Microbiome digest, October 17, 2014

Resistance one year after antibiotic treatment, skin microbiome in atopic dermatitis, bacterial 16S rRNA load in the lungs, the rat oral microbiome, and microbes in cheese. And an exciting new discovery by Stanford scientists. Have a great weekend!

 

Multiple site human microbiome

Development of antimicrobial resistance in the normal anaerobic microbiota during one year after administration of clindamycin or ciprofloxacin – Mamun-Ur Rashid – Anaerobe

“Clindamycin or ciprofloxacin or placebo was given for 10 days in three groups. Skin, nasal, saliva, faeces sampling at day -1 and 11, 1, 2, 4 and 12 months.“

Shared microbiome in gums and the lung in an outpatient population – Patrick R. Schmidlin – Journal of Infection

“PCR to determine four periopathogens and seven less pathogenic species in both the periodontal pocket and bronchial protected specimen brush was used. “

Human skin microbiome

* Review: Role of the skin microbiome in atopic dermatitis – Alexander Salava and Antti Lauerma – Clinical and Translational Allergy

“Molecular genetics have dramatically changed our vision of the micro-organisms colonizing the human skin and recently well-documented changes in the skin microbiome in atopic dermatitis have become evident.”

Human respiratory microbiome

* The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial – Geraint B Rogers – The Lancet Respiratory Medicine

“Microbiota composition was determined by 16S rRNA gene sequencing of sputum samples from participants in the BLESS trial”

A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2 – Marc A. Sze – PLOS ONE

“qPCR and ddPCR were performed on these samples using primers spanning the V2 region on the 16S rRNA gene along with negative controls. Total 16S counts were compared between the two methods.”

Human gut microbiome

* With pictures! Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian

“However, to date, much of the literature addresses the procedure from a physician’s point of view, and can therefore be lacking in practical detail. As nurses are often the ‘unsung heroes’ of the procedure, it is timely to address the subject from a nursing perspective.”

The Intestinal Microbiota and Microenvironment in Liver – Hong-Di Ma- Autoimmunity Reviews

“But the interplay between the intestinal tract and the liver may explain the increased association with autoimmune liver diseases and inflammatory bowel diseases. “

Alterations of gut barrier and gut microbiota in food restriction, food deprivation and protein-energy wasting – L. Genton – Clinical Nutrition

“This review… highlights the complex interactions between the components of gut barrier in depleted states due to food deprivation, food restriction and protein energy wasting and shows that these interactions are multidirectional”

Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis – Ye Feng- Journal of Microbiology, Immunology and Infection

“Both the 16S polymerase chain reaction approach and the whole genome shotgun approach were adopted for the next-generation sequencing technology. “

Chronic ethanol consumption alters intestinal microbiota impairing immune function – T. Barr – Alcohol

The gastrointestinal microbiome – functional interference between stomach and intestine – Loris R. Lopetuso – Best Practice & Research Clinical Gastroenterology

“This review focuses and speculates on the possible interactions between gastric microorganisms and intestinal microbiota and on the consequences of this interplay in modulating gut health.”

Animal models of microbiome research

Can Pre-Weaning Modulation of Intestinal Microbiota by Oligosaccharides or Amoxicillin Program Adult One in Rats? – Fanny B. Morel – Nutrition

“As revealed by a targeted qPCR approach, programming of adult intestinal microbiota seems to vary according to the nature of the pre-weaning microbiotal modulator.”

Animal microbiome

* Characterization of the rat oral microbiome and the effects of dietary nitrate – Embriette R. Hyde – Free Radical Biology and Medicine

“Demonstrates the utility of using metagenomics techniques to characterize the healthy rat tongue microbiome and to compare it to the healthy human tongue microbiome.”

Soil microbiome

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils – Olivier Zablocki – Applied and Environmental Microbiology

“The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized.”

Food microbiology

Microbial communities involved in Kashar cheese ripening – Oğuz Aydemir – Food Microbiology

“The molecular classification and identification of 594 LAB isolates during Kashar cheese ripening were performed through (GTG)5–PCR fingerprinting of their genomic DNA followed by verification of the (GTG)5–PCR clusters obtained after numerical analysis through 16S rRNA gene sequencing of representative isolates. “

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)
Cristina Riquelme – International Journal of Food Microbiology

“Pyrosequencing of tagged amplicons of the V3–V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.”

Metagenomics/Bioinformatics

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models – Matthew N. Benedict – PLOS Computational Biology

“Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. “

Microbes in the news

‘Critical Conversation’ to focus on human microbiome – Sue Wuetcher – UB Reporter, University at Buffalo

“David Relman, the Thomas C. and Joan M. Merigan Professor and professor of microbiology and immunology at the Stanford University School of Medicine, will speak on “Your Inner Self: The Human Microbiome in Health and Disease””

 

Bik’s Weekend Picks

Want to Ace That Test? Get the Right Kind of Sleep – Benedict Carey – New York Times

“Scientists now argue that a primary purpose of sleep is learning consolidation, separating the signal from the noise and flagging what is most valuable.”

‘Human face of science’: Researchers dance to raise funds for cancer study – RT.com

“Biomedicine scientists in Barcelona have released a music clip aimed at raising funds for medical research, as well as promoting their profession’s “human face.” The video’s release comes amid low levels of public interest in science throughout Spain.”

In science, popularity breeds unreliability – Tom Siegfried – Science News

“In recent decades, pressure to publish and seek publicity has distorted the scientific enterprise. Scientists need grants. Getting published raises the likelihood of getting those grants. “

Satire: Scientists Discover Two New Kinds Of Bird Poop – The Allium

“Scientists at Stanford University have revealed that they have discovered two new species of bird poop that defy classification. These are the first new species of poop that have been discovered in thirty five years. The findings have been reported this week in the journal Nature.”

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