A special issue of Science with 2 papers on lifestyle factors that determine composition of the stool microbiome in large human cohorts, variation in microbiome LPS immunogenicity contributes to autoimmunity, SEM analysis of cave speleothem microbial communities, and saliva bacteria in Chicha (Ecuadorian beer).
Jobs and Events
Early Career Microbiome Meal, during European Respiratory Society Meeting 2016 London, September 2016
Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio – Greg Caporaso – MicroBEnet
General microbiome
A special Science Issue called The Microbiota At Work: 
Introduction: Manipulating the Microbiota – Caroline Ash, Kristen Mueller – Science
Review: Cross-species comparisons of host genetic associations with the microbiome – Julia K. Goodrich – Science
Review: How colonization by microbiota in early life shapes the immune system – Thomas Gensollen – Science
Review: Antibiotic use and its consequences for the normal microbiome – Martin J. Blaser – Science
Review: The healthy human microbiome – Jason Lloyd-Price – Genome Medicine
Pregnancy and birth
Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants – T. Matsuki – Beneficial Microbes
Human oral microbiome
Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE
Human respiratory microbiome
[PDF] The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res
Human reproductive tract microbiome
[PDF] Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps – Rui-Li Fang – Am J Transl Res
Opinion: Cervicovaginal Microbiomes–Threats and Possibilities – Gregor Reid – Trends in Endocrinology & Metabolism
Review: Foodomics as part of the host-microbiota-exposome interplay – Lorenza Putignani – Journal of Proteomics
Human gut microbiome
Population-level analysis of gut microbiome variation – Gwen Falony – Science
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science
Durable coexistence of donor and recipient strains after fecal microbiota transplantation – Simone S. Li – Science
Review: Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens – Eric G. Pamer – Science
Associations between dietary flavonoid intake and gut microbiota in a group of adults with cystic fibrosis (CF) – L. Li – Journal of Nutrition & Intermediary Metabolism
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans – Tommi Vatanen – Cell
Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals – Sergio Serrano-Villar – EBioMedicine
Serologic microbial associated markers can predict Crohn’s disease behaviour years before disease diagnosis – R. S. Choung – Alimentary Pharmacology & Therapeutics
Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology
Review: Human gut microbiota and healthy aging: Recent developments and future prospective – Manish Kumar – Nutrition an Healthy Aging
Animal and other models
Soluble and Insoluble Fiber Differentially Impact Canine Fecal Microbiome and Circulating Metabolome – Matthew Irick Jackson – The FASEB Journal
Germ-free and antibiotic-treated mice are highly susceptible to epithelial injury in DSS colitis – Cristina Hernández-Chirlaque – Journal of Crohn’s and Colitis
High intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity – Emmanuel Denou – American Journal of Physiology
Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium – Joshua C. Mccann – Frontiers in Microbiology
Review: Oral microbial biofilm models and their application to the testing of anticariogenic agents – Christina P.C. Sim – Journal of Dentistry
Animal microbiome
Patterns of bacteria-host associations suggest different ecological strategies between two reef building cold-water coral species – Anne-Leila Meistertzheim – Deep Sea Research Part I: Oceanographic Research Papers
Plant, root, and soil microbiome
Characterizing and handling different kinds of AM fungal spores in the rhizosphere – Xueguang Sun – World Journal of Microbiology and Biotechnology
Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field – Qianhan Shang – World Journal of Microbiology and Biotechnology
Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils – Xi-En Long – Environmental Science and Pollution Research
The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur) – S. Meaden – Environmental Microbiology Reports
Universal indicators for oil and gas prospecting based on bacterial communities shaped by light-hydrocarbon microseepage in China – Chunping Deng – Journal of Microbiology and Biotechnology
Performance of 16s rRNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies – Bram Beckers – Frontiers in Microbiology
Water and extremophiles
The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum – Fatima Foflonker – Algal Research
Microbial communities in a range of carbon dioxide fluxes from a natural volcanic vent in Campo de Calatrava, Spain – Irena Fernández-Montiel – International Journal of Greenhouse Gas Control
On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats – Igor Stelmach Pessi – Journal of Phycology
Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean – Andreas Krupke – Frontier in Marine Science
Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment – Yung Mi Lee – Korean Journal of MIcrobiology
Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave – Cohord Mason – The Journal of Experimental Microbiology & Immunology
Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes – Gaston E. Small – Biogeochemistry
Built environment microbiome
Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air
Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology
Food microbiology
Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha) – Ana L. Freire – PeerJ
A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology
Bioinformatics and metagenomics
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design – Christoph Mayer – Molecular Biology and Evolution
Microbial ecology
The Evolution of Quorum Sensing as a Mechanism to Infer Kinship – Jonas Schluter – PLOS Computational Biology
Co-existence facilitates interspecific biofilm formation in complex microbial communities – Jonas S Madsen – Environmental Microbiology
Viruses and phages
Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints – W. C. Wilson – Virus Genes
Techniques
[Video Protocol] Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – Journal of Visualized Experiments
Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE
The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res
Microbes in the news
Your gut bacteria are more than what you eat – Elizabeth Pennisi – Science
With quotes from me! New research confirms thriving gut bacteria is linked to a healthier body – Russell Brandom – The Verge
Want more good bugs in your gut? Try yogurt. And coffee – Patrick Skerrett – STAT News
This Bacteria Strain Offers a Curious Mix of Hope and Danger. The Elizabethkingia strain could cure malaria, but it’s also sickened dozens in Wisconsin – Lisa Margonelli – Slate
The Benefits of Slathering Your Newborn Baby with Vaginal Bacteria – Rebecca Schiller – Vice Broadly
A Timely Gut Check. At the American Museum of Natural History, meet your microbiome – Ralph Gardner – The Wall Street Journal
A Comprehensive Survey of Pre-Clinical Microbiology Curricula Among United States Medical Schools – Dora Melber – Clinical Infectious Diseases
Mayo Clinic Ventures Firm Explores Commercialization Of Gut Microbe Treatment – Don Jacobson – Twin City Business
Microbes and art
Quilting with soil: soil microorganisms had “painted” their efforts on the cloth in an unexpected variety of colors. – Martha Pings – Soils
Science, publishing, and career
Is most published research really false? – Jeffrey T Leek, Leah R Jager – bioRxiv
Who’s downloading pirated papers? Everyone. In rich and poor countries, researchers turn to the Sci-Hub website – John Bohannon – Science
The frustrated science student behind Sci-Hub – John Bohannon – Science
Plagiarism: A worm poking holes into the quality of our academic work – Christine Osae – The New Times
Bik’s Picks
Doctor ready to perform first human head transplant – Ross Kenneth Urken – News Week
Microbiome Digest - Bik's Picks 