Thanks to all of you who gave nice feedback on this endeavour of publishing weekly a reading list of what’s interesting to us!

A shorter list this week, as we are having a long bank holiday week-end in Australia for ANZAC Day. Nonetheless, very interesting studies came, as always! Hope this list of noteworthy things in microbiome(s), AMR and pathogen ecology/genomics is useful to some!

Noteworthy studies and publications

(a) Microbiome

• Improving microbial phylogeny with citizen science within a mass-market video game.
  Roman Sarrazin-Gendron et al. Nature Biotechnology — 15 April 2024.
  Comment: Quite a unique proof-of-principle effort of combining microbiome science with citizen science, this time by crowdsourcing a multiple alignment task of 1 million 16S ribosomal RNA sequences obtained from human microbiome studies into a minigame inside the video game Borderlands 3. An interesting news article about it can be found here. Actual real-life benefits from it are still a bit nebulous to me, but it definitely is a cool project!

• Rome III criteria capture higher irritable bowel syndrome SNP-heritability and highlight a novel genetic link with cardiovascular traits.
  Leticia Camargo Tavares et al. Cellular and Molecular Gastroenterology and Hepatology — 18 April 2024.
  Comment: Irritable bowel syndrome (IBS) is a complex disease which can present with various diverse symptoms, which means that the few different ways to diagnose it will impact how we research it. This interesting study from colleagues at Monash University in Melbourne (and others) uses the UK Biobank and the LifeLines cohorts to highlight new genetic links between IBS and cardiovascular diseases when diagnosis follows the Rome III criteria.

• Exploring Host-Commensal-Pathogen Dynamics in Cell Line and Organotypic Human Intestinal Epithelial Models.
  Nening M. Nanlohy, Nina Johannesson et al. iScience — 18 April 2024.
  Comment: It’s often very valuable to have an intermediate in vitro validation model between in silico and in vivo investigations of host-microbes interactions. In this new interesting study from the lab of Susana Fuentes (RIVM, Netherlands), authors present a new in vitro model system to study host-commensal-pathogen interaction and immune responses, using cell cultures and human intestinal enteroids. It seems to respond well to co-cultures too!

• Effect of 1-year lifestyle intervention with energy-reduced Mediterranean diet and physical activity promotion on the gut metabolome and microbiota: a randomized clinical trial.
  Jesús F García-Gavilan, Alessandro Atzeni et al. American Journal of Clinical Nutrition — 29 February 2024.
  Comment: From a few months ago, this is from the interesting (PREDIMED)-Plus RCT from Spain investigating the effects of a 1 year of intensive intervention (Mediterranean diet and exercise regime) on fecal metabolites, gut microbiome and CVD risk factors in overweight people, to measure impacts and changes of lifestyle changes on health. Results highlight notable differences in patient following by dieticians vs. self-imposed on weight reduction and general health. Fecal metabolites and the gut microbiome are impacted, with Eubacterium and Dorea being highlighted. One of our collaborative 2021 FINRISK study on microbiome association with healthy food choices led by Kari Koponen (in the same journal) had also highlighted Eubacterium to be linked with healthier food choices, so there might be something there!

• Ultra-processed foods and food additives in gut health and disease.
  Kevin Whelan et al. Nature Reviews Gastroenterology & Hepatology — 22 February 2024.
  Comment: Also from a few months ago, this very timely review from Benoit Chassaing’s lab on how ultra-processed foods impact the gut microbiome and health. Very good nutrition and immunology examples, a quite exhaustive review!

• Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.
  Ernestina Hauptfeld et al. Nature Communications — 20 April 2024.
  Comment: Promising new tool to improve MAG recovery when assembling metagenomes. I particularly like the integrative approach; maybe could be one to test? Happy for comments if you already have.

(b) Microbial ecology, evolution and AMR

• Non-antibiotic pharmaceuticals are toxic against Escherichia coli with no evolution of cross-resistance to antibiotics.
  Rebecca J. Hall et al. npj Antimicrobials and Resistance — 15 April 2024.
  Comment: There is an interesting (and complex) debate on whether microbial adaptation to compounds that are not thought to be antimicrobial could actually be and drive antimicrobial resistance or cross-resistance. In this brief but interesting study, authors observed toxicity (inferred through reduced optical density of in vitro cultures) of acetaminophen (paracetamol), ibuprofen, propranolol (beta-blockers) and metformin on the lab strain E. coli K-12 MG1655. Interestingly, a 30-day exposure experiment did not show an increased cross-resistance with antibiotics.

(c) Other general interest

• Phylogenomics and the rise of the angiosperms.
  Zuntini et al. — 24 April 2024.
  Comment: If like me you like to see “new things having their genome sequenced”, this is for you. A major genomics study has been published in the field of plant biology, wit a new phylogeny being presented for angiosperms, inbluding ~60% of all genera (n=8000), a 15-fold increase in numbers compared to previous efforts. Figure 1 is a beautiful poster-worthy tree, and other results include attempts at timing the phylogeny and insights into diversification of angiosperms in the Mesozoic and Cenozoic Eras.