Category Archives: Food Microbiology

June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

May 25, 2016

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The sinonasal microbiome in chronic rhinosinusitis, walnut consumption in a mouse model, and treatment of cows with antibiotics has effects on dung beetle microbiomes.

Jobs and Grants

Assistant professor of food science, microbial ecology – Penn State

American Gastroenterological Association Invites Applications for Gut Microbiome Award – Philanthropy news digest

Three Post-Doctoral Fellowships for Tropical Microbial Ecologists in Panama – Smithsonian Tropical Research Institute

Events

1st International Conference on the Marine Microbiome – Discovery & Innovation for science and industry, 27 June 2016 — 30 June 2016, Berlin, Germany

Pregnancy and birth

Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women – Luisa F Gomez-Arango – Diabetes

Human oral microbiome

Minireview: A practical guide to the oral microbiome and its relation to health and disease – K Krishnan – Oral Diseases

Human respiratory microbiome

Review: A systematic review of the sinonasal microbiome in chronic rhinosinusitis – Martin Anderson – American Journal of Rhinology & Allergy

Human gut microbiome

Letter: Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis – Malte Christoph Rühlemann – Gut

Review: Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children – Evalotte Decker – Gut Microbes

Human vaginal microbiome

Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis – Gary Ventolini – Women’s Health

Animal experiments

Pulmonary Th17 Antifungal Immunity Is Regulated by the Gut Microbiome – Jeremy P. McAleer – The Journal of Immunology

Microbial modulation of behavior and stress responses in zebrafish larvae – Daniel J. Davis – Behavioural Brain Research

Effects of walnut consumption on colon carcinogenesis and microbial community structure – Masako Nakanishi – Cancer Prevention Research

Animal microbiome

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata – Sonny T. M. Lee – Frontiers in Microbiology

Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus – Aneta Nowakiewicz – PLOS ONE

Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles – Tobin J. Hammer – Proceedings of the Royal Society B

Immune response and gut microbial community structure in bumblebees after microbiota transplants – Kathrin Näpflin – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing – Linkun Wu – Scientific Reports

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize – Giovanni Vigliotta – Journal of Environmental Management

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil – Stefano Covino – Science of the Total Environment

Water microbiome

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed – Liyan Song – Microbial Ecology

Built environment microbiome

Review: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review – Marcus H. Y. Leung – Microbiome

Review: Use of Homogeneously-Sized Carbon Steel Ball Bearings to Study Microbially-Influenced Corrosion in Oil Field Samples – Gerrit Voordouw – Frontiers in Microbiology

Food microbiology

Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective – Ileana Vigentini – Frontiers in Microbiology

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Bioinformatics

mockrobiota: a public resource for microbiome bioinformatics benchmarking – Nicholas A Bokulich – PeerJ Preprints

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals – Yevgeny Nikolaichik

Techniques

Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics – Linn Sgie – Nature Communications

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly – Christopher Huptas – BMC Research Notes

Microbes in the news

Inner Workings: Ancient teeth reveal clues about microbiome evolution – Jyoti Madhusoodanan – PNAS

Study shows cows on antibiotics produce dung with higher levels of greenhouse gases – DW

May 20, 2016

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Updated microbial census, building healthy gut communities, antibiotics might worsen symptoms in transplant patients, another gut-brain connection, and FiveThirtyEight’s Gut Science week.

Events

Bioinformatics for the Microbiome Symposium at Stanford – Friday, May 27

General microbiology

Status of the Archaeal and Bacterial Census: an Update – Patrick D. Schloss – mBio

Suddenly everyone is a microbiota specialist! – Stefan A. Boers – Clinical Microbiology and Infection

Intricacies of assessing the human microbiome in epidemiologic studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Sepsis in preterm infants causes alterations in mucosal gene expression and microbiota profiles compared to non-septic twins – María Cernada – Scientific Reports

From our lab, Editorial: Gut microbiota: How to build healthy growth-promoting gut communities – David A. Relman – Nature Reviews Gastroenterology & Hepatology

Human oral microbiome

Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting – Luwei Liu – PLOS ONE

Human skin, eye, and ear microbiome (also see under Animal Experiments below)

Microbiology of Middle Ear Infections: Do You Hear What I Hear? – Donna M. Wolk – Clinical Microbiology Newsletter

Review: Impact of Microbiome on Ocular Health – Abirami Kugadas – The Ocular Surface

Human respiratory microbiome

Azithromycin therapy during RSV bronchiolitis: upper airway microbiome alterations and subsequent recurrent wheeze – Yanjiao Zhou – Journal of Allergy and Clinical Immunology

Human urinary tract microbiome

Research Highlight: Stones: Gut microbiome is unique in kidney stone disease – Rebecca Kelsey – Nature Reviews Urology

Human gut microbiome

Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition – Matthieu Million – Scientific Reports

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease – Steven N. Baldassano – Scientific Reports

Hypothesis: Targeting the Ecology Within: The Role of the Gut-Brain Axis and Human Microbiota in Drug Addiction – Patrick D. Skosnik – Medical Hypotheses

Editorial: FMT — enduring strains – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Metabolic Health: The Potential Beneficial Effects of a Medium Chain Triglyceride Diet in Obese Individuals – Sabri Ahmed Rial – MDPI Nutrients

Fecal Microbiota Transplantation

Predictors of Early Failure After Fecal Microbiota Transplantation for the Therapy of Clostridium Difficile Infection: A Multicenter Study – Monika Fischer – The American Journal of Gastroenterology

Animal experiments

Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis – Luisa Möhle – Cell Reports

Gut bacteria influence the birth of new brain cells in mice – Jessica Hamzelou – New Scientist

Editorial: Microbiota Alterations in Inflammatory Bowel Diseases: From Correlation to Causality – Benoit Chassaing – CMGH Cellular and Molecular Gastroenterology and Hepatology

Commentary: Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction – Domenico Santoro – Journal of Investigative Dermatology

Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Plant, root, and soil microbiome

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain) – Gema Bárcenas-Moreno – Science of The Total Environment

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis – Ning Ling – Soil Biology and Biochemistry

Mycorrhiza and heavy metal resistant bacteria enhance growth, nutrient uptake and alter metabolic profile of sorghum grown in marginal soil – Faten Dhawi – Chemosphere

Built environment microbiome

Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures – D. Vázquez-Nion

Pollution and waste microbiology

Microbial diversity and community structure in an antimony-rich tailings dump – Enzong Xiao – Applied Microbiology and Biotechnology

Food microbiology

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, proteomics, metabolomics

An adaptive association test for microbiome data: R package MiSPU – Chong Wu – Genome Medicine

Review: The information science of microbial ecology – Aria S Hahn – Current Opinion in Microbiology

Editorial: Proteomic interrogation of the gut microbiota: potential clinical impact – Sven-Bastiaan Haange – Expert Review of Proteomics

Microbial community metabolic modeling: A community data-driven network reconstruction – Christopher S. Henry – Journal of Cellular Physiology

More microbiology

Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice – Yusuke Shono – Science Translational Medicine

Some antibiotics may worsen complications in transplant patients – Science Daily

Microbes in the news

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker

Everybody Is Constipated, Nobody Is Constipated – Maggie Koerth-Baker

What Your Poop Says About You – Christine Laskowski

Probiotics Won’t Fix All Your Health Problems – Katherine Hobson

What Your Poop Says About You – Christine Laskowski

Is Gut Science Biased? – Anna Maria Barry-Jester

How Your Gut Affects Your Mood – Christie Aschwanden – FiveThirtyEight

Your Mouth Has Bacteria “That Could Grow on Mars,” Says a NASA Scientist – Especially if you had cheese sometime recently – Neel V. Patel – Inverse

Science, publishing, and career

Preprints for the life sciences – Jeremy M. Berg – Science

May 17, 2016

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Live blogging from the Michigan Microbial Meeting, microbiomes of Tibetan macaques and Pika, climate gases from SAR11, mycobiome of stored peanuts, and the deep biosphere.

Events

Ongoing now, with live written coverage: Michigan Meeting ““Unseen Partners: Manipulating Microbial Communities that Support Life on Earth.”

Bioinformatics for the Microbiome Symposium – Stanford Medicine – Friday May 27, 2016

Symposium: With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology – Jan 4-8 2017, New Orleans

General microbiome

Microbiome Data Science: Understanding Our Microbial Planet – Nikos C. Kyrpides – Trends in Microbiology

Animal experiments

Antiviral effect of vitamin A on norovirus infection via modulation of the gut microbiome
Heetae Lee – Scientific Reports

A single gene of a commensal microbe affects host susceptibility to enteric infection – Mi Young Yoon – Nature Communications

Conference abstract: The Impact of Dietary Soy on Gut Microbiome – India R Gill – The FASEB Journal

Animal microbiome

Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana) – Binghua Sun – Scientific Reports

Pika population density is associated with composition and diversity of gut microbiota – Huan Li – Frontiers in Microbiology

Review: The bovine milk microbiota: insights and perspectives from -omics studies – Mol Biosyst

Plant, root, and soil microbiome

Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale – Haichuan Cao – Scientific Reports

Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe – Joseph R. Jenkins – GCB Bioenergy

Biochar as a novel niche for culturing microbial communities in composting – Daquan Sun – Waste Management

Review: Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions –
Hezi Tenenboim – Trends in Plant Science

Temperature sensitivity of soil microbial communities: an application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Biogeosciences

Water and extremophile microbiome

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol – Jing Sun – Nature Microbiology

News coverage: 
Story behind the paper: Climate gases from SAR11 – Stephen Giovannoni – Nature Microbiology Community Blog
Tiny organisms have huge effect on world’s atmosphere – Science Daily

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Depth-dependent and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific – Ryo Kaneko – Journal of Oceanography

Exploring the interaction patterns among taxa and environments from marine metagenomic data – Ze-Gang Wei – Quantitative Biology

Review: Analysis of Low-Biomass Microbial Communities in the Deep Biosphere – Y. Morono – Advances in Applied Microbiology

Undergraduate thesis: Oases of Microbial Life in the Highest Elevation Fumaroles on Earth – Adam Solon – University of Colorado-Boulder

Food microbiology

Variation in fungal microbiome (mycobiome) and aflatoxins during simulated storage of in-shell peanuts and peanut kernels – Fuguo Xing – Scientific Reports

Microbiology of death

Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates – Miguel Iniesto – Scientific Reports

Pollution and waste microbiology

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond – Enzong Xiao – Environmental Pollution

pH modulates arsenic toxicity in Bacillus licheniformis DAS-2 – K. Tripti – Ecotoxicology and Environmental Safety

News coverage: Bacteria discovered to remove arsenic from soil – BK Mishral – Times of India

More microbiology

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice – Stefan O. Reber – PNAS

News coverage: Immunization with bacteria promotes stress resilience, coping behaviors in mice, CU-Boulder study finds – University of Colorado Boulder

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation – Sudip Das – PNAS

Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population – Saurabh R. Gandhi – PNAS

Microbes and art

Creating art with bacteria at New England Biolabs – Jennie Oemig – Wicked Local Beverly

Microbes in the news

Interviewing the Founder of the World #1 Microbiome Investment fund: Isabelle De Cremoux – Labiotech

How Soil Microbes Fight Climate Change – They’re our microscopic allies in making dirt a major resource for storing excess carbon – Esther Ngumbi – Scientific American

Everything You Need to Know About Obama’s New Microbiome Initiative – Tiny organisms. Big budgets. – Kastalia Medrano – Inverse

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker – Five Thirty Eight
What Your Poop Says About You – Christine Laskowski – Five Thirty Eight

FAQ on Microbiology of Built Environments from the American Academy of Microbiology – Jonathan Eisen – MicroBEnet

At A Texas Body Farm, Studying The Decay Of Donated Corpses – Kai Kupferschmidt – World Crunch

Children with and without multiple sclerosis have differences in gut bacteria – EurekAlert

Bathroom Reader: A Brief History of the Toilet – Zack Fediay – uBiome Blog

Linfield Wine Lecture Series: Managing Expectations: The Microbiome in Agriculture – Jack Gilbert – Linfield College

Science, publishing, and career

Point of View: Avoiding a lost generation of scientists – Justin Q Taylor – eLIFE

Twitter won’t count links and photos as part of your 140 characters – Dave Gershgorn – PopSci

Bruno Lemaitre on Science and Narcissism – Leonid Schneider – For Better Science

Screen Shot 2016-05-17 at 10.58AM, May 17.jpg

Illustration by Leonid Schneider

May 14, 2016

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Your weekend microbiome update.

Human Respiratory microbiome

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid – Kentaro Akata – BMC Pulmonary Medicine

The cystic fibrosis lower airways microbial metagenome – Patricia Moran Losada – ERJ Open Research

Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk – Christian Rosas-Salazar – American Journal of Respiratory and Critical Care Medicine

Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry – Jessica A. P. Carlson-Jones – PLOS ONE

Human ear microbiome

MALDI-TOF mass spectrometry reveals a highly complex bacterial profile of otitis media with effusion – Zoltán Papp – International Journal of Pediatric Otorhinolaryngology

Human gut microbiome

Editorial: Heartbeat: The gut microbiota and heart failure – Catherine M Otto – Heart

Editorial: Dietary metabolism, gut microbiota and acute heart failure – WH Wilson Tang – Heart

Trimethylamine N-oxide and prognosis in acute heart failure – Toru Suzuki – Heart

Animal experiments

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium – Ting-Chin David Shen – PLOS ONE

Effects of alternative plant-based feeds on hepatic and gastrointestinal histology and the gastrointestinal microbiome of sablefish (Anoplopoma fimbria) – Linda D. Rhodes – Aquaculture

Addendum: Rebooting the Microbiome – Sean Munoz – Gut Microbes

Typos, horrible experiment, and controversial findings. Proceed with care: An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Rabindra K. Mandal – Scientific Reports

Animal microbiome

Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits – Yuliaxis Ramayo-Caldas – The ISME Journal

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) – Genevieve Bennett – American Journal of Primatology

Jellyfish: Aurelia aurita ephyrae reshape a coastal microbial community – Luca Zoccarato – Frontiers in Microbiology

Mosquito C-type lectins maintain gut microbiome homeostasis – Xiaojing Pang – Nature Microbiology

Plant, root, and soil microbiome

D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria – Atanas D Radkov – Microbes and Environments

MycoDB, a global database of plant response to mycorrhizal fungi – V. Bala Chaudhary – Scientific Data

Effects of soil substrate quality, microbial diversity and community composition on the plant community during primary succession – Jan Frouz – Soil Biology and Biochemistry

Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics – Chuanyu Yang – PLOS ONE

Fire-severity effects on plant–fungal interactions after a novel tundra wildfire disturbance: implications for arctic shrub and tree migration – Rebecca E. Hewitt – BMC Ecology

Water and extremophile microbiome

The symbiotic relationship of sediment and biofilm dynamics at the sediment water interface of oil sands industrial tailings ponds – T. Reid – Water Research

Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough – Taiki Katayama – FEMS Microbiology Ecology

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions – Sergei V. Bukin – Frontiers in Microbiology

The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale – Zhang, Binglin – Environmental Research Letters

Microbial dynamics of the extreme-thermophilic (70 °C) mixed culture for hydrogen production in a chemostat – Fang Zhang – International Journal of Hydrogen Energy

Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles – Fumito Shiraishi – Earth and Planetary Science Letters

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Biofilm transplantation in the deep sea – Irene Wagner-Döbler – Molecular Ecology

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting – Weipeng Zhang – Molecular Ecology

Food microbiology

Composition and function of sourdough microbiota: From ecological theory to bread quality – Michael Gänzle – International Journal of Food Microbiology

Comparison of DNA-based techniques for differentiation of production strains of ale and lager brewing yeast – J. Kopecká – Journal of Applied Microbiology

Infection microbiology

Review: Polymicrobial-Host Interactions During Infection – Hong Tay Wei – Journal of Molecular Biology

Bioinformatics and metagenomics

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology – Jesús A. Ballesteros – Molecular Biology and Evolution

Evaluating techniques for metagenome annotation using simulated sequence data (CC) – Richard J. Randle-Boggis – FEMS Microbiology Ecology

Computational methods for predicting genomic islands in microbial genomes – Bingxin Lu – Computational and Structural Biotechnology Journal

Microbial ecology

Quorum Sensing Communication Modules for Microbial Consortia – Spencer R. Scott – ACS Synthetic Biology

Ecological Opportunity, Evolution, and the Emergence of Flea-borne Plague – B. Joseph Hinnebusch – Infection and Immunity

Microbes in the news

NOAA Research on Microbial Communities Contributes to National Microbiome Initiative – Edward Pritchard – NOAA

Parasites Influence Makeup of Human Gut Microbiome, BoG Speaker Reports – GenomeWeb

May 2, 2016

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Pregnancy and birth

Review: Impact of early gut microbiota on immune and metabolic development and function – Mei Wang – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics –
Saswat Mishra – Biosensors and Bioelectronics

Human gut microbiome

Underlying molecular and cellular mechanisms in childhood irritable bowel syndrome – Bruno P. Chumpitazi – Molecular and Cellular Pediatrics

Plant, root, and soil microbiome

Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs – J.M. Rinta-Kanto – FEMS Microbiology Ecology

Built environment microbiome

Ciprofloxacin residue and antibiotic-resistant biofilm bacteria in hospital effluent – Jérôme Ory – Environmental Pollution

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Pollution and waste microbiology

Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge – Hajer Ennouri – Bioresource Technology

Food microbiology

Microbiological characterisation and volatiles profile of model, ex-novo, and traditional Italian white wheat sourdoughs – Valery Ripari – Food Chemistry

Microbes in the news

PTSD could be prevented with gut microbes, study suggests – Catharine Paddock – Medical News Today

3 years, 3 countries, 222 children: Big gut data tracks impact of hygiene on microbiome – Will Chu – Nutraingredients

Debunking “microbiome causes autism” myths – Exposing Autism One

DNA Genotek’s microbiome collection and stabilization blog. Advancing microbiome discoveries: An update on our grant winners – Megan McGrath – DNA Genotek

SCSU students present antibiotic research on Capitol Hill – Brian Zahn – New Haven Register

Mumbai: Microbiology students create trim almond truffle – Phorum Dalal – Mid Day

Students get a close up view on microbiology. Presentation demonstrated how bacteria plays a role in everyday life – Carolyn Blackburne – Your 4 State

Enlightening the World of Five-Year-Olds: Hand Washing Activity Shines Light on Germs – University of South Carolina Upstate

Using the microbiome to predict risk of infection following chemotherapy – Emmanuel Montassier & Dan Knights – BioMed Central Blog

Novel, bacteria-repelling biomaterial could increase the success of medical implants – Science Daily

Scientists reveal the secret of antibiotic-resistant bacteria – Phys.org

Citizen-scientists to help swimmers ID bacteria-filled lakes – The Eagle

Science, publishing, and career

This hilarious Twitter account uses Lego to show the realities of academia – Jacinta Bowler – Science Alert

Image Manipulation: Cleaning Up the Scholarly Record – Phil Davis – The Scholarly Kitchen

Bacteria in state’s drinking water is ‘public health crisis’ – Gazette Extra
Bik’s Picks

Five Small Animals That Messed With Big Science – Victoria Jaggard – National Geographic

May 1, 2016

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Events

Bioinformatics for the Microbiome – Stanford Center for Genomics and Personalized Medicine – May 27, 2016

General microbiome

Microbiome sequencing: challenges and opportunities for molecular medicine – Thomas Clavel – Expert Review of Molecular Diagnostics

Human skin microbiome

An In vitro Model for Bacterial Growth on Human Stratum Corneum – Danique A. van der Krieken – Acta Dermato-Venereologica

Human respiratory microbiome

Launching into the Deep: Does the Pulmonary Microbiota Promote Chronic Lung Inflammation and Chronic Obstructive Pulmonary Disease Pathogenesis? – Marc A. Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Targeting the gut to protect the bladder: Oral Phage therapy approaches against urinary Escherichia coli infections? – Harald Brüssow – Environmental Microbiology

Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease – Takuo Emoto – Heart and Vessels

Review: Gut microbiota: an Indicator to Gastrointestinal Tract Diseases – Trupti Patel – Journal of Gastrointestinal Cancer

Review: Gut microbiome and kidney disease: a bidirectional relationship – Souhaila Al Khodor – Pediatric Nephrology

Animal models

Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice – Jin Li – Circulation

The effects of maternal and post-weaning diet on gut microbiota and glucose metabolism in mice offspring – Jia Zheng – Bioscience Reports

Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota – Brittany E. Harlow – PLOS ONE

Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows – Marija Kaevska – Canadian Journal of Microbiology

Molecular exploration of fecal microbiome in quinoa-supplemented obese mice – Jose F. Garcia-Mazcorro – FEMS Microbiology Ecology

Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice – Lovisa Heyman-Lindén – Food and Nutrition Research

The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems – Victor Schmidt – Applied and Environmental Microbiology

Insights into the biodiversity of the gut microbiota of broiler chickens – Leonardo Mancabelli – Environmental Microbiology

Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups – Wilma T. Steegenga – Molecular Nutrition & Food Research

Animal microbiome

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan- Environmental Microbiology

Global microbialization of coral reefs – Andreas F. Haas – Nature Microbiology

Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria – Jan Hubert – Microbial Ecology

Review: Diagnosis and interpretation of intestinal dysbiosis in dogs and cats – Jan Suchodolski – The Veterinary Journal

Plant, root, and soil microbiome

Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea – Margrét Auður Sigurbjörnsdóttir – FEMS Microbiology Ecology

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites – Frederic Mahe – bioRxiv

Edaphic properties override the influence of crops on the composition of the soil bacterial community in a semiarid agroecosystem – Luke D. Bainard – Applied Soil Ecology

Effects of land use change on the composition of soil microbial communities in a managed subtropical forest – Xiaoping Guo – Forest Ecology and Management

Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach – Nathaniel A. Lyngwi – PLOS ONE

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems – Ian R Sanders – The ISME Journal

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter – Thea Whitman – The ISME Journal

Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa – I. Moroenyane – Microbial Ecology

Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance – Cécile E. Thion – FEMS Microbiology Ecology

Ecological restoration alters microbial communities in mine tailings profiles – Yang Li – Scientific Reports

Water and extremophile microbiome

Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton – Mathias Milici – Frontiers in Microbiology

Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench – Jonathan Tarn – Frontiers in Microbiology

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? – Mario Moreno-Pino – FEMS Microbiology Ecology

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring – Zhou Jiang – Scientific Reports

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – J. Goordial – Environmental Microbiology

Built environment microbiome

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Food microbiology

Overlap of spoilage microbiota between meat and meat processing environment in small-scale vs large-scale retail distribution – Giuseppina Stellato – Applied and Environmental Microbiology

Fermentative capabilities and volatile compounds produced by Kloeckera/Hanseniaspora and Saccharomyces yeast strains in pure and mixed cultures during Agave tequilana juice fermentation – Ivonne Wendolyne González-Robles – Antonie van Leeuwenhoek

Pollution and waste microbiology

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater – Scientific Reports – You-Wei Cui

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.– Alejandro Palomo – The ISME Journal

Bioinformatics and metagenomics

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2 – Johan Bengtsson-Palme – Ecological Informatics

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data – Mohamed Mysara – BMC Bioinformatics

Minireview: Tracking strains in the microbiome: insights from metagenomics and models – Ilana L. Brito – Frontiers in Microbiology

Viruses and phages

Review: Endogenized viral sequences in mammals – Nicholas F. Parrish – Current Opinion in Microbiology

Probiotics

Probiotic Cream: Viability of Probiotic Bacteria and Chemical Characterization – Lutfiye Yilmaz-Ersan – Journal of Food Processing and Preservation

Transcriptomics

Use of Metatranscriptomics in Microbiome Research – Stavros Bashiardes – Bioinform Biol Insights

More microbiology

Complex molecular mixtures under cycling gradients as basis for lifes origins – Bert Poolman – bioRxiv

Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ – Laura Villanueva – Environmental Microbiology

Review: Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits – Kai Hillman – Current Opinion in Microbiology

Microbes in the news

Findings from the Gut—New Insights into the Human Microbiome – Karen Weintraub – Scientific American

What our gut tells us about the ‘hygiene hypothesis’ – Veronica Meade-Kelly – MedicalXpress

Russian scientists prove Antarctic bacteria brought from other continents – TASS

Beer made from belly button fluff has a bit of the brewer in every glass – Jenni Ryal – Mashable @7centBrewery

Yep, This Brewery Makes Beer Using Bacteria From People’s Belly Buttons: “7 cent Brewery” – Alec MacDonald – Elite Daily

Bacteria from Burning Tree mastodon survived 13,000 years – Laura Arenschield – Dispatch

Echo Bay woman caught harvesting bacteria at gardening event – Jeff Klassen – Soo Today

Weakened coral reefs are facing the threat of algae colonisation – Kemal Atlay – SBS Australia

Junk Food Is Bad For Plants, Too – How a steady diet of fertilizers has turned crops into couch potatoes – Anne Biklé and David R. Montgomery – Nautilus

From running shoes to carbon sinks: four surprising uses for algae – ABC Future Tense

Science, publishing, and career

“Everyone” Downloads Research Papers Illegally – Science magazine just published a great piece on the utility of Sci-Hub. Unfortunately, its defense of its own business model is flawed – Justin Peters – Slate

April 28, 2016

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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: Screen Shot 2016-04-28 at 12.42PM, Apr 28 1.jpg

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

Bacteria beneficial to plants have spread across California – UC Riverside study shows spread of Bradyrhizobium has important implications for biofertilizers – EurekAlert

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

April 24, 2016

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Effect of gluten-free diet, broad and accurate taxonomic resolution with multiple genes, ice-nucleating bacteria, indoor bacteria, fungi, and archaea.

Human oral microbiome

Changes in the Oral Moisture and the Amount of Microorganisms in Saliva and Tongue Coating after Oral Ingestion Resumption: A Pilot Study -Natsuki Kishimoto – The Open Dentistry Journal

Human gut microbiome

The influence of a short-term gluten-free diet on the human gut microbiome – Marc Jan Bonder – Genome Medicine

Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study – C. J. Stewart – Diabetic Medicine

The Influence of Prebiotic Arabinoxylan Oligosaccharides on Microbiota Derived Uremic Retention Solutes in Patients with Chronic Kidney Disease: A Randomized Controlled Trial – Ruben Poesen – PLOS ONE

Minireview: Human microbiome versus food-borne pathogens: friend or foe – Jonathan Josephs-Spaulding – Applied Microbiology and Biotechnology

Opinion: Strain-level dissection of the contribution of the gut microbiome to human metabolic disease – Chenhong Zhang – Genome Medicine

Review: Impact of the gut microbiota on inflammation, obesity, and metabolic disease – Claire L. Boulangé – Genome Medicine

Review: Translational aspects of the microbiome—to be exploited – Edit Mikó – Cell Biology and Toxicology

Animal models

Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats – Frank A Duca – Diabetes

Gene expression of Lactobacillus plantarum and the commensal microbiota in the ileum of healthy and early SIV-infected rhesus macaques – Benjamin L. Golomb – Scientific Reports

Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet – Sonja N. Heinritz – PLOS ONE

Plant, root, and soil microbiome

(also filed under New Techniques below) New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Detection of plant growth enhancing features in psychrotolerant yeasts from Patagonia (Argentina) – María Cecilia Mestre – Journal of Basic Microbiology

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community – John M Gladden – Biofuels

Soil biochar amendment shapes the composition of N2O-reducing microbial communities – Johannes Hartera – Science of the Total Environment

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau – Yong Zhang – Science of the Total Environment

Water and extremophile microbiome

Ice-nucleating bacteria control the order and dynamics of interfacial water – Ravindra Pandey – Science Advances

Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties – Anas Abdulaziz – Journal of Basic Microbiology

Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities – Yuya Nakamura – Applied Microbiology and Biotechnology

Evidence of adaptation, niche separation and microevolution within the genus Polaromonas on Arctic and Antarctic glacial surfaces – Jan Gawor – Extremophiles

Built environment microbiology

Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants – Fabian Weikl – PLOS ONE

Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics – Sepideh Pakpour – Microbial Ecology

Food microbiology

Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii subsp. Bulgaricus – Kim I. Sørensen – Applied and Environmental Microbiology

Microbiota of an Italian Grana like cheese during manufacture and ripening unraveled by 16S rRNA-based approaches – Valentina Alessandria – Applied and Environmental Microbiology

Taxonomy, new techniques, bioinformatics

New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes – Gregorio Iraola – bioRxiv

Reviews: Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents – Scott F. Gilbert – Nature Reviews Genetics

Microbes in the news

How the world’s chillest bacteria make ice. They may be responsible for creating clouds and rain – Alessandra Potenza – The Verge

How The Bacteria In Your Gut Could Be Used To Treat Mental Illness. New research finds that altering gut bacteria in mice changes the way their brains work – Carolyn Gregoire – Huffington Post

Five ‘fake’ water firms in Mombasa shut after tests confirm bacteria – Elkana Jacob – The Star Kenya

Investigators reduce sugar content of yogurt without reducing sweetness: using microbiological methods that predate the era of genetic technologies – Science Daily

How Toronto’s germs are different from those in other cities. New study reveals each community has its own unique blend of fungi and bacteria — a microbial signature – Robin Levinson King – The Star

Microbes and art

Living Art: Meet the Woman Making Sculptures With Bacteria from Her Skin, UK-based artist Mellissa Fisher – Stephanie Leke – Broadly The Vice

April 23, 2016

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Pint of Science, oral microbiome dynamics, rheumatoid arthritis, mineral turnover in the rhizosphere, and the subzero microbiome.

Events

Pint of Science San Francisco Bay Area (also in other cities all over the world): 23-25 May 2016, combining beer and science

Pregnancy and birth

Microbiome and Fetus: A Relationship for Life – Janet Teodori – Journal of Prenatal & Perinatal Psychology & Health

The Tree(s) of Life: The Human Placenta and My Journey to Learn More about It – Carolyn B. Coyne – PLOS Pathogens

Human oral microbiome

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome – Niklas Grassl – Genome Biology

Human vaginal microbiome

Effects of low dose estrogen therapy on the vaginal microbiomes of women with atrophic vaginitis – Jian Shen – Scientific Reports

Human gut microbiome

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients – Tossawan Jitwasinkul – Journal of Global Antimicrobial Resistance

Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease – Jun Shimizu – PLOS ONE

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis – Jun Chen – Genome Medicine

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. Nov. – Khelaifia Saber – OMICS

Review: Bugging inflammation: role of the gut microbiota – Sj Shen – Clinical & Translational Immunology

Review: Modulating Composition and Metabolic Activity of the Gut Microbiota in IBD Patients – Mario Matijašić – MDPI Int J Mol Sci

Animal models

Effect of Dietary Carboxymethyllysine on glucose and insulin sensitivity, cecal fatty acids and the plasma metabolome in mice fed the Total Western Diet – Robert Edwin Ward – The FASEB Journal

Animal microbiome

The Microbiome of Animals: Implications for Conservation Biology – Simon Bahrndorff – International Journal of Genomics

Review: Herbivore dung as food for dung beetles: elementary coprology for entomologists – Peter Holter – Ecological Entomology

Plant, root, and soil microbiome

Plant–Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere – R. Alegria Terrazas – Advances in Applied Microbiology

Dynamics of endophytic bacteria in plant in vitro culture: quantification of three bacterial strains in Prunus avium in different plant organs and in vitro culture phases – Mona Quambusch – Plant Cell, Tissue and Organ Culture (PCTOC)

Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils – Mengmeng Wang – Plant and Soil

Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings – Silvia Gschwendtner – Plant and Soil

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community – Ana Mellado – New Phytologist

Rhizosphere priming effect on soil organic carbon decomposition under plant species differing in soil acidification and root exudation – Xiaojuan Wang – New Phytologist

Water and extremophile microbiome

Viral metabolic reprogramming in marine ecosystems – Bonnie L Hurwitz – Current Opinion in Microbiology

Review: The subzero microbiome: Microbial activity in frozen and thawing soils – Mrinalini P. Nikrad – FEMS Microbiology Ecology

Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins – Virginia P Edgcomb – The ISME Journal

Waste and pollution microbiology

Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge – Hajer Ennouri – Bioresource Technology

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters – Stefano Fazi – Microbial Ecology

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms – Yunhua Xiao – Applied Microbiology and Biotechnology

Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments – S. Jane Fowler – Frontiers in Microbiology

Food microbiology

The Potential of the Incorporation of Essential Oils and Their Individual Constituents to Improve Microbial Safety in Juices: A Review – Evandro Leite de Souza – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics and metagenomics

The Metagenomic Pizza: a simple recipe to introduce bioinformatics to the layman – Marie-Claude Blatter – EMBnet

MOCAT2: a metagenomic assembly, annotation and profiling framework – Jens Roat Kultima – Bioinformatics

Temporal microbiome road-maps guided by perturbations – Beatriz García-Jiménez – bioRxiv

Fundamental Limits of Pooled-DNA Sequencing – A. Najafi – ArXiv

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity – Nam-Phuong Nguyen – NPJ Biofilms

Microbial Ecology

Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

Viruses and phages

Giant viruses at the core of microscopic wars with global impacts – Adrien Villai – Current Opinion in Virology

Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction – V Furtak – Eurosurveillance

Metabolomics

Review: Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions – Linda S. Zhang – Genome Medicine

Microbes in the news

Your office is a veritable petri dish of bacteria – Sarah Kaplan – The Washington Post

We’re home to trillions of cells that aren’t ours and they’re keeping us alive – Katherine Ellen Foley – Quartz

These oral bacteria are linked to an increased chance of getting pancreatic cancer – Laurie McGinley – The Washington Post