Our post today has been remodeled after some small technical problems, but here’s your fresh Friday digest of microbiome papers!

Events and jobs

Full-time visiting faculty position in biochemistry and microbiology (2017-18)
College of the Holy Cross – Worcester, Massachussets

Microbiology Laboratory Technician
Symbio Laboratories – Brisbane, Australia

Team Manager – Microbiology
AstraZeneca – Cambridge, UK

27th European Congress of Clinical Microbiology & Infectious Diseases
Vienna – Austria

General microbiome

Cryptic biogeochemical cycles: unravelling hidden redox reactions
Andreas Kappler – Environmental Microbiology

Multi-site human microbiome

Microbe-microbe and host-microbe interactions drive microbiome dysbiosis and inflammatory processes
AD Proal – Discovery Medicine

The human microbiome: an emerging tool in forensics
Jarrad T. Hampton-Marcell – Microbial Biotechnology

The salivary microbiome is altered in the presence of a high salivary glucose concentration
J. Max Goodson – Plos One

Human vaginal microbiome

Review: The role of Escherichia coli in reproductive health: state of the art.
P. Cools – Research in Microbiology

Survival of vaginal microorganisms in three commercially available transport systems.
Allison L DeMarco – Anaerobe

Human gut microbiome

Small Intestinal Bacterial Overgrowth Is Associated with Non-Alcoholic Fatty Liver Disease.
A. Fialho – Journal of Gastrointestinal and Liver Disease

Review: Roles of the intestinal microbiota in pathogen protection.
C. Ubeda – Clinical Translational Immunology

Atopic dermatitis and gut microbiota
M. Lindberg – British Journal of Dermatology

Editorial: The gut microbiota and psychiatric illness
Glenda MacQueen – Journal of Psychiatry and Neuroscience

Commentary: For Health Disparities, Don’t Ignore the Microbiome
Jennifer Abbasi – JAMA

Faecal microbiota transplantation protects against radiation-induced toxicity.
M Cui – EMBO Molecular Medicine

Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites and Metabolic Pathways
Bei Gao – Chemical Research in Toxicology

Animal experiments

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice.
Giada de Palma – Science Translational Medicine

Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice
Aurelijus Burokas – Biological Psychiatry

Animal microbiome

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Mathieu Groussin – Nature Communications

Transition of the intestinal microbiota of dogs with age.
H. Masuoka – Biosciences Microbiota Food Health

Comparative analysis of gut microbiota of mosquito communities in central Illinois.
EJ Muturi – PLoS Neglected Tropical Diseases

Transformation, Proliferation, and Influence on Host Performance by Three Gut Bacteria in the Rice Water Weevil (Coleoptera: Curculionidae)
Yunshan Huang – Annals of the Entomological Society of America

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island
Jan M. Meyer – Environmental Microbiology

MALDI-TOF MS identification of microbiota associated with pest insect Diabrotica speciosa
Bruno Perlatti – Agricultural and Forest Entomology

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria
Alyce Taylor-Brown – Environmental Microbiology

Plant, root, and soil microbiome

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil
Pengfei Liu – Environmental Microbiology

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China
Mi-Hwa Lee – Journal of Food Science

Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars
AK Mahoney – Frontiers in Plant Science

Water and extremophile microbiome

Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea
Vadim Dubinsky – Environmental Microbiology

Bacterial activity in hydrogenetic ferromanganese crust from the Indian Ocean: a combined geochemical, experimental and pyrosequencing study
PP Sujith – Environmental Earth Sciences

Stoichiometry of Prochlorococcus, Synechococcus, and small eukaryotic populations in the western North Atlantic Ocean
Steven E. Baer – Environmental Microbiology

Built environment

Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation.
N. de Jonge – Bioresource Technology

Spread from the Sink to the Patient: in situ Study Using Green Fluorescent Protein (GFP) Expressing- Escherichia coli to Model Bacterial Dispersion from Hand Washing Sink Trap Reservoirs
Shireen Kotay – Applied and Environmental Microbiology

Phages and viruses

Pre-print: How to name and classify your phage: an informal guide
Evelien M. Adriaenssens – bioRxiv

Review: Tumor-associated macrophages: implications in cancer immunotherapy
Amy J Petty – Immunotherapy

Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules
Shugeng Feng – FEMS Microbiology Ecology

Techniques

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Sylwia Zielinska – MicrobiologyOpen

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Jason L. Weirather – F1000 Open Research

A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella
Sonia Paytubi – Frontiers in Microbiology

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Mohamed Mysara – GigaDB

Misc

Highlights: Evolving as a holobiont
Lauren A. Richardson – Plos Biology

Microbes in the news

Gut microbes and poor artery health – researchers probe possible link
Jim Scott – CU Boulder Today

A light digest for today’s Sunday morning. A variety of human microbiome papers and a review on the evolution of antimicrobial resistance.

Human respiratory microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Poala J Marino. Journal of Critical Care.

Human nearly-sterile sites

Short communication: Epicardial Adipose Tissue Microbial Colonization and Inflammasome Activation in Acute Coronary Syndrome. Daniela Pedicino. International Journal of Cardiology.

Human gut microbiome

Microbiota Disruption Induced by Early Use of Broad Spectrum Antibiotics is an Independent Risk Factor of Outcome after Allogeneic Stem Cell Transplantation. Daniela Weber.
Biology of Blood and Marrow Transplantation.

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept. Vera Slomka. Clinical Periodontology.

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. A. Sloan Devlin. Cell Host & Microbe.

Animal experiments

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes. Julia H. Kreznar. Cell Reports.

Microbes in the environment

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. M Herrmann. Microbial Ecology.

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats. Adriano Cabal. Microbiology Open.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa. Relebohile Matthew Matobole. Marine Drugs.

Food microbiology

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods. Luana Martins Perin. Food Microbiology.

Perspective: New insights on the use of wine yeasts. Francesca Comitini. Current Opinion in Food Science.

Phages and viruses

Pre-print: Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments. Samuel L. Díaz Muñoz. bioRxiv.

Biotechnology

Virulence Inhibitors from Brazilian Peppertree Block Quorum Sensing and Abate Dermonecrosis in Skin Infection Models. Amelia Muhs. Scientific Reports.

Evolution

Review: Epistasis and the Evolution of Antimicrobial Resistance. Alex Wong. Frontiers Microbiology.