Another week, another digest of what has caught our eye in the field of microbiome research, microbial genomics and ecology, and others. Grant application week this week, so not a lot of studies. Comments in blue are personal and hopefully useful to some. A reminder that you can subscribe to this weekly list via WordPress (bottom right of the screen) or the RSS feed.

Hopefully interesting to some! Keep sharing! 🙂

Noteworthy studies and publications

(a) Microbiome

• A high-fat diet promotes cancer progression by inducing gut microbiota–mediated leucine production and PMN-MDSC differentiation
  Jiewen Chen, Xiyuan Liu et al. PNAS — 6 May 2024.
  Comment: Authors show that a high fat diet acts on the gut microbiome and promotes breast cancer/melanoma progression, describing a “gut–bone marrow–tumor” axis. Microbes produce leucine, which activating polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) production. Desulfovibrio seems to be implicated, and is detected in cancer patients with worse outcomes.

• A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.
  Joshua M. Kirsch et al. Cell Host & Microbe — 1 April 2024.
  Comment: Paper from a month ago, looking at the extent of insertion sequences (IS) in the human microbiota. They provide with a new IS database and observe that gut bacteria have diverse IS maintained over long timescales, but is sensitive to perturbation by nutrients and/or bacteriophages. Interestingly, IS insertions are enriched in “hot spots” in the accessory genomes of bacteria, particularly in susCD/tonB transporters, which encode high-affinity substrate-uptake receptors for carbohydrates and cofactors. All in all, this seems to highlight IS as being an interesting evolutionary and adaptive mechanism to perturbations in the microbiota.

• Can the Evidence-Based Use of Probiotics (Notably Saccharomyces boulardii CNCM I-745 and Lactobacillus rhamnosus GG) Mitigate the Clinical Effects of Antibiotic-Associated Dysbiosis?
  Dan Waitzberg et al. Advances in Therapy — 30 January 2024.
  Comment: I’ve been told at University 15 years ago that it is a good idea to take probiotics after antibiotics, to promote “good bacteria” after AB-induced dysbiosis (quotes are to insist on the vagueness of this statement). I had missed this interesting study from a few months ago, in which authors suggest that the administration of specific probiotic strains of interest (a yeast, Saccharomyces boulardii CNCM I-745 and a bacterium, Lactobacillus rhamnosus GG) within 48h of starting antibiotics can promote a return to the pre-antibiotic state faster than without.

• Worming into infancy: Exploring helminth-microbiome interactions in early life
  Andrei Bogza, Irah L. King et al. Cell Host & Microbe — 8 May 2024.
  Comment: A much needed high-quality review on this topic. Most of microbiome research is performed in high-income country, but in low-income countries (LMICs), most children are co-infected with helminths, which have been proven to induce considerable changes on the microbiome and have very important impact on morbidity. This echoes in my mind with the 2011 study from Fumagalli et al. showing that pathogen (helminth) pressure was probably one of the main selective pressure throughout human evolution.

• Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer’s disease mouse models.
  Caroline Wasén et al. Nature Communications — 3 April 2024.
  Comment: In the same week showing that APOE4 homozygotes have nearly 100% penetrance for a distinct form of AD, I was reminded of this month-old study on the contribution of the microbiome in AD’s pathogenesis, by suppressing immune mediated amyloid clearance by microglia in mice, and seems to be mediated by members of the Bacteroidota phylum. A very complex multi-factorial disease indeed.

(b) Microbial genetics, ecology, evolution and AMR

• Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict.
  David Geller-McGrath et al. eLife — 2 May 2024.
  Comment: A very promising looking method to predict metabolic pathways and interactions in genomes with a focus on incompleteness, which is quite an important addition compared to other approaches like METABOLIC. We’ll definitely give it a try.

• Wild birds and the ecology of antimicrobial resistance: an approach to monitoring.
  Tullia Guardia et al. The Journal of Wildlife Management — 24 April 2024.
  Comment: The fight against worldwide AMR takes multiple OneHealth approaches, as the spread can be clinical, enviornmental and affect many hosts beyond humans. In this interesting review, authors highlight wild birds as important sentinel and carriers for AMR, but there are many challenges and outstanding questions regarding transmission. Sensible recommendations included for surveillance standardization.

• Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.
  Md. Hassan uz-Zaman et al. Plos Biology — 7 May 2024.
  Comment: It is almost unbelievable (and puzzling — personal opinion) that the LTEE is staying relevant for some for so long. In this paper, Jeff Barrick, Howard Ochman and colleagues look at where new bacterial (E. coli) genes come from. They suggest that within the very controlled and in vitro environment of the LTEE, promoters can arise from transposable elements to create “new” genes. Interesting!

(c) Other general interest

• Association of ultra-processed food consumption with all cause and cause specific mortality: population based cohort study.
  Zhe Fang et al. BMJ — 8 May 2024.
  Comment: An impactful exhaustive study from USA with >30 years of follow up of more than 115,000 people, highlighting outcomes from consuming ultra-processed foods (UPFs). Higher intake of UPFs was associated with slightly higher all cause mortality, not just caused by cancer and CVD. Associations varied but ready-to-eat meat/poultry/seafood-based UPFs showed particularly strong associations with mortality. In a meta-analysis, UPFs were shown to be linked to 40% higher risk of T2D, 35% higher risk of CVD, 23% higher risk of hypertension, 55% higher risk of obesity, 81% higher risk of metabolic syndrome and 50% higher risk of CVD mortality. Article about it in the New York Times.

• Physiological integration of taste and metabolism.
  Josephine M. Egan — New England Journal of Medicine — 9 May 2024.
  Comment: The mini-abstract of this review is very short and speaks for itself: “Much of what we learned in school about how we taste is wrong. Progress in understanding how taste works is providing insights that may help in the management of obesity, diabetes, and other illnesses“. A great and enlightening read, with very nice figures.

• Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations
  Sonya R. Erlandson et al. Environmental Microbiome — 7 May 2024.
  Comment: An environmental microbiology paper, but the approach was quite interesting and innovative. Authors wanted to look at what changes occur in the soil microbial communities when crops grow and rotate in the same field. To do so, they created ‘soil sentinels’, which are permeable bags of autoclaved soil acting as a substrate for wild microbes to colonize, buried those and looked at their microbial composition at different intervals. They show that the approach work, and seems to capture microbial taxa that actually differentiate crops much better than if whole soil communities would be compared.

Noteworthy preprints:

• Goldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes
  Athina Gavriilidou et al. bioRxiv — 2 May 2024.
  Comment: Promising tool to explore pangenomic co-occurrence (and “co-avoidance”) in microbial genomes, with a particular care on distinguishing linkage due to shared ancestry from traces of actual co-selection. We’re definitely going to check this out but let us know if you are too.

• Adaptation to skin mycobiota promotes antibiotic tolerance in Staphylococcus aureus.
  Caitlin H. Kowalski et al. bioRxiv — 5 May 2024.
  Comment: The skin microbiome (as all the other microbiomes) is not just composed of bacteria, and yet, the non-bacterial parts are routinely plainly ignored by many studies. In this study, authors show that a fungal species, Malassezia sympodialis reduces skin colonization by Staphylococcus aureus through bactericidal activity. Some S. aureus strains with mutations in the GTP pyrophosphokinase Rel can resist this antagonism, which seems to coincide with multidrug emergence in the same strains.

• A description of Lineage 1 Mycobacterium tuberculosis from Papua, Indonesia.
  Hanif Ahmad Kautsar Djunaedy et al. medRxiv — 8 May 2024
  Comment: This study from Phil Ashton and international colleagues describes tuberculosis isolates in a poorly-studied region. They show that a majority of Papuan M. tuberculosis (71.4%) are from the L1.2.1.2.1 sublineage. Genomic analysis suggests frequent introductions and a long-standing presence of MTB L1 in the region, widespread transmission across different districts and ethnic groups in Papua and very little drug resistance (11.9%), attributed to limited healthcare infrastructure and ineffective treatment programs in the region.

Other noteworthy things:

• Nerd alert. The Mycology unit at the Royal Botanical Gardens at Kew (UK) have released a very funny tweet thread comparing Met Gala outfits to fungi.