An average sized digest today, full of animal studies, publications on the microbiome of  various sources of water, and a range of plant/root/soil science.  Enjoy!

General microbiome

A unified conceptual framework for prediction and control of microbiomes – James C Stegen – Current Opinion in Microbiology

Multi-site human microbiome

Meanings, measurements, and musings on the significance of patterns in human microbiome variation – Stephanie L Schnorr – Current Opinion in Genetics & Development

Human respiratory microbiome

The Lung Microbiome in Health and Respiratory Diseases – Marimón, José M – Clinical Pulmonary Medicine

Human gut microbiome

Gut Microbiota-Stimulated Innate Lymphoid Cells Support β-Defensin 14 Expression in Pancreatic Endocrine Cells, Preventing Autoimmune Diabetes – Michela Miani – Cell Metabolism

Hookworms Make Us Human: The Microbiome, Eco‐immunology, and a Probiotic Turn in Western Health Care – Jamie Lorimer – Medical Anthropology Quarterly

Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer – Michael A. Liss – European Urology

The effects of grape and red wine polyphenols on gut microbiota – A systematic review – Victoria Nash – Food Research International

Common traits between the beige fat-inducing stimuli – Ozren Stojanović – Current Opinion in Cell Biology

Animal experiments

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period – Enrique Doster – Frontiers in Microbiology

Effects of rice bran and fermented rice bran suspensions on caecal microbiota in dextran sodium sulphate-induced inflammatory bowel disease model mice – Junna Shibayama – Food Bioscience

Donkey milk lysozyme ameliorates dextran sulfate sodium-induced colitis by improving intestinal barrier function and gut microbiota composition – Lun Jiang – Journal of Functional Foods

Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs – Fengping He – Biochemical and Biophysical Research Communications

[Correction] The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet – Christine A.Olson – Cell

Animal microbiome

Comparative Analysis of Ileal and Cecal Microbiota in Aged Rats – Sun Min Lee – Journal of Cancer Prevention

Dietary values of macroalgae Porphyra haitanensis in Litopenaeus vannamei under normal rearing and WSSV challenge conditions: Effect on growth, immune response and intestinal microbiota – Jin Niu – Fish & Shellfish Immunology

The murine female intestinal microbiota does not shift throughout the estrous cycle – Jessica G. Wallace – PLOS One

Plant, root, and soil microbiome

Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems – Hyunmin Koo – Life

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria – Marta Kinnunen – The ISME Journal

Identifying components of mixed and contaminated soil samples by detecting specific signatures of control 16S rRNA libraries – A.A. Igolkina – Ecological Indicators

Influence of ancient anthropogenic activities on the mangrove soil microbiome – Luciano F. Huergo – Science of The Total Environment

Feeding behaviour of epi-anecic earthworm species and their impacts on soil microbial communities – Kevin Hoeffner – Soil Biology and Biochemistry

Manipulation of microbial community in the rhizosphere alleviates the replanting issues in Panax ginseng – Linlin Dong – Soil Biology and Biochemistry

Metagenomic insights into the phylogenetic and functional profiles of soil microbiome from a managed mangrove in Malaysia – Gunaselvam Priya – Agri Gene

Water and extremophile microbiome

Metagenomic evidence of microbial community responsiveness to phosphorus and salinity gradients in seagrass sediments – Matthew W Fraser – Frontiers in Microbiology

Microbial community dynamics and assembly follows trajectories of an early spring diatom bloom in a semi-enclosed bay – Huajun Zhang – Applied and Environmental Microbiology

Do composition and diversity of bacterial communities and abiotic conditions of spring water reflect characteristics of groundwater ecosystems exposed to different agricultural activities? – Karsten Karczewski – Wiley Microbiology Open

Microbial community dynamics at high organic loading rates revealed by pyrosequencing during sugar refinery wastewater treatment in a UASB reactor – Liguo Zhang – Frontiers of Environmental Science & Engineering

Insights into the succession of the bacterial microbiota during biodrying of storage sludge mixed with beer lees: Studies on its biodiversity, structure, associations, and functionality – Tiantian Liu – Science of The Total Environment

Food microbiology

Algae in food- a general review –  Sylwia Ścieszka – Critical Reviews in Food Science and Nutrition

Microbial analysis of commercially available US Queso Fresco – Maxwell J.Holle – Journal of Dairy Science

Bioinformatics

Establishing a mucosal gut microbial community in vitro using an artificial simulator – LinShu Liu – PLOS One

Techniques

Flow cytometry as a potential method of measuring bacterial viability in probiotic products: A review – Martin G.Wilkinson – Trends in Food Science & Technology

Ed’s non-microbiology picks 

Cancer cells engineered with CRISPR slay their own kin

Back-and-forth exchanges boost children’s brain response to language

Recurrent Glioblastoma Treated with Recombinant Poliovirus – Annick Desjardins – The New England Journal of Medicine

Knowing less but presuming more: Dunning-Kruger effects and the endorsement of anti-vaccine policy attitudes – Matthew Motta – Social Science & Medicine

New research could banish guilty feeling for consuming whole dairy products

US emissions of methane – a potent greenhouse gas – are 60% higher than EPA thinks