Microbiome digest, November 5, 2014

Bioinformatic tools for tree building and metagenomics, microbiome of iPads in hospitals, and stool samples from indigenous cultures.
Human clinical microbiome

MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing – Arun Rawat – PLOS ONE

“We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes.”

Human gut microbiome

Human Fecal Microbiome–Based Biomarkers for Colorectal Cancer – Vilvapathy Narayanan – Cancer Prevention Research

“A recent study by Zackular and colleagues… provides an important way forward here in showing that specific analysis of multiple aspects of the microbiome composition in toto provides reliable detection of both precancerous and cancerous lesions. “

Plant microbiome

Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes – Alba Silipo – Nature Communications

“Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A.”

Microbiome of the built environment

* Surface Microbiology of the iPad Tablet Computer and the Potential to Serve as a Fomite in Both Inpatient Practice Settings as Well as Outside of the Hospital Environment – Elizabeth B. Hirsch – PLOS ONE

“Thirty iPads belonging to faculty with a variety of practice settings were sampled to determine the presence and quantity of clinically-relevant organisms.”

Bioinformatic tools

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation – Kalliopi Trachana – PLOS ONE

“Therefore, we constructed high quality “gold standard” orthologous groups that can serve as a benchmark set for orthology inference in bacterial species.”

Towards more accurate ancestral protein genotype–phenotype reconstructions with the use of species tree-aware gene trees – Mathieu Groussin – Molecular Biology and Evolution

“Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer and loss (DTL) of genes statistically increases ASR accuracy.”

IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies – Lam-Tung Nguyen – Molecular Biology and Evolution

“We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented.”

Sampling and DNA extraction techniques

Nasal Screening for MRSA: Different Swabs – Different Results! – Philipp Warnke – PLOS ONE

“This study investigates the performance of different swab-types in nasal MRSA-screening by utilizing a unique artificial nose model to provide realistic and standardized screening conditions.”

Microbes in the news

Les Dethlefsen from our lab did an excellent “AMA” (ask me anything) on Reddit/Science today, on the human gut microbiota. Read the questions and Les’ answers here.

* Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures – Daniella Lowenberg – PLOS Blogs

“Suspecting that this excrement is rich in biological clues, a group of researchers conducted experiments to investigate fecal microbiomes and published a study in PLOS ONE detailing insights into the diets and lifestyles of two ancient indigenous cultures of Puerto Rico”

Quantifying the Microbiome and the State of Crowd Science with Jessica Richman (1h Podcast) – The Quantified Body

“…we have an excellent guest today to bring us up to date on all this. Jessica Richman, is CEO and co-founder of uBiome.”

* If you think your city subway only consists of smelly disgruntled commuters, think again… – Marcus Leung – MicroBEnet

“Have you ever wondered what microbes are around you when you take public transport? Personally, I think about it every day during my two-hour subway commute to and from our lab here in Hong Kong.”

Science, publishing, and career

Metascience could rescue the ‘replication crisis’ – Jonathan W. Schooler – Nature

“Metascience, the science of science, uses rigorous methods to examine how scientific practices influence the validity of scientific conclusions. “

Interactive notebooks: Sharing the code – Helen Shen – Nature

“The free IPython notebook makes data analysis easier to record, understand and reproduce.”

Column: It takes time and a team to win grants – Ingrid Eisenstadter – Nature

“All our applicants are people who were bright enough to get PhDs and MDs, but the proposals we receive tend to share the same flaws, whether they come from recent graduates or from researchers with years of experience.”

Elsevier bad for your h-index? – Ferniglab

“The negotiations between the Dutch universities and Elsevier have foundered…., which means that from 1 January 2015, Dutch researchers will no longer have access to Elsevier journals.”

Sexy molecules! Comedian Megan Amram talks ‘Science… for Her!’ (Q&A) – Amanda Kooser -CNET

“”Parks and Recreation” writer Megan Amram offers up a “raunchy, crazy” textbook full of carbon dating, physics as nail art and kale.”

Bik’s Picks

YouTube video: Brian Cox visits the world’s biggest vacuum chamber – Human Universe: Episode 4 Preview – BBC Two

“…what happens when a bowling ball and a feather are dropped together under the conditions of outer space (vacuum – EB).”

Study in paradise: Stanford professors turn Hawaii into a living science classroom – Bjorn Carey – Stanford News

“Students in the School of Earth Science’s Wrigley Field Program in Hawaii spend the quarter measuring vegetation, coral reefs and volcanoes to understand the dynamics of one of the planet’s most interesting ecosystems.”

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