September 9, 2019

Good Morning! Many research articles are posted! Highlights include a study describing hyper targeted phages in the human gut and a virome database, and construction of a pathway in a heterologus organism to pruduce secondary bile molecules for efforts to engineer and control bacterial metabolites in diseases. Happy readings!

Human oral microbiota
Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing – Ihara et al. – mSystems

Human vaginal microbiome
Life history recorded in the vagino-cervical microbiome – Jie et al. – bioRvix

Human gut microbiome
*A metabolic pathway for bile acid dehydroxylation by the gut microbiome – Funabashi et al. – bioRxiv

Probiotics for Gastrointestinal Symptoms and Quality of Life in Autism: A Placebo-Controlled Pilot Trial – Arnold et al. – Journal of Child and Adolescent Psychopharmacology

Animal experiments
The characteristics of gut microbiota and commensal Enterobacteriaceae isolates in tree shrew (Tupaia belangeri) – Gu et al. – BMC Microbiology

Modulation of high fat diet-induced microbiome changes, but not behaviour, by minocycline – Hasebe et al. – Brain, Behavior, and Immunity

Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale – Randall et al. – Microbiome

Animal microbiome
Linking pollen foraging of megachilid bees to their nest bacterial microbiota – Voulgari-Kokota et al. – Ecology and Evolution

Plant, root and soil microbiome
Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers – Isobe et al. – The ISME Journal

Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet – Veach and Zeglin – Microbial Ecology

Stable Microbial Community and Specific Beneficial Taxa Associated with Natural Healthy Banana Rhizosphere – Europe PMC Journal of Microbiology and Biotechnology

Copepod carcasses in the subtropical convergence zone of the Sargasso Sea: implications for microbial community composition, system respiration and carbon flux – Tang et al. – Journal of Plankton Research

Predominance of soil vs root effect in rhizosphere microbiota reassembly – Zhao et al. – FEMS Microbiology Ecology

Bacterial rhizosphere community profile at different growth stages of Umorok (Capsicum chinense) and its response to the root exudates – Devi et al. – International Microbiology

The Burning of Sugarcane Plantation in the Tropics Modifies the Microbial and Enzymatic Processes in Soil and Rhizosphere – Trujillo-Narcia et al. – Journal of Soil Science and Plant Nutrition

Biocontrol and plant growth-promoting ability of plant-associated bacteria from tomato (Lycopersicum esculentum) under field condition – Amaresan et al. – Microbial Pathogenesis

Time-series analysis of phosphorus-depleted microbial communities in carbon/nitrogen-amended soils – Mise et al. – Applied Soil Ecology

The Bacterial Microbiome Associated with Arid Biocrusts and the Biogeochemical Influence of Biocrusts upon the underlying Soil – Moreira-Grez et al. – Frontiers in Microbiology

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition – Jackrel et al. – mBio

Water and extremophile microbiome
Copepod carcasses in the subtropical convergence zone of the Sargasso Sea: implications for microbial community composition, system respiration and carbon flux – Tang et al. – Journal of Plankton Research

Built-environment
Genome-centered omics insight into the competition and niche differentiation of Ca. Jettenia and Ca. Brocadia affiliated to anammox bacteria – Zhao et al. – Applied Microbiology and Biotechnology

Food microbiology
Modeling and regulation of higher alcohol production through the combined effects of the C/N ratio and microbial interaction – Jiang et al. – Journal of Agricultural and Food Chemistry

Phages and viruses
*CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog – Cell Host & Microbe

Bioinformatics
MITRE: inferring features from microbiota time-series data linked to host status – Bogart et al. – BMC Genome Biology

Phylogenetic Tree-based Microbiome Association Test – Kim et al. – Bioinformatics

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