February 26, 2016

IVF outcomes, large oral microbiota study, Pygmies and Bantu, GF animal models, correlation detection strategies, and sashimi in Portugal.

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Transition from infant- to adult-like gut microbiota – E. Avershina – Environmental Microbiology

Abnormal vaginal microbiota may be associated with poor reproductive outcomes: A prospective study in IVF patients – T. Haahr – Human Reproduction

Human oral microbiome

Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study – Toru Takeshita – Scientific Reports

Human gut microbiome

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns – Andres Gomez – Cell Reports

Inflammatory Bowel Disease Affects the Outcome of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection – Alexander Khoruts – Clinical Gastroenterology and Hepatology

Gut microbiota composition and relapse risk in pediatric MS: A pilot study – Helen Tremlett – Journal of the Neurological Sciences

Analysis of Gastric Microbiota by Pyrosequencing: Minor Role of Bacteria Other Than Helicobacter pylori in the Gastric Carcinogenesis – Hyun Jin Jo – Helicobacter

Review: Crohn’s Disease: Evolution, Epigenetics, and the Emerging Role of Microbiome-Targeted Therapies – Ersilia M. DeFilippis – Current Gastroenterology Reports

Review: Immune recognition and response to the intestinal microbiome in type 1 diabetes – Alexandra Paun – Journal of Autoimmunity

Review: Intestinal microbiota: from sequencing to function – Julia-Stefanie Frick – International Journal of Medical Microbiology

Models of microbiome research

Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behaviour – Pauline Luczynski – International Journal of Neuropsychopharmacology

Vancomycin treatment alters humoral immunity and intestinal microbiota in an aged mouse model of Clostridium difficile infection – Edward van Opstal – The Journal of Infectious Diseases

Culex quinquefasciatus larval microbiomes vary with instar and exposure to common wastewater contaminants – Marcus J. Pennington – Scientific Reports

Microbial succession in response to pollutants in batch-enrichment culture – Shuo Jiao – Scientific Reports

Manipulation of the gut microbiota using resistant starch is associated with protection against colitis-associated colorectal cancer in rats – Ying Hu – Carcinogenesis

Animal microbiome

Managing Amphibian Disease with Skin Microbiota – Douglas C. Woodhams – Trends in Microbiology

Plant, root, and soil microbiome

Fungal phylogenetic diversity drives plant facilitation – Alicia Montesinos-Navarro – Oecologia

Positive plant–soil feedbacks of the invasive Impatiens glandulifera and their effects on above-ground microbial communities – Z Pattison – Weed Research

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Spatial scale drives patterns in soil bacterial diversity – Sarah L. O’Brien – Environmental Microbiology

Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods – David S. Duncan – Soil Biology and Biochemistry

Water and extremophile microbiome

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs – Jacob P. Beam – Frontiers in Microbiology

Food microbiology

Influence of season and type of restaurants on sashimi microbiota – S. Miguéis – The European Journal of Public Health

Mitigation of Biofilm Formation on Corrugated Cardboard Fresh Produce Packaging Surfaces Using a Novel Thiazolidinedione Derivative Integrated in Acrylic Emulsion Polymers – Michael Brandwein – Frontiers in Microbiology

Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs – Evelyne Mann – Meat Science


Correlation detection strategies in microbial data sets vary widely in sensitivity and precision – Sophie Weiss – The ISME Journal

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

An algorithm for designing minimal microbial communities with desired metabolic capacities – Alexander Eng – Bioinformatics

Posted this previously, but now peer reviewed: Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ


High-resolution microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition – Jakob Zimmermann – European Journal of Immunology

More microbiology

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycle –
Jordi van Gestel – PLOS Computational Biology
Microbes in the news

Human Gut Microbiome Evolution: From Hunter-Gatherers to a Western Lifestyle – Discover

Giving up hunting and gathering changed our gut microbiome – Eric Smillie – Newsweek

The social microbiome of the social honey bee – Irene Newton – MicroBEnet

Video: The Microbiome Project: Surgery – Jack Gilbert and colleagues discuss – Argonne National Laboratory

Newly discovered microbes in marine sponges, turtles, rockfish, and termites – Microbe Post

Penn Researcher Contributes Engineering Expertise to Solving Dental Maladies – University of Pennsylvania

Living bacteria-powered lights hit the market – New Scientist

What Are You Smoking? Bacteria Found at Local Hookah Bars – Bianca Lopez – University of Tampa

Science, publishing, and career

“That was a really bad Friday for us:” WIRED warns four stories were plagiarized – Ivan Oransky – Retraction Watch

Bik’s picks

Arctic shipworm discovery alarms archaeologists: a new species of the wood-chomping mollusks is loose in the Arctic – Eli Kintisch – Science


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