Microbiome digest, October 10, 2014

A quiet day in microbiome literature. Some general microbiome reviews, a phage commonly found in insect symbionts, and an unusual fecal transplant.

General microbiome

Viruses and the Microbiota – Christopher M. Robinson and Julie K. Pfeiffer – Annual Review of Virology

“This review examines the known effects and mechanisms by which microbiota influence mammalian virus infections.”

Review: The Microbiota, Chemical Symbiosis, and Human Disease – Matthew R. Redinbo – Journal of Molecular Biology

“Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments – nasal, lung and gastrointestinal (GI) tract – is reviewed with a focus on new knowledge about the taxa, species, proteins and chemistry that promote health and impact progression toward disease.”

Human gut microbiome

Alien Invasions and Gut “Island Biogeography” – Edward F. DeLong – Cell

“Now, Seedorf et al. show that microbiota from a variety of disparate habitats can successfully colonize and compete in the mammalian gut environment.”

Review: The small intestine microbiota, nutritional modulation and relevance for health – Sahar El Aidy – Current Opinion in Biotechnology (April 2015 issue!)

“This review highlights the recent advances made in the study of the human small intestine microbiota”

The Opposing Forces of the Intestinal Microbiome and the Emerging Pathobiome – Jennifer Defazio – Surgical Clinics of North America

Insect microbiome

Arsenophonus insect symbionts are commonly infected with APSE, a bacteriophage involved in protective symbiosis – Olivier Duron – FEMS Microbiology Ecology

“APSE was found in association with two-thirds of the Arsenophonus strains examined and from a variety of insect groups such as aphids, white flies, parasitoid wasps, triatomine bugs, louse flies, and bat flies.”

Microbes in the news

Beyond the call: Scientist self-administers fecal transplant in search for healthy microbiome – Helen Clark – GizMag

“Jeff Leach’s first-person narrative bookends a fascinating discussion on the changing nature of gut bacteria in many Western societies”

Dr. Raphael Kellman’s Microbiome Diet – Faith Middleton, Lori Mack, Jonathan McNicol – WNPR News

“Repair and boost the bacteria in the gut with the right food, prebiotics and probiotics, and you’ll feel better and lose weight. That’s the theory of Dr. Raphael Kellman of New York, author of The Microbiome Diet.”

The Mad Science Behind OMSI’s Greatest Exhibits – Nathan Tucker

“During my visit, the primary focus is on the shop’s next big traveling exhibition, an NSF-funded exploration of the human microbiome called The Zoo in You. “

Study Shows Rebiotix Microbiota-based Drug Candidate Targeted at Recurrent C. difficile Infection is Highly Effective – PR Newswire – SysCon

“Results for groundbreaking multi-center study of lead drug candidate RBX2660 (microbiota suspension) presented at IDWeek 2014”

Bik’s Picks

Gross! Or is it? University pushes peeing in the shower to save water – Megan Holohan – Today

“The campaign, aptly titled “Go with the Flow,” claims that if every student peed in the shower once daily, the university would save about $230,000 a year on water.”

‘Giant leap’ to type 1 diabetes cure – James Gallagher – BBC News Healthy

“A team at Harvard University used stem cells to produce hundreds of millions of the cells in the laboratory.”

Want to stay thin? Strap ice packs around body – Kounteya Sinha – Times of India

“Exposure to cold temperatures can convert white fat tissue from the thighs and belly to beige fat that burns calories for heat.“


General microbiology and science, August 12, 2014

Prokaryotic Essential Genes, 10 years of next-generation sequencing, a short podcast on the Hadza microbiome, and Ebola.



Protein Localization Analysis of Essential Genes in Prokaryotes – Chong Peng & Feng Gao – Nature Scientific Reports

“Here, a comprehensive protein localization analysis of essential genes in 27 prokaryotes including 24 bacteria, 2 mycoplasmas and 1 archaeon has been performed. “


Review: Ten years of next-generation sequencing technology – Erwin L. van Dijk – Trends in Genetics

“Here we provide an overview of the evolution of NGS and discuss the most significant improvements in sequencing technologies and library preparation protocols.”

More Microbiology

CISAC experts tackle public health & policy questions on Ebola – Beth Duff-Brown – Stanford University

“We ask CISAC biosecurity experts to answer several questions about Ebola and the public health concerns and policy implications. “

Rapid and reagentless detection of microbial contamination within meat utilizing a smartphone-based biosensor – Pei-Shih Liang – Nature Scientific Reports

“An 880 nm near infrared LED was irradiated perpendicular to the surface of ground beef, and the scatter signals at various angles were evaluated utilizing the gyro sensor and the digital camera of a smartphone.”

Academic Minute Podcast: Microbiota of the Hadza Tribe – Alyssa Crittenden, UNLV

“My colleagues and I have, for the first time, characterized the hunter-gatherer gut microbiome– working with a population of foragers in East Africa, the Hadza of Tanzania.”

Women in Science

Why are the media so obsessed with female scientists’ appearance? –  Alice Bell – The Guardian

“Yet another profile of Susan Greenfield feels the need to dwell on her ‘long, youthfully blond hair’. Why are the media so rubbish at covering women in science?”

Bik’s Picks

Under- and over-water halves of Gyrinidae beetle eyes harbor different corneal nanocoatings providing adaptation to the water and air environments – Artem Blagodatski – Nature Scientific Reports

“In this study we analyze the micro- and nanostructure of the split eyes of two Gyrinidae beetles genera, Gyrinus and Orectochilus. “

Antarctic midge’s genome is smallest in insects to date: Bare-bones genome is adaptation to deep freeze – Science Daily

“Scientists who sequenced the genome of the Antarctic midge suspect the genome’s small size — the smallest in insects described to date — can probably be explained by the midge’s adaptation to its extreme living environment.”