Today’s Digest provides much food for thought. Highlights include how to identify keystone species, a seminal review on the long-term and short-term effects of C-section on mom and child’s health, and a new de novo assembler for short metagenomic reads.

General microbiology

Antibiotic export by efflux pumps affects growth of neighboring bacteria – Xi Wen et al. – Scientific Reports

Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures – Brooke L. Deatherage Kaiser et al. – PLoS One

Biodiversity‐function relationships in methanogenic communities – Pawel Sierocinski et al. – Molecular Ecology

Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria – Gathanayana Pathiraja et al. – Science of the Total Environment

An improved neutral community model for temporal observations in microbial communities – Li Jie & Shen Xuzhu – Ecological Modelling

** Identifying Keystone Species In The Microbial Community Based On Cross-sectional Data – Min Li et al. – Current Gene Therapy

Does quorum sensing interference affect the fitness of bacterial pathogens in the real world? – Yiying Liu et al. – Environmental Microbiology

Pregnancy and early life

Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow’s Milk Protein Allergy under a Restricted Diet – María Díaz et al. – Nutrients

** Review: Short-term and long-term effects of caesarean section on the health of women and children – Jane Sandall et al. – Lancet

Human skin microbiome

The Skin Microbiota in Patients Hospitalized for Cellulitis and Association With Outcome – Duncan R Cranendonk et al. – Clinical Infectious Diseases

Human multi-site microbiome

Continuous Antibiotic Prophylaxis in Pediatric Urology – Douglas W.Storm et al. – Urologic Clinics of North America

Human gut microbiome

Impact of antibiotic use on survival in patients with advanced cancers treated on immune checkpoint inhibitor phase I clinical trials – S Sen et al. – Journal of Experimental Medicine

Review: Visceral pain: gut microbiota, a new hope? – Matteo M Pusceddu & Melanie G Gareau – Journal of Biomedical Science

Review: Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions – Beth Burgwyn Fuchs et al. – Future Microbiology

Fecal Microbiota Transplant for Recurrent Clostridium Difficile Infection in Pediatric Inflammatory Bowel Disease – Cho, Stanley et al. – Journal of Pediatric Gastroenterology and Nutrition

Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients – Saima Naz et al. – Cellular Immunology

Alterations of Gut Microbiome in the Patients With Severe Fever With Thrombocytopenia Syndrome – Honghai Xu et al. – Frontiers in Microbiology

Review: Role of Gut Microbiota in the Development and Treatment of Colorectal Cancer – LIN C. et al. – Digestion

Human gut-microbiome-brain axis

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey et al. – Developmental Psychology

Animal experiments

Grape polyphenols reduce gut-localized reactive oxygen species associated with the development of metabolic syndrome in mice – Peter Kuhn et al. – PLoS One

Host developmental toxicity of BPA and BPA alternatives is inversely related to microbiota disruption in zebrafish – Tara R Catron et al. – Toxicological Sciences

Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats – Brunella Posteraro et al. – Alcoholism Clinical & Experimental Research

Liver tumorigenesis is promoted by a high saturated-fat diet specifically in male mice and is associated with hepatic expression of the proto-oncogene Agap2 and enrichment of the intestinal microbiome with Coprococcus – Kim B Pedersen et al. – Carcinogenesis

Animal microbiome

Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises – Chava L. Weitzman et al. – Royal Society Open Science

Review: Understanding the Milk Microbiota – Stephanie A.Metzger et al. – Veterinary Clinics of North America: Food Animal Practice

Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival – Christopher McMullen et al. – Veterinary Microbiology

Plant, root and soil microbiome

Review: The impact of microbes in the orchestration of plants’ resistance to biotic stress: a disease management approach – Matthew Chekwube Enebe & Olubukola Oluranti Babalola – pplied Microbiology and Biotechnology

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts – Xuepeng Sun et al. New Phytologist

Facilitation promotes invasions in plant-associated microbial communities – Wei, Zhong et al. – Ecology Letters

Water and extremophile microbiome

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations – David A. Aromokeye et al. – Frontiers in Microbiology

Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting – Keshao Liu et al. – Science of The Total Environment

Food microbiology

Review: Fermentation trip: amazing microbes, amazing metabolisms – Rong Feng et al. – Annals of Microbiology

Phages and viruses

Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1) – Mike Dyall-Smith et al. – Genes

Technology

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer – Sae Ashikawa et al. – Journal of Medical Microbiology

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study – Jan Tkadlec et al. – Clinical Microbiology and Infection

Bioinformatics

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results – Aitor Blanco-Míguez et al. – PLoS One

Review: Integrating–omics data into genome-scale metabolic network models: principles and challenges – Charlotte Ramon et al. – Essays in Biochemistry

** High-quality genome sequences of uncultured microbes by assembly of read clouds – Alex Bishara et al. – Nature Biotechnology

Microbes in the news

Cecilia Jonsson Serenades Sewage Bacteria – Sofia Bergmann – Berlin Art Link