January 5, 2015

Happy New Year!

Human oral microbiome

Salivaomics – David T.W. Wong – The Journal of the American Dental Association

Human respiratory microbiome

The Bergen COPD microbiome study (MicroCOPD): rationale, design, and initial experiences – Rune Grønseth – European Clinical Respiratory Journal

Human skin microbiome

Interactions between host factors and the skin microbiome – Adam SanMiguel, Elizabeth A. Grice – Cellular and Molecular Life Sciences

Molecular Characterization of the Skin Fungal Microbiota in Patients with Seborrheic Dermatitis – Akiomi Tanaka – Clinical & Experimental Dermatology Research

Human gut microbiome

Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine – Silvia Caballero and Eric G. Pamer – Annual Review of Immunology

* Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases – Jie Liang – Journal of Digestive Diseases

Special Issue: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile – Melinda A Engevik – American Journal of Physiology – Gastrointestinal and Liver Physiology

Gut Fungal Microbiota: The Yin and Yang of Inflammatory Bowel Disease –
Richard, Mathias L. – Inflammatory Bowel Diseases

Gut-Microbiota and Mental Health: Current and Future Perspectives
Ajit Kumar Thakur – Journal of Pharmacology & Clinical Toxicology

Microbiota, Biofilms and Helicobacter Pylori in the Diseases of Gastroduodenal Zone – G.Sh. Isaeva , V.B. Ziatdinov – Kazan Medical Journal

Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers – Kristin Schmidt – Psychopharmacology

The Human Microbiome, Ecological Ontology, and the Challenges of Community – Gregory W. Schneider and Russell Winslow – Perspectives in Biology and Medicine

Microbiome of pregnancy and birth

* Temporal dynamics of the very premature infant gut dominant microbiota – Fabien Aujoulat – BMC Biology

The Preterm Placental Microbiome Varies in Association with Excess Maternal Gestational Weight Gain – Kathleen M. Antony – American Journal of Obstetrics and Gynecology

* Study in 2 million children: Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal models

Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques – Kai-tao Hu – International Journal of Infectious Diseases

Investigating the long-term effect of subchronic phencyclidine-treatment on novel object recognition and the association between the gut microbiota and behavior in this animal model of schizophrenia – B. Pyndt Jørgensen – Physiology & Behavior

Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis – Mingzhang Guo – Journal of Ethnopharmacology

Animal microbiome

Stability of the Gorilla Microbiome Despite SIV Infection – Andrew H. Moeller – Molecular Ecology

Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota – Guillaume Carissimo – PNAS USA

* Microbiota shifts in the surface mucopolysaccharide layer of corals transferred from natural to aquaria settings – Zoe A. Pratte – Journal of Invertebrate Pathology

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis – Cléa Bauvais – Marine Environment Research

Plant microbiome

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development – Laura B. Martínez-García – New Phytologist

* A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates – Pedro Beschoren da Costa – PLOS ONE

The application of Arabidopsis thaliana in studying tripartite interactions among plants, beneficial fungal endophytes and biotrophic plant-parasitic nematodes – Alfonso Martinuz – Planta

Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities – Manuel Delgado-Baquerizo – Functional Ecology

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress – Nidhi Bharti – Microbial Ecology

Promoting effect of Fusarium oxysporum [f.sp. strigae] on abundance of nitrifying prokaryotes in a maize rhizosphere across soil types – Mary K. Musyoki – Biological Control

Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts – James D. Bever – New Phytologist

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities – T. E. Anne Cotton – New Phytologist

Soil and sediment microbiome

Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey – Hua Fang – Environmental Science & Technology

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem – Ximei Zhang – PLOS ONE

A Novel Sister Clade to the Enterobacteria Microviruses (family Microviridae) Identified in Methane Seep Sediments – Sam Bryson – Environmental Microbiology

Dynamics of Plant Nutrients, Utilization and Uptake, and Soil Microbial Community in Crops Under Ambient and Elevated Carbon Dioxide – Shardendu K. Singh – Nutrient Use Efficiency: from Basics to Advances

Water microbiome

Physical controls of variability in North Atlantic phytoplankton communities – Andrew D. Barton – Limnology and Oceanography

Origins and environmental mobility of antibiotic resistance genes, virulence factors, and bacteria in a tidal creek’s watershed – Andrei L. Barkovskii – Journal of Applied Microbiology

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities – Francisco J. R. C. Coelho – Global Change Biology

The Food Web of Boiling Springs Lake Appears Dominated by the Heterolobosean Tetramitus thermacidophilus Strain BSL – William H.H. Reeder IV – Journal of Eukaryotic Microbiology

Microbiome of digesters and wastewater

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters – David Wilkins – Applied and Environmental Microbiology

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities – David R. Johnson – Applied and Environmental Microbiology

Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia – Adey Feleke Desta – PLOS ONE

Enhancement of sludge granulation in anaerobic acetogenesis by addition of nitrate and microbial community analysis – Yang Li – Biochemical Engineering Journal

Microbiome of the built environment

Indoor Fungi: Companions and Contaminants – A. Nevalainen – Indoor Air

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – M. Takahashi – Journal of Applied Microbiology

Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina – Patricia Elizaquível – International Journal of Food Microbiology


Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not – Jessica Hedge, Daniel J. Wilson – mBio

Reply to “Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources” – Jason T. Ladner – mBio


Response of Peripheral Rhythms to the Timing of Food Intake – Megumi Hatori, Satchidananda Panda – Methods in Enzymology


The near-quantitative sampling of genomic DNA from various food-borne Eubacteria – Peter Irwin – BMC Microbiology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system – Patrick D. Schloss preprint

Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems – Jarrad T. Hampton-Marcell – Springer Protocols Handbooks

Protocols for Handling, Storing, and Cultivating Oil Sands Tailings Ponds Materials for Microbial and Molecular Biological Study – J. M. Foght – Springer Protocols Handbooks

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples (video) – Yan Wei Lim – JOVE

Microbes in the news

Book: Principals of Microbial Diversity – James W. Brown – ASM Press

Bacteria hold clues to our health – Heather Kelly – CNN

11+ things everyone needs to know about microbes – Jonathan Eisen – MicrobeNet

How to Build a Healthy Microbiome, Before, During, and After Birth – Kelly Brogan – Mercola.com

Mining the microbiome: How the microbes that share our bodies could help prevent cancer – Leigh MacMillan – Vanderbilt-Ingram

The Surprising Link Between Gut Bacteria And Anxiety – Carolyn Gregoire – Huffington Post

Stress, Depression, & The Bacteria In Your Gut – Video with Professor John F. Cryan – Richard Zwolinski – PsychCentral

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus – Jonathan Eisen – The Tree of Life

Gut Microbiome Rebounds After Colonoscopy Bowel Preparation – Lara C. Pullen – Medscape

Elevator buttons at hospitals have more bacteria than the toilets – Nicole Oran – MedCityNews

Can Mars be terraformed with bacteria? The Cyano Knights think so! Scott Sutherland – The Weather Network

Cholera’s Method of Killing Identified – Jim Algar – Tech Times

Science, publishing and career

A Stronger Post-Publication Culture Is Needed for Better Science – Hilda Bastian – PLOS Medicine

Advocating for women in hiring decisions – Dr. Mellivora – Tenure She Wrote

Science and art

Stylish Silk Scarves, Dyed With Bacteria – Liz Stinson – Wired.com

Bik’s Picks

The global distribution of diet breadth in insect herbivores – Matthew L. Forister – PNAS USA

‘Bad luck’ of random mutations plays predominant role in cancer, study shows – Science Daily

Experimental Diet Pill Tricks Body into Thinking It Ate – Bahar Gholipour – Live Science



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