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!

Thank you to Svetlana Perović for recently sharing these reading lists as part of the great Microbiome Digest, which you should check out too! 🙂 A reminder that you can subscribe to this weekly list via WordPress (bottom right of the screen) or the RSS feed. I also advertise these posts on Twitter, BlueSky and LinkedIn, but feel free to share them wherever. Hopefully this is interesting to some, let us know! 🙂

I’ll be travelling in the next few weeks, but hopefully able to keep a steady streams of these coming.

Noteworthy studies and publications

(a) Microbiome

• Tunable control of B. infantis abundance and gut metabolites by co-administration of human milk oligosaccharides.
  Abilgail L Reens et al. Gut Microbes— 8 January 2024.
  Comment: I had missed this one from a few months ago, but it is a good one for those interested in precision microbiome engineering! In this study, authors use a synbiotic mix of bacteria and nutrients to control a microbial influence in infants. They looked at what happens after co-delivering Bifidobacterium infantis (an important species in infant microbiomes) with human milk oligosaccharides. As is the goal for synbiotics, they observe that the HMO favours the creation of a stable ecological niche for B. infantis to colonize, and together, they impact gut metabolites in the host.

• Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data.
  Gleb Goussarov et al. MicrobiologyOpen— June 2022.
  Comment: From a few years ago, everything you have always wanted to know about metagenome-assembly and MAGs but were too afraid to ask at this point! Very clear and informative.

• Short-term dietary fiber interventions produce consistent gut microbiome responses across studies.
  Cynthia I. Rodriguez et al. mSystems — 14 May 2024.
  Comment: Interesting read of this review re-analyzing 16S rRNA studies from 21 dietary fiber interventions from 12 studies in humans (n=2,564 samples from 538 subjects) and showing that the effects of increased fiber consumption seem to be comparable across studies, with the identification of particular genera with consistant responses (increased/decreased abundances after treatment).

• Microbial dark matter could add uncertainties to metagenomic trait estimations.
  Ernest D. Osburn et al. Nature Microbiology — 13 May 2024.
  Comment: Interesting comment on soil microbiology (but also applicable to human microbiomes) and the presence of non-bacterial DNA linked to function. Authors jazzily coin this as “microbial dark matter” but it is now an exciting time (and also high time) to be working on other domains of life present in ecosystems, such as archaea and others.

• Gut microbiome co-abundance networks varies with age, sex, smoking status and body mass index.
  Christophe Boetto et al. medRxiv — 1 May 2024.
  Comment: Really likely to be another very impactful study from the Milieu Interieur consortium in France. In this preprint, authors looked at co-abundance networks in the gut microbiome and described their various aspects exhaustively to find factors linked to variation in these networks. These sort of studies really touch on to the ecology of microbiomes and how dynamic of a system they are. Looking forward to seeing the paper published.

(b) Microbial genetics, ecology, evolution and AMR

• Intraspecies warfare restricts strain coexistence in human skin microbiomes.
  Christopher P. Mancuso et al. bioRxiv — 7 May 2024.
  Comment: As a Staphylococcus enthusiast myself (it is a weird thing to say out of context), how to not be thrilled when seeing a new strain ecology study drop from the Tami Lieberman lab in Boston! In this new preprint, authors profiled ~15,000 pairwise interactions between different skin S. epidermidis strains from 18 individuals and 6 families and found a lot of within-species antagonism linked to strains fitness success, with various mechanistic reasons and linked to horizontal gene transfer. Wonderful job.

• Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii
  Maaike S. Besteman et al. Environmental Microbiology Reports — 10 May 2024.
  Comment: Examples of syntrophy between bacteria and archaea are starting to be studied in detail. Examples include some acetogenic bacteria, which convert fatty acids (butyrate, propionate) with the requirement of H₂ consumption from methanogenic archaea. This recent work from the Netherlands goes a bit further in the characterization of this functional interaction by examining co-cultures of Syntrophomonas wolfei (bacterium) and Methanospirillum hungatei (methanogenic archaeon) with and without addition of the acetate-scavenger archaeon Methanothrix soehngenii using transcriptomics evidence, highlighting the importance of acetate scavengers in the syntrophic functional community degrading fatty acids.

• Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance.
  Stephanie S. R. Souza et al. npj Antimicrobials and Resistance — 7 May 2024.
  Comment: Very nice longitudinal study characterizing circulating lineages of Staphylococcus aureus causing bloodstream infections in a single hospital (New Hampshire, USA) along a 12-years period. Authors look at the dynamics of lineages and AMR over time, and observe that ST5 and ST8 were more prevalent, with 24 distinct AMR genes conferring susceptibility to 9 classes of antibiotics. Both ST5/8 seemed to have independent acquisitions of beta-lactam resistance. Nice use of time-calibrated phylogenies too with such a collection of strains.

• Three concurrent mechanisms generate gene copy number variation and transient antibiotic heteroresistance.
  Hervé Nicoloff et al. Nature Communications — 10 May 2024.
  Comment: There is what the sequence analysis tells you, and then there is real life. In real clinical settings, transient resistance to antibiotics is observed. This heteroresistance has very biological and ecological reasons and is described as a “medically relevant phenotype where small antibiotic-resistant subpopulations coexist within susceptible bacterial population“. In this study using Klebsiella pneumoniae in mice models, authors investigate 3 mechanisms of gene copy number variation that lead to heteroresistance, whether by tandem amplification, plasmid copy number increase or transposition of AMR genes onto cryptic plasmids. And when checking real life samples, all three of these also seem to happen in bloodstream E. coli isolates.

• Widespread horizontal gene transfer between plants and bacteria.
  Shelly Haimlich et al. ISME Communications — 13 May 2024.
  Comment: Great study working on the hypothesis that spatial ecological proximity between plant-associated bacteria and their hosts could promote cross-kingdom horizontal gene transfer, a rare but not unseen phenomenon. Using the highly-sequenced plant model Arabidopsis and its myriad of associated metagenomic datasets, authors look for events of HGT and suggest that 75 unique genes seem to have been transferred, including DET2 involved in phytohormones biosynthesis.

• Bile acids activate the antibacterial T6SS1 in the gut pathogen Vibrio parahaemolyticus.
  Sarah Schiffmann et al. bioRxiv — 12 May 2024.
  Comment: Vibrio parahaemolyticus is a marine bacterium that can cause seafood-borne illness in humans. This preprint suggests a mechanism for this virulence and host invasion, by identifying a secretion system (T6SS) used to translocate toxins across membranes and activated by human secondary bile acids.

• Full factorial construction of synthetic microbial communities.
  Juan Diaz-Colunga et al. bioRxiv— 5 May 2024.
  Comment: Sometimes it’s interesting to be able to test how various different species or strains interact together in synthetic medium, but can be cumbersome to design if you have more than a few. In this preprint, authors share their method to design and implement 96-well plate-based experiments to inoculate various synthetic microbial consortia together for future phenotyping, and also cleverly demonstrate feasibility using colorants in the cultures and light spectra analysis. My first thoughts would be to pay particular attention to technical replicates, as wall-specific batch effect and well cross-contamination are not uncommon with 96-well plates (especially if not using a robotic liquid handler). But very cool!

(c) Other general interest

• Indexing All Life’s Known Biological Sequences
  Mikhail Karasikov et al. bioRxiv — 14 May 2024.
  Comment: No less! Some similar indexing efforts were done in the microbial field, but in this preprint from ETH Zurich, authors found a clever way to index petabases of DNA from most large sequencing public repositories and make it searchable on this website. Could be useful to generate hypotheses somehow! Happy to hear more about interesting possible uses.

• Whole-body magnetic resonance imaging at 0.05 Tesla.
  Yujaio Zhao et al. Science — 10 May 2024.
  Comment: I am absolutely not qualified enough to look at this in detail, but it looks promising enough to be noteworthy? Science has a recent article presenting a new and much cheaper alternative for MRI scanning, which uses a magnet of far less magnetic flux density (0.05T vs 1.5-3T in current MRI), and importantly operates much faster (<10mins) with far less noise, and is much cheaper. I suspect this could have a great impact on medicine in places where current MRI scanners are definitely unaffordable.

• Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes.
  Yan-Ling Qi et al. Nature Communications — 14 May 2024.
  Comment: Cool effort in this environmental metagenomic assembly of 2,949 archaeal MAGs from 12 phyla and comprising 392 newly identified species. Authors look at predicted functions in the genomes and provide new insights into the metabolism and ecology of these organisms in geothermal springs. Always amazed to see these efforts describing new uncultured, unknown diversity. What a great time to be a microbiologist!

• Differences across the lifespan between females and males in the top 20 causes of disease burden globally: a systematic analysis of the Global Burden of Disease Study 2021.
  Vedavati Patwardhan et al. The Lancet Public Health — May 2024.
  Comment: There is an urgent need for gender-responsive approaches to health for better equity in the future. In this paper, based on the Global Burden of Disease Study 2021 data, authors look at differences in major causes of disease burden between females and males, across regions of the world and their evolutions since 1990. A trove of very useful information!