October 12, 2016

Infants with bronchiolitis, vitamin D receptor GWAS study, long-term effects of stool transplants, genome reduction in insect endosymbionts, San Francisco Bay denitrifying communities, resistomes in metagenomic datasets, Picodroplet WGA for metagenomics.

Jobs and events

Scientist/Senior Scientist opening at WholeBiome

Upcoming mothur and R workshops – Pat Schloss – Mothur

Pregnancy and early life

Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk – Manli Y. Davis – Microbiome

Human general and multisite microbiome

Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia – Jatinder Singh – mSphere

Review: The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review – Rosario Lucas López – APMIS

Human oral microbiome

Does obesity influence the subgingival microbiota composition in periodontal health and disease? – Suellen da Silva Maciel – Journal of Clinical Periodontology

Human respiratory microbiome

Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients – Darius Seidler – PLOS ONE

Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis – Kohei Hasegawa – European Respiratory Journal

Human urinary tract microbiome

Changes in Urinary Microbiome Populations Correlate in Kidney Transplants With Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies
B. D. Modena – American Journal of Transplantation

Human reproductive tract microbiome

Evidence that the endometrial microbiota has an effect on implantation success or failure – Immaculada Moreno – American Journal of Obstetrics & Gynecology

Human gut microbiome

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes – Anna Heintz-Buschart – Nature Microbiology

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota – Jun Wang – Nature Genetics

A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition – Ludovic Giloteaux – American Journal of Case Reports

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis – Wenjun Liu – Scientific Reports

Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection – Jonna Jalanka – BMC Medicine

Press: Healing effect of fecal microbiota transplantation lasts for long – Science Daily

Integrity of the Human Faecal Microbiota following Long-Term Sample Storage – Elahe Kia – PLOS ONE

Review: Signals from the gut microbiota to distant organs in physiology and disease -Bjoern O Schroeder – Nature Medicine

Review: The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke – Katarzyna Winek – Neurotherapeutics

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Commentary: Microbiome: Should we diversify from diversity? – Katerina V.-A. Johnson – Gut Microbes

Review: I-Cubed (Infection, Immunity, and Inflammation) and the Human Microbiome – David S. Younger – Neurologic Clinics

Animal models

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches – Masatoshi Morikawa – PLOS ONE

Spatial and Temporal Shifts in Bacterial Biogeography and Gland Occupation during the Development of a Chronic Infection – Daniela Keilberg – mBio

Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction – Jun Chen – Genome Medicine

Animal microbiome

Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats – Kerri L. Coon – Molecular Ecology

Review: Dissecting genome reduction and trait loss in insect endosymbionts – Amparo Latorre – Annals of the New York Academy of Sciences

Review: Beneficial microorganisms for honey bees: problems and progresses – Daniele Alberoni – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

The interplay between soil structure, roots, and microbiota as a determinant of plant–soil feedback – Joana Bergmann – Ecology and Evolution

Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees – O. Nicolitch – Soil Biology and Biochemistry

Bacterial selection for biological control of plant disease: criterion determination and validation – Monalize Salete Mota – Brazilian Journal of Microbiology

Killing two birds with one stone: Natural rice rhizospheric microbes reduce arsenic uptake and blast infections in rice – Venkatachalam Laksmanan – Frontiers in Plant Science

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization – Lawrence G. Oates – Agriculture, Ecosystems & Environment

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Chatting With a Tiny Belowground Member of the Holobiome: Communication Between Plants and Growth-Promoting Rhizobacteria – R. Sharifi – Advances in Botanical Research

Water and extremophile microbiome

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance – Jessica A. Lee – Microbial Ecology

Molecular diversity of plankton in a tropical crater lake switching from hyposaline to subsaline conditions: Lake Oloidien, Kenya – Wei Luo – Hydrobiologia

Distinct biogeographical patterns of marine bacterial taxonomy and functional genes – John Matthew Haggerty – Global Ecology and Biogeography

Waste and pollution microbiology

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system – Jiaojiao Niu – Scientific Reports

Comparison of the microbial community composition of pristine rock cores and technical influenced well fluids from the Ketzin pilot site for CO2 storage – Linda Pellizzari – Environmental Earth Sciences

Food microbiology

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir – Aaron M. Walsh – mSystems

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase – Ahmed Abdelfattah – Horticulture Research

Bioinformatics and metagenomics

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis – Maria Hammond – Microbiome

The structure and diversity of human, animal and environmental resistomes – Chandan Pal – Microbiome


TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees – Wen Huang – Molecular Biology and Evolution



Mining gut microbiome oligopeptides by functional metaproteome display – Jonas Zantow – Scientific Reports

More microbiology

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron – Nathan D. Schwalm III – mBio

Living together in biofilms: the microbial cell factory and its biotechnological implications – Mercedes Berlanga – Microbial Cell Factories

Microbes in the news

The Virus With Spider DNA. How did part of a black-widow venom gene end up in a virus that infects one of the world’s most successful bacteria? – Ed Yong – The Atlantic

The Human Microbiome – ASM Cultures microbiome special featuring top scientists and biotech companies

The superhero in your vagina – Kendall Powell – Mosaic Science

Legionella Bacteria Detected at 4 American Airlines Hangars – ABC News

Study Sees Link Between Allergies and the Infant Gut – Robert Lee Hotz – Wall Street Journal

Breasts have their own microbiome – and it could influence your cancer risk
Your breast has its own unique ecosystem – Bec Crew – Science Alert

Researchers restored a colony of microbes in the gut – Ian Graber-Stiehl – Popular Science

Microbes and money

Second Genome Partners with King’s College London to Evaluate the Influence of the Microbiome in Landmark EAT Study – PR Newswire

MicroBiome Therapeutics’ NM504 For Improving Blood Glucose Regulation Is First Microbiome Modulator to Receive U.S. Patent Allowance – PR Web

Seres’s pioneering microbiome drug fails mid-stage trial – Mark Ratner

Farmers Are Manipulating Microbiomes to Help Crops Grow – Sarah Zhang – Wired

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