Noteworthy things — Week 15 (08/04/2024)

Third week of doing this! It would seem that it is appreciated on socials! I am currently sharing these posts on Twitter/X, BlueSky & LinkedIn but please do disseminate this page as you see fit! A couple of other points:

  • RSS integration: also, upon being asked about it, I looked into how folks can subscribe to these posts, and it seems that adding this url to your RSS feed reader might work! (I’ve tried with Feedly, that I use, and it seems to work fine).
  • Format of these posts: I’m also experimenting with brief comments (in blue below), let me know if those are useful or not, how you would improve readability etc. I haven’t yet figured out how to best do this so any feedback is welcome.

Finally, good luck to all Australian readers here who might be in the middle of NHMRC and ARC writing-up!

Noteworthy studies and publications

(a) Microbiome

  • A pan-cancer analysis of the microbiome in metastatic cancer.
    Thomas W. Battaglia, Iris L. Mimpen et al. Cell — 9 April 2024.
    Comment: Quite impressive integrative study of matched datasets (metagenomics, genomics, transcriptomics, and clinical data) for 4,160 metastatic tumor biopsies from the Hartwig pan-cancer metastasis cohort (on 26 cancer types). In the light of previous “debate” on the topic, tumor-resident bacteria DNA could be detected, and assembled into species-level MAGs, revealing that bacterial diversity is associated with specific cellular and molecular tumor immunity features. Interesting, the main culprit seems to still be a main culprit: Fusobacterium DNA abundance associated with poor immunotherapy response in a non-small cell lung cancer (NSCLC) validation cohort. Aside from this comment, there is already controversy on the methods (link on Twitter), as cancer/fetal microbiomes are quite (rightfully) debated subjects.

  • Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice.
    Tatsuya Dokoshi et al. Nature Communications — 8 April 2024.
    Comment: The study provides direct evidence of a skin-gut axis by showing that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome (in mice), including increased expression of host defense genes in the colon (Muc2 and Reg3) and changes the composition and behavior of intestinal bacteria, some of which are seen to penetrate the intestinal epithelium and enhance colitis from DSS.

  • Circulating microbiome DNA as biomarkers for early diagnosis and recurrence of lung cancer.
    Haiming Chen, Yi Ma et al. Cell Reports Medicine — 5 April 2024.
    Comment: There’s been an increasing realisation over the years that circulating blood could contain quite a lot of microbiome-derived features like DNA (and probably transiently some actual microbes), and this nice report shows that circulating microbiome DNA can be used as a (predictive) biomarker of incident lung cancer (using a moderately small cohort of 416 participants before splitting into training/validation groups).

  • Gut bacteria-driven homovanillic acid alleviates depression by modulating synaptic integrity.
    Mingliang Zhao et al. Cell Metabolism — 5 April 2024.
    Comment: Another interesting gut-brain axis study coming up, this time on the role of homovanillic acid (HVA), a neurotransmitter linked to depression when depleted. Authors have found that gut Roseburia intestinalis promotes the abundance of Bifidobacterium longum for HVA production, and that complementation with HVA, or B. longum, or R. intestinalis alleviated depression in mice. Proposed mechanism is that HVA restores synaptic function by inhibiting autophagic death. Very cool!

  • The endotoxin hypothesis of Alzheimer’s disease.
    Guy Brown & Michael Heneka. Molecular Neurodegeneration — 1 April 2024.
    Comment: Interesting commentary on the possible infectious aethiolgy of Alzheimer’s Disease. AD patients have higher than normal levels of LPS endotoxin in their blood and there is a current hypothesis that LPS from gut, lungs or gums may increase blood LPS, which may directly or indirectly increase the pathology of Aβ, TAU and microglia, to exacerbate Alzheimer’s disease. This adds to some earlier hypotheses that HSV-1 could also contribute. Would be interesting to see how this conflates with APOE ε4 status.

  • Recommendations for the Use of Dietary Fiber to Improve Blood Pressure Control.
    Hamdi Jama et al. Hypertension — 8 April 2024.
    Comment: This new paper from the Marques Lab (Melbourne, Aus.) builds on previous work showing evidence that fibre intake can lower blood pressure via an increase in microbial production of short-chain fatty acids. This new publication interestingly formalises suggested recommendations for this.

(b) Microbial ecology, evolution and AMR

  • Co-selection for antibiotic resistance by environmental contaminants.
    Laura May Murray et al. npj antimicrobials and resistance — 1 April 2024.
    Comment: Very interesting review from the University of Exeter (UK) summarizing what is known about the influence of micropollutants on AMR spread in the environment, including metals, non-antibiotic drugs (ibuprofen or even the antidepressant fluoxetine!) or even fungicides (like mancozeb).

  • Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.
    Désirée A. Schmitzab et al. (Kümmerli lab). ISME Communications — 27 March 2024.
    Comment: It is a very important challenge in microbiology to experimentally functionally study complex assembled community of microbes interacting with each other. This study provides with interesting considerations derived from in vitro monocultures and supernatant analyses.

  • Differential development of antibiotic resistance and virulence between Acinetobacter species.
    Elizabeth Darby et al. mSphere — 5 April 2024.
    Comment: A lot has been described for the pathogen Acinetobacter baumannii but far less comparatively for another species in the genus, A. lwoffii. Authors present one of the first comprehensive study on this species, which has emerging pathogenic potential and has thus remained more antibiotic-sensitive than A. baumannii.

(c) Other general interest

  • Nitrogen-fixing organelle in a marine alga.
    Coale et al. Science — 10 April 2024.
    Comment: Not every day you see the discovery of a new organelle in a eukaryotic species!! Meet the “nitroplast”, nitrogen-fixing organelle identified in the green alga Candidatus Atelocyanobacterium thalassa.

  • Beta-Blockers after Myocardial Infarction and Preserved Ejection Fraction.
    Troels Yndigegn et al. New England Journal of Medicine — 7 April 2024.
    Comment: The early clinical trials for routinely prescribing beta-blockers after heart attacks were performed decades ago, and we now have better tools to assess their efficacy. A new randomized trial in people with preserved ejection fraction (EF>50%) shows they’re not helpful or necessary.

  • Elemental psychopathology: distilling constituent symptoms and patterns of repetition in the diagnostic criteria of the DSM-5.
    Miriam K. Forbes et al. Psychological Medicine — 4 September 2023.
    Comment: If you sometimes wonder (like me, as a microbiologist) why the gut-brain axis is so hard to study robustly in humans, this could be one of the reasons to keep in mind. In this study (summarized very well by Nicholas Fabiano on Twitter here) authors map the repetition among the 1419 symptoms described in 202 diagnoses of adult psychopathology in section II of the DSM-5 and finds that although ~65% of distinct symptoms are unique to a single diagnosis, ~70% of the diagnoses also have at least one symptom repeated in another diagnosis and/or “chapters” (categories). Symptoms of major depressive disorder (MDD) seem to also repeat the most frequently. This shows how tricky it can be to categorise invididuals with mental health symptoms for downstream analyses.

Noteworthy preprints:

  • CELEBRIMBOR: Pangenomes from metagenomes.
    Joel Hellewell, Samuel Horsfield et al. bioRxiv –9 April 2024.
    Comment: If you’re assembling metagenomes into MAGs, you know they are often (almost always?) incomplete, which raises issues when trying to infer core genes (and pangenomes in general). This new method incorporates genome completeness estimations (e.g. checkM) to probabilistically estimate a more accurate core/accessory gene identification.

Other noteworthy things: