Microbiome digest, August 7, 2014

Microbiome and caries, colorectal cancer, and inflammatory bowel diseases. Microbiomes of fish, dogs, and mosses, microscopic life in an asphalt lake, and the Picks.

Human mouth microbiome

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing – Junko Obata – PLOS ONE

“In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the 16S rRNA gene.”

Human gut microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer – Joseph P. Zackular, Mary A.M. Rogers, Mack T. Ruffin IV, and Patrick D. Schloss – Cancer Prevention Research

“Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas.”

Manipulation of Microbiome, a Promising Therapy for Inflammatory Bowel Diseases – Dapeng Jin, Hongyu Zhang, and Jun Sun – Clinical & Cellular Immunology

“In this review, we summarize the current knowledge of how changes in microbiota may affect the pathogenesis of IBD. “

A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota – Bruce R. Hamaker, Yunus E. Tuncil – Journal of Molecular Biology

“the article encourages the building of a framework of information to manipulate the colon microbiota in a predicted way for improved health”

 

Human microbiome after death

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans – Ismail Can – Journal of Microbiological Methods

“We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers”

Animal models of human microbiome

Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats
S.M. O’Mahony – Neuroscience

“Neonatal antibiotic treatment leads to an increase in visceral sensitivity in adulthood in rats.”

Dog microbiome

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque – Ian J Davis, Christopher Bull, Alexander Horsfall, Ian Morley and Stephen Harris – BMC Microbiology

“Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. ‘

Fish microbiome

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish – Lenka Gerzova – PLOS ONE

“In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents.”

Insect microbiome

The mosquito microbiota influences vector competence for human pathogens – Nathan J Dennison, Natapong Jupatanakul, George Dimopoulos – Current Opinion in Insect Science

“Understanding the interaction between the vector, its microbiota and transmitted pathogens will provide novel opportunities to limit disease transmission.”

Plant microbiome

Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Faisal Hammad Mekky Koua – Saudi Journal of Biological Sciences

“..we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan.”

Soil and water microbiome

Two Neumann U students discover new types of viruses – CatholicPhilly.com

“They collected arthrobacter (a bacteria present in soil) from under trees and near lakes, found and filtered out the phages that were present, and then studied phage anatomy and life cycles.”

Water droplets in oil are microhabitats for microbial life – Rainer U. Meckenstock – Science

“In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. “

Microbiome of the built environment

Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings – Jörg D. Ettenauer – PLOS ONE

“In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques.”

Metagenomics

High-resolution metagenomics – Eran Mick & Rotem Sorek – Nature Biotechnology

In this issue, Nielsen et al. present a powerful method for interpreting metagenomic data at the level of individual genomes without relying on reference sequences of cultured isolates, which can be generated for only a small fraction of microbial life.

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

“But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.”

Science and Career

Ph.D.’s, come out of the closet! – Lina Nilsson – Science

“If you promise not to tell Fisher’s Ph.D. adviser (or mine), I’ll let you in on this well-hidden truth: Fisher isn’t planning to pursue an academic career.”

Bik’s Picks

Stress during pregnancy can be passed down through generations, rat study shows – Science Daily

Scientists investigating pregnancies in four generations of rats show that inherited epigenetic effects of stress could affect pregnancies for generations.”

This Is Your Brain on Fish – James Hamblin – The Atlantic

Thicker, stronger, and more resilient. Once a week is all it takes, new research says.”

10 Great Novels That Will Make You More Passionate About Science – Charlie Jane Anders – io9

A lot of the best science fiction features scientists who solve problems and make breakthroughs.”

Scientist looking forward to weekend of binge-experimenting – The Allium

Imperial college Scientist Dr. Lou Pole announced earlier today that he was going to spend the entirety of this weekend binge-experimenting.”

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