprint, authors look at soil samples to demonstrate that storage at -80°C, even after a complete thaw, preserves microbial diversity better than storage of extracted DNA at -20°C for extended periods (unsurprising perhaps). They also show that fungal richness and the overall composition of bacterial and fungal communities in soil samples are highly resilient to both short-term thawing events and long-term frozen storage.

• Modelling interactions that determine core gut microbiome stability to predict microbiome perturbation by opportunistic pathogens
  P.T. van Leeuwen et al. bioRxiv — 15 July 2024.
  Comment: A billion-dollar question (no, really) in microbiome science is to understand well how colonizing bacteria (probiotics, opportunistic pathogens, etc) establish, interact, integrate or not complex microbial communities and microbiomes. In this preprint, authors compare how E. coli or Bacteroides ovatus differ in their colonization strategies on a synthetic microbial community (complemented by co-culture growth experiments). Bacteroides tends to replace existing bacteria while E. coli tends to integrate into the microbiome. It is a simplified model, but still interesting to contextualise in a broader context.

• Gut microbial factors predict disease severity in a mouse model of multiple sclerosis
  Alex Steimle, Mareike Neumann et al. Nature Microbiology — 15 July 2024.
  Comment: Some very interesting approaches in this mice/microbiome study! Authors first used both gnotobiotic mice with defined synthetic microbiota and SPF mice with complex microbiotas, to look at the role of specific microbial strains and their interactions within the gut on the experimental autoimmune encephalomyelitis (EAE) model (most widely used animal model for human MS and mimics key pathological and clinical features). They find that the impact of a single commensal like A. muciniphila (previously associated with the disease) on disease development is significantly influenced by the broader microbial community and cannot be assessed in isolation. More interestingly, they also see that IgA coating index of gut bacteria, particularly Bacteroides ovatus, is a potent predictor of individual disease severity, as opposed to the presence of the bacteria alone, which shows the power of looking at co-abundance networks and at function when associating microbial features to diseases.

• How bile acids and the microbiota interact to shape host immunity
  Michael H. Lee et al. Nature Reviews Immunology — 15 July 2024.
  Comment: Quite authoritative review updating the knowledge on the intricate interactions between bile acids, the gut microbiota, and host immunity. It includes examples on the continued identification of microbially conjugated bile acids (MCBAs) and their modulatory immune effects. An interesting highlight for me was also that MCBAs can have a stronger effect after binding receptors like FXR and TGR5 than primary bile acids (produced by the host), highlighting their key importance. Some interesting links with IBD are also presented.

• CompareM2 is a genomes-to-report pipeline for comparing microbial genomes
  Carl M. Kobel et al. bioRxiv — 17 July 2024.
  Comment: For anyone doing MAGs out there and who has used CompareM before, here’s the new version of it, with some useful benchmarks from authors. This version integrates several analyses such as QC, annotation, function and species calling as well as comparative analyses like computation of core/pan genomes and phylogenetics. Link to the CompareM2 Github.

• Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
  Aarthi Ravikrishnan et al. bioRxiv — 11 July 2024.
  Comment: On the importance of the gut microbiome in aging and in population-dependent effects in microbiome research! In this nice preprint, authors analyse metagenomic data from 234 healthy community-living octogenarians from Singapore (enrolled in the SG90 cohort) to identify gut microbial hallmarks of healthy aging. They identify reduced species richness and a metabolic potential expansion towards alternative butyrate synthesis pathways, with key species like Alistipes shahii and Bacteroides xylanisolvens becoming more abundant. Interestingly, they find novel associations involving Parabacteroides goldsteinii (a potential probiotic) and Klebsiella pneumoniae (a pathobiont). By comparing results to other Asian cohorts (SPMM, CPE, T2D), they interestingly find some that are only consistently seen in Asian and not European cohorts.

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

• Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation
  Valentine Cyriaque et al. Nature Communications — 12 July 2024.
  Comment: Plasmids constitute an interesting ecological cost/benefit balance for their microbial hosts and there’s been considerable research trying to understand this beyond modeling and theoretical arguments. Here, authors use a novel scRNA-seq approach in Pseudomonas putida to show that plasmid-encoded genes are differentially expressed among bacterial cells, with key plasmid functions correlating with host cell activity. They uncover a distinct bacterial subpopulation that particularly does not transcribe conjugation-related genes, implying a potential bet-hedging strategy for plasmid persistence within bacterial communities.

• Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype
  Aldert Zomer et al. PNAS — 11 July 2024.
  Comment: Intriguing and original study looking at the genetic basis of microbial pigmentation and the reflective colouring of colonies observed on synthetic media! Similar to green bird feathers, authors show the presence of “structural colour” in microbial colonies that are vividly iridescent and compare their genomes to other types of coloured colonies using a bacterial GWAS approach, to uncover a set of genes linked to biosynthesis of pigments (uroporphyrin and pterins, also found in butterfly wings) but also carbohydrate metabolism. They go on to build a classifier to predict structural colouring directly from sequences. I am not sure I know what practical translatable finding will be derived from this yet, but this is clearly very cool!

• Density-dependent network structuring within and across wild animal systems
  Gregory F. Albery et al. bioRxiv — 2 July 2024.
  Comment: This ecology paper is an enormous effort (>100 authors on the preprint) attempting to link wild animal density to interaction networks, using data from all around the world from 55k individual animals across 34 wildlife systems. I did not really understand every single aspect of the work (which is very ecological), but I take some findings from it regarding pathogen transmission, in the context of One Health perhaps: as the number of animals in a given area increases (higher population density), the chances of those animals coming into contact with each other also increases. The study found that as density increases, animals are more likely to share the same space, which could lead to the spread of diseases that are transmitted indirectly, such as through the environment (e.g., contaminated water or soil). However, the increase in social interactions, like touching or grooming, does not increase at the same rate. This means that while animals might be closer together in space, they may not necessarily be interacting socially more often, which could affect how diseases that require direct contact spread. Authors suggest that animals might change their behavior at high densities to avoid too much contact, possibly to reduce the risk of disease transmission or to cope with limited resources or space. Interesting to see such big data analyses in the field of ecology and pathogen transmission!

(c) Other general interest

• Transoceanic pathogen transfer in the age of sail and steam
  Elizabeth N. Blackmore & James O. Lloyd-Smith PNAS — 16 July 2024.
  Comment: In this work, authors use historical data (including ship passenger lists and manifests, ship population data, journey times, ship types, points of origin for ships arriving to multiple locations, etc) along with pathogen natural history parameters (incubation time, infectiousness, R0 numbers) to build mathematical models quantifying the historical risks of shipborne pathogen introduction during the 15th-19th centuries. Authors challenges longstanding narratives that suggested a rapid and inevitable spread of pathogens across the globe following European exploration, highlighting the complexity and variability of historical pathogen transfer. Furthermore, they show the importance of ship size and population density in facilitating sustained pathogen circulation on long voyages, with larger and more crowded ships presenting greater risks of pathogen introduction, and suggesting that the advent of steam over sail (unsurprisingly) accelerated the risk of pathogen transfer. It remains a modelling study, but it is an interesting take!

• Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
  Marcela Sandoval-Velasco, Olga Dudchenko, Juan Antonio Rodríguez, Cynthia Pérez Estrada et al. Cell — 11 July 2024.
  Comment: Ridiculously fun developments in ancient DNA studies with this one. Authors used a novel approach (PaleoHi-C) on a single preserved skin sample of a 52,000-year-old woolly mammoth, successfully reconstructing its 3D genome architecture, including chromosomal territories, loops, and compartments. It revealed a distinct tetradic inactive X chromosome structure in elephantids. Authors suggest that it is the particular dehydration conditions that led to the exceptional preservation of tissue structure in this sample, arresting molecular movement. Those two (one – two) pieces in popular press are also well-written and explain more.