February 1, 2017

General Microbiome

Microbial Partnerships of Pathogenic Oomycetes-M Larousse-PLoS Pathogens

Biocontrol of Virulent Ralstonia solanacearum isolates by an Indigenous Bacillus cereus-H Mandal-Journal of Agricultural Technology

Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities-P Rubbens-PLoS ONE

Assessment of Metabolic changes in Mycobacterium smegmatis wild type and alr mutant strains: evidence for a new pathway of D-alanine biosynthesis.-DD Marshall-Journal of Proteome Research

Invasions of Host-Associated Microbiome Networks-CL Murall-Advances in Ecological Research

Review: Microbiome engineering: Current applications and its future.-JL Foo-Biotechnology Journal

Review: Microbes and Mental Health: A Review.-R Rieder-Brain, Behavior, and Immunity

Temporal dynamics of microbial communities in microcosms in response to pollutants-Shuo Jiao-Molecular Ecology

Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system-Zhou Li-Environmental Microbiology

Pregnancy and Early Life

Helicobacter pylori infection is associated with an altered gastric microbiota in children-KM Brawner-Mucosal Immunology

Multi-site Human Microbiome

Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity-MW Hall-npj Biofilms and Microbiomes

Human Respiratory Microbiome

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants-BD Wagner-PLoS ONE

Metagenomic Analysis of Airborne Bacterial Community and Diversity in Seoul, Korea, during December 2014, Asian Dust Event-Seho Cha-PLoS ONE

Human Skin Microbiome

Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals.-Rodrigues Hoffman A-Veterinary Dermatology

Human Nearly Sterile Sites

Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori-Teresa Alarcon-Molecular Pathogenesis and Signal Transduction by Helicobacter pylori

Blood microbiota as a potential noninvasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully-Zongxin Ling-Heptatology

Epidemiological investigation of Candida species causing bloodstream infection in paediatric small bowel transplant recipients-Mallory J. Suhr-Mycoses

Human Gut Microbiome

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease-Timothy R. Sampson-Cell

The Intestinal Microbiome, the Immune System and Spondyloarthropathy-ME Costello-Next-Generation Therapies and Technologies for Immune-Mediated Inflammatory Diseases

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations-ND Chu-PLoS ONE

The development and role of microbial-host interactions in gut mucosal immune development-CR Stokes-Journal of Animal Science and Biotechnology

Pd-237 The Microbiome of the Colonic Mucosal-luminal Interface in Crohn’s Disease Patients in Endoscopic Remission-J Jacobs-Inflammatory Bowel Diseases

Progress with treating the microbial dysbiosis associated with irritable bowel syndrome.-JS Pearson-Current Opinion in Gastroenterology

Fecal microbiota transplantation for gastrointestinal disorders.-T Malikowski-Current Opinion in Gastroenterology

The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?-J Dore-Therapie

Review: Clostridium difficile colitis: A clinical review.-GK Ong-American Journal of Surgery

Biotransformation of Total Saponins in Siraitia Fructus by Human Intestinal Microbiota of Normal and Type 2 Diabetic Patients:Comprehensive Metabolites Identification and Metabolic Profile Elucidation Using LC-Q-TOF/MS.-G Zhou-Journal of Agricultural Food Chemistry

Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study-Mitsuharu Matsumoto-PLoS ONE

Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine-Wolfgang Stremmel-PLoS ONE

Animal Experiments

P-327 Prolonged Restraint Stressor Exposure in Outbred Cd-1 Mice Impacts Microbiota, Colonic Inflammation, and Short Chain Fatty Acids in Colonic Inflammation-R Maltz-Inflammatory Bowel Diseases

EGCG Prevents High Fat Diet-Induced Changes in Gut Microbiota, Decreases of DNA Strand Breaks, and Changes in Expression and DNA Methylation of Dnmt1 and MLH1 in C57BL/6J Male Mice.-M Remely-Oxidative Medicine and Cellular Longevity

Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice.-G Boudry-Journal of Dairy Science

The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs-Nick D. Jeffery-PLoS ONE

Animal Microbiome

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate-KR Amato-Microbial Ecology

Two biomass preparation methods provide insights into studying microbial communities of intestinal mucosa in grass carp (Ctenopharyngodon idellus)-NT Tran-Aquaculture Research

Changes in the Bacteriome of Honey Bees Associated with the Parasite Varroa destructor, and Pathogens Nosema-J Hubert-Invertebrate Microbiology

Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder.-J Sun-Scientific Reports

Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine-Rahat Zaheer-PLoS ONE

Plant, Root and Soil Microbiome

Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia-Feras F. Lafi-Genome Announcements

Community structure, species variation, and functional characterization of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars-AK Mahoney-Frontiers in Plant Science

Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem-G Rodriguez-Caballero-Science of the Total Environment

Plant Growth Promoting Activity of Pink Pigmented Facultative Methylotroph-Methylobacterium extorquens MM2 on Lycopersicon esculentum L.-P Subhaswaraj-Journal of Applied Biology and Biotechnology

… Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere-N D’Agostino-Genome Announcements

Microbial species and functional diversity in rice rhizosphere of high-yield special ecological areas.-P LiYuan-Journal of Agricultural Resources and Environment

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana-R Garcia-Suarez-Journal of Applied Microbiology

Community Structures of Arbuscular Mycorrhizal Fungi in Soils and Plant Roots Inhabiting Abandoned Mines of Korea-H Park-Mycobiology

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado-ASF de Araujo-Journal of Microbiology

Thesis: Potential risk factors associated with the microbiota of grass roots in the Kimberley region of Western Australia-B Achemedei

Soil Microbial Communities in Natural and Managed Cloud Montane Forests-EH Chang-Forests

Functional Genes That Distinguish Maize Phyllosphere Metagenomes in Drought and Well-Watered Conditions-Barbara A Methe-bioRxiv

Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.-H Liu-Scientific Reports

Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.-X Zhou-Scientific Reports

Water and Extremophile Microbiome

Production and Characterization of Organic Solvent-Tolerant Cellulase from Bacillus amyloliquefaciens AK9 Isolated from Hot Spring-M Irfan-Applied Biochemistry and Biotechnology

Significant seasonal variations of microbial community in an acid mine drainage lake in Anhui Province, China-C Hao-Environmental Pollution

Bacterial Community Structure and Functional Potential in the Northeastern Chukchi Sea-KM McFarlin-Continental Shelf Research

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis-NI Won-International Journal of Environmental Research and Public Health

Radiative energy budgets of phototrophic surface-associated microbial communities and their photosynthetic efficiency under diffuse and collimated light-M Lichtenberg-bioRxiv

Anaerobic Dechlorination of Tetrachlorobisphenol A in River Sediment and Associated Changes in Bacterial Communities-J Zhang-Water, Air & Soil Pollution

Microbial community changes in methanogenic granules during the transition from mesophilic to thermophilic conditions.-X Zhu-Applied Microbial Biotechnology

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.-AS Wymore-Microbial Ecology

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls-Petra Pop Ristova-PLoS ONE


Toward a Personalized Approach in Prebiotics Research-M Dey-Nutrients

Phages and Viruses

Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates-Lenka Mikalova-PLoS ONE

Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea-Jinik Hwang-PLoS ONE


Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks-S Prigent-PLoS Computational Biology

P-310 Yi Characterizing Gut Metagenome Variation with Host Contamination Using Nanopore Sequencing-J Wang-Inflammatory Bowel Diseases

MetaTopics: an integration tool to analyze microbial community profile by topic model-J Yan-BMC Genomics

Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow-C Wu-Journal of Natural Products

Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages-Jordyn Bergsveinson-AIMS Microbiology

Microbes in the News

Seres plots path back from phase 2 microbiome blowup-FierceBiotech


Which foods can improve your gut bacteria?-BBC News


Branding BIOHM, The Tesla Of Probiotics-Forbes


For A Healthier Mind, Trust Your Gut-GOOD Magazine


Fecal Transplants May Improve Autism By Targeting Gut Bacteria-Huffington Post


Are prebiotics or probiotics effective against dermatitis?-EurekAlert


Dynamic duo could quickly identify deadly bacteria in hospitals-New Atlas
Bacteria in estuaries have genes for antibiotic resistance-Phys.Org


January 21, 2017

Events and Jobs

MS in Microbiology & Cell Science from the University of Florida

QC analyst II-Microbiology

Medical Lab Assistant in Microbiology Essex BMS

General microbiome

*Review: Host-microbiota interactions: epigenomic regulation-Vivienne Woo-Current Opinion in Immunology

The emerging importance and challenges of the human mycobiome-Heidi H. Kong-Virulence

Human respiratory microbiome

*Review: Microbiomes in respiratory health and disease: an Asian-Pacific perspective-Sanjay H. Chotirmall-Respirology

Extracellular vesicles, a key mediator to link environmental microbiota to airway immunity-Youngwoo Choi-Allergy, Asthma and Immunology Research

The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia-Tetyana Zakharkina-Thorax

Human skin microbiome

Experimental metagenomics and ribosomal profiling of the human skin microbiome-Pamela Ferretti-Experimental Dermatology

Human nearly-sterile sites

The gut-brain axis in healthy females: lack of significant association between microbial composition and diversity with psychiatric measures-Susan C. Kleiman-PLoS One

Characterization of microbial communities within aggressive prostate cancer tissues-Melissa A. Yow-Infectious Agents and Cancer

Human gut microbiome

A highly active endo-levanase BT1760 of a dominant mammaliam gut commensal Bacteroides thetaiotaomicron cleaves not only various bacterial levans, but also levan of timothy grass-Karin Mardo-PLoS One

Treatment of recurrent Clostridium difficile infection using fecal microbiota transplantation in patients with inflammatory bowel disease-Krista M. Newman-Gut Microbes

Animal experiments

Effect of Vanadium and Tea Polyphenols on Intestinal Morphology, Microflora and Short-Chain Fatty Acid Profile of Laying Hens-Z.H. Yuan-Biological Trace Element Research

Characterization of gut microbiome dynamics in developing pekin ducks and impact of management system-Aaron A. Best-Frontiers in Microbiology

Animal microbiome

Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium-Laura M. Cox-International Journal of Systematic and Evolutionary Microbiology

Plant, root and soil microbiome

Soil microbiome is more heterogeneous in organic than in conventional farming system-Manoeli Lupatini-Frontiers in Microbiology

Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil-L. Canfora-Scientific Reports


Can probiotics modulate human disease by impacting intestinal barrier function?-Peter A. Braun-British Journal of Nutrition

Mulberry anthocyanin biotransformation by intestinal probiotics-Jing-Rong Cheng-Food Chemistry

Phages and viruses

Low-level predation by lytic phage philPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus-Lucia Fernandez-Scientific Reports

Microbes in the news

Seeking structure with metagenome sequences-phys.org

FishTaco method pinpoints bacterial species responsible for each functional imbalance in microbiome-News Medical Life Sciences

What does your armpit say abou you? Museum exhibit takes a look-Corbie Hill-The News & Observer

Is your diet changing your gut bacteria?-Robin Arora-Desilit- Yahoo News

Symbiont-derived antimicrobials contribute to the control of the lepidopteran gut microbiota-Yongqi Shao-Cell Chemical Biology

Hypertension opens the flood gates to the gut microbiota-W. Robert Taylor-Circulation Research

Moth gut bacteria could help create new antibiotics-Claire Maldarelli-Raw Story

New £5 Notes Are Riddled With Bacteria – But It’s The Good Kind-Holly Brockwell-Gizmodo

80 million bacteria are exchanged with each kiss-Humanitas University

Study shows how bacteria can lessen the body’s defenses-Amy Wallace-UPI

Study ties inflammation, gut bacteria to type I diabetes-Serena Gordon-UPI