Category Archives: Metagenomics & Bioinformatics

May 21, 2016

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Helminths positively associated with allergy, baboon vaginal microbiome, nitrogen fixation in poplar trees, boreal lakes as analogues for the Archaean ocean, and PERMANOVA-S as alternative for weighted Unifrac.

Events

2016 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting and Exhibition – July 24-30, New Orleans, LA

General
Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science – Steven J. Hallam – Current Opinion in Microbiology

Human oral microbiome

Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodontally healthy young adults – Florence Carrouel – Frontiers in Microbiology

Species level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population – Nezar Noor Al-hebshi – Journal of Oral Microbiology

Review: Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria – S. Sukumar – Journal of Dental Research

Human gut microbiome

Helminths are positively associated with atopy and wheeze in Ugandan fishing communities: results from a cross-sectional survey – E. L. Webb – Allergy

Stool frequency is associated with gut microbiota composition – Fatemeh Hadizadeh – Gut

The gut-adherent microbiota of PSC–IBD is distinct to that of IBD – Mohammed Nabil Quraishi – Gut

Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas– Yingying Lu – Scientific Reports

Haloferax massiliensis sp. nov., the first human-associated halophilic archaea – Saber Khelaifia – New Microbes and New Infections

Review: The influence of commensal and pathogenic gut microbiota on prion disease pathogenesis – David S. Donaldson – Journal of General Virology

Animal experiments

Effect of Dietary Fibers on Cecal Microbiota and Intestinal Tumorigenesis in Azoxymethane Treated A/J Min/+ Mice – Birgitte Moen – PLOS ONE

Food-grade antimicrobial ɛ-polylysine transiently perturbs the structure of the murine gut microbiome – Xiaomeng You – The FASEB Journal

Animal microbiome

Baboon vaginal microbial flora – Jael A. Obiero – Journal of Medical Primatology

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle – Arfan Abrar – Animal Science Journal

Dietary-driven variation effects on the symbiotic flagellate protist communities of the subterranean termite Reticulitermes grassei Clément – S. Duarte – Journal of Applied Entomology

Plant, root, and soil microbiome

Variable Nitrogen Fixation in Wild Populus – Sharon L. Doty – PLOS ONE

Press: Bacteria in branches naturally fertilize trees – Michelle Ma – University of Washington

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – GigaScience

Conference abstract: Microbial communities associated with the biotransformation potential of insensitive explosives in surface soils – F. Crocker – 2016 SIMB Annual Meeting and Exhibition

Water and extremophile microbiome

Millions of Boreal Shield Lakes can be used to Probe the Evolution of Archaean Ocean Life – Sherry Schiff – bioRxiv

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution – Beatriz Díez – PLOS ONE

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms – Daniel S Jones – ISME Journal

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage – Sara Billerbeck – Nature Microbiology

Drinking water, waste and pollution microbiology

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions – Yingyu Law – Scientific Reports

Conference abstract: Microbial survival in drinking water systems – A. Pinto – 2016 SIMB Annual Meeting and Exhibition

Bioinformatics

PERMANOVA-S: Association test for microbial community composition that accommodates confounders and multiple distances – Zheng-Zheng Tang – Bioinformatics

More microbiology

ppGpp couples transcription to DNA repair in E. coli – Venu Kamarthapu – Science

Press: Factor preserves DNA integrity in bacteria despite assault from antibiotics – Science Daily
Spatial organization shapes the turnover of a bacterial transcriptome – Jeffrey R Moffitt – eLIFE

The Small World Initiative™: An Innovative Crowdsourcing Platform for Antibiotics – Ana Maria Barral – The FASEB Journal

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities – Yinghua Zha – PLOS ONE

Microbes in the news

Featuring my work (but not my quotes): The inner lives of dolphins – Marine mammals carry an unexpected microbial mix – Steve Fyffe – Stanford Medicine Magazine

About Stanley Falkow and Denise Monack: Microbe mentoring: The recipe for success includes independence, a gentle shove and a good stiff drink – Kathy Zonana – Stanford Medicine Magazine

President Obama Awards the National Medals of Science & Technology and Innovation. Stanford Professor of Microbiology Stanley Falkow get his award at 11:30 min in this video.

Students are developing bacteria that eat plastic polluting our oceans. Om nom. – Josh Hrala – Science Alert

A Comprehensive Survey of Preclinical Microbiology Curricula Among US Medical Schools – Dora J. Melber – Clinical Infectious Diseases

University Of California, San Diego Invests $12 Million In Its Own Microbiome Research Efforts! – Vinny – University Herald

Bik’s Picks

Striking Immune Phenotypes in Gene-Targeted Mice Are Driven by a Copy-Number Variant Originating from a Commercially Available C57BL/6 Strain – Vinay S. Mahajan

Press: Immune Defect Detected in Knockout Mice – Tanya Lewis – The Scientist

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 19, 2016

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Two papers on triclosan effects, genome reduction in a common soil bacterium, spatial patterns of ocean microbes, and deep sequencing in unexplained fever cases.

Triclosan and microbiome

Two very different papers about the effect of triclosan on the microbiome:

Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome – Angela C. Poole – mSphere

Antimicrobial in Common Toothpaste Doesn’t Impact Gut, Oral Microbiome – ASM

but:

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A. Gaulke – PLOS ONE

The Case Against Antibacterial Soap Is Getting Stronger – Alexandra Sifferlin – Time

Human oral microbiome

Undergraduate thesis: Exploring a possible correlation between the human oral microbiome and body mass index – Ivy S. McDermot – University of Colorado Boulder

Human gut microbiome

Irritable Bowel Syndrome special in Nature: 
Irritable bowel syndrome – Michelle Grayson
Microbiome: Bacterial broadband – Michael Eisenstein

HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases – Sergio Serrano-Villar – Scientific Reports

Review: The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni – Therapeutic Advances in Gastroenterology

Animal experiments

Microbiome-metabolome responses in the cecum and colon of pig to a high resistant starch diet – Yue Sun – Frontiers in Microbiology

Animal microbiome

Characterisation of the bacterial community structures in the intestine of Lampetra morii – Yingying Li – Antonie van Leeuwenhoek

Review: Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications – R.M. Stumpf – Biological Conservation

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterial lineage – Tess Brewer – bioRxiv

Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla – Yong-Po Zhao – Scientific Reports

Review: Microbial inoculation of seed for improved crop performance: issues and opportunities – Maureen O’Callaghan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean – Nyree J. West – Frontiers in Microbiology

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat – Erik C. L. Trampe – Frontiers in Microbiology

Waste and pollution microbiology

Diversity of ammonia-oxidizing bacteria and archaea in response to different aeration rates during cattle manure composting – Lei Yan – Ecological Engineering

Microbes and infection

Deep sequencing approach for investigating infectious agents causing fever – T. N. Susilawati – European Journal of Clinical Microbiology & Infectious Diseases

Metagenomics and bioinformatics

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data – Eric Z. Chen – Bioinformatics

Review: Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis – Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan – Evolutionary Bioinformatics

More microbiology

Structure of the T4 baseplate and its function in triggering sheath contraction – Nicholas M. I. Taylor – Nature

How viruses infect bacteria: A tale of a tail – EurekAlert

A platform for the discovery of new macrolide antibiotics – Ian B. Seiple – Nature

Microbes in the news

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters
University of South Florida Scientists Discover Antarctic Sponge Extract Can Help Kill MRSA – University of South Florida
Arctic Sponge Extract May Be Potent Against MRSA – Xuan Pham – Lab Roots

These bacteria are all over your wallet and smartphone
“Due to rising temperatures, we will NOT be accepting boob or sock money.” – Maria Lamagna – MarketWatch

Tampa Bay: Bacteria threatens Bay Area palm trees #Phytoplasma

Panda poop study provides insights into microbiome, reproductive troubles – EurekAlert

Indian gut similar to Bangladeshis, omnivorous animals, claims study
We acquire them from our mothers during birth, pass on to us through the breast milk and live with us till we die – Anuradha Mascarehnas – Indian Express

Science, publishing, and career

Ecology: The sea-otter whisperer – Jane Lubchenco – Nature

Bik’s Picks

MinION in space: Virologist Kate Rubins is set to make history as the first person to sequence DNA in space – Frontline Genomics

With lighting by my husband’s company Xicato: Arts: California on camera. The re-opening of the San Francisco Museum of Modern Art – John Gilbey – Nature

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 13, 2016

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Today brought us great news from the White House Office of Science and Technology Policy (OSTP): the National Microbiome Initiative (NMI). Look on Twitter for our tweets tagged with #NMI.

National Microbiome Initiative and news coverage

Fact Sheet: Announcing the National Microbiome Initiative – The White House Office of Science and Technology Policy

Microbes shape our world – and a new White House initiative will figure out how – Rachel Feltman – The Washington Post

Obama administration to launch microbiome initiative, heeding scientists’ calls – David Nather – STAT News

The White House Launches the National Microbiome Initiative: Half a billion dollars are being pledged to study the microbes in humans, crops, soils, oceans, and more – Ed Yong – The Atlantic

Pleasantly surprised by the National Microbiome Initiative – Jonathan Eisen – The Tree of Life

New microbiome center to combine UChicago, Marine Biological Laboratory, Argonne expertise – EurekAlert

Events

Bioinformatics for the Microbiome – Stanford – Friday May 27th, with talks by Rob Knight, Ami Bhatt, Susan Holmes, Tomer Altman, Justin Sonnenberg, Sharon Greenblum, Ben Callahan and more.

Pint of Science Festival, May 23-25, San Francisco: Science talks in the finest watering holes of the Bay Area. Several microbiology talks!

Time is Running Out for “Culture as Medium” exhibit at Baltimore Under Ground Science Space (BUGSS) – Anne M. Estes – Mostly Microbes

Festival of Genomics – 27-29 June 2016 Boston

General microbiome

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges – Martin J. Blaser – mBio

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis – Marco Fondi – Genome Biology and Evolution

Pregnancy and birth

News: Antibiotics, gut bugs and the young – Hilary Browne – Nature Reviews Microbiology

Human skin microbiome

Cross your legs before reading this one: Genital anaerobic bacterial overgrowth and the PrePex male circumcision device, Rakai, Uganda – Cindy M. Liu -The Journal of Infectious Diseases

Human gut microbiome

Gut microbiota in early pediatric multiple sclerosis: a case−control study – H. Tremlett – European Journal of Neurology

Review: Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle – Christopher M. Jakobson – PLOS Pathogens

Plant, root, and soil microbiome

The Sphagnum microbiome: new insights from an ancient plant lineage – Joel E. Kostka – New Phytologist

Bioinformatics and metagenomics

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R – Timothy G. Stephens – PeerJ

Microbes in the news
Is a Disrupted Gut Microbiome at the Root of Modern Disease?—with Dr. Justin Sonnenburg – Chris Kresser – Revolution Health Radio

Fatal attachment: How pathogenic bacteria hang on to mucosa and avoid exfoliation – EurekAlert

This MIT professor is using bee poop to map an invisible world – Melia Robinson – TechInsider

Microbes and art

ASM Agar Art 2016 People’s Choice voting – vote for the best contribution.

Science, publishing, and career

Top Medical Journals Give Women Researchers Short Shrift – Lauren Silverman – NPR

May 11, 2016

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Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

May 10, 2016, 2nd edition

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Nitrate and oral microcosms, microbial tryptophan metabolism effects on astrocytes, creating germ free plants, a systematic review of the (lack of) effect of probiotics on the gut microbiome, and a phage/host prediction tool.

Event

Starts today: Food-Microbiome Interaction: Implications for Health & Disease – New York Academy of Sciences and the Quadram Institute at The Royal Society in London

Pregnancy and birth

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood – J. Metsälä – Clinical & Experimental Allergy

Review: Obesity and overweight: Impact on maternal and milk microbiome and their role for infant health and nutrition – Izaskun Garcia-Mantrana – Molecular Nutrition and Food Research

Human respiratory microbiome

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities – Marcos Pérez-Losada – AIMS Microbiology

Human oral microbiome

Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms – Jessica E. Koopman – Microbial Ecology

Human skin microbiome

A systematic review and meta-analysis on Staphylococcus aureus carriage in psoriasis, acne and rosacea – J. E. E. Totté – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups – Deepak Yadav – Gut Pathogens

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials – Nadja B. Kristensen – Genome Medicine

Tissue Microbiome Profiling Identifies An Enrichment of Specific Enteric Bacteria In Opisthorchis viverrini Associated Cholangiocarcinoma – Kern Rei Chng – EBioMedicine

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

Review: Could physical exercise help modulate the gut microbiota in chronic kidney disease? – Marta Esgalhado – Future Microbiology

Review: The Gut Microbiota and Immune System Relationship in Human Graft-versus-Host Disease – Lucrezia Laterza – Mediterranean Journal of Hematology and Infectious Diseases

Review: Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions? – David Endesfelder – Current Diabetes Reports

Animal experiments

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions – Alejandro Salgado-Flores – PLOS ONE

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants – Sheerli Kruger Ben Shabat – The ISME Journal

Book Chapter: Germ-Free Mice Model for Studying Host–Microbial Interactions – Yogesh Bhattarai – Mouse Models for Drug Discovery – Springer

Animal microbiome

Review: Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds – Anak Agung Gede Indraningrat – Marine Drugs

Plant, root, and soil microbiome

Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes – Rebekah J. Robinson – Scientific Reports

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils – Jean-Baptiste Ramond – Journal of Basic Microbiology

Plants of the Fynbos biome harbour host species-specific bacterial communities – Tsakani Miyambo – FEMS Microbiology Letters

Extremophile microbiome

In situ hydrogen dynamics in a hot spring microbial mat during a diel cycle – Niels Peter Revsbech – Applied and Environmental Microbiology

Metabolomics

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor – Veit Rothhammer – Nature Medicine

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands – Bruno Lamas – Nature Medicine

Review: Urolithins, the rescue of ‘old’ metabolites to understand a ‘new’ concept: metabotypes as a nexus between phenolic metabolism, microbiota dysbiosis and host health status – Francisco A. Tomás-Barberán – Molecular Nutrition & Food Research

Metagenomics and bioinformatics –

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – J. A. Frank – Scientific Reports

OrfM: A fast open reading frame predictor for metagenomic data – Ben J. Woodcroft – Bioinformatics

Phages and viruses

HostPhinder: A Phage Host Prediction Tool – Julia Villarroel – MDPI Viruses

More microbiology

Nonclinical Safety Assessment of SYN-004: An Oral β-lactamase for the Protection of the Gut Microbiome From Disruption by Biliary-Excreted, Intravenously Administered Antibiotics – John F. Kokai-Kun – International Journal of Toxicology

Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system – Ki Soo Park – Science Advances

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans – Narasimha Anaganti – Journal of Biosciences

Microbes in the news

Stool Bank OpenBiome Is Expanding to Somerville. The bank wants more Boston-area residents to donate – Jamie Ducharme

Do probiotics have an effect on healthy adults? It’s too early to tell – EurekAlert

The Microbiome in Pediatric Rheumatic Diseases – Matthew Stoll – The Rheumatologist

May 7, 2016

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Drosophila male-killing spiroplasma, chitin in potting soil, temperature constraints for complex life, a book on microbial diversity, and monitoring sewer health.

General microbiome

Review: Design, analysis and application of synthetic microbial consortia – Xiaoqiang Jia – Synthetic and Systems Biotechnology

Review: Metabolic network modeling of microbial interactions in natural and engineered environmental systems – Octavio Perez-Garcia – Frontiers in Microbiology

Opinion: Mirror, mirror on the wall: which microbiomes will help heal them all? – Renuka R. Nayak – BMC Medicine

Hypothesis: Do microbiotas warm their hosts? – Eugene Rosenberg – Gut Microbes

Human respiratory microbiome

Microbiome diversity in the sputum of patients with pulmonary tuberculosis – P. Krishna – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Literature review: The gut microbiota: a major player in the toxicity of environmental pollutants? – Sandrine P Claus – NPJ Biofilms and Microbiomes

Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study – Zoltan Pataky – Digestive Diseases and Sciences

n=1: Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report – Bumjo Oh – Clinical Nutrition Research

Conference abstract: Associations Between Physical Activity and the Intestinal Microbiome of College Freshmen – Corrie M Whisner – The FASEB Journal

Animal experiments

Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis – Becky Cheng – Current Biology

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities – Kevin D. Kohl – Frontiers in Microbiology

Conference abstract: Soy positively impacts cecal microbiota of ovariectomized rats selectively bred for low aerobic capacity – Tzu-Wen Liu – the FASEB Journal

Animal microbiome

Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response – Jianhua Zhang – PLOS ONE

Plants, roots, and soil microbiome

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology – Jane Debode – Frontiers in Microbiology

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semiarid woodland in Patagonia, Argentina – Paula Berenstecher – Functional Ecology

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China – Jianli Ding – Applied Soil Ecology

Conference abstract: Multi-omics of the Soil Microbiome – Janet K Jansson – The FASEB Journal

Review: Life cycle specialization of filamentous pathogens — colonization and reproduction in plant tissues – Janine Haueisen – Current Opinion in Microbiology

Review: Interspecific hybridization impacts host range and pathogenicity of filamentous microbes – Jasper RL Depotter – Current Opinion in Microbiology

Water and extremophile microbiome

From climate models to planetary habitability: temperature constraints for complex life – Laura Silva – arXiv preprint

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems – Roberto Danovaro – Science Advances

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer – Robert Danczak – Frontiers in Earth Science

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

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling – Kenneth Wasmund – mBio

Book: Their World: A Diversity of Microbial Environments – Editors: Christon J. Hurst – Springer

Review: Marine microorganisms as a promising and sustainable source of bioactive molecules – G. Romano – Marine Environmental Research

Waste and pollution microbiology

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed – Elliott P. Barnharta – International Journal of Coal Geology

Review: Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments? – Viviana Fonti – Science of The Total Environment

Review: Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure – Sevcan Aydin – Applied Microbiology and Biotechnology

Viruses and phages

Editorial overview: The megaviromes – Didier Raoult – Current Opinion in Microbiology

More microbiology

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development – Ryan H. Hansen – PLOS ONE

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria – Kelly C Wrighton – The ISME Journal

Research Highlight: A time to gather chromosomes together – Naomi Attar – Nature Reviews Microbiology

Conference abstract: Metabolic Exchange In Microbial Communities – Andrei Osterman – The FASEB Journal

Microbes in the news

Pipe Dreams: Tapping into the Health Information in Our Sewers – Carrie Arnold – Environmental Health Perspectives

Deep sea microbes may be key to oceans’ climate change feedback – Howard Lee – The Guardian

Exploiting Male Killing Bacteria Could Control Insect Pest Species in the Future – SciCasts

Fifty people warned about possible exposure to drug-resistant bacteria at University of Alberta Hospital – Keith Gerein

May 4, 2016

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Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology

Bioinformatics

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research

Techniques

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review