May 3, 2016

Counting the microbial species on Earth, goat rumen microbiome development, red kangaroos who died a tragic death, fungi in burgundy vineyards, Archaea in  Yellowstone, and image irregularities at a Pfizer lab in La Jolla.

Jobs and Events

Postdoctoral Fellowship Opportunity: Microbiology of the Built Environment – Sloan Foundation

Bioinformatics for the Microbiome, May 27 – Stanford Center for Genomics and Personalized Medicine, $49

General microbiology

Scaling laws predict global microbial diversity: Earth is home to as many as 1 trillion (10exp12) microbial species – Kenneth J. Locey – PNAS

Pregnancy and birth

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study – Silvia Arboleya – MDPI International Journal of Molecular Sciences

Review: Young microbes for adult obesity – M. Serino – Pediatric Obesity

Review: Microbial therapeutic interventions – Nicole G. Grady – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis – Isabela N. Rôças – PLOS ONE

Human respiratory tract microbiome

Nasopharyngeal Microbiota, Host Transcriptome and Disease Severity in Children with Respiratory Syncytial Virus Infection – Wouter A.A. de Steenhuijsen Piters – Am J Respir Crit Care Med.

Human reproductive tract microbiome

Detection of DNA viruses in prostate cancer – Vitaly Smelov – Scientific Reports

Human gut microbiome

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study – T. Odamaki – Beneficial Microbes

Fecal microbiota transplant for Clostridium difficile infection in older adults – William M. Tauxe – Therapeutic Advances in Gastroenterology

Review: Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis – Motoyoshi Nagai – International Immunopharmacology

Review: Gut Microbiome in CKD: challenges and opportunities – Anitha Nallu – Translational Research

Editorial: Transplanting a Microbial Organ: the Good, the Bad, and the Unknown – Dionysios A. Antonopoulos – mBio

Animal models
A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice – Brian Collins – The Journal of Nutritional Biochemistry

Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures – Jacob Bak Holm – The Journal of Nutritional Biochemistry

Colonic Inflammation Accompanies An Increase of β-Catenin Signaling and Lachnospiraceae/Streptococcaceae in the Hind Gut of High-Fat Diet-Fed Mice – Huawei Zeng – The FASEB Journal

Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice – J-Y Yang – Mucosal Immunology

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota – Aaron C. Ericsson – PLOS ONE

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses – J. P. Brooks – Journal of Environmental Quality

Exploring the Goat Rumen Microbiome from Seven Days to Two Years – Lizhi Wang – PLOS ONE

Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection – Juan J. Quereda – PNAS

Animal microbiome

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus) – Meirong Li – World Journal of Microbiology and Biotechnology

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida) – Jan Hubert – Journal of Economic Entomology

Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia – Jing-Jing Khoo – Ticks and Tick-borne Diseases

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence – Robert A. Quinn – Proceedings of the Royal Society B

Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture – Arjun Singh – Journal of Basic Microbiology

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau – Xiao Dan Huang – Archaea

Horse Species Symposium abstracts: Journal of Animal Science
Recent advances in the microbiome and physiology of the hindgut of the horse and dog – F. Camargo
Canine intestinal microbiology and metagenomics: From phylogeny to function – B. C. Guard – Journal of Animal Science
The microbiome of the horse hindgut: History and current knowledge – V. Julliand

Plant, root, and soil microbiome

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations – Jincai Ma – Science of the Total Environment

Microbial diversity limits soil heterotrophic respiration and mitigates the respiration response to moisture increase – Fen-Guo Zhang – Soil Biology and Biochemistry

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil – Sabine A. Ragot – Plant and Soil

Genetically modified WYMV-resistant wheat exerts little influence on rhizosphere microbial communities – Zhenhua Zhang – Applied Soil Ecology

Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands – Vincent E.J. Jassey – European Journal of Protistology

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of burgundy vineyards – Marie-Lara Bouffaud – Oeno One

Review: Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability—A Review – Pravin Vejan – MDPI Molecules

Chapter: Mycorrhizas in Agroecosystems – Marcela C. Pagano – Recent Advances on Mycorrhizal Fungi

Water and extremophile microbiome

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water – Maria Aguilar – The Journal of Eukaryotic Microbiology

Drift in ocean currents impacts intergenerational microbial exposure to temperature – Martina A. Doblin – PNAS

Low Genome Content Diversity of Marine Planktonic Thaumarchaeota – Haiwei Luo – Environmental Microbiology Reports

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park – Zackary J. Jay – Environmental Microbiology

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment

A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake – Kweku Afrifa Yamoah – Biogeosciences

Review: Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence – Lisa A. Levin – Frontiers in Marine Science

ReviewMicrobial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling – Orissa M Moulton – Frontiers in Ecology and the Environment

Book: Biotechnology of Extremophile – Springer

Waste and pollution microbiology

Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface – Silas H.W. Vick – International Journal of Coal Geology

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Built environment microbiology

Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care? – Gary M. King – Sowing Seeds in the City

Bioinformatics, transcriptomics, metagenomics

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies – Elena Bushmanova – Bioinformatics

Feature: Microbiology: the road to strain-level identification – Vivien Marx – Nature Methods

Protocol BookData Mining Techniques for the Life Sciences – Springer
Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era – Massimiliano Orsini
Update on Genomic Databases and Resources at the National Center for Biotechnology Information – Tatiana Tatusova
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijanić

More microbiology

Riches of phenotype computationally extracted from microbial colonies – Tzu-Yu Liu – PNAS

Microbes in the news

UB’s microbiome hunters. These are exciting times at UB as its work on the human genome and microbiome matures. – Research Foundation for The State University of New York

Video: How Your City Has Its Own Unique Microbiome – Discovery News – YouTube

Wrapping up multiple sclerosis at UCSF – Claire Conway – UC San Francisco

Stalking Cave Bacteria to Make Secret Weapons Against Superbugs: Dr. Naowarat Cheeptham – Sam Grobart – Bloomberg

Seres Therapeutics Announces Achievement of Target Enrollment of SER-109 Phase 2 Study for the Prevention of Recurrent Clostridium difficile Infection – Business Wire

Bacteria use traffic-cop-like mechanism to infect gutWSU scientists discover mechanism critical to pathogens’ success – EurekAlert

Tesla’s Bioweapon Defense Mode can protect you from bacteria, and reduce pollution
Cars. Tesla’s AC unit is available on the Model X and the new Model S – Alphr

Bacteria Hysteria

This odor-fighting, bacteria-killing underwear is made with pure silver – Christian de Looper – Yahoo Digital Trends
Millions of people are drinking mold and bacteria with their coffee. This is how to avoid it! – David Wolfe

Science, publishing and career

Image integrity concerns in papers from a Pfizer lab – Leonid Schneider – For Better Science

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