Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of interesting gut microbiome papers and preprints. In particular, Beller et al. looked at the succession of microbial communities in the infant gut from birth to 1 year of age. This digest also contains some very interesting works on environmental microbiome, as an example, Wasmund et al. investigated bacterial taxa able to degrade extracellular DNA in marine sediments.
For those interesting in bioinformatic tools and methods, this digest also contains the description of novel data ressources and tools. In particular, Pellow et al. present a new tool, SCAPP, allowing for a better assembly of plasmids from metagenomes.
Finally, today’s non-microbiology pick is a paper looking critically at the open source citation advantage effect (the hypothesis that articles made available open access may benefit from an increased number of citation) by conducting a meta-analysis of previous studies.
Have a great Weekend!
Multi-site human microbiome
Review: The human microbiome and COVID-19: A systematic review – Yamamoto et al. – Plos One
Human gut microbiome
The gut microbiome and type 2 diabetes status in the Multiethnic Cohort – Maskarinec et al. – Plos One
Preprint: Niche partitioning facilitates coexistence of closely related gut bacteria – Brochet et al. – BiorXiV
Preprint: Successional Stages in Infant Gut Microbiota Maturation – Beller et al. – BiorXiV
Fetal meconium does not have a detectable microbiota before birth – Kennedy et al. – Nature Microbiology
Animal experiments
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study – Tal et al. – NPJ Biofilms and Microbiomes
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance – Liu et al. – Nature Microbiology
Animal microbiome
Preprint: Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea – Delwart et al. – BiorXiV
Plant, root, and soil microbiome
Microbiomes of commercially-available pine nuts and sesame seeds – Fay et al. – Plos One
Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication – Van Cauwenberghe et al. – ISME Journal
Water and extremophile microbiome
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments – Wasmund et al. – Nature Microbiology
Phages and viruses
Preprint: High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems – Meaden et al. – BioRxiV
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome – Nayfach et al. – Nature Microbiology
Bioinformatics
SCAPP: an algorithm for improved plasmid assembly in metagenomes – Pellow et al. – Microbiome
A standardized archaeal taxonomy for the Genome Taxonomy Database – Rinke et al. – Nature Microbiology
My non-microbiology picks
Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles – Langham-Putrow et al. – Plos One
Microbiome Digest - Bik's Picks 