Bonjour from Paris, France ! Today’s digest contains a selection of really interesting preprints and published studies. In their review, Heilbronner and collaborators explore the role of bacteriocins, small antibacterial molecules produced by many commensal bacteria in human-associated microbiomes. The role of the bacteriocins in the human microbiome is of particular importance since they could be leveraged to specifically target colonizing pathogens while sparing mutualistic patners.
If you are interested in exploring new bioinformatic methods, I recommend taking a look at the study from Cheng and collaborators, who applied a novel iterative random forest approach to explore marine microbiome during algal blooms. They show how this model allow to identify conditions that are important causal factors of algal bloom dynamics.
Today’s non-microbiology pick is an opinion piece reflecting on the possible methods to develop the field of computational biology, ensure proper training and career development in this discipline and allow a greater collaboration between domain biologist and data scientists in multidisciplinary teams.
Have a great Tuesday!
Events and jobs
Virtual conference: Harnessing the plant microbiome – October 22-24, 2021
University of California, Davis, USA
Virtual conference: Reshaping the Microbiome through nutrition – November 17-19, 2021
General microbiome
Review: The microbiome-shaping roles of bacteriocins – Heilbronner et al. – Nature Reviews Microbiology
Human gut microbiome
Preprint: Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19 – Schult et al. – BioRXiv
Review: Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health – Dogra et al. – microorganisms
Animal experiments
Preprint: Mice with a humanized immune system are resilient to transplantation of human microbiota – Zhou et al. – BioRXiv
Animal microbiome
Preprint: Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes – Coon et al. – BioRXiv
Water and extremophile microbiome
A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms – Cheng et al. – Scientific reports
Built environment
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years – Wang et al. – Microbiome
Phages and viruses
Preprint: A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use – Hegarty et al. – BioRXiv
Bioinformatics
Preprint: SynTracker: a synteny based tool for tracking microbial strains – Enav and Ley – BioRXiv
My non-microbiology pick
A field guide to cultivating computational biology – Way et al – PLOS biology
Microbiome Digest - Bik's Picks 