Microbiome digest, August 20, 2014

Ocular microbiome, life under ice, and gut microbiome and behavior.

Human ocular microbiome

Assessment of ocular surface microbiota in keratoconus patients – a pilot study – M Gajecka – Acta Ophthalmologica

“Culture-based microbiology methods are used in the investigation to preliminary examine the OS microbiota. Simultaneously, microbial genetic material is extracted from the eye swabs for further qualitative and quantitative analyzes using molecular biology methods (real-time PCR, NGS).”

Microbial detection in clinical samples

Elevated Levels of Circulating DNA in Cardiovascular Disease Patients: Metagenomic Profiling of Microbiome in the Circulation – Vasudevan Dinakaran – PLOS ONE

“This work was aimed to study the circulating human microbiome in CVD patients and healthy subjects.”

Animal models of microbiome

A Possible Link between Food and Mood: Dietary Impact on Gut Microbiota and Behavior in BALB/c Mice – Bettina Pyndt Jørgensen – PLOS ONE

“Behavioral changes were accompanied by a significant change in GM composition of mice fed a high-fat diet” “Denaturation gradient gel electrophoresis (DGGE) was used to investigate differences in the composition of the GM.”

Mammalian microbiome

Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus – Jana Sachsenröder – Journal of General Virology

“Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids.”

Water microbiome

A microbial ecosystem beneath the West Antarctic ice sheet – Brent C. Christner – Nature

“Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. “

See also: Lakes under the ice: Antarctica’s secret garden – Douglas Fox – Nature

“Samples from a lake hidden under 800 metres of ice contain thousands of microbes and hint at vast ecosystems yet to be discovered.”


A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis – Liviu P. Dinu – PLOS ONE

“This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. “

Viruses and phages (see also the rat/rotavirus paper above)

Unveiling viral–host interactions within the ‘microbial dark matter’ – Manuel Martínez-García – Nature Communications

“Using this method, we pinpoint viruses infecting the ubiquitous hyperhalophilic Nanohaloarchaeota, included in the so-called ‘microbial dark matter’ (the uncultured fraction of the microbial world).”

Microbes in the news

Archiving: Don’t let microbial samples perish – Noah Fierer and Craig Cary – Nature

“Microbial ecologists must coordinate to archive sample collections and genetic material.”

Microbiology: Microbiome science needs a healthy dose of scepticism – William P. Hanage – Nature

“To guard against hype, those interpreting research on the body’s microscopic communities should ask five questions”

Science, publishing and career

Editorial: Finding the root – The NIH is right to investigate whether bias makes grant awards unfair – Nature

“The idea that scientists who volunteer time and energy to review NIH grants could be biased against qualified minority researchers is a tough pill to swallow. “

Today’s YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015 – Jonathan Eisen – The Tree of Life

Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg. “


Equally productive women are tenured less -Beryl Lieff Benderly – Science

“Women received tenure less often than men with equal productivity in three disciplines studied by Kate Weisshaar, a Ph.D. student in sociology at Stanford University.”

Bik’s Picks

Solar energy that doesn’t block the view – Science Daily

“Researchers have developed a new type of solar concentrator that when placed over a window creates solar energy while allowing people to actually see through the window. “

If Seals Hadn’t Introduced Tuberculosis To The New World, Europeans Would Have – Science 2.0

A new study documents that again, finding isolated Mycobacterium pinnipedii from skeletons found in Peru which are at least 1000 years old. The pathogen is a relative of the TB bacterium that affects seals, so it likely that seals carried the pathogens from Africa to the Peruvian coast.”

Which Hot New Lab Coat Should You Buy This Season? – Fake Science

“We’ve found the hottest coats from Paris, Milan, and Batavia, Illinois and put them into our patented quiz. Take it and find out which lab coat will have you steaming up the beakers!”


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