Category Archives: Human skin

November 14, 2016

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Infant gut microbiota, oral microbiota of farmworkers with pesticide exposure, critically ill patients, probiotics and Alzheimer’s, Sutterella is a commensal.

Events

Cheese Cultures & Microbiology Class, December 2, 2016, Petaluma – California Artisan Cheese Guild – Eventbrite

Pregnancy and early life

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol – Julia Simioni – BMC Pediatrics

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital – Tarek Itania – Anaerobe

Human oral microbiome

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology

News: Study finds link between pesticide exposure and microbiome changes – Brooks Hays – UPI
Pesticide exposures can cause changes in oral microbiome – ASM

Molecular detection of bacteria associated to caries activity in dentinal lesions – Beatriz Gonçalves Neves – Clinical Oral Investigations

Review: Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review – Miguel Padial-Molina – J Oral Maxillofac Res

Human skin microbiome

A Precision Microbiome Approach Using Sucrose for Selective Augmentation of Staphylococcus epidermidis Fermentation against Propionibacterium acnes – Yanhan Wang – Int J Mol Sci

A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes – Maria Allhorn – Scientific Reports

Skin bacteria could protect against disease – Science Daily

Human vaginal microbiome

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm – Joana Castro – Pathogens and Disease

Human gut microbiome

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study – Jacqueline M. Lankelma – Intensive Care Medicine

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. – Kaisa Hiippala – Frontiers in Microbiology

Review: Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC) – Jochen Mattner – Int J Mol Sci

Animal microbiome

Review: Microbiota-host interplay at the gut epithelial level, health and nutrition – Jean-Paul Lallès – Journal of Animal Science and Biotechnology

Plant, root, and soil microbiome

Root bacterial endophytes alter plant phenotype, but not physiology – Jeremiah A. Henning – Peer J

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria – Pious Thomas – Microbial Ecology

Water microbiome

Unraveling the microbial community of a cold groundwater catchment system – Burga Braun – Water Research

Built environment microbiome

Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations – Min Gao – Environmental Pollution

Metabolomics

Review: Emerging roles of xenobiotic detoxification enzymes in metabolic diseases – Michael C. Petriello – Reviews on Environmental Health

Probiotics

Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind, and controlled trial – Elmira Akbari -Frontiers in Aging Neuroscience

News: Probiotics improve cognition in Alzheimer’s patients – Medical Xpress

More microbiology

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence – Yok Hian Chionh – Nature Communications

Cracking the code for dormant bacteria. Newly discovered genetic code controls bacterial survival during infections – Anne Trafton – MIT News Office

Microbes in the news

Monitoring in Real Time the Formation and Removal of Biofilms From Clinically Relevant Pathogens – PR Web

From the American College of Rheumatology Annual Scientific Meeting: Gut bacteria may be a trigger for antiphospholipid syndrome – EurekAlert

Three University of Maryland students are sending bacteria samples into space – Rachel Kuipers – the Diamondback

University of Texas at Dallas named “Milestones in Microbiology” – Joanna Urban – ASM

Bethany professor Matthew Swearingen receives research grant – Weirton Daily Times

Scientists try bacteria to halt invasive cheatgrass overwhelming the West – Keith Ridler – LA Times

November 10, 2016

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Fanconi anemia, Clostridium subcluster decreased in UC, ectomycorrhizas in oak forests, cryoconite hole anaerobes.

Human oral microbiome

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia – C.P. Furquim – Journal of Dental Research

Human gut microbiome

A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients – Kozue Takeshita – Inflammatory Bowel Diseases

Composition of gut microbiota in infants in China and global comparison – Ya-Shu Kuang – Scientific Reports

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease – Paul Giacomin – Scientific Reports

Making sense of the cause of Crohn’s – a new look at an old disease – Anthony W. Segal – F1000 Research

Metaanalysis: The Emerging Role of the Gut Microbiome in Adult Patients With Multiple Sclerosis – Pamela K. Newland – Journal of Neuroscience Nursing

Review: Escherichia coli Nissle 1917 in Ulcerative Colitis Treatment: Systematic Review and Meta-analysis – Giuseppe Losurdo – Journal of Gastrointestinal and Liver Diseases

Human blood and tissue microbiology

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections – Vibeke Børsholt Rudkjøbing – BMC Infectious Diseases

Review: Mechanisms of Bacterial Colonization of Implants and Host Response – Christof Wagner – Advances in Experimental Medicine and Biology

Animal models

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease – Ainsley M. Robinson – Inflammatory Bowel Diseases

Microbiota induces tonic CCL2 systemic levels that control pDC trafficking in steady state – M Swiecki – Mucosal Immunology

Siderophore-based immunization strategy to inhibit growth of enteric pathogens – Martina Sassone-Corsia – PNAS

Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice – Shaoqian Zhao – Journal of Molecular Endocrinology

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories – François-Joël Gatesoupe – BMC Microbiology

Plant, root, and soil microbiome

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition – Chengdong Huang – Field Crops Research

First detection of Endogone ectomycorrhizas in natural oak forests – Kohei Yamamoto – Mycorrhiza

[PFD] Grape berry bacterial inhibition by different copper fungicides – Guilherme Martins – BIO Web of Conferences

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Z Dai – Scientific Reports

Water and extremophile microbiome

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome – Marek K. Zdanowski – Microbial Ecology

Food microbiology

Sensory, microbiological and physico-chemical characterization of Klila, a traditional cheese made in the south-west of Algeria – Benamara R. N. – African Journal of MIcrobiology Research

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? – Bokai Zhu – Environment International

Built environment microbiology

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of MIcrobiology Research

Bioinformatics and metagenomics

Book chapter: DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data – Ilaria Granata – Dynamics of Mathematical Models in Biology

More microbiology

Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs – Kenneth Shatzkes – mBio

Predatory bacteria offer potential solution to drug resistance problem – Phys.org
Predatory Bacteria Can Cannibalize Drug-Resistant Bugs – Seeker

Bik’s non-microbiology Picks

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing – Mary A. Majumder – PLOS Biology

Origins of Biodiversity – Michael J. Benton – PLOS Biology

Microbes in the news

Researchers exploring new platform for detecting pathogenic bacteria using bacteriophages – News Medical

Novel vaccines block iron scavenging by bacteria. Agents starve bacteria by raising antibodies to capture the small molecules the microbes release to harvest iron – Stu Borman – Chemical & Engineering News

What’s lurking in the water in Shedd Aquarium – Lisa Bertagnoli – Chicago Business

New biophotonic light sensor can detect Legionella bacteria in minutes – News Medical

Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and the market

Clinical Microbiology Market Expected to Reach $6.72 billion by 2022 – Medgadget

Science, publishing, and career

Rosalind’s Ghost: Biology, Collaboration, and the Female – Caroline Wagner – PLOS Biology

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender – Xiao Han T. Zeng – PLOS Biology

November 2, 2016

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Microbiome and precision medicine, bacterial responses to the Deepwater Horizon oil spill, bacterial dynamics in a water distribution system, and uBiome launches a clinical gut test.

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz – Trends in Pharmacological Sciences

Press: Making the microbiome part of precision medicine – EurekAlert

Probiotics / Skin microbiome

Bacterial Etiology and Risk Factors Associated with Cellulitis and Purulent Skin Abscesses in Military Trainees – Ryan C. Johnson – PLOS ONE

Local Application of Probiotic Bacteria Prophylaxes against Sepsis and Death Resulting from Burn Wound Infection – Anne Argenta – PLOS ONE

Animal microbiome

Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Fever – Soo Jin Jeon – PLOS ONE

Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation – Henk J. van Lingen – PLOS ONE

Water microbiome

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill – Kim M Handley – bioRxiv

Built environment microbiome

Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System – E. I. Prest – PLOS ONE

Bioinformatics and metagenomics

Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification – Florian P Breitwieser – bioRxiv

Microbes in the news

‘Living buildings’ could use bacteria for heat, electricity and repairs – Helen Massy-Beresford – Horizon Magazine

Bacteria can’t get a grip on self-healing, slippery surface
Inspired by nature, a high-tech, low-adhesive coating for medical devices could help prevent infection – EurekAlert

Biocement from genetically modified bacteria could react to changes in environment – Brian Wang – Next Big Future

Purple bacteria shine path to super-efficient light harvesting – University of Queensland

Microbes on the marketplace

uBiome Announces World’s First Sequencing-Based Clinical Microbiome Test – PR Web
uBiome launches gut microbiome sequencing test, reels in Series B – FierceBiotech

The ultimate guide to DIY DNA testing kits – April Long – Elle

Microbiome Study Suggests an Opportunity to Reduce Healthcare Facility Costs by 30%. Poor Indoor Air Quality and Healthcare Associated Infections (HAIs) as Key Burdens – Digital Journal

 

November 1, 2016

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Ribosomal gene sequencing as a clinical diagnostic tool, probiotic microcins in the inflamed gut, toxic sugar metabolism by a bee symbiont, bacteria as indicators of soil condition, viruses of the human body.

General microbiome

Omics Approaches To Probe Microbiota and Drug Metabolism Interactions – Robert G. Nichols – Chemical Research in Toxicology

Review: Microbial interactions: ecology in a molecular perspective – Raíssa Mesquita Braga – Brazilian Journal of Microbiology

Human skin microbiome

Understanding the role of Propionibacterium acnes in acne vulgaris: the critical importance of skin sampling methodologies – Hélène Omer – Clinics in Dermatology

Human respiratory microbiome

Editorial: Macrolides, inflammation and the lung microbiome: untangling the web of causality – Robert P Dickson – Thorax

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Emerging pathogenic links between microbiota and the gut–lung axis
– Kurtis F. Budden – Nature Reviews Microbiology

Human gut microbiome

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions – Daniel E Almonacid – bioRxiv

Detecting beer intake by unique metabolite patterns – Gözde Gürdeniz – Journal of Proteome Research

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

The infant gut microbiome correlates significantly with rotavirus vaccine response in rural Ghana – Vanessa C. Harris – Journal of Infectious Diseases
Could the gut microbiome be key to understanding and improving rotavirus vaccine performance in high disease burden settings? – Journal of Infectious Diseases

Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors – M L Stoll – Genes and Immunity

Can the composition of the intestinal microbiota predict the development of urinary tract infections? – Casper DJ den Heijer – Future Microbiology

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Good Bugs, Bad Bugs in the Gut: The Role of Microbiota Dysbiosis in Chronic Gastrointestinal Consequences of Infection – Andre G Buret – American Journal of Gastroenterology

Review: Soy and Gut Microbiota: Interaction and Implication for Human Health – H Huang – J Agric Food Chem

Review: The gut microbiome and hypertension – M Pevsner-Fisher

Probiotics

Microcins mediate competition among Enterobacteriaceae in the inflamed gut – Martina Sassone-Corsi – Nature

Press: How good gut bacteria wrest control from the bad – Cosmos Magazine

Novel encapsulation improves recovery of probiotic strains in fecal samples of human volunteers – Volker Mai – Applied Microbiology and Biotechnology

Psychobiotics and the Manipulation of Bacteria–Gut–Brain Signals – Amar Sarkar – Trends in Neurosciences

Press: Psychobiotics: What Do We Know and Where Do We Go? – Laurie Anne Walden – Contagion Live

Review: Eosinophils, probiotics, and the microbiome – Helene F. Rosenberg – Journal of Leukocyte Biology

Animal experiments

Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice – Jing-jing Wang – Scientific Reports

Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Animal microbiome

Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicola – Hao Zheng – mBio

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites – Aram Mikaelyan – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacteria as emerging indicators of soil condition – Syrie M. Hermans – Applied and Environmental Microbiology

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens – Longfei Jiang – Scientific Reports

Endophytic Bacillus cereus effectively controls Meloidogyne incognita on tomato plants through rapid rhizosphere occupation and repellent action – Haijing Hu – Plant Disease

Drivers of yeast community composition in the litter and soil of a temperate forest –
Tereza Mašínová – FEMS Microbiology Ecology

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat – Michele Perazzolli – BMC Genomics

The root growth of wheat plants, the water conservation and fertility status of sandy soils influenced by plant growth promoting rhizobacteria – Naeem Khan – Symbiosis

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices – Jae-Hyung Ahn – Journal of Microbiology

Partitioning the effect of composition and diversity of tree communities on leaf litter decomposition and soil respiration – Mark Davidson Jewell – Oikos

Effects of Land use on the Structural Diversity of Soil Bacterial Communities in South Eastern Iran – Ghobad Jalali – Biosciences Biotechnology Research

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Antarctic strict anaerobic microbiota from Deschampsia antarctica vascular plants rhizosphere reveals high ecology and biotechnology relevance – Rafael José Marques Peixoto – Extremophiles

The influence of the host plant is the major ecological determinant of soil presence of the nitrogen-fixing root nodule symbiont, Cluster II Frankia – Kai Battenberg – Applied and Environmental Microbiology

Review: Fungal endophytes and their interactions with plants in phytoremediation: A review – Zujun Deng – Chemosphere

Water and extremophile microbiome

Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the north Atlantic ocean – Elisa Guerrero-Feijóo

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products – Miguel David Marfil-Santana – Journal of Microbiology

Food microbiology

Different flour microbial communities drive to sourdoughs characterized by diverse bacterial strains and free amino acid profiles – Giuseppe Celano – Frontiers in Microbiology

Built environment microbiome

Drinking water: One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria – Antonia Bruno – Microbiology Open

Weathering of a Roman Mosaic—A Biological and Quantitative Study on In Vitro Colonization of Calcareous Tesserae by Phototrophic Microorganisms – Addolorata Marasco – PLOS ONE

Bioinformatics and metagenomics

Phylogenetic Dirichlet-multinomial model for microbiome data – Yunfan Tang – arXiv

More microbiology

Bacterial evolution: Genomics of metabolic trade-offs – Martin F. Polz – Nature Microbiology

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

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences – Huimin Zhang – Molecular Biotechnology

Review: 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

Viruses of the Human Body. Some of our resident viruses may be beneficial – Eric Delwart – The Scientist

Naval Special Warfare Trainees Face Tiny Enemy: Bacteria – Sara G. Miller – Live Science

Could a disrupted sleep also disturb your gut? – Fiona Pepper for The Health Report

Researchers think they’ve finally figured out why bacteria only causes acne in some people. And how to stop it. – Fiona MacDonald – Science Alert

Microbes and the market

uBiome CEO Jessica Richman Joins Sean Parker, Maria Shriver, Arianna Huffington and Others, Speaking at Fortune Brainstorm HEALTH

Science, publishing, and career

2016 Life Sciences Salary Survey. Most researchers feel stimulated by their work but are dissatisfied with their compensation, according to this year’s results – Karen Zusi – The Scientist

October 31, 2016

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Happy Halloween! Today is the first day at my new employer uBiome. But the blog continues. Today’s blog features the gut microbiome of Type 2 Diabetes patients and the transportome of mycorrhiza.

Human skin microbiome

Inhibition of HDAC8 and HDAC9 by microbial short-chain fatty acids breaks immune tolerance of the epidermis to TLR ligands – James A. Sanford – Science Immunology

Press: Acne Gives Up Secret That Points to New Treatments – Amy Norton – WebMD

Human gut microbiome

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

Animal microbiome

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome – Lizi Bensoussan – Environmental Microbiology

Plant, root, and soil microbiome

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza – Kevin Garcia – Trends in Plant Science

Microbes in the news

Bacteria, other contaminants make costume contact lenses risky – NBC

Nurses’ Scrubs Carry Bad Bacteria. Healthcare workers, patients, and environment form ‘transmission triangle’ – Liz Highleyman – MedPage Today

A Word from Dr. Pfenninger: The weird disease of tetanus – John L. Pfenninger – Midland Daily News

Doctors transfer the power of gut bacteria – Emery Cowan – AZ Daily Sun

October 28, 2016

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Still in Albuquerque at UNM where I gave a talk today hosted by Joe Alcock. Another great example of how Twitter (at least some parts of it!) can bring scientists together.

Two studies published in Nature Genetics this month coupling variations in the human gut microbiome with genetic variations in the human genome. Also: predicting facial skin microbiome and how does Wolbachia do it?

Human skin microbiome

Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome – Souvik Mukherjee – Scientific Reports

Human gut microbiome

Editorial: The gut microbiome—an emerging complex trait – Andrew K Benson – Nature Genetics
Association of host genome with intestinal microbial composition in a large healthy cohort – Williams Turpin – Nature Genetics
The effect of host genetics on the gut microbiome – Marc Jan Bonder – Nature Genetics

Can the composition of the intestinal microbiota predict the development of urinary tract infections? – Casper DJ den Heijer – Future Microbiology

Review: Personalized microbiome-based approaches to metabolic syndrome management and prevention – H Shapiro – J Diabetes (NCBI link)

Animal microbiome

Microbiota associated with Bactrocera carambolae and B. dorsalis (Insecta: Tephritidae) revealed by next-generation sequencing of 16S rRNA gene – Hoi-Sen Yong – Meta Gene

The microbiome of neotropical ticks parasitizing on passerine migratory birds – Khemraj Budachetri – Ticks and Tick-borne Diseases

Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification – Guowei Zhou – Scientific Reports

Commentary: Open questions: how does Wolbachia do what it does? – Francis M. Jiggins – BMC Biology

Plant, root, and soil microbiome

Inducing the rhizosphere microbiome by biofertilizer application to suppress banana Fusarium wilt disease – Lin Fu – Soil Biology and Biochemistry

A new primer set for DNA metabarcoding of soil Metazoa – E. Capra – European Journal of Soil Biology

Functional foods

The effect of bacteriophages on the acidification of a vegetable juice medium by microencapsulated Lactobacillus plantarum – Claude P. Champagne – Food Microbiology

More microbiology

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae – M. Tofazzal Islam – BMC Biology

Microbes in the news

Gaining new insights into the health promoting properties of kefir – Waterford Today

Antibiotics Linked to Sepsis Risk. Disturbing healthy bacteria during hospital admission associated with later sepsis – Michael Smith – MedPage Today

 

October 20, 2016

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Events

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

Correspondence: Improving 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

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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

Techniques

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

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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

Editorial: What’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

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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