March 16, 2017.

A long review today, lots of environmental microbiome, a few papers on the methods, virus and microbial biotechnology sections and at the end a Nature announcement for transparency policy updates, aiming for better research reproducibility.

Oral Microbiome

Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome
S. S. Garcia – Journal of Dental Research

Human nearly-sterile sites

Review: Microbiome effects on immunity, health and disease in the lung
Shakti D. Shukla – Clinical & Translational Immunology

Animal Microbiome

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle
Sigmund Jensen – Marine Ecology

Animal experiments

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves
Y. F. Deng – Scientific Reports

Antiprotozoal Effect of Saponins in the Rumen Can Be Enhanced by Chemical Modifications in Their Structure
Eva Ramos-Morales – Frontiers in Microbiology

Plant, root, and soil microbiome

Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands
Xiao-Bo Wang – The ISME Journal

Phosphate solubilizing microbes: an effective and alternative approach as
biofertilizers
Kumar Anand – International Journal of Pharmacy and Pharmaceutical Sciences

Master’s thesis: An Investigation Of The Tri-Trophic Interactions In
The Rhizosphere Of Medicago Truncatula Using A
Functional Microbiome Approach
Amanda Anne Rosier – University of Delaware

Water and extremophile microbiome

Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal
Jing Wang – Frontiers in Microbiology

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis
Niranjan Nitin Parulekar – PlOS One

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology

Built environment

Impact of water heater temperature setting and water use frequency on the building plumbing microbiome
Pan Ji – The ISME Journal

Food microbiology

Effects of cellulase-producing bacteria on bacterial community structure and diversity during fermentation of Chinese liquor grains
J. H. Guo – The Journal of The Institute of Brewing

Microbial Biotechnology

The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors
Shelesh Agrawal – Microbiology Open

Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China
Yan Li – Frontiers in Microbiology

General Microbiology

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria
Masahiro Kanno – Nature Communications

Short communication: Membrane vesicle-mediated bacterial communication
Masanori Toyofuku – The ISME Journal

Brief Report: Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1
Jiayue Yang – Environmental Microbiology Reports

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio
Anne-Catherine Ahn – PlOS One

Review article: The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics
Caroline S. Rempe – Frontiers in Microbiology

Phages and viruses

Mini-Review: Driving HIV-1 into a Vulnerable Corner by Taking Advantage of Viral Adaptation and Evolution
Shigeyoshi Harada – Frontiers in Microbiology

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome
Daniel Aguirre de Cárcer – PlOS One

Review: The concept of commensal viruses almost 20 years later: redefining borders in clinical virology
Diem-Lan Vu & Laurent Kaiser – Clinical Microbiology and Infection

Statistics / Bioinformatics

A fast small-sample kernel independence test for microbiome community-level association analysis
Xiang Zhan – Biometrics

Revealing large metagenomic regions through long DNA fragment hybridization capture
Cyrielle Gasc & Pierre Peyret – Microbiome

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
Sara Ciucci – Scientific Reports

Microbes in the news

Snow Bacteria, A Pandora’s Box? – GlacierHub

Phage therapy shown to kill drug-resistant superbug (link to original paper included) – HealthCanal

A Microbe Hunter Plies Her Trade In Space – NPR

Science, publishing, and career

Announcement: Transparency upgrade for Nature journals – Nature

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