October 21, 2016

Oral bacteria in esophageal cancer samples, spring blooms of coastal phytoplankter, and a microbial anthropologist in the Jungle.


Meeting: Chemistry of Microbiomes in Human Environments – 11/9/16 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Press: Presence of certain oral bacterium in esophageal cancer samples associated with shorter survival – Medical Xpress

Human vaginal microbiome

Review: Role of microbial flora in female genital tract: A comprehensive review – Subramanyam Dasari – Asian Pacific Journal of Tropical Disease

Plant, root, and soil microbiome

Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling – Jiachao Zhang – PLOS ONE

Diversity indices using arbuscular mycorrhizal fungi to evaluate the soil state in banana crops in Colombia – Germán Mahecha-Vásquez – Applied Soil Ecology

Water microbiome

Physiological and ecological drivers of early spring blooms of a coastal phytoplankter – Kristen R. Hunter-Cevera – Science

Microbial community dynamics in semi-commercial RAS for production of Atlantic salmon post-smolts at different salinities – Ingrid Bakke – Aquacultural Engineering

Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production – Ida Rud – Aquacultural Engineering

Built environment microbiome

Shoe soles as a potential vector for pathogen transmission: a systematic review – T. Rashid – Journal of Applied Microbiology

Microbes in the news

A Microbial Anthropologist in the Jungle – Maria Gloria Dominguez-Bello – Cell

African Soil Microbiology Project – Elizabeth Bach – Global Soil Biodiversity

Researchers Say Plant Bacteria Could Provide its Own Salvation – Interesting Engineering

I’m a Doctor. If I Drop Food on the Kitchen Floor, I Still Eat It. – Aaron E. Carroll – The New York Times
Letters to the Editor: Eat Food From the Floor? Microbiology and Mores – The New York Times

Dr Brad McKay explains the complex world of vaginal bacteria – Brad McKay – News.com.au

What’s making lifeguards sick at La Jolla Cove? – Brandon Lewis – CBS8

Spotlight on Grants: Nickel and cobalt in Streptococcus – Siti Nur Amalina – Microbe Post

ASM’s Microbes After Hours Microbes After Hours: The Necrobiome – Microbial Life After Death

Bik’s Non-Microbiology Picks

We used to sell cigarettes in hospitals. 5 practices that may soon look just as outdated – Melissa Bailey – STAT News

October 20, 2016


2016-2017 Dannon Gut Microbiome, Yogurt and Probiotics Fellowship Grant Application Form
Also see: Leading Yogurt Company Challenges Students to Unearth New Data on the Gut Microbiome, Yogurt and Probiotics with $50K Grant Program. Dannon® will award two $25K grants to further scientific research – PR Newswire

Third Annual Microbiome Symposium – Penn Vet – October 26 and 27, 2016
Penn’s microbiome conference turns eye toward antibiotic use in livestock
Text by Katherine Unger Baillie – Penn Current

Q4 microbiome conferences roundup: Are you looking for a good scientific microbiome research symposium? Over the next three months, you have six exciting microbiome conferences from which to choose. – Megan M. MacBride – Taconic

Disappointing lack of diversity here: #YAMMM: 29 speakers, 4 women. Microbiome Drug Development Summit, 24-26 January 2017, Paris, France

General microbiome

An introduction to microbiome analysis for human biology applications – Katherine R. Amato – American Journal of Human Biology

Human oral microbiome

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Human respiratory microbiome

Role of microbiome in the pathophysiology and disease course of asthma – Singanayagam A – Curr Opin Pulm Med

Human skin microbiome

Review: Topographical and physiological differences of the skin mycobiome in health and disease – Jay-Hyun Jo – Virulence

Human vaginal microbiome

A fruitful alliance: the synergy between Atopobium vaginae and Gardnerella vaginalis in bacterial vaginosis-associated biofilm – Liselotte Hardy – Sexually Transmitted Infections

Human gut microbiome

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Similar Fecal Microbiota Signatures in Patients With Diarrhea-Predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

Review: Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches – R. Balfour Sartor – Gastroenterology

Review: The Microbiome and Human Disease Pathogenesis: How do you do what you do to me …? – Edward N. Janoff – Translational Research

Animal models

Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing – Geon Goo Hana – Veterinary Microbiology

Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine – Drew D. Kiraly – Scientific Reports

Animal microbiome

Developmental and ecological benefits of the maternally transmitted microbiota in a dung beetle – Daniel B. Schwab – The American Naturalist

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis – Joost T.P. Verhoeven – FEMS Microbiology Ecology Letters

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities – Jessica L. Ray – Molecular Ecology

Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater’s Prairie Chicken – Yan Zhang – Microbial Ecology

Plant, root, and soil microbiome

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists – Ai Kawahara – PLOS ONE

Review: Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Water microbiome

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor – Katsunori Yanagawa – ISME J

More microbiology

CorrespondenceImproving Microbiology Research: the Problems Are Less Statistical and More Biological – Dennis F. Lawler – mBio

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Microbes in the news

Tasmanian devil milk fights superbugs – BBC News
Tasmanian devil milk kills several deadly superbugs that are resistant to existing drugs – Science Alert

There’s a breast microbiome, and it’s different in women with breast cancer – Erin Blakemore – Washington Post

Research Highlight: A protective protozoan in mucosal infection – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Outbreak of Biofilm-Forming Achromobacter xylosoxidans Due to Environmental Transmission – Infection Control Today

The Emergent Microbiome: A Revolution for the Life Sciences – Part VII, The Microbiome and Immunotherapy I – Dilworth IP – Lexology

New science museum exhibit explores ‘the secret world’ inside us: N.C. Museum of Natural Sciences in downtown Raleigh opens a new special exhibit this weekend – WRAL.com

Vedanta Biosciences Granted First European Patent Broadly Covering Pharmaceutical Compositions for Microbiome Therapeutics Based on Bacterial Consortia – Business Wire

Science, publishing, and career

Married to the(ir) job: living with an academic. Scholars and their significant others share the good, the bad and the ugly – Times Higher Education

Investigation Finds Pathologist Guilty of Systemic Misconduct – Bob Grant – The Scientist

Women need to be seen and heard at conferences. A neuroscience initiative is boosting the number of female invited speakers at meetings. Other disciplines should do the same – Nature

The Bearded Lady Project . Q&A: Lexi Jamieson Marsh and Ellen Currano: Face to face – Alexandra Witze – Nature

October 19, 2016

Blogging from SJC today on my way to Vancouver. Oral microbes correlated with food-triggered migraines, spinal cord injuries, comparison of 8 DNA extraction kits on 3 sample types, mockrobiota.

Jobs and Events

Flying to Vancouver today to give a short talk at DNA Genotek’s Microbiome Breakfast Session at #ASHG2016

Fall Mid-Atlantic Microbiome Meetup (M3) – November 1-2, University of Maryland

Human oral microbiome

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort – Antonio Gonzalez – mSystems

Press: Migraines could be caused by gut bacteria, study suggests – Hannah Devlin – The Guardian
Scientists think they’ve found why chocolates and wine cause migraines for some very unlucky people – Katherine Ellen Foley – Quartz

Human skin microbiome

The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes – Paul Capewell – eLife

Human respiratory microbiome
The Prevalence of Antibiotic-resistant Staphylococcus aureus Nasal Carriage among Industrial Hog Operation Workers, Community Residents, and Children Living in their Households: North Carolina, USA – Sarah M. Hatcher – Environmental Health Perspectives

Press: Drug-resistant staph bacteria prevalence higher in young children living with hog workers – EurekAlert

Animal models

Gut dysbiosis impairs recovery after spinal cord injury – Kristina A. Kigerl – Journal of Experimental Medicine

Press: Researchers show how spinal cord injury causes profound changes in gut microbiota – News-Medical Net
Gut bacteria can aid recovery from spinal cord injury, study suggests – Science Daily


Eight commercial kits, 16 procedures, 3 sample types: Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition – Berith E. Knudsen – mSystems

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking – Nicholas A. Bokulich – mSystems

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography – Stephen Nayfach – Genome Research

Press: From Genome Research: Strain-level profiling yields new insights into mother-infant microbiomes – EurekAlert

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J. Joseph – PeerJ

Microbes in the news

Tapping the Human Gut Microbiome, Part 1: The Next Frontier for Novel Therapeutics – Christian Furlan Freguia – GenEngNews
Tapping the Human Gut Microbiome, Part 2: From the Bottom Up – Christian Furlan Freguia – GenEngNews

The microbiome: Looking at microbes as more than pathogens – Ryan T. Ranallo – Healio

Harnessing The Plant Microbiome For Cleaner, Pesticide-Free Agriculture – Ben Schiller – FastCoexist

Bacteria named in Mighty Taco outbreak; chain denies fault – Food Safety News

Clemson students get bacteria named after them. New strain of Legionella named for students who studied it – Carla Field – Wyff4

Bacteria ‘alarm clock’ may cause repeat infections in patients – Kate Wighton – Imperial.ac.uk

Microbes and Money

Igniting a Microbiome Revolution: Era7 Bioinformatics Syncs with Capital Cell – Erin Hobey – CrowdFundInsider
Igenbio Inc offers metagenome analysis services for clinical and industrial applications – Reuters

October 18, 2016

Vaginal probiotics, forensic analysis of skin bacteria on fabrics, Wolbachia in nematodes, ivy phyllosphere, microbial life in two polar extremes, how to improve the indoor environment, and mass spec analysis of human habitat molecules.

Pregnancy and early life

Vaginal Probiotic Administration in the Management of Preterm Premature Rupture of Membranes – Daskalakis G.J. – Fetal Diagnosis and Therapy

General human microbiome

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Human respiratory microbiome

Review: Host–Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization – Michelle E. Mulcahy – Trends in Microbiology

Human skin and tissue microbiome

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences

Not a word about extraction controls, so proceed with caution: Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis – Elvira E. Ziganshina – PLOS ONE

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Risk of Developing Celiac Disease – Cenit, Maria C. – Journal of Clinical Gastroenterology

EditorialWhat’s in Your GI Microbiome? – Martin H. Floch – Journal of Clinical Gastroenterology

Animal and in vitro models

Study of the Ability of Bifidobacteria of Human Origin to Prevent and Treat Rotavirus Infection Using Colonic Cell and Mouse Models – Mélanie Gagnon – PLOS ONE

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism – Limin Zhang – mSystems

A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets – Isabelle Le Huërou-Luron – European Journal of Nutrition

An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract – Marzorati, Massimo – Journal of Clinical Gastroenterology

Animal microbiome

Sea lions: Protein and RNA extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations – W Espinosa-de Aquino – Methods in Ecology and Evolution

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish – D Kušar – Journal of Fish Diseases

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts – Amanda M. V. Brown – Scientific Reports

Plant, root, and soil microbiome

Disentangling interactions between microbial communities and roots in deep subsoil – Martina I. Gocke – Science of the Total Environment

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock – Alexandre Bagnoud – Nature Communications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation – Xihui Xu – Environmental Science and Pollution Research

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment

Water and extremophile microbiome

Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation – Eunhee Lee – Limnology and Oceanography

Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem – Jeff S. Bowman – BioScience

Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal neuston – A. D. Galach’yants – Microbiology

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains, Buryat Republic) – E.S. Kashkak – Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Built environment microbiome

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats – Daniel Petras – Analytical Chemistry

Food microbiology

Raw Ready-to-Eat Seafood Safety: Microbiological Quality of the Various Seafood Species Available at Fishery, Hyper, and Online Market – H.W. Kim – Letters in Applied Microbiology

Bioinformatics and metagenomics

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources – Nicolas Tsesmetzis – Standards in Genomic Sciences

IMG/M: integrated genome and metagenome comparative data analysis system
I-Min A. Chen – Nucleic Acids Research

Review: The present and future of de novo whole-genome assembly – Jang-il Sohn – Briefings in Bioinformatics

Microbes in the news

Soaking A Bunch Of Toads In Their Own Bacteria Could Save Their Lives – Krista Langlois – Five Thirty Eight

Bacteria Hysteria

Why your office could be making you sick: Keyboards ‘contain 20,000 MORE bacteria than a toilet bowl’– Stephen Matthews – Daily Mail

How to clean and disinfect your keyboard and mouse – Ed Rhee – CNET

Science, publishing, and career

A Tale of Two Women and Their Careers in Science – Anna Katie – YouTube

Promoting Responsible Scientific Research – American Society for Microbiology

October 17, 2016

Fecal markers on child hands in Bangladesh, Clostridium difficile in pet dogs, intertidal microbes, and variability in household airborne bacteria.

Human skin microbiome

Occurrence of host-associated fecal markers on child hands, household soil, and drinking water in rural Bangladeshi households – Alexandria B. Boehm – Environmental Science & Technology Letters

Human respiratory microbiome

Data Mining of Lung Microbiota in Cystic Fibrosis Patients – Jianguo Li – PLOS ONE

Review: A future perspective on neurodegenerative diseases: Nasopharyngeal and gut microbiota – Fazlurrahman Khan – Journal of Applied Microbiology

Human urinary and reproductive tract

Methods only, no results (or: how to write two papers instead of one): Methodology for a vaginal and urinary microbiome study in women with mixed urinary incontinence – Yuko M. Komesu – International Urogynecology Journal

Human oral microbiome

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study – Xiaozhou Fan – Gut

Human gut microbiome

High-throughput sequencing identifies distinct fecal and mucosal gut microbiota correlating with different mucosal proteins – Li-na Dong – PeerJ Preprint

Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder – Ping Lin – Journal of Affective Disorders

Differential Changes in Gut Microbiota After Gastric Bypass and Sleeve Gastrectomy Bariatric Surgery Vary According to Diabetes Remission – Rinki Murphy – Obesity Surgery

Review: Antibiotics and the Intestinal Microbiome : Individual Responses, Resilience of the Ecosystem, and the Susceptibility to Infections – Sophie Thiemann – Current Topics in Microbiology and Immunology

Animal experiments

Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice – Valeriy A. Poroyko – Scientific Reports

The impact of orally administered phages on host immune response and surrounding microbial communities – Yingying Hong – Bacteriophage

Animal microbiome

More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes – Nathan E. Stone – PLOS ONE

Press: NAU Crew Finds Bacteria Clue by Scooping Pooch Poo – Arizona Public Media

Rumen microbiota for wild boreal cervids living in the same habitat – Kjartan Østbye – FEMS Microbiology Letters

Structure and culture of the gut microbiome of the Mormon cricket Anabrus simplex – Chad C Smith – bioRxiv Preprint

Plant, root, and soil microbiome

Microbial legacies alter decomposition in response to simulated global change – Jennifer BH Martiny – ISME Journal
Water microbiome

Spatial and Halophytes Associated Microbial Communities in Intertidal Coastal Region of India – Doongar R. Chaudhary – International Journal of Phytoremediation

Built environment microbiome

High temporal variability in airborne bacterial diversity and abundance inside single-family residences – Joanne B. Emerson – Indoor Air

Microbes in the news

UMass microbiologist Kristen DeAngelis awarded $2.5 million grants to study how soil microbes contribute to global warming – Lucas Ropek

Bdellovibrio, the cannibalistic drug coming to humanity’s rescue – Mallory Locklear – Ars Technica

Nuclear Waste Repositories Safer With Bacteria – iTechPost

UA Museum hopes to display giant whale skeleton after bacteria clean up the bones for a couple of years – Dermot Cole – ADN

Nikon Small World Photomicrography Competition Popular Vote Gallery

October 15, 2016

Bacteria in wounds, Oxalobacter and kidney stones, harbor seals, sables, leeches, response to afforestation, subglacial lake, polluted river water.

Human skin and wound microbiome

Bacterial Contribution in Chronicity of Wounds – Kashif Rahim – Microbial Ecology

Human gut microbiome

The fecal microbiota as a biomarker for disease activity in Crohn’s disease – Danyta. I. Tedjo – Scientific Reports

Review: Fungi in the healthy human gastrointestinal tract – Heather E. Hallen-Adams – Virulence

Animal and other experiments

Anti-obese effects of two lactobacilli and two bifidobacteria on ICR mice fed on a high fat diet – Zhipeng Li – Biochemical and Biophysical Research Communications

Skin microbiome promotes mast cell maturation by triggering stem cell factor (SCF) production in keratinocytes – Zhenping Wang – Journal of Allergy and Clinical Immunology

Diet-related gut bacterial dysbiosis correlates with impaired development, increased mortality and Nosema disease in the honeybee (Apis mellifera) – Patrick W. Maes – Molecular Ecology

Oxalobacter formigenes–Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells – Donna Arvans – Journal of the American Society of Nephrology

Press: Factors secreted by gut bacteria may help combat kidney stones – Science Daily

Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype – Jordi Mayneris-Perxachs – The American Journal of Clinical Nutrition

Animal microbiome

Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina) – Daniela Numberger – MicrobiologyOpen

Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene – Yu Guan – AMB Express

Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential – Jeremiah N. Marden – Frontiers in Microbiology

Plant, root, and soil microbiome

Interkingdom Responses to Bacterial Quorum Sensing Signals Regulate Frequency and Rate of Nodulation in Legume–Rhizobia Symbiosis – Andrew G. Palmer – ChemBioChem

Development of Soil Bacterial Communities in Volcanic Ash Microcosms in a Range of Climates – Dorsaf Kerfahi – Microbial Ecology

Response of soil microbial community to afforestation with pure and mixed species – Anna Gunina – Plant and Soil

Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities – Asma Asemaninejad – Microbial Ecology

The role of arbuscular mycorrhizal fungi in grain production and nutrition of sorghum genotypes: Enhancing sustainability through plant-microbial partnership – Adam B. Cobb – Agriculture, Ecosystems & Environment

Arbuscular mycorrhizal fungal assemblages in biological crusts from a Neotropical savanna are not related to the dominant perennial Trachypogon – R.M. Hernández-Hernández – Science of the Total Environment

Review: Belowground nitrogen transfer from legumes to non-legumes under managed herbaceous cropping systems. A review – Malinda S. Thilakarathna – Agronomy for Sustainable Development

Water and extremophile microbiome

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes – Chan Lan Chun – Science of The Total Environment

A monotonically declining elevational pattern of bacterial diversity in freshwater lake sediments – Jin Zeng – Environmental Microbiology

Grazers structure the bacterial and algal diversity of aquatic metacommunities – Julia Birtel – Ecology

Changes of the bacterial abundance and communities in shallow ice cores from Dunde and Muztagata glaciers, Tibetan Plateau – Yong Chen – Frontiers in Microbiology

Physiological ecology of microorganisms in Subglacial Lake Whillans – Trista J. Vick-Majors – Frontiers in Microbiology

Built environment microbiome

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station – Maximilian Mora – Frontiers in Microbiology

Waste and pollution microbiology

Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient – Jenna L. Shelton – Frontiers in Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats – Mathilde Jeanbille – Frontiers in Microbiology

Bioinformatics and metagenomics

Bacterial human virulence genes across diverse habitats as assessed by in silico analysis of environmental metagenomes – Ditte A. Søborg – Frontiers in Microbiology

Microbes in the news

Reflections on 1500 blog posts at #microbenet – David Coil – Microbe.net

Staff Pick: ‘I Contain Multitudes’ by Ed Yong – Publishers Weekly

Mapping the Subway’s Microbiome – Grégory Fléchet – CNRS News

Your child’s microbiome, and why its health matters – Jennifer Graham – Statesboro Herald

Enquiring About Tolerance (EAT) study: Second Genome, King’s College London study eczema, food allergies in infants – Healio

The ‘Swiss Agent’: Long-forgotten research unearths new mystery about Lyme disease – Charles Piller – STAT News

What radiation-resistant space fungus can do for drug discovery – Shayla Love – STAT News

3 New Vaccines Against ‘Black Death’ Plague Bacteria Show Promise – Rachael Rettner – Live Science

Scientists engineer ‘glow in the dark’ bacteria – to help spot the bugs that cause food poisoning – Lizzie Parry – The Sun

If you want to make bacteria glow, give it a virus – Ben Coxworth – New Atlas

How the Gut Microbiome May Help Us Prevent IBD – Science Blog

October 14, 2016

The pubic hair microbiome, lung transplant virome, IBS microbiome signature, coprolites, antibacterial molecules for babies the Tasmanian Devil pouch, Archaea in Mars simulation, white pudding, functional mapping pipeline,

Human oral microbiome

Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis – G.P. Schincaglia – Journal of Dental Research

The microbial community shifts of subgingival plaque in patients with generalized aggressive periodontitis following non-surgical periodontal therapy: a pilot study – Jing Hang – Oncotarget

ReviewThe Autoimmunity-Oral Microbiome Connection – N Nikitakis – Oral Diseases

Human respiratory microbiome

The Perioperative Lung Transplant Virome: Torque Teno Viruses are Elevated in Donor Lungs and Show Divergent Dynamics In Primary Graft Dysfunction – A. A. Abbas – American Journal of Transplantation

Composition and immunological significance of the upper respiratory tract microbiota – L. Patrick Schenck – FEBS Letters

Human skin and hair microbiome

Individualization of pubic hair bacterial communities and the effects of storage time and temperature – Diana W. Williams – Forensic Science International: Genetics

Gram-positive anaerobe cocci (GPAC) are underrepresented in the microbiome of filaggrin-deficient human skin – Patrick L.J.M. Zeeuwen – The Journal of Allergy and Clinical Immunology

Review: Microbiome in healthy skin, update for dermatologists – B. Dréno – Journal of the European Academy of Dermatology and Venereology

Human reproductive tract microbiome

Challenging dogma: the endometrium has a microbiome with functional consequences! – Linda C. Giudice – American Journal of Obstetics & Gynecology

Human gut microbiome

Intestinal microbiota in adult patients with Short Bowel Syndrome: Preliminary results from a pilot study – Stefania Boccia – Clinical Nutrition

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome – Julien Tap – Gastroenterology

The dual role of Escherichia coli in the course of ulcerative colitis – Magdalena Pilarczyk-Zurek – BMC Gastroenterology

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Dysbiosis in the ICU: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Parasites, microbiota and metabolic disease – Sonakshi Bhattacharjee – Parasite Immunology

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: Human Coprolites as a Source for Paleomicrobiology – Sandra Appelt – Microbiology Spectrum

Animal models

Behavioural and Neurochemical Consequences of Chronic Gut Microbiota Depletion during Adulthood in the Rat – A.E. Hoban – Neuroscience

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses – Zhipeng Li – Environmental Microbiology Reports

Microbial community mapping in intestinal tract of broiler chicken – Yingping Xiao – Poultry Science

Animal microbiome

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria – Jeroen A. J. M. van de Water – Microbial Ecology

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii) – E. Peel – Scientific Reports

Plant, root, and soil microbiome

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems – S. Uroz – Soil Biology and Biochemistry

Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea – Ludovic Henneron – Oikos

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions – Vishal Kumar – Frontiers in Plant Science

Water microbiome

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes – M. Romina Schiaffino – Environmental Microbiology

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake – Patricia M. Valdespino-Castillo – Microbial Ecology

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River – Wenhui Wang – Scientific Reports

Microbes in space

Survivability and Growth Kinetics of Methanogenic Archaea at various pHs and Pressures: Implications for Deep Subsurface Life on Mars – Navita Sinha – Planetary and Space Science

Food microbiology

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: The example of white pudding – Emilie Cauchie – International Journal of Food Microbiology

Microbial diversity in pitted sweet cherries (Prunus avium L.) as affected by high-hydrostatic pressure treatment – Julia Toledo del Árbol – Food Research International

Built environment microbiology

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia

Techniques / Fungi

Accurate Estimation of Fungal Diversity and Abundance Through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing – D. Lee Taylor – Applied and Environmental Microbiology

Bioinformatics and metagenomics

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli – Minseung Kim – Nature Communications

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies – Jiwoong Kim – BMC Bioinformatics

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Extremophiles found in a lake, and this is great news for biotech – Colm Gorey – Silicon Republic

‘I want my teeth back’: Kids infected with jaw-eating bacteria after dental treatment – Katie Mettler – Sacramento Bee

Microbiome biotech joins Peter Thiel’s Breakout Labs project – Fierce Biotech

Science, publishing, and career

Book:  Fungible Life: Experiment in the Asian City of Life – Aihwa Ong – Amazon