Today’s digest features studies on glycosaminoglycans degradation by urinary microbiome, social network of honeybees, improved DNA extraction for low biomass samples, the LotuS2 tool for amplicon sequencing analysis, and more. Happy Monday!
Gut microbiome
Review: The role of the microbiota in the management of intensive care patients – Piotr Szychowiak – Annals of Intensive Care
Review: The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) – Rahel S. König – Frontiers in Immunology
Review: Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System – Richa Jalodia – Journal of Neuroimmune Pharmacology
Urinary microbiome
*A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota – Vivian H. Nguyen – Frontiers in Cellular and Infection Microbiology
Vaginal microbiome
Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease – Janet E Hill – Inflammatory Bowel Diseases
Skin microbiome
*Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – Cell Host & Microbe
Water microbiome
Tenets of a Holistic Approach to Drinking Water-Associated Pathogen Research, Management, and Communication – Caitlin Proctor – Water Research
Animal microbiome
Review: Possibilities and limits for using the gut microbiome to improve captive animal health – Jessica Diaz & Aspen T. Reese – Animal Microbiome
The mosquito microbiome includes habitat-specific but rare symbionts – Hans Schrieke – Computational and Structural Biotechnology Journal
*The gut microbiota affects the social network of honeybees – Joanito Liberti – bioRxiv
Techniques and methods
Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome – Guoshun Xu – BMC Genomics
Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – Cell Report Methods
When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome – Simone Bihl – Gut Microbes
*Microvolume DNA extraction methods for microscale amplicon and metagenomic studies – Anna R. Bramucci – ISME Communications
Bioinformatics
*LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis – Ezgi Özkurt – bioRxiv
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities – Derek M. Bickhart – Nature Biotechnology