March 10, 2015

Human microbiome, general

Abstract: Targeted Genomic Characterization, Uncultured Bacteria from Human Microbiota, Project – Mircea Podar – Environmental Metagenomics

Review: The Emerging Role of Metagenomics in the Diagnosis of Infectious Diseases – Jun Li and Qiang Feng – SOJ Microbiology & Infectious Diseases

Review: Chapter 4 – Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome – Philip Chuang – Comprehensive Analytical Chemistry

Microbiome of pregnancy and birth

In vitro impact of human milk oligosaccharides on Enterobacteriaceae growth – Jennifer L Hoeflinger – Journal of Agricultural and Food Chemistry

Human oral microbiome

Review: Distribution of Genes Related to Antimicrobial Resistance in Different Oral Environments: A Systematic Review – Ludmila Coutinho Moraes

Human gastric and gut microbiome

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia – Dariush Nasrollahzadeh – Scientific Reports

Review: Autism and Our Intestinal Microbiota – Reddy B.L. and Saier M.H – Journal of Molecular Microbial Biotechnology

Human reproductive organ microbiome

The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in Korea – Hea Young Oh – Clinical Microbiology and Infection

Animal models of microbiome research

Helicobacter pylori infection can affect energy modulating hormones and body weight in germ free mice – Yalda Khosravi – Scientific Reports

Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases – Huang, Edmond Y. – Inflammatory Bowel Diseases

Animal microbiome

Characterization of intestinal bacterial communities of western lowland gorillas (Gorilla gorilla gorilla), central chimpanzees (Pan troglodytes troglodytes), and a forest elephant (Loxodonta africana cyclotis) living in Moukalaba-Doudou National Park in Gabon – Sayaka Tsuchida – Tropics

Editorial: Phylogeny: Are arthropods at the heart of virus evolution? – Gytis Dudas, Darren J Obbard – eLIFE

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses – Ci-Xiu Li – eLIFE

Review: Marsupial oral cavity microbiome – Philip S Bird – Microbiology Australia

Review: The marine mammal microbiome: current knowledge and future directions – Tiffanie M Nelson – Microbiology Australia

Review: Mammalian microbiomes – Linda L Blackall – Microbiology Australia

Plant microbiome

Analysis of the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in phosphate solubilization – Margrét Auður Sigurbjörnsdóttir – Microbiology

The response of root-associated bacterial community to the grafting of watermelon –
Ning Ling – Plant and Soil

Soil and sediment microbiome

Call for papers: BIODESERT: Exploring and Exploiting the Microbial Resource of Hot and Cold Deserts – BioMed Research International

Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment – Patrícia S. Costa – PLOS ONE

Establishing microbial diversity and functions in weathered and neutral Cu–Pb–Zn tailings with native soil addition – Xiaofang Li – Geoderma

A novel sub-phylum method discriminates better the impact of crop management on soil microbial community – Florine Degrune – Agronomy for Sustainable Development

Grazing intensity in subarctic tundra affects the temperature adaptation of soil microbial communities – Sari Stark – Soil Biology and Biochemistry

Phytoremediation Using Microbial Communities: I – Mohammad Miransari – Phytoremediation

Effects of soil management practices on soil microbial communities and development of southern blight in vegetable production – Tiehang Wu – Applied Soil Ecology

Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem – Alena K. Oliver – Forest Ecology and Management

Short-term effects of simulated below-ground carbon dioxide leakage on a soil microbial community – I. Fernández-Montiel – International Journal of Greenhouse Gas Control
Review: Microbial communities and their primary to early diagenetic mineral phases; the record from Neoproterozoic microbialites of Qarn Alam, Oman – M. Mettraux – Microbial Carbonates in Space and Time: Implications for Global Exploration and Production

Water microbiome

Review: Halophilic microbial communities and their environments – Aharon Oren – Current Opinion in Biotechnology

Bioreactor microbiome

Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater – Yu Miao – Water Research

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples – Boonfei Tan – ISME Journal

Microbiome of the built environment

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin – Environmental Science & Technology

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance – Nicholas A Bokulich – eLIFE

Metabolomics and transcriptomics

Microbial community transcriptional networks are conserved in three domains at ocean basin scales – Frank O. Aylward – PNAS USA

Review: The use of evolutionary approaches to understand single cell genomes – Haiwei Luo – Frontiers in Microbiology

Book: Encyclopedia of Metagenomics – Genes, Genomes and Metagenomes – Basics, Methods, Databases and Tools – Nelson, Karen E. Some interesting book chapters include:

  • MEMOSys: Platform for GenomeScale Metabolic Models – Stephan Pabinger and Zlatko Trajanoski – Genes, Genomes and Metagenomes
  • Insights into Environmental Microbial Denitrification from Integrated Metagenomic, Cultivation, and Genomic Analyses – Stefan J. Green
  • Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences -Weizhong Li
  • Use of Bacterial Artificial Chromosomes in Metagenomics Studies, Overview – Lingling Wang
  • A 123 of Metagenomics – Torsten Thomas

Viruses and phages

The Importance of Virology at a Time of Great Need and Great Jeopardy – Michael J. Imperiale and Arturo Casadevall – mBio

A metagenomics and case-control study to identify viruses associated with bovine respiratory disease – Terry Fei Fan Ng – Journal of Virology


Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species – Morgane Rossi-Tamisier – International Journal of Systematic and Evolutionary Microbiology

A single protocol for extraction of gDNA from bacteria and yeast – Laurie Vingataramin and Eric H. Frost – BioTechniques

Microbes in the news

Are you overweight? The clue’s in your poo – Robert Pickup – The Conversation

New research finds queen bee microbiomes are starkly distinct from worker bees – Indiana University Bloomington

Queen Bee Microbiomes Are not Like Those of Worker Bees – Entomology Today

Launch of the AMI Microbiome Podcast – American Microbiome Insitute

Dog bacteria might benefit human health – Kalli Ricka Wolf – Tucson Sentinel

A Short History of the Discovery of Viruses – MicrobiologyBytes

How Bacteria Work – Marianne Spoon – How Stuff Works

Resistance: The Film, a documentary on antibiotic resistance.

Science and art

Science and Culture: High concept art and experiments – Calla Cofield – PNAS USA

Science, publishing, and career

The postdoc series: What is a postdoc? – Julie Gould – Nature

Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida and M. Àngels Colomer – PNAS USA

A Second Chance for Fraudsters? What’s behind paper retractions? – Adam Marcus and Ivan Oransky – Labtimes

Bik’s Picks

Chameleons’ Color-Changing Secret Revealed – Laura Geggel – LiveScience

This plant can feel bugs eating it alive. Can scientists improve its self defense? – Darryl Fears – Washington Post

Picture of the Week: Plastiglomerate – Chau Tu – ScienceFriday



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