June 12, 2017

An unusually quiet Monday to start your week of microbiome literature. In the methods section, some new protocols from Springer’s “Diagnostic Bacteriology” volume. Enjoy!

General microbiome

Review: Influences of environmental bacteria and their metabolites on allergies, asthma and host microbiota
G Jatzlauk et al. – Allergy

Human gut microbiome

Microbiome and NAFLD: Potential Influence of Aerobic Fitness and Lifestyle Modification
Matthew R. Panasevich – Physiological Genomics

Mucosa-associated microbiota signature in colorectal cancer
R. Gao et al. – European Journal of Clinical Microbiology & Infectious Diseases

Microbial diseases

Pre-print: Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA
Maho Yokoyama et al. – bioRxiv

Animal experiments

Alteration of gut microbiota in association with cholesterol gallstone formation in mice
Qihan Wang et al – BMC Gastroenterology

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts
Meriem Belheouane et al. – Microbiome

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids
Jennifer L. Morrow et al – Microbiome

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome
Sara M. Wolff et al – Microbiome

Plant, root, and soil microbiome

Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA
DS Jones et al. – Applied and Environmental Microbiology

Water, estuarine and sediment microbiome

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor
N Stern et al. – Applied and Environmental Microbiology

Microbial biotechnology

Efficacy of Bacillus amyloliquefaciens as biocontrol agent to fight fungal diseases of maize under tropical climates: from lab to field assays in south Kivu
Parent Zihalirwa Kulimushi et al. – Environmental Science and Pollution Research

Food microbiology

RNA-based amplicon sequencing highlights the impact of the processing technology on microbiota composition of artisanal and industrial PDO Lard d’Arnad
I Ferrocino et al. – Applied and Environmental Microbiology

General microbiology and evolution

Nitrogen-source stabilization of quorum sensing in the Pseudomonas aeruginosa bioaugmentation strain SD-1
M Wang et al – Applied and Environmental Microbiology

Phages and viruses

Pre-print: Gene networks provide a high-resolution view of bacteriophage ecology
Jason Shapiro & Catherine Putonti – bioRxiv

Bioinformatics and statistics

MetabolitePredict: a de-novo human metabolomics prediction system and its applications in rheumatoid arthritis
Quan Qiu Wang & Rong Xu – Journal of Biomedical Informatics

Techniques and methods

Protocol: Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization
Silvia Fontenete et al. – Diagnostic Bacteriology

Protocol: Detection of Helicobacter pylori DNA in Formalin-Fixed Paraffin-Embedded Gastric Biopsies Using Laser Microdissection and qPCR
María Fernanda Loayza Villa et al. – Diagnostic Bacteriology

Protocol: Characterization of Sinus Microbiota by 16S Sequencing from Swabs
Thad W. Vickery et al. – Diagnostic Bacteriology

Protocol: Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples
Amanda Claire Brown & Mette T. Christiansen

Microbes in the news

Bacteria Behind Legionnaires’ Disease Found at New York Police Station
Ashley Southall – The New York Times

Science, publishing, and career

Microbiology Graduate Program – University of California

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