Viruses and metagenomics, the soil of Central Park, and sweat eating bacteria.
Ecology
Loops and autonomy promote evolvability of ecosystem networks – Jianxi Luo – Scientific Reports
“To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. “
Erosion of functional independence early in the evolution of a microbial mutualism
Kristina L. Hillesland – PNAS USA
“We show that as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations in conditions forcing cooperation with the archaeon Methanococcus maripaludis, it lost a key metabolic trait that would be required for it to grow alone in most environments.”
Tree diversity does not always improve resistance of forest ecosystems to drought – Charlotte Grossiord – PNAS USA
“Within our study network of 160 forest stands across Europe, we found that mixed species forests are less exposed to drought stress in some regions only. “
Phages, viruses, and metagenomics
Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains – Maria Paloma S. Barros – PLOS ONE
“This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. “
Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater – Tiong Gim Aw – Journal of Virological Methods
“In this study, NGS and bioinformatics have been employed for the direct detection and characterization of viruses in wastewater and of viruses isolated after cell culture. “
Metagenomics / Bioinformatics
“The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. “
Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets
Seyhan Yazar – PLOS ONE
“We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets”
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation – Brejnev Muhizi Muhire – PLOS ONE
“Here we present Sequence Demarcation Tool (SDT), …that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences.”
A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes – Naruekamol Pookhao – Bioinformatics
“We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities.”
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus – Emmanuel Prestat – Nucleic Acids Research
“A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. “
Microbes in the News
Soil Microbiome of Central Park – Jef Akst – The Scientist
“The soil of New York City’s Central Park is bursting with biodiversity spanning all three domains of life, according to a study published today”
Supporting the “Good” Gut Microbes – Anna Azvolinksy – The Scientist
“During systemic infection, mice kick-start the production of a specific sugar to feed and protect the beneficial bacteria in their guts while fighting pathogenic strains.”
Sweat-Eating Bacteria: Acne Miracle Cure? – Discovery News
“A new, small study has shown that applying a topical creme containing the bacteria leads to healthier skin and could be used to treat acne and promote healing in wounds.”
Women in Science
* Sexism in Science – sbhatnagar3 – Phylogenomics Blogspot
“Please don’t treat these seminars as a fashion show. It distracts the people away from your work”.”
Bik’s Picks
Behavior of bats at wind turbines – Paul. M. Cryan – PNAS USA
“Bats are dying in unprecedented numbers at wind turbines, but causes of their susceptibility are unknown. “
Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism – David M. Scantlebury – Science
“We show that daily energy expenditure (DEE) of cheetahs was similar to size-based predictions and positively related to distance traveled.”
Previously unseen details of seafloor exposed in new map – Science Daily
“Twice as accurate as the previous version, the new map features a much more vivid picture of seafloor structures, including thousands of previously uncharted mountains.”
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Microbiome Digest - Bik's Picks 