October 10, 2015

The Eukaryome of the human gut, core microbiome in rumen, overweight kitties, and viral metagenomics of a hot spring.

Human gut microbiome

Repertory of Eukaryotes (Eukaryome) in the Human Gastrointestinal Tract: Taxonomy and Detection Methods – Ibrahim Hamad – Parasite Immunology

Diversity of Duodenal and Rectal Microbiota in Biopsy Tissues and Luminal Contents in Healthy Volunteers – Gangping Li – Journal of Microbiology and Biotechnology

Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease – Bashar Aqel, John K. DiBaise – Nutrition in Clinical Practice

Review: Gut Microbiome: What We Do and Don’t Know – Gail A. Cresci and Emmy Bawden – Nutrition in Clinical Practice

Editorial: Contribution of Gut Bacteria to Lipid Levels Another Metabolic Role for Microbes? – Hooman Allayee, Stanley L. Hazen

Human vaginal microbiome

Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota – Kenetta L. Nunn – mBio

Models of microbiome research

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity
Denise Morais da Fonseca – Cell

Animal microbiome

Overweight and the feline gut microbiome – a pilot study – I. N. Kieler – Journal of Animal Physiology and Animal Nutrition

Bovine mastitis may be associated with the deprivation of gut Lactobacillus – C. Ma – Beneficial Microbes

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range – Gemma Henderson – Scientific Reports

Plant, root, and soil microbiome

Evaluating a multigene environmental DNA approach for biodiversity assessment
Alexei J. Drummond – GigaScience (via PMC)

Sheep grazing and soil bacterial diversity in shrublands of the Patagonian Monte, Argentina – Nelda L. Olivera – Journal of Arid Environments

Climatic conditions, soil fertility and atmospheric nitrogen deposition largely determine the structure and functioning of microbial communities in biocrust-dominated Mediterranean drylands – Raul Ochoa-Bon – Plant and Soil

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters – Amélia Bourceret – Microbial Ecology

Water and extremophile microbiome

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins – Dorina Seitaj – PNAS
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs – Sóley Ruth Gudbergsdóttir – Environmental Microbiology

Waste treatment microbiology

Characterization of microbial communities in water and biofilms along a large scale SWRO desalination facility: Site-specific prerequisite for biofouling treatments – Adi Levi – Desalination

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans – Massimo C Pernice – The ISME Journal


A Global Metabolomic Analysis of a Mammalian Host Infected with Bacillus anthracis
Chinh T.Q. Nguyen – Infection and Immunity

Sequencing techniques

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
Tatsuya Unno – Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

Differential analysis of biological networks – Da Ruan – BMC Bioinformatics

SPINGO: a rapid species-classifier for microbial amplicon sequences – Guy Allard – BMC Bioinformatics

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection – Xiao Ding – BMC Bioinformatics

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology – Feng Ju and Tong Zhang – Environmental Science & Technology

A Comparison of Base-calling Algorithms for Illumina Sequencing Technology – Ashley Cacho – Briefings in Bioinformatics


A Validated High Resolution Mass Spectrometry-based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype – Julie Vanden Bussche – Analytical Chemistry

Microbes in the news

Should We Bank Our Own Stool? – Moises Velasquez-Manoff – New York Times

Researchers use gut bacteria composition to genetically classify colorectal tumors – EurekAlert

Bacteria take on stinky problem in Kenner – Christie Walton – Fox8Live

MSU faculty member earns grant award for biofilm methodology research: Darla Goeres was recently awarded a Burroughs Wellcome Innovation in Regulatory Science Award. – Montana State University

Biotech of the week: Enterome, the Leading French Microbiome Start-up – LaBiotech

Conference Coverage: ID week: Drug Resistance: What Happens Inside the Nose? – HCP Live

Antibiotic use and cancer risk: Repeat exposure poses harm: interview with Ben Boursi – Healio



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