May 8, 2017

First, a job opportunity in my PI’s lab: please forward or apply! Papers today are spread over multiple topics, with more in soil and water, and an emphasis on ecological ideas for the general microbiome.

Events and jobs
Bioinformatics Research Associate – Harvard T.H. Chan School of Public Health

General microbiome
Perspective: Multi-stability and the origin of microbial community types – Didier Gonze – ISME

Microbial consortia at steady supply – Thibaud Taillefumier – eLife

Human oral microbiome
Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome – Steven Knapp – Frontiers in Cellular and Infection Microbiology

Human gut microbiome
Opinion: What happened to Koch’s Postulates in Diarrhea? – Shamima Sultana – Environmental Microbiology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics – Sonny T.M. Lee – Microbiome

Animal experiments
TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome – Robert D. Stedtfeld – FEMS Microbiology Ecology

A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep – Saad Al-Masaudi – Frontiers in Microbiology

Plant, root, and soil microbiome
Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances – Bingxin Li – Science of the Total Environment

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations – Yunfu Gu – PLoS One

Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence – Nicholas A. Barber – Environmental Microbiology

Arbuscular and Ectomycorrhizal Fungi Associated with the Invasive Brazilian Pepper Tree (Schinus terebinthifolius) and Two Native Plants in South Florida – Karim Dawkins – Frontiers in Microbiology

Water and extremophile microbiome
Differential responses of marine, mesohaline, and oligohaline bacterial communities to the addition of terrigenous carbon – DPR Herlemann – Environmental Microbiology

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia – Hauke F. Kegler – Frontiers in Microbiology

Built environment
Long-term successional dynamics of microbial association networks in anaerobic digestion processes – Linwei Wu – Water Research

Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition – A. Anisa Cokro – Water Research

Probiotics / prebiotics
Review: Effectiveness of Probiotic, Prebiotic, and Synbiotic Therapies in Reducing Postoperative Complications: A Systematic Review and Network Meta-analysis – Nongyao Kasatpibal – Clinical Infectious Diseases

Review: Effect of Probiotics on Metabolic Outcomes in Pregnant Women with Gestational Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials – Bonnie L. Taylor – Nutrients

Techniques
Rapid Pathogen Identification in Bacterial Pneumonia Using Real-time Metagenomics – Kathryn M Pendleton – American Journal of Respiratory and Critical Care Medicine

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics – Andrea C. Duarte – Frontiers in Microbiology

Microbes in the news
Gold processing bacteria help to recycle electronics – Tim Sandle – Digital Journal

Continued exposure to bacteria from decomposing bodies took its toll on workers – Mahesh Avadhuta – Deccan Chronicle

Bacteria Hysteria
Rob Mancini: Why do folks insist on providing bad food safety advice? – Ben Chapman – BarfBlog

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