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
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
Techniques
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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Microbiome Digest - Bik's Picks 