Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

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General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News