I hope everyone is staying safe and healthy during this pandemic. Today’s digest will start with a few articles on COVID-19 before moving on to microbiome papers.
Preprint: A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing – Itokawa et al.
Preprint: FDA approved drugs with broad anti-coronaviral activity inhibit SARS-CoV-2 in vitro – Weston et al.
Protein Structure and its Sequence Reanalysis of 2019-nCov Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1 – Zhang et al. – ACS Publications
Antithetic population response to antibiotics in a polybacterial community – Laporta & Ojalvo – ScienceAdvances
Review: Toward a dynamical understanding of microbial communities – Rainey & Quistad – Royal Society Publishing
Pregnancy and early life
Beyond the Bacterial Microbiome: Virome of Human Milk and Effects on the Developing Infant – Mohandas & Pannaraj – Karger
Human vaginal microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study – Usyk et al. – PLOS Pathogens
Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta et al. – Springer Link
Human gut microbiome
Review: Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature – Frame & Jackson – Nutrition Reviews
Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long et al. – Nature
The effects of daily fasting hours on shaping gut microbiota in mice – Li et al. – BMC Microbiology
Human oral microbiome
Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports
Effects of Chlorhexidine mouthwash on the oral microbiome – Bescos et al. – Scientific Reports
Microbiome diversity and composition varies across body areas in a freshwater turtle – McKnight et al. – Microbiology Society
Gut microbiota shifts in the giant tiger shrimp, Penaeus monodon, during the postlarvae, juvenile, and adult stages – Cicala et al. – Springer Link
Plant and soil microbiome
Community-driven Metadata Standards for Agricultural Microbiome Research – Dundore-Arias et al. – APS Publications
Do cover crops benefit soil microbiome? A meta-analysis of current research – Kim et al. – ScienceDirect
Water and extremophile microbiome
Linking regional shifts in microbial genome adaptation with surface ocean biochemistry – Garcia et al. – The Royal Society Publishing
The potential impact of bacterial communities exposed to crude oil and light on the growth of the harmful algal blooming species Karenia brevis (Dinophyceae) – Park & Buskey – CSIRO Publishing
Machine-learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection – Ciucci et al.
Infrared absorptions as indicators for Pseudomonas aeruginosa and Acinetobacter baumannii – Yamamoto et al.
Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments – Lloyd et al.
A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms – Long et al.