February 3, 2018

Today’s digest is short, but has exciting reads on how machine learning is improving prediction of antibiotic resistance genes.

General Microbiome

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Puentes-Téllez PE. Microbial Ecology

Review: Role of antimicrobial peptides in controlling symbiotic bacterial populations. Mergaert P. Natural Product Reports

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment.Tek EL. FEMS Microbiology Ecology

Gut Microbiome

The mechanistic link between health and gut microbiota diversity.Larsen OFA. Scientific Reports

REVIEW:The Role of Gut Microbiome and Associated Metabolome in the Regulation of Neuroinflammation in Multiple Sclerosis and Its Implications in Attenuating Chronic Inflammation in Other Inflammatory and Autoimmune Disorders.Dopkins N. Immunology

Plant, Soil, and Water Microbiome

Lithobiontic life: “Atacama rocks are well and alive”. Gómez-Silva B.Antonie Van Leeuwenhoek

Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China. Hu Y. Journal of Microbiology

Arbuscular Mycorrhizal Fungi and Plant Chemical Defence: Effects of Colonisation on Aboveground and Belowground Metabolomes. Hill EM. Journal of Chemical Ecology

Comparison of plants with C3 and C4 carbon fixation pathways for remediation of polycyclic aromatic hydrocarbon contaminated soils. Sivaram AK. Scientific Reports

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions. Szabó A. Exremophiles

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity.Dennis PG. Scientific Reports

Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing. Miao J. Archives of Microbiology

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities.Bell E. Environmental Microbiology

Animal Experiments and Microbiome

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. Zhang W. ISME Journal

Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Banerjee S. Microbiology

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors. Dada N. Scientific Reports

Virome

The virome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals the first report of DNA fragments corresponding to replicating non-retroviral RNA viruses in Fungi.Turina M. Environmental Microbiology

Techniques/Protocols

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.Arango-Argoty G. Microbiome

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