May 5, 2015, part 2

There was so much literature today (more than 600 papers!) that I am doing a second digest today.

Human reproductive tract microbiome

Investigation and Characterization of the Microbiome of the Upper Female Reproductive Tract [10] – Shana M. Miles – Obstetrics & Gynecology

Animal and other models

Akkermansia muciniphila Adheres to Enterocytes and Strengthens the Integrity of the Epithelial Cell Layer – Justus Reunanen – Applied and Environmental Microbiology

Animal microbiome

Effect of Diet on the Rumen Microbial Community Composition of Growing Cattle and the Role It Plays in Methane Emissions – Allison L. Knoell – Digital Commons University of Nebraska – Lincoln

Amphibian Symbiotic Bacteria Do Not Show a Universal Ability To Inhibit Growth of the Global Panzootic Lineage of Batrachochytrium dendrobatidis – Rachael E. Antwis – Applied and Environmental Microbiology

Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias? – Giulia Zancolli – Microbial Ecology

Plant root, soil and sediment microbiome

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng – Chunping Xiao – Journal of Ginseng Research

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland – David J Eldridge – The ISME Journal

The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics – Rubén López-Mondéjar – Soil Biology and Biochemistry

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core – Assia Kaci – Environmental Science and Pollution Research

Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China – L. Ma – Biogeosciences

Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing – Aditi Sengupta – Microbial Ecology

Soil Microorganisms Contribute to Plant Nutrition and Root Health – Mark S. Coyne and Robert Mikkelsen – Better Crops

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia – R. Devereux – Geobiology

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN – Soil, Air, Water

Response of maize and soil microorganisms to decomposing poplar root residues after shallow or homogenous mixing into soil – Hikal Gad – Journal of Plant Nutrition and Soil Science

Water microbiome

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California – Ryan S. Mueller – Genome Announcements

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment – Gabriel Y. Ponce-Soto – Frontiers in Microbiology

Review: Marine-derived fungi: diversity of enzymes and biotechnological applications
Rafaella C. Bonugli-Santos – Frontiers in Microbiology

Review, but contains mostly plagiarized text: The Importance of Marine Genomics to Life – Popoola Raimot Titilade – Journal of Ocean Research


Spatial microbial community structure and biodiversity analysis in “extreme” hypersaline soils of a semiarid Mediterranean area – Loredana Canfora – Applied Soil Ecology

Ecoenzymatic stoichiometry at the extremes: How microbes cope in an ultra-oligotrophic desert soil – Yunuen Tapia-Torres – Soil Biology and Biochemistry

Microbial and Enzyme Activities of Saline and Sodic Soils – Kripal Singh – Land Degradation & Development

Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons – Elyse A. Rodgers-Vieira – Applied and Environmental Microbiology

Carbon Source Preference in Chemosynthetic Hot Spring Communities – Matthew R. Urschel – Applied and Environmental Microbiology

Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity – Heather E. Adams – Frontiers in Microbiology

Bioreactor microbiology

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration – Jin-Feng Liu – Frontiers in Microbiology


Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions – Cheryl-Emiliane T. Chow – Frontiers in Microbiology

More microbiology

Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Review: Sugar coating: bacterial protein glycosylation and host–microbe interactions – Felicia Y.Y. Tan – Trends in Biochemical Sciences

Assay for estimating total bacterial load: relative qPCR normalization of bacterial load with associated clinical implications – Ivan Brukner – Diagnostic Microbiology and Infectious Disease

Review: A review on computational systems biology of pathogen–host interactions – Saliha Durmuş – Frontiers in Microbiology

Metagenomics and bioinformatics

Contact genomics: Scaffolding and phasing (meta)genomes using chromosome 3D physical signatures – Jean-Francois Flot – FEBS Letters

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations – Hong Xue – mBio

Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon – Sima Tokajian – Frontiers in Cellular and Infection Microbiology

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data – Stefan Spring – Frontiers in Microbiology

Review: Strategies and approaches in plasmidome studies – uncovering plasmid diversity disregarding of linear elements? – Julian R. Dib – Frontiers in Microbiology

Microbes in the news

Your Beard Is Covered in Bacteria: So is everything else. Don’t fall for the latest viral freak-out – David Coil – Slate

LongreadGut Feelings – The Mysteries of the Microbiome – Jo Chandler – The Monthly

Bik’s Picks

Dolphins Living in Closer Quarters Are Friendlier – Lori Cuthbert – Discovery

Space might make astronauts dumber, study shows – Craig Hlavaty –

We could use some in California – pipeline, please! Where does all the water go? Watch Oregon’s mysterious Lost Lake disappear down a lava tube – Aileen Donnelly – National Post


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