October 27, 2015

Gut biogeography, soil transplants, donkey penises, Chicago public beaches, deep-sea mussels, dust particles in the International Space Station, and red pepper influence on kimchi microbiology


About the world within us: This week, Penn Vet, Penn Medicine, and the Children’s Hospital of Philadelphia will host their second annual microbiome symposium – Sandy Bauers – Philly.com

Call for Volunteers: Gut Microbiota Samples – AGA is now recruiting volunteers to have their gut analyzed. Submit your name by Dec. 7 to be considered

General human microbiome

Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches – José E. Belizário – Frontiers in Microbiology

Pregnancy and birth microbiome

The Early Intestinal Microbiota of Healthy Korean Newborns – Eu Kyoung Lee – Iran J Pediatr

Human oral microbiome

Microbiome interaction with sugar plays an important role in relapse of childhood caries
Jing Tian – Biochemical and Biophysical Research Communications

Human respiratory microbiome

The microbiome of the maxillary sinus and middle nasal meatus in chronic rhinosinusitis – O.A. Ivanchenko – Rhinology

Human skin microbiome

The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients – Charles W. Lynde – Journal of Cutaneous Medicine and Surgery

Human gut microbiome

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India – Anna Johnning – BMC Microbiology

Regulation of lung immunity and host defense by the intestinal microbiota – Derrick R. Samuelson – Frontiers in Microbiology

Intestinal Microbiota Profiles of Healthy Pre-School and School-Age Children and Effects of Probiotic Supplementation – Wang C. – Annals of Nutrition and Metabolism

Effect of Whole-Grain Barley on the Human Fecal Microbiota and Metabolome – Maria De Angelis – Applied and Environmental Microbiology

Microbiota studies in the bile duct strongly suggest a role for H. pylori in extrahepatic cholangiocarcinoma – Francisco Avilés-Jiménez- Clinical Microbiology and Infection

Review: A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes – Yueqiong Ni – mBio

Review: Gut biogeography of the bacterial microbiota – Gregory P. Donaldson – Nature Reviews Microbiology

Review: The Microbiome in Mental Health: Potential Contribution of Gut Microbiota in Disease and Pharmacotherapy Management – Stephanie A. Flowers – Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy

Review: Impact of Gut Microbiota on Obesity, Diabetes, and Cardiovascular Disease Risk – Luca Miele – Current Cardiology Reports

Editorial: Faecal transplants – Tim Spector, Rob Knight – British Medical Journal

Microbiome models

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection – Jason L. Kubinak

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model – Marisol Aguirre – Research in Microbiology

The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Frontiers in Microbiology

Review: Selective manipulation of the gut microbiota improves immune status in vertebrates – Ana Montalban-Arques – Frontiers in Immunology

Animal microbiome

With a picture of the sampling site! Bacterial and fungal microflora on the external genitalia of male donkeys (Equus asinus) – Carla L. Carleton – Animal Reproduction Science

Zoo animalsHuman Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

InsectsMicrobial ecology-based methods to characterize the bacterial communities of non-model insects – Erica M. Prosdocimi – Journal of Microbiological Methods

CattleThe nasopharyngeal microbiota of feedlot cattle – Devin B. Holman – Scientific Reports

CattleThe rumen microbial metagenome associated with high methane production in cattle – R. John Wallace – BMC Genomics

GooseComparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing – Wen Wang – Microbiological Research

BatsBacterial diversity indicates dietary overlap among bats of different feeding habits – Sunil Banskar – Microbiological Research

Copepods: Biotransformation of petroleum hydrocarbons and microbial communities in seawater with oil dispersions and copepod feces – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Mussels: Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels – Lizbeth Sayavedra – eLIFE

SnailEnrichment and Identification of Cellulolytic Bacteria from the Gastrointestinal Tract of Giant African Snail, Achatina fulica – Kiran D. Pawar – Applied Biochemistry and Biotechnology

CoralIntraspecific diversity among partners drives functional variation in coral symbioses – John Everett Parkinson – Scientific Reports

CoralVariations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system – Huda Mahmoud – Marine Pollution Bulletin

CoralMicrobiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria – Julie L Meyer – The ISME Journal

ZebrafishIdentification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine – W. Zac Stephens – mBio

ArthropodThe microbiome of Folsomia candida: an assessment of bacterial diversity in a Wolbachia-containing animal – V. Agamennone – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Dynamics of bacterial community structure on intertidal sandflat inhabited by the ghost shrimp Nihonotrypaea harmandi (decapoda: Axiidea: Callianassidae) in tomioka bay, amakusa, Japan – Minoru Wada – Gene

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest
Dulce Flores-Rentería – Soil Biology and Biochemistry

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities – Francesco Vitali – Microbiological Research

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China – Weibing Xun – Environmental Microbiology

Microbial responses to southward and northward Cambisol soil transplant – Mengmeng Wang – Microbiology Open

Review: Incorporating the soil environment and microbial community into plant competition theory – Po-Ju Ke – Frontiers in Microbiology

Review: Root Microbiome Assemblage is Modulated by Plant Host Factors – Venkatachalam Lakshmanan – Advances in Botanical Research

Water microbiome

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats – Hon Lun Wong – Scientific Reports

Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches – Kema Malki – Data in Brief

Cyanobacterial reuse of extracellular organic carbon in microbial mats – Rhona K Stuart – The ISME Journal

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton – Sedimentology

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan – Takuro Nunoura – Environmental Microbiology

Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget? – Antony Meunier, Stéphan Jacquet – Biology Open

Active populations of rare microbes in oceanic environments as revealed by bromodeoxyuridine incorporation and 454 tag sequencing – Koji Hamasaki – Gene

Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment – Tao He – Applied Microbiology and Biotechnology

[Mini review] metagenomic studies of the Red Sea – Hayedeh Behzad – Gene

Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities and different biofilm 3D architectures – Ibtissem Doghri – BMC Microbiology

Genome-wide tuning of protein expression levels to rapidly engineer microbial traits – Emily F. Freed – ACS Synthetic Biology

Built Environment microbiology

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities – Aleksandra Checinska – Microbiome

Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing – Jing You – Applied Microbiology and Biotechnology

Food microbiology

The influence of red pepper powder on the density of Weissella koreensis during kimchi fermentation – Bo Kyoung Kang – Scientific Reports

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant – Maria Calasso – Food Microbiology

Extremophile microbiology

Hot spring deposits: Tracing Biosignature Preservation of Geothermally Silicified Microbial Textures into the Geological Record – Kathleen A. Campbell – Astrobiology

Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland – Hanna Miettinen – Frontiers in Microbiology

Bioinformatics and metagenomics

mBLAST: Keeping up with the Sequencing Explosion for (Meta) Genome Analysis – Curtis Davis – Journal of Data Mining in Genomics & Proteomics

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia – William C. Nelson – Applied and Environmental Microbiology

V-GAP: Viral genome assembly pipeline – Yoji Nakamura – Gene

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community – Robert M. Bowers – BMC Genomics

MinION Analysis and Reference Consortium: Phase 1 data release and analysis [version 1; referees: awaiting peer review] – Camilla L.C. Ip – F1000 Research

Review: Machine learning for metagenomics: methods and tools – Hayssam Soueidan, Macha Nikolski – Arxiv

Review: Novel Computational Technologies for Next-Generation Sequencing Data Analysis and Their Applications – Chuan Yi Tang – International Journal of Genomics

Microbes in the news

Potentially Dangerous Bacteria Thrive At The International Space Station, NASA Warns
– Katrina Pascual – Tech Times
What’s In The Microbiome Of Space? – Science 2.0

Decoding the DNA of lung bacteria to keep you healthy – Leah Cuthbertson – Imperial College London

US researchers delve into make-up of gut bacteria in horses – HorseTalk

Microbial engineering finds a home at SEAS: genetic engineering on biofilms – Adam Zewe – Harvard

Cultures: a small magazine tackling big issues – Special Kids Edition – ASM

Hurricane Patricia Victims Use Chlorine To Fight Bacteria – Operation Blessing

Bacteria can communicate like brain cells. This is a bacterial world. We just live in it. – Bradley J. Fikes – San Diego Union Tribune

Jessica Richman Wants People to Track Their Microbiomes – Wall Street Journal



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