Noteworthy things — Week 21 (20/05/2024)

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

  • The gut–airway microbiome axis in health and respiratory diseases.
    Mustafa Özçam & Susan V. Lynch Nature Reviews Microbiology — 22 May 2024.
    Comment: We are starting to understand a bit better the dynamics between oral, airway and gastrointestinal microbial communities and their role in respiratory diseases. This review is a great resource and has very nice figures about it. Make sure to check our 2023 JACI study led by Dr Yang Liu, on the use of gut microbes to predict incident respiratory diseases.

  • Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration
    Ariadna Fernández-Calvet et al. Nature Communications — 16 May 2024.
    Comment: One of my favourites this week. Some enterobacteria can produce self-aggregating amyloid fibers (such as curlis in E. coli) that are critical during early attachment to surfaces and subsequent biofilm formation. The similarity with how amyloid fibers self-aggregate in some age-related neurodegenerative diseases has not gone unnoticed and a few studies have tried to link the two already. This new one is quite impactful in the matter; authors show that the abundance of certain biofilm-related genes in the gut microbiome can be correlated with Parkinson’s disease incidence, and go further by proving using C. elegans and mice models that bacterial biofilm-derived amyloids can induce α-synuclein aggregation, and promote key pathological features of PD in mice when injected in their brains.

  • Systematic analysis of gut bacterial carcinogen metabolism and its functional consequences
    Boyao Zhang et al. bioRxiv — 21 May 2024.
    Comment: An original preprint from the EMBL at Heidelberg! The fate of known carcinogenic products in our bodies is not well known (apart from the end outcome) and this study shows that 34 bacterial species representative of the human lower intestine are able to biotransform 41/68 known carcinogen products in vitro. Those included cigarette smoke, industrial reagents or clinical drugs (picked from their toxicity on the Ames test and presence on the EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database). Authors go on to test how this interacts with the host response to carcinogens and suggest an interplay between host/microbiome for exposome-induced tumorigenesis.

  • Segatella copri strains adopt distinct roles within a single individual’s gut
    Xieyue Xiao et al. bioRxiv — 20 May 2024.
    Comment: Combining comparative microbial genomics can critically enhance our understanding of the microbiome, and shed light on strain variation, whether within-individuals or between. This preprint does that on Segatella copri (formerly from the ill-defined Prevotella copri complex and now aptly renamed in honour of Nicola Segata). Authors isolated and cultured and sequenced 63 S. copri strains from a single participant with S. copri abundances at ~75% of all detected gut taxa) from a Fijian cohort and compared them. This added knowledge on variation in metabolic capabilities, cellular morphologies, SCFA production yield, and translated to the observation that only some S. copri isolates induced strong transcriptional responses from Caco-2 epithelial cells. Good discussion too on the limitations of metagenomics to distinguish clades (vs. culturing + sequencing/typing).

  • Gardnerella diversity and ecology in pregnancy and preterm birth
    Hanna L. Berman et al. mSystems — 16 May 2024.
    Comment: In the same spirit, authors looked here at within- and between-individual strain variation in Gardnerella sp. from vaginal microbiomes. They show that that single microbiomes can contain all currently known species of Gardnerella and that multiple similar species can exist within the same environment, prompting more questions on how these strains interact in individuals. Looking at cohort data suggests that some species appear more commonly in certain populations, highlighting the need for large surveys to capture the whole genus diversity.

(b) Microbial genetics, ecology, evolution and AMR

  • Anaerobiosis modulates the performance of antimicrobial resistance genes in Enterobacteriaceae
    Laura Ortiz et al. bioRxiv — 17 May 2024.
    Comment: Always been a bit bugged when MIC tests are performed at the bench (in full aerobic conditions) in contrast with the microaerophilic or even anaerobic environment that bacteria would actually encounter in a patient (wounds, gut, etc). In this preprint, authors looked at whether different atmospheric oxygen conditions could influence resistance in E. coli and K. pneumoniae. Guess what, it does! *shocked* This suggests that anaerobiosis conditions should really be taken into consideration when trying to predict resistance levels in bacterial pathogens. Nice work!

  • Global epistasis and the emergence of function in microbial consortia.
    Juan Diaz-Colunga, Abigail Skwara et al. PNAS — 6 May 2024.
    Comment: I did not follow all the mathematical and modelling details but I quite enjoyed the central idea and concept presented here. It stems from the observation that statistic models can predict the effect of a species on a community-level function, akin to epistasis reported in genetics. This “ecological global epistasis” stems from widespread species-by-species interactions, and can potentially be interacted with to modulate functions from microbial communities. Tweet thread from the lead author here!

  • Bacterial cell differentiation enables population level survival strategies.
    Trisha N. Chong & Lucy Shapiro mBio — 21 May 2024.
    Comment: Very interesting microbial ecology minireview on the various ways bacteria act as multi-cellular organisms within functional communities, structures etc. This includes biofilms, swarming and fruiting bodies as well as some pathogenicity processes. “Obligate” differentiation (the case of Caulobacter crescentus) is also discussed.

  • Inducible transposon mutagenesis for genome-scale forward genetics.
    David W. Basta et al. bioRxiv — 21 May 2024.
    Comment: Tn-seq is a very proven and popular microbial mutagenesis technique, whereby you deactivate genes using transposons that are randomly (or not) inserted throughout the microbial genome. There are some drawbacks to it, mainly that sometimes Tn insertion is inefficient, and it is also easy to deactivate essential genes and therefore not be able to study the resulting non-viable mutants. In this preprint, authors present a new method called InducTn-seq, which allows for the induction of mutagenesis and a temporal control of transposon insertion. One of the major outcomes suggested is the possibility to move beyond a binary outcome of gene essentiality to a more quantitative measure of fitness. As a proof-of-concept, authors use a mouse model of colitis to identify more functions involved in infection.

  • Shaping of microbial phenotypes by trade-offs.
    Manlu Zhu & Xiongfeng Dai Nature Communications — 18 May 2024.
    Comment: Very exhaustive review on how trade-offs (at various levels) shape microbial biology, ecology and evolution. Authors talk about trade-offs between growth and adaptability, growth and survival, generalist and specialists (the most interesting to me). A long but good read.

(c) Other general interest

  • The promise and pitfalls of synteny in phylogenomics.
    Jacob L. Steenwyk & Nicole King et al. Plos Biology — 20 May 2024.
    Comment: Synteny (the order of genes) has been an interesting addition to the reconstruction of various species phylogenetic trees, in particular for deep branches with uncertainty. In this critical essay, authors discuss the state of using synteny for phylogenetics, with very interesting examples (humans/apes, sponges/ctenophores, fishes, etc).

  • Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.
    Dylan J. Taylor, Jordan M. Eizenga, Qiuhui Li et al. Annual Review of Genomics and Human Genetics — 25 April 2024.
    Comment: A few years ago (surprisingly recently), the concept of human pangenomes came a bit more into light (it’s been decades we study this in microbes), facilitated by advances in whole genome sequencing of humans. This review summarizes very well the state of this field including the resolution of centromeres in human genomics, and what are the benefits of including non-reference sequences for maximizing human diversity and representativity. New reference pangenomes are discussed too. To our microbiome-minded minds, considering the human pangenome is useful when wanting a more efficient human read filtering, incorporating pangenomic sequences and not just the artificial hg38 reference (check the nice method from Michael Hall to do this; we’ve used it and it works relatively well; adds ~1000s of additional human reads to filter per sample out vs. hg38 even on European samples).

  • iSeq: An integrated tool to fetch public sequencing data.
    Haoyu Chao et al. bioRxiv — 22 May 2024.
    Comment: Happy to hear the thoughts of others using this, if any; we will certainly give it a go. This is a tool aiming to facilitate sequence recovery from repositories from the command line. A few others exist, but this one seems promising (?).

  • The anthropogenic fingerprint on emerging infectious diseases.
    Rory Gibb et al. medRxiv — 22 May 2024.
    Comment: Likely a very impactful preprint in the field of pandemic preparedness and the causes of zoonotic spillovers. Using outbreak reporting data, authors look at which factors affect the risk of zoonotic outbreak worldwide for major pathogens. Living in mosaic landscapes (at the border of forests or fragmented environments) is found to be a factor, exacerbated by regular decreases in precipitations (and climate change). Outbreak reporting is mostly affected by socio-economic aspects and geography, such as time and distance to healthcare facility. Good data analysis study, with a lot to unpack!