Noteworthy things — Week 16 (15/04/2024)

Fourth post and going well! This is what we gathered this week in the fields of microbiome science, pathogen genomics and other! Hopefully of interest to some 🙂

Noteworthy studies and publications

(a) Microbiome

  • Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.
    Xin Zhou, Xiaotao Shen et al. Cell Host & Microbe — 10 April 2024.
    Comment: Very good longitudinal, multi-body site study on the human microbiome! Highlights are that the stability of the microbiome seems to vary among individuals and body sites (not unexpected), but interestingly, more “individualized” microbial genera look like they are more stable over time. Also, disease induces coordinated microbial dynamics at each body site, which suggests a systemic response from disease impacting microbes, and finally, authors show that microbiome stability and skin microbial composition are altered with insulin resistance.

  • Utilization of the microbiome in personalized medicine.
    Karina Ratiner et al. Nature Reviews Microbiology — 18 December 2023.
    Comment: Very thorough review from a group in Israel, formalising the various knowledge and approaches enabling the use of microbiome modification in precision medicine. Very useful ref for many in the field, I’m sure!

  • Stratification of Fusobacterium nucleatum by local health status in the oral cavity defines its subspecies disease association.
    Madeline Krieger, Yasser AbdelRahman et al. Cell Host & Microbe — 10 April 2024.
    Comment: As multi-omics and/or extensively phenotyped datasets become larger and more body sites in the same individuals become more “matched”, the importance of the oral microbiome in general health starts to be confirmed (it always had kind of been hypothesized). This paper highlights that the human dental plaque and oral abscesses can harbor multiple types of oral fusobacteria, that F. nucleatum subspecies prevalence stratifies by ecological niches and that subsp. animalis seems to dominate in absesses. Interestingly too, authors suggest that F. nucleatum should be reclassified, as it clearly seems to harbour ecologically and taxonomically distinct (currently called) subspecies. Very nice “Preview” article in the same issue too.

  • The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut.
    Cassandra E. Gheorghe, Sarah-Jane Leigh et al. Cell Reports. — 15 April 2024.
    Comment: Interesting further links between the gut-brain axis and tryptophan metabolism. Chronic stress affects tryptophan metabolism in the gut in such a very sensitive manner that it is observable as diurnal oscillations in this mice study. Authors used metabolomics to see that Trp metabolism was one of the most affected pathway after stress, and Trp-producing gut bacteria are the most affected by diurnal rhythmicity.

  • Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host.
    Gabriel Vasconcelos Pereira & Marie Boudaud et al. Cell Host & Microbe — 10 April 2024.
    Comment: Interesting new IBD study in mice, highlighting the importance of mucus-degrading microbiota in the disease. In this integrative approach, authors show that a combination of genetics, reduced dietary fiber & mucolytic bacteria can trigger IBD in mice. More specifically, mucus loss can promote type 1 T helper (Th1) cells (which produce interferon-gamma, IL-2, and TNF-beta), which drives colitis. Interestingly a fiber-free exclusive enteral nutrition seems to promote bacterial isobutyrate and prevent colitis.

  • Fermented foods and gastrointestinal health: underlying mechanisms.
    Arghya Mukherjee et al. Nature Reviews Gastroenterology & Hepatology 21:248–266 (2024)
    Comment: Fermented foods are increasingly recognized as health-promoting. This interesting review presents the benefits of fermented foods in gut health and disease, and how the microbiota and associated bioactive compounds are thought to have a broader effect.

  • Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.
    Xiaowen Feng & Heng Li, Genome Biology — 11 April 2024.
    Comment: New promising metagenome-assembly tool? Authors present a novel “reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs” after observing that “even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs.”

(b) Microbial ecology, evolution and AMR

  • Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis.
    Xinran Wang et al. Nature Metabolism — 12 April 2024.
    Comment: Streptomyces sp. are notoriously very abundant in biosynthetic gene clusters (BGCs), and their metabolic flexibility and are used in bioengineering for creating mutants with particular metabolic abilities, for example for industrial production of particular compounds. Aside from this strategy, not much else is done to enhance the efficiency of these cloned BGCs but in this study, authors examined whether you could identify other genes that have co-evolved with the BCGs, and whether they improved biosynthetic abilities if you cloned them along with the BCGs. And they did!

  • Many purported pseudogenes in bacterial genomes are bona fide genes.
    Nicholas P. Cooley & Erik S. Wright BMC Genomics — 15 April 2024.
    Comment: This is somehow not a surprising fact, as often are all bioinformatics-driven “dogma” in biology. This paper explores how much of the genes that are annotated as pseudogenes may be wrongly so due to technical limitations. The conclusions of the paper: “many pseudogenes in microbial genome assemblies are actually genes; high read coverage is required for correct assembly and indicate an inflated number of pseudogenes due to internal stops is indicative of poor overall assembly quality.”

  • Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation.
    Mariliis Hinnu et al. Scientific Reports — 22 March 2024.
    Comment: Authors use fluorescent reporters to measure how exactly antibiotics can cause translation errors in bacteria. From the abstract: “Bactericidal amikacin induced preferably stop-codon readthrough at a moderate level. Bacteriostatic azithromycin on the other hand induced both frameshifting and stop-codon readthrough at much higher level. Single cell analysis revealed that fluorescent reporter-protein signal can be lost due to leakage from a fraction of bacteria in the presence of antibiotics, demonstrating the complexity of the antimicrobial activity”

  • Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis.
    Husain Poonawala et al. Antimicrobial Agents and Chemotherapy — 8 April 2024.
    Comment: A pretty interesting study in my book! This study looks at transcriptomic response to 17 antibiotics in M. tuberculosis. Authors focus on the response speed of M. tuberculosis to antibiotics, but I am kind of fascinated at the amount of genes responding to antibiotics, and wondering about individuality in AB response in bacteria and whether it could explain differences in MICs or other.

(c) Other general interest

  • Survival and rapid resuscitation permit limited productivity in desert microbial communities.
    Stefanie Imminger et al. Nature Communications — 17 April 2024.
    Comment: What happens to bacteria when environmental conditions fluctuates and become unfavourable? We assume most of them are going dormant? Some of them die? Do functional communities survive somehow? I love these “real life” microbiology investigations like this one, where authors simulated rain on biocrust microbial communities from a desert and looked at microbial survival and resuscitation. Conclusions: desert communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity at the community level.

Other noteworthy things:

  • Mark the date! Dr Calum Walsh (University of Melbourne) is the next speaker at the Australasian Human Microbiome Research Network (AHMRN) Journal Club series to present his 2023 paper on “Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach“. More info on the talk available here. It will be on the 30th May 2024 at 12.30 ACST | 13.00 AEST | 4:00 GMT+1.
  • Biorender is a popular service to help scientists build pretty figures and diagrams but there seems to be some discussion on how expensive it is vs. how much copyright do authors retain when using the service. As part of this discussion on Twitter, free and more open alternatives have been recently pointed out, such as Bioicons, or MindTheGraph.
  • Nature Reviews Genetics is now publishing a new article type called ‘Tools of the Trade’ in which early career researchers – graduate students, postdocs or new PIs – can discuss their new method, tool or technique. More info on this Twitter thread.
  • Being in Australia, we love Tasmanian devils (obviously) and we love cancer genomics too (no link with Australia). Max Stammnitz (Centre for Genomic Regulation, Barcelona) published a very interesting Twitter thread on what could go wrong when tumour cells are sequenced at shallow depth (in this case, transmissible cancers affecting Tassie devils), and how it can impact results.
  • There has been quite relatable and heartbreaking (sometimes) commentaries on this new Nature news piece entitled “Citizenship privilege harms science”. Obviously for many it will not come as a surprise as it is sadly a common reality and experience for international academics around the world. Visas and passport inequality affects science negatively, whether for job mobility or conferences purposes.