February 8, 2016

Plasmid-mediated salt tolerance in the gut microbiota, Tuft cells and immunity, microbes of the Cerrado, impact of sequencing technique on microbiota analysis, and a new microbiome tool on the cloud.


Introducing Nephele, NIAID’s new cloud-based microbiome analysis tool. Webinar on March 7. See also under Bioinformatics below.

Human oral microbiome

Research highlight: FISHing in the oral microbiota – Naomi Attar – Nature Reviews Microbiology

Human gut microbiome

Intestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Evidence for plasmid mediated salt tolerance in the human gut microbiome and potential mechanisms – Eileen Broaders – FEMS Microbiology Ecology

Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD – Thomas Lee – Gut

Review: Novel Strategies for Applied Metagenomics – Moore-Connors, Jessica M. – Inflammatory Bowel Diseases

Research highlight: ntestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Models of microbiome research

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut – Michael R. Howitt – Science

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance – H. Yan – Journal of Animal Physiology and Animal Nutrition

Beneficial Effects of Fecal Microbiota Transplantation on Ulcerative Colitis in Mice – Zhihui Tian – Digestive Diseases and Sciences

Plant, root, and soil microbiome

Soil bacterial communities associated with natural and commercial Cyclopia spp. – Anneke Postma – FEMS Microbiology Ecology

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere – Siddarthan Venkatachalam – Plant Biology

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils – Alinne Pereira de Castro – PLOS ONE

Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost – M. García-Jaramillo – Science of The Total Environment

Opinion: Plant microbiota affects seed transmission of phytopathogenic micro-organisms – Matthieu Barret – Molecular Plant Pathology

Built environment microbiome

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children – Karen C. Dannemiller – The Journal of Allergy and Clinical Immunology

Antibiotics in drinking water in Shanghai and its contribution to antibiotic exposure of school children – Hexing Wang – Environmental Science & Technology

Pollution and waste microbiology

Characterisation of biofilm and planktonic bacterial and fungal communities transforming high molecular weight polycyclic aromatic hydrocarbons – Benjamin D Folwell – Applied and Environmental Microbiology

Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment – Yanjun Ma – FEMS Microbiology Ecology

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water – Mathew L. Frankel- PLOS ONE

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Impacts of pristine and transformed Ag and Cu engineered nanomaterials on surficial sediment microbial communities appear short-lived – Joe D Moore – Environmental Science & Technology

Food microbiology

Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters – Ene Viiard – PLOS ONE


Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis – Adam G. Clooney – PLOS ONE

Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array – Shawn P. Brown – Molecular Ecology Resources


Probiotic and Functional Characterization of Bifidobacteria of Indian Human Origin – Nancy Awasti – Journal of Applied Microbiology


Nephele, microbiome analysis without boundaries. NIAID’s new tool offering cloud-based storage, file transfer, and analysis.

Note: 16S is not the same as metagenomics: Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets – Sunil Nagpal – PLOS ONE

Microbes in the news

Smart Science: Wolbachia Bacteria Might Stop Zika and Dengue Viruses – Judy Stone – Forbes

The science of treating depression during pregnancy – Josie Glausiusz – Quartz

GIANTmicrobes – When Teachers Throw Things – Anne Estes

Gut bacteria may influence alcoholics’ liver damage – Kathryn Doyle – Reuters
Scientists Seek Answers on Zika in Other Viruses – Carl Zimmer – New York Times

Bears’ Hibernation Linked To Unusual Changes In Their Gut Microbes – Samantha Mathewson – Nature World News

Bears hibernate ‘with bacterial help’ – Jonathan Webb – BBC News

The Tardigrade story a.k.a. Open Science Wins – Surya Saha – Storify

This Bacteria-Powered Microrobot Navigates via Electric Fields – Michael Byrne – Motherboard

Sainsbury’s Recall Camembert Cheese Products Over Food Poisoning Concerns – Natasha Hinde – The Huffington Post UK

EFSA update: Fully defining microbiota cause-and-effect: Yolanda Sanz provides update –
Will Chu – Nutraingredients

Satire: Trump Proposes Ban On All Microbiome Researchers “Until We Know What They Are Up To” “When I become president, we are going to make American poo great once again.” – The Allium

Bacteria Hysteria

What’s hiding in your handbag? Contact 6 tests purses for bacteria – Katrina Cravy – Fox

Bik’s Picks

Natural History Museums Are Teeming With Undiscovered Species – Ed Yong – The Atlantic

New species of tarantula found near Folsom Prison named for Johnny Cash – Rachel Feltman – Washington Post



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