Wow, this was a busy day with about 700 new articles for y’all to screen. Here we go:
Events
May 7th Webinar: George Weinstock Ph.D., will present “The Human Microbiome: Impact on Health and Disease.”
May 13th Webcast at 11am EDT – “Innovations in the microbiome” with Annick Mercenier and Enea Rezzonico – Nature Publishing Group
Human oral microbiome
Periodontal disease in a remote Asian population: association between clinical and microbiological parameters – Christine Kvarnvik – Journal of Investigative and Clinical Dentistry
Human gut microbiome
Comparison of the gut microbiota of people in France and Saudi Arabia – M. Yasir – Nutrition and Diabetes
Fecal microbiota characteristics of patients with colorectal adenoma detected by screening: A population-based study – James J. Goedert – EBioMedicine
Review: Archaea associated with human surfaces: not to be underestimated – Corinna Bang , Ruth A. Schmitz – FEMS Microbiology Reviews
Review: Keeping bugs in check: The mucus layer as a critical component in maintaining intestinal homeostasis – Martin Faderl – IUBMB Life
Review: A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host – Christoph A Thaiss – Gut Microbes
Review: Effect of Helicobacter pylori Infection on the Composition of Gastric Microbiota in the Development of Gastric Cancer – Cao L. · Yu J. – GastroIntestinal Tumors
Review: Immunogenetic control of the Intestinal Microbiota – Eric Marietta – Immunology
Review: Type 2 diabetes and gut microbiome: at the intersection of known and unknown – Smitha Upadhyaya – Gut Microbes
Review: Host-Microbiota Interactions in the Intestine – Elson C.O. – Digestive Diseases
Review: Control of commensal microbiota by the adaptive immune system – Husen Zhang – Gut Microbes
Animal models of microbiome research
Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets – Zhen Luo – Archives of Animal Nutrition
Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum – Refaat Ras – International Journal of Parasitology
Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats – Michaela D. J. Blyton – Environmental Microbiology Reports
Regulation by gut commensal bacteria of carcinoembryonic antigen-related cell adhesion molecule expression in the intestinal epithelium – Yasuaki Kitamura – Genes to Cells
Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition – Elena Gorokhova – Environmental Science & Technology
Role of intestinal microbiota in the generation of polyphenol-derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research
Animal microbiome
Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts – Joanito Liberti – Molecular Ecology
Microbial and sponge loops modify fish production in phase-shifting coral reefs – Cynthia B. Silveira – Environmental Microbiology
Coral symbiotic algae calcify ex hospite in partnership with bacteria – Jörg C. Frommlet – PNAS USA
Plant, plant root and soil microbiome
Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy – Kosuke Shiraishi – Scientific Reports
Role of root microbiota in plant productivity – Andrzej Tkacz and Philip Poole – Journal of Experimental Botany
Seasonal variation of bacterial endophytes in urban trees – Shu Yi Shen – Frontiers in Microbiology
Plant polysaccharides initiate underground crosstalk with bacilli by inducing synthesis of the immunogenic lipopeptide surfactin – Delphine Debois – Environmental Microbiology Reports
Banana leaf and glucose mineralization and soil organic matter in microhabitats of banana plantations under long-term pesticide use – Elena Blume – Environmental Toxicology and Chemistry
Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria – Sebastian Lòpez-Fernàndez – Frontiers in Microbiology
Decreases in soil moisture and organic matter quality suppress microbial decomposition following a boreal forest fire – Sandra R. Holden – Soil Biology and Biochemistry
Soil bacterial community response to sulfadiazine in the soil–root zone – Rüdiger Reichel – Journal of Plant Nutrition and Soil Science
Three-dimensional structure and cyanobacterial activity within a desert biological soil crust – Hagai Raanan – Environmental Microbiology
Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open
Microbial 16S gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements – Anna Lavecchia – Biology and Fertility of Soils
Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils – David VanInsberghe – The ISME Journal
Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study – Felipe Bastida – Applied Soil Ecology
Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities – Daniel S. Read – Environmental Science and Pollution Research
Functional diversity of soil microbial communities under Scots pine, Norway spruce, silver birch and mixed boreal forests – Chodak Marcin – Pedobiologia
Water microbiome
Metabolic cascades in marine microbial communities – Andreas F. Haas and Forest Rohwer – PNAS USA
A Rickettsiales Symbiont of Amoebae with Ancient Features – Frederik Schulz – Environmental Microbiology
Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene – Yu-Mei Wei – Environmental Science and Pollution Research
Cyanobacterial dynamics in shallow Lake Apopka (Florida, U.S.A.) before and after the shift from a macrophyte-dominated to a phytoplankton-dominated state – Matthew N. Waters – Freshwater Biology
Extremophile microbiome
Open Access: Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming – Alexander Tøsdal Tveit – PNAS USA
Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil – Lori A. Phillips – Soil Biology and Biochemistry
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem – Karen Andrade – The ISME Journal
Microbiome of the built environment
From Lab to Field: The Influence of Urban Landscapes on the Invasive Potential of Wolbachia in Brazilian Aedes aegypti Mosquitoes – Heverton Leandro Carneiro Dutra – PLOS Neglected Tropical Diseases
Bioreactor microbiology
Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome – Zhiping Wang – Microbial Ecology
Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage – Matthew D. Porter – Microbial Ecology
Food microbiology
Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing – Qian Peng – Current Microbiology
Microbial Ecology
Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology
Effect of audible sound in form of music on microbial growth and production of certain important metabolites – Niral Sarvaiya, Vijay Kothari – Microbiology
Techniques
Optimized DNA extraction and metagenomic sequencing of airborne microbial communities – Wenjun Jiang – Nature Protocols
http://www.nature.com/nprot/journal/v10/n5/full/nprot.2015.046.html
Bioinformatics
phylogeo: an R package for geographic analysis and visualization of microbiome data –
Zachary Charlop-Powers and Sean F. Brady – Bioinformatics
PhD thesis: Statistical models for large-scale comparative metagenome analysis – Kathrin Petra Aßhauer – Georg-August-Universität Göttingen
Metagenomics
Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe – Irena I. Artamonova – Environmental Microbiology
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes – Bing Li – The ISME Journal
Metabolomics and proteomics
Review: Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota – Weili Xiong – Proteomics
Fate of microbial metabolites of dietary polyphenols in rats: is the brain their target destination? – Mattia Gasperotti – ACS Chemical Neuroscience
Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders – Colin Heberling – International Journal of Molecular Sciences
Navigating through metaproteomics data: A logbook of database searching –
Thilo Muth – Proteomics
Phages and viruses
Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity – Welkin H Pope – eLIFE
Linking environmental prokaryotic viruses and their host through CRISPRs
– Laura Sanguino – FEMS Microbiology Ecology
Microbes in the news
The Healthy Birth: Dyad or Triad? Exploring Birth and the Microbiome – Anne Estes – Science & Sensibility
Designing a Hospital to Better Fight Infection (about the Hospital Microbiome Project) – Robert Lee Hotz – Wall Street Journal
and
WSJ article on the Hospital Microbiome Project – Elisabeth Bik – MicroBEnet
Facts About Our Microbial Menagerie – Infection Control Today
Don’t Trust The Goats; Their Ticks Could Make You Sick – Poncie Rutsch – NPR
Tiny Creatures: The World of Microbes – Anne M. Estes – Mostly Microbes
Time-lapse movie of growth and death in bacterial communities – David Esteban – Experiment.com
An arms race of microbial proportions: A war between bacteria and bacteriophages is being fought at the genetic level – Jason Tetro – Popular Science
Microbes and money
uBiome Launches Clinical Laboratory: launch of their CLIA-regulated clinical laboratory to provide clinical tests based on its unique microbial assays – Globe News Wire
New report sheds light on the Global human microbiome market – size, share, segments analysis and outlook to 2020 – Whatech.com
Science, publishing and career
Five Non-Academic Careers for which Ph.D. Holders are Uniquely Qualified… – Colin White – Nature Careers
Study: Peer Review Predicts Success – Ruth Williams – The Scientist
Discussion paper: Appearance and Gender Bias in Academia – Tali Regev – Tel Aviv University
Bik’s Picks
Source of Antarctica’s Eerie ‘Bleeding Glacier’ Found – Becky Oskin – Live Science
Video: Watch an Algae Cell Turn Itself Inside Out – Douglas Main – NewsWeek
How do you find a Burmese python in the Everglades? – Michael Casey – CBS News
[hr]
Microbiome Digest - Bik's Picks 