Category Archives: Human oral

October 17, 2015

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Fungal infection in brains of Alzheimer patients (already generating a lot of discussion on Twitter), solving a bloody mess in leeches, crosstalk in sewage cleaning plant roots, stromatolite microbiomes, halophilic viruses, and a new tool called Schmutzi.

General human microbiome

Different Brain Regions are Infected with Fungi in Alzheimer’s Disease – Diana Pisa – Scientific Reports

Human (and dog) oral microbiome

Microbiological Analysis of Anaerobic Bacteria Isolated from Periodontal
Pockets in Cases of Periodontal Disease in Dogs and Humans – Magdalena Gołyńska – Dentistry

Human gut microbiome

Review: Changes seen in gut bacteria content and distribution with obesity: causation or association? – David S. H. Bell – Postgraduate Medicine

Review: Obesity, Diet and the Gut Microbiota – Anthony R. Bird – Current Nutrition Reports

Animal models

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice – Adina Howe – The ISME Journal

Bacterial community response to changes in a tri-trophic cascade during a whole-lake fish manipulation – Jatta Saarenheimo – Ecology

Animal microbiome

Solving a bloody mess: B-vitamin independent metabolic convergence among gammaproteobacterial obligate endosymbionts from blood-feeding arthropods and the leech Haementeria officinalis – Alejandro Manzano-Marín – Genome Biology and Evolution

Plant, root, and soil microbiome

Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots – Enrico Baldan – PLOS ONE

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest – Albert Barberán – Ecology Letters

Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis – Bin Luo – Scientific Reports

Impacts of root symbiotic associations on interspecific variation in sugar exudation rates and rhizosphere microbial communities: a comparison among four plant families – Atushi Okubo – Plant and Soil

Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition – Jun Zeng – Soil Biology and Biochemistry

Influence of Microbial Composition on the Carbon Storage capacity of the Mangrove soil at the land-ocean boundary in the Sundarban Mangrove Ecosystem, India – Subhajit Das – Geomicrobiology Journal

Extremophile microbiome

Analysis of metagenomic data reveals common features of halophilic viral communities across continents – S. Roux – Environmental Microbiology

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis – Giorgio Casaburi – Environmental Microbiology

Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community – Surendra Vikram – Environmental Microbiology

Plants impact structure and function of bacterial communities in Arctic soils – Manoj Kumar – Plant and Soil

Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches – Antonio García-Moyano – Microorganisms

Waste treatment microbiology

Assessment of human virus removal during municipal wastewater treatment in Edmonton, Canada – Yuanyuan Qiu – Journal of Applied Microbiology

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis – Chih-Ming Kao – Journal of Hazardous Materials

Metagenomics and bioinformatics

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology – Peter D. Karp – Briefings in Bioinformatics

Jflow: a workflow management system for web applications – Jérôme Mariette – Bioinformatics

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA – Gabriel Renaud – Genome Biology

Microbes in the news

Inside the Grim World of the Phytoplasmas ‘Zombie’ Plant Bacteria – Michael Byrne – Motherboard

The Future of Dieting Is Personalized Algorithms Based on Your Gut Bacteria – Melissa Dahl – Huffington Post

From migraine to microbiome, 20 companies to watch at big BIO investor event – Ron Leuty – San Francisco Business Times

Microbial considerations in rosacea treatment: Greater understanding of that demodex mites play may uncover new therapeutic options – Lisette Hilton – Dermatology Times

Science, publishing, and career
Men set their own cites high: Gender and self-citation across fields and over time – Molly M. King
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October 16, 2015

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Chronic wound microbiota of almost 3000 patients, two periodontitis papers, biography among Agave microbiotas, and microbial ecology of Antarctic aquatic systems.

Pregnancy and birth

Commentary: Metaproteomic analysis adds a functional glimpse into host–microbe succession in an infant’s GI – Joshua E. Elias – Proteomics

Editorial: Microbiomes – Embracing complexity – Pratik Jagtap – Proteomics

Human oral microbiome

Oral Microbiota, Periodontal Status and Osteoporosis in Postmenopausal Women – Scarlette Hernández-Vigueras – Journal of Periodontology

Relationship between periodontitis-associated subgingival microbiota and clinical inflammation by 16S pyrosequencing – A Camelo-Castillo – Journal of Clinical Periodontology

Plastic teeth that don’t allow bacteria to grow on them: 3D-Printable Antimicrobial Composite Resins – Jun Yue – Advanced Functional Materials

Human skin microbiome

Analysis of the chronic wound microbiota of 2,963 patients by 16S rDNA pyrosequencing – Randall D. Wolcott – Wound Repair and Regeneration

Human gut microbiome

A Gut Odyssey: The Impact of the Microbiota on Clostridium difficile Spore Formation and Germination – Aimee Shen – PLOS Pathogens

Review: Gut microbiota and obesity – Philippe Gérard – Cellular and Molecular Life Sciences
Animal microbiome

Evaluation of feed grade sodium bisulfate impact on gastrointestinal tract microbiota ecology in broilers via a pyrosequencing platform – Si Hong Park – Poultry Science

Birds: Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans – Kazunari Ushida – Journal of Veterinary Medical Science

First Evidence of an Important Organic Matter Trophic Pathway between Temperate Corals and Pelagic Microbial Communities – J. A. Fonvielle – PLOS ONE

Plant, root, and soil microbiome

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species – Devin Coleman-Derr – New Phytologist

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members – Aurore Stroobants – Soil Microbiology

Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation tests – Noël J. Diepens – Environmental Science & Technology

Letter to the Editor: Plant microbiota: implications for human health – Leena von Hertzen – British Journal of Nutrition

Water microbiome

Impact of multiple anthropogenic stressors on freshwater: how do glyphosate and the invasive mussel Limnoperna fortunei affect microbial communities and water quality? – Haydée Pizarro – Ecotoxicology

Bacterial and protist community changes during a phytoplankton bloom – John K. Pearman – Limnology and Oceanography

Research Highlight: Wired communities – Denise Waldron – Nature Reviews Microbiology

Extremophile microbiome

Review: Microbial ecology of Antarctic aquatic systems – Ricardo Cavicchioli – Nature Reviews Microbiology

Built environment microbiome

Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area – Juanjuan Wang – Water Research

Microbes in the news

Crohn’s disease causes, symptoms, treatments and role of gut bacteria – Rebecca Bowslaugh – Bel Marra Health

Microbial Signatures Predict Post-op Recurrence in Crohn’s – David Wild – GastroEndoNews
Deep-sea corals in the Red Sea: reservoirs of hope – Sedeer El-Showk – Nature Asia

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences – Part III, Psychobiotics – Jessica Miles and Anthony D. Sabatelli – JD Supra

Researchers find an answer to invasive cheatgrass: Will this native bacteria finally thwart one of the most invasive weeds in North America? – Gloria Dickie – High Country News

Not a great title: 3D printed teeth to keep your mouth free of bacteria – Jacob Aron – New Scientist

Not for the faint of heart: Bacteria of maggots causes fatal septicemia in man – Chris Whitehouse – Outbreak News Today – Refers to this article in Emerging Infectious Diseases

Microbiology and Art

This is the Most Beautiful View of Poo You’re Ever Going to See – Jamie Condliffe – Gizmodo

Science, publishing, and career

How do we define and measure scientific literacy? – Joseph Timpona – Blogs at Plos

Your Data to Explore: An Interview with Anne Wojcicki from 23andMe – Jane Gitschier – PLOS Genetics
After sexual harassment reports, famed astronomer resigns from UC Berkeley – Rachel Feltman – Washington Post

Geoff Marcy incident indicative of larger problem – Ellen Simms – The Daily Cal

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October 13, 2015

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Tongue coating microbiota, fecal microbiota in Tibetan and Chinese Han, the gut mycobiome in obesity, and the Hoopoe’s uropygial gland.

Pregnancy and birth

Review: Neonatal Gut Microbiota and Human Milk Glycans Cooperate to Attenuate Infection and Inflammation – David S Newburg – Clinical Obstetrics & Gynecology

Research highlight: Early life dysbiosis increases asthma risk – Naomi Attar – Nature Reviews Microbiology

Review: Gut Microbiome and the Development of Food Allergy and Allergic Disease – Benjamin T. Prince – Pediatric Clinics of North America

Human oral microbiome

Variations of Tongue Coating Microbiota in Patients with Gastric Cancer – Jie Hu – BioMed Research International

Review: Microbial Nucleic Acid Sensing in Oral and Systemic Diseases – K.E. Crump – Journal of Dental Research

Human respiratory microbiome

Review: The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection – Alexander J. Adami – Tuberculosis

Human gut microbiome

Comparative analyses of fecal microbiota in Tibetan and Chinese Han living at low or high altitude by barcoded 454 pyrosequencing – Long Li & Xin Zhao – Scientific Reports

Obesity changes the human gut mycobiome – M. Mar Rodríguez – Scientific Reports

Review: Understanding Luminal Microorganisms and Their Potential Effectiveness in Treating Intestinal Inflammation – Ince, M. Nedim – Inflammatory Bowel Diseases

Review: Brain-gut-microbiota axis in Parkinson’s disease – Agata Mulak, Bruno Bonaz – World Journal of Gastroenterology

Research Highlight: In transit – Denise Waldron – Nature Reviews Microbiology

Review: Gut microbiota and non-alcoholic fatty liver disease [PDF]-  Paraskevas Gkolfakis – Hepatobiliary Pancreat Dis Int

Animal microbiome

The Hoopoe’s Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird – Sonia M. Rodríguez-Ruano – PLOS ONE

Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus – E. Jousselin – Molecular Ecology Resources

Plant, root, and soil microbiome

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences – Shailendra Yadav – Archaea

Waste treatment microbiology

The Relationship between Microbial Community Evenness and Function in Slow Sand Filters – Sarah-Jane Haig – mBio

Metagenomics and bioinformatics

Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach – Shun’ichi Ishii – Scientific Reports

Exact approaches for scaffolding – Mathias Welle – BMC Bioinformatics

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities – Andreas Henschel – PLOS Computational Biology

Viruses and phages

A classification system for virophages and satellite viruses – Mart Krupovic – Virology Division News

Microbial Ecology

Research Highlight: Single-locus changes perturb community structure – Denise Waldron – Nature Review Genetics
Single gene locus changes perturb complex microbial communities as much as apex predator loss – Deirdre McClean – Nature Communications

Microbes in the news

New intro biology lab tests for germs on campus – Sydney Schaedel – The Daily Pennsylvanian

A Whale of a Tale: Gut microbiome of right whales and other baleen species shares characteristics with those of both cows and meat-eating predators – Bioscience Technology

Science and art

Artist Jennifer Angus Covers the Smithsonian’s Walls With Bugs – Lauren Palmer – ArtNet

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October 7, 2015

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Human oral microbiome

The Microbiome in Populations with a Low and High Prevalence of Caries – I. Johansson – Journal of Dental Research

Human gut microbiome

Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children – S. M. Bahr – Translational Psychiatry

Geriatric respondents and non-respondents to probiotic intervention can be differentiated by inherent gut microbiome composition – Suja Senan – Frontiers in Microbiology

Review: Intestinal microbiota and the innate immune system – a crosstalk in Crohn’s disease pathogenesis – Lea-Maxie Haag – Frontiers in Immunology

Review: The human gut virome: a multifaceted majority – Lesley A. Ogilvie – Frontiers in Microbiology

Review: Microbiota and host immune responses: a love-hate relationship –
Sarah Tomkovich – Immunology

Conference report: Gut microbiota and brain function: An evolving field in neuroscience – Jane A. Foster – International Journal of Neuropsychopharmacology

Animal microbiome

French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives – G. Minard – Frontiers in Microbiology

Plant, root, and soil microbiome

Deterministic processes vary during community assembly for ecologically dissimilar taxa – Jeff R. Powell – Nature Communications

A meta-analysis approach for assessing the diversity and specificity of belowground root and microbial volatiles – Denis Schenkel – Frontiers in Plant Science

Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth – Maskit Maymon – Frontiers in Plant Science

Water microbiome

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle
David J. Lea-Smith – PNAS

Review: Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities – BoonFei Tan – Frontiers in Microbiology

Extremophile microbiome

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential – Richard Allen White III – Frontiers in Microbiology

Built environment microbiology

Typo in title, some plagiarized text, and poor English but still including here: Metagenomic Human Repiratory Air in a Hospital Environment – Yi Yu Lai – PLOS ONE

Food microbiology

Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs – Emilie Lhomme – International Journal of Food Microbiology

Waste microbiology

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry – Priyanka Kumari – PLOS ONE

Phages and viruses

Mammalian Host-Versus-Phage immune response determines phage fate in vivo – Katarzyna Hodyra-Stefaniak – Scientific Reports

Microbial Ecology

Review: Microbiomes: unifying animal and plant systems through the lens of community ecology theory – Natalie Christian – Frontiers in Microbiology

Metagenomics and bioinformatics

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes
Sarah Temmam – PLOS ONE

Microbes in the news

“revolutionary poop platform”: Biomiic’s Platform Will Give People Microbiome Data From Crap: How Joseph Moon, Koji Yasuda and Soohong Kim are changing genomics Harvard iLab – Bostinno

Get To Know Your Poop Bacteria With This New iPhone App – Stephanie M. Lee – BuzzFeed

Could This Tough Bacteria Survive on Mars? – Irene Klot – Discovery

Bacteria in the world’s oceans produce millions of tonnes of hydrocarbons each year – Phys.org

Archaea: A headline on the front page of the New York Times for November 3, 1977, read “Scientists Discover a Way of Life That Predates Higher Organisms”. – Laura Eme, W. Ford Doolittle – Current Biology

The science of retweets – Science Daily
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October 5, 2015

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Characterizing and classifying the oral microbiome, homeostasis in the lung microbiome, collecting airborne microbes, and earthworms feeding on microbiomes.

Human oral microbiome

An accurate and efficient experimental approach for characterization of the complex oral microbiota – Wei Zheng – Microbiome

Phylogenetic approaches to microbial community classification – Jie Ning and Robert G. Beiko – Microbiome

DGGE: Stability of saliva microbiota during moderate consumption of red wine – Elvira Barroso – Archives of Oral Biology

Human respiratory tract microbiome

Review: Homeostasis and its Disruption in the Lung Microbiome – Robert P. Dickson – Am J Physiol Lung Cell Mol Physiol

Human gut microbiome

Faecalibacterium prausnitzii subspecies–level dysbiosis in the human gut microbiome underlying atopic dermatitis – Han Song – Journal of Allergy and Clinical Immunology

Animal models

Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4 – Barbara U. Metzler-Zebeli – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Waste treatment microbiology

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures – Manuel Aira – FEMS Microbiology Ecology

Food microbiology

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques – Mia Ryssel – International Journal of Food Microbiology

Air / Built environment microbiome

Passive dust collectors for assessing airborne microbial material – Rachel I. Adams – Microbiome

Microbes in the news

Beating parasites wins three scientists Nobel prize for medicine: “I think the microbes might almost deserve it more than I do” – Reuters

Nobel Prize Doctors still spreading word of bacteria find – Cathy O’Leary – The West Australian

Intrapartum antibiotics associated with altered infant gut microbiome – Maren Shapiro and Leah Bressler – 2MinuteMedicine

L’eau de bacteria: A whiff of the future? Biotech firms explore using microorganisms to produce flavors, fragrances – Benjamin Plackett – The Charlotte Observer

uBiome Co-Founder Jessica Richman Scoops Top Prize At IVY Awards, uBiome Is Finalist In MedTech Innovator of 2015 – PR Web

Podcast: Our microbiome and our health. Guests: Gary Wu, Tracy Bale, Frederic Bushman – RadioTimes

Microbiome Monday: Animals and Their BFFs – American Museum of Natural History

Permafrost-eating bacteria: a new twist on thawing Arctic and global warming – Thomas S Bianchi – The Conversation

Microbes may play a major role in cloud formation and wet weather – Richard Gray – Daily Mail

Volkswagen: Diesel transplants reveal likely culprit behind DeiselGate: car microbiomes -featuring Jeferina Gordon, Josephine Candelsman, and Hands Dieter Poetsch – – Morten Blaser – The Megabiome

Bacteria Hysteria

Take care when reusing bags: Reusing carrier bags for a diverse range of contents puts consumers at risk of bacterial contamination – Worthing Herald

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September 30, 2015

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Gut virome in infants, metabolome of Mediterranean diet, zebrafish gut assembly, antibiotic use and psoriasis risk, Roseobacter proteomics, and MetaPhlAn2.

Pregnancy and birth

The gut virome and bacterial microbiome—the early years – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Early life dynamics of the human gut virome and bacterial microbiome in infants –
Efrem S Lim – Nature Medicine

Human oral microbiome

Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis – Szymon P Szafrański – NPJ Biofilms and Microbiomes

Urease and Dental Plaque Microbial Profiles in Children – Evangelia Morou-Bermudez – PLOS ONE

High prevalence of colonization of oral cavity by respiratory pathogens in frail older patients with oropharyngeal dysphagia – O. Ortega – Neurogastroenterology & Motility

Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance – Ana Paula Vieira Colombo – Microbial Pathogenesis

Human gut microbiome

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome – Francesca De Fillippis – Gut

Review: Clinical and Pathophysiological Consequences of Alterations in the Microbiome in Cirrhosis – Jane Macnaughtan – American Journal of Gastroenterology

Animal models

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut – Sandi Wong – mBio

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis –
Peter Zanvit – Nature Communications

Plant, root, and soil microbiome

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Oily waste containing natural radionuclides: does it cause stimulation or inhibition of soil bacterial community? – Polina Galitskaya – Journal of Plant Nutrition and Soil Science

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Water microbiome

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

Extremophile microbiome

Perspective: The discovery of Antarctic RNA viruses: a new game changer – Ricardo Cavicchioli – Molecular Ecology

Metagenomics and bioinformatics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling – Duy Tin Truong – Nature Methods

Metabolomics, proteomics

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products – Chad W. Johnston – Nature Communications

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

CRISPRs

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins – Joseph Bondy-Denomy – Nature

Review: CRISPR-Cas immunity in prokaryotes – Luciano A. Marraffini – Nature

Microbes in the news

Study Links Skin Microbiome to Infections – Skin Inc

Ancient ‘Superman’ microbe’s ability to withstand damage to its DNA could be key to unlocking cancer cure, Chinese scientists say – Stephen Chen – South China Morning Post

Another Frontier in Microbiome Research: Preterm Birth – Julie A. Jacob – JAMA

Science, publishing, and career

A taxonomy of authorship roles – Credit Casrai

Bik’s Picks

What if everyone lived to 100? – Georgina Peters – London Business School Review

Gene-Edited “Micropigs” to Be Sold as Pets: The institute in Shenzhen, China, that creates the pigs quoted an initial price tag of $1,600 – David Cyranoski – Scientific American / Nature

1500-Year-Old Mosaic Map Found – Rossella Lorenzi – Discovery

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September 29, 2015

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Gut microbiota in first year of life, the mouse gut metagenome, microbiome and metabolome of cats and dogs, and lichen and flea microbes found in amber.

Pregnancy and birth

Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study – MB Azad – BJOG: An International Journal of Obstetrics & Gynaecology

Human oral microbiome

Oral Microbiome in Chinese Patients with Aggressive Periodontitis and Their Family Members – Yi Li – Journal of Clinical Periodontology

Characterizing Diversity of Lactobacilli Associated with Severe Early Childhood Caries: A Study Protocol – Yihong Li – Advances in Microbiology

Human gut microbiome

Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire: a proof-of-concept study – Pierre H.H. Schneeberger – Infection, Genetics and Evolution

Editorial: Rifaximin, a Molecule with Newly Discovered Anti-inflammatory Properties May Help Shaping the Microbiome and Its Interaction with Host Immunity – F. Pandolfi – Mini-Reviews in Medicinal Chemistry

PhD Thesis: A Computational Tool for Investigating Mechanistic Relationships in the Colon-Diet-Flora Complex – Arun S. Moorthy – University of Guelph

Animal models

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells – Koji Atarashi – Cell

Research Highlights: Keeping track of gut bacteria – Irene Jarchum – Nature Methods

Animal microbiome

A catalog of the mouse gut metagenome – Liang Xiao – Nature Biotechnology

Keynote presentation: The importance of the microbiome and metabolome in health and disease of dogs and cats – Jan Suchodolski – Acta Veterinaria Scandinavica

Antimicrobial use in swine production and its effect on the swine gut microbiota and antimicrobial resistance – Devin B. Holman – Canadian Journal of Microbiology

Pathogen Loading From Canada Geese Faeces in Freshwater: Potential Risks to Human Health Through Recreational Water Exposure – T. J. Gorham – Zoonoses and Public Health

Review: Coral – The World’s Most Diverse Symbiotic Ecosystem – Linda L. Blackall – Molecular Ecology

New Brazilian giant viruses isolation from environmental samples using a panel of protozoa – Fábio P. Dornas – Frontiers in Microbiology

A New Genus of Fleas with Associated Microorganisms in Dominican Amber – George Poinar Jr. – Journal of Medical Entomology

Isolation and Identification of Pathogenic Filamentous Fungi and Yeasts From Adult House Fly (Diptera: Muscidae) Captured From the Hospital Environments in Ahvaz City, Southwestern Iran – Hamid Kassiri – Journal of Medical Entomology

Plant, root, and soil microbiome

Mycorrhizal diversity, seed germination and long-term changes in population size across nine populations of the terrestrial orchid Neottia ovata – Hans Jacquemyn – Molecular Ecology

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) – Nicolas Delhomme – PLOS ONE

Order of arrival structures arbuscular mycorrhizal colonization of plants – Gijsbert D. A. Werner – New Phytologist

Elevated atmospheric CO2 increases microbial growth rates in soil: results of three CO2 enrichment experiments – Evgenia Blagodatskaya – Global Change Biology

Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds – Vívian N. Gonçalves – Environmental Microbiology

The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression – Manuela Krüger – Molecular Ecology

Lichen-associated fungi from Paleogene amber – Elina Kettunen – New Phytologist

Changes in soil bacterial communities and diversity in response to long-term silver exposure – Sotirios Vasileiadis – FEMS Microbiology Ecology

Review: Diversity, distribution and biotechnological potential of endophytic fungi – You-Kun Zheng – Annals of Microbiology

Water microbiome

Assessment of microbial populations within Chicago area nearshore waters and interfaces with river systems – Emily Sible – Data in Brief

Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River – Mariya W. Smith – Frontiers in Microbiology

Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs – Beth H. Baker – Water Research

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments – Dong Li – Environmental Microbiology

Bacterial community shift drives antibiotic resistance promotion during drinking water chlorination – Shuyu Jia – Environmental Science & Technology

Waste microbiology

The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters – Junpeng Rui – Biotechnology for Biofuels

Microbial Ecology

Interspecific diversity reduces and functionally substitutes for intraspecific variation in biofilm communities – Kai Wei Kelvin Lee – The ISME Journal

Bioinformatics

MG7: Configurable and scalable 16S metagenomics data analysis – Alexey Alekhin – BioRxiv

Robust Parameter Estimation for Biological Systems: A Study on the Dynamics of Microbial Communities – Matthias Chung – ArXiv

Techniques

Review: Contemporary molecular tools in microbial ecology and their application to advancing biotechnology – Mamoon Rashid – Biotechnology Advances

Microbes in the news

In intro biology lab, students become research subjects – Julia Liss – Michigan Daily

β-glucan-enriched Pasta Boosts Good Gut Bacteria, Reduces Bad Cholesterol – Science 2.0

Two medical students hope to treat superbug with donations to their ‘poo bank’ – Western Daily Press

Bacteria in ancient flea may be ancestor of the Black Death: Plague bacteria may be 20 million years old– Oregon State University

Antarctic bacteria could hold secret to finding life on Mars – University of Tasmania
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September 27, 2015

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General microbiome

Power Law Analysis of the Human Microbiome – Zhanshan Sam Ma – Molecular Ecology

Pregnancy and birth

Review: Probiotics and necrotizing enterocolitis – Paul Fleming – Pediatric Surgery International

Human oral microbiome

The efficacy of two oral hygiene regimens in reducing oral malodour: a randomised clinical trial – Magda Feres – International Dental Journal

Human respiratory tract microbiome

PhD Thesis: Investigating the host and bacterial factors in cystic fibrosis that promote persistence of infection in the lung – Daniel James Smith – University of Queensland

Human gut microbiome

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants – Roberto Berni Canani – The ISME Journal

Review: Reciprocal interaction of diet and microbiome in inflammatory bowel diseases – Monika Schaubeck – Current Opinion in Gastroenterology

Review: Resistant starches for the management of metabolic diseases – Laure B. Bindels – Current Opinion in Clinical Nutrition & Metabolic Care

Animal models

Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna – Martijn Callens – The ISME Journal

Animal microbiome

Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption – J. Stoops – Food Microbiology

Indigenous microbiota and Leishmaniasis – Mateus Eustáquio de Moura Lopes – Parasite Immunology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B Hadapad – Pest Management Science

Plant, root, and soil microbiome

Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes – Fabiola Miranda-Sánchez – Environmental Microbiology

Non-random species loss in bacterial communities reduces antifungal volatile production – W. H. Gera Hol – Ecology

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment – Mohammad Bahram – The ISME Journal

Plant and root-endophyte assembly history: interactive effects on native and exotic plants – Benjamin A. Sikes – Ecology

Review: Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach – Fernando Carlos Gómez-Merino – Acta Physiologiae Plantarum

Review: Engineering Microbiomes to Improve Plant and Animal Health – U.G. Mueller – Trends in Microbiology

Water microbiome

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River – Bonnie L. Brown – Standards in Genomic Sciences

Extremophile microbiome

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy – Judith M Klatt – The ISME Journal

Emerging spatial patterns in Antarctic prokaryotes – Chun Wie Chong – Frontiers in Microbiology

Waste microbiology

Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels – Maria Westerholm- Biotechnology for Biofuels

Food microbiology

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing – Ruo-si Fang – Journal of Food Sciences

Isolation and characterization of bacteriocinogenic lactic bacteria from M-Tuba and Tepache, two traditional fermented beverages in México – Norma M. de la Fuente-Salcido – Food Science & Nutrition

Built environment microbiology

Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel – Nahum Y. Shpigel – PLOS ONE

Microbial Ecology

Transient dynamics of competitive exclusion in microbial communities – Stilianos Louca – Environmental Microbiology

Metagenomics and bioinformatics

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens – Bastian Greshake – Molecular Ecology Resources

Review: Recovering full-length viral genomes from metagenomes – Saskia Smits – Frontiers in Microbiology

Editorial: The main challenges that remain in applying high-throughput sequencing to clinical diagnostics – Michael Loeffelholz & Yuriy Fofanov – Expert Review of Molecular Diagnostics

Microbes in the News

uBiome Supports Oral Disease Prevention with Donations and Study – PR Web

Probiotic Formula Reverses Cow’s Milk Allergies by Changing Gut Bacteria of Infants – Lab Manager

Microbes and art

Microbe artwork shows the limits of antibiotics – University of Oxford

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September 22, 2015

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Effect of hookworm infection on microbiome of celiac subjects, neutrophil ageing, altering the bone niche, and a personal microbial cloud.

Pregnancy and birth

Influence of a combination of probiotics on bacterial infections in very low birthweight newborns – Zlatka Kanic – Wiener klinische Wochenschrift

Microbiome of death

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses – Seung Hak Yang – Genetics and Molecular Biology

Human respiratory tract microbiome

Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics – Leah J. Hauser – International Forum of Allergy & Rhinology

Human oral microbiome

Comparison of Subgingival and Peri-implant Microbiome in Chronic Periodontitis – Zhang, Qian – Chinese Journal of Dental Research

The novel association between red complex of oral microbe and body mass index in healthy Japanese: a population based cross-sectional study – Kanae Matsushita – Journal of Clinical Biochemistry and Nutrition

Human gut microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects – I. Rangel – Alimentary Pharmacology & Therapeutics

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial – Hyuk Yoon – Journal of Clinical Biochemistry and Nutrition

Review: Improving healthspan via changes in gut microbiota and fermentation – Michael J. Keenan – AGE

Review: Gastric Microbiota – Gianluca Ianiro – Helicobacter

Thesis: High-resolution analysis of the human intestinal microbiota stability landscape – Tineka Blake – Aalto University

Animal models

An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea – Yemeng Li – RCS Advances

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche – Yubin Luo – Cell Metabolism

The levonorgestrel-releasing intrauterine system is associated with delayed endocervical clearance of Chlamydia trachomatis without alterations in vaginal microbiota – E.R. Liechty – Pathogens and Disease

Goldfish: Correlations of Gut Microbial Community Shift with Hepatic Damages and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure – Haifeng Kan – Environmental Science & Technology

Neutrophil ageing is regulated by the microbiome – Dachuan Zhang – Nature

Animal microbiome

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea – Qingsong Yang – Aquatic Ecosystem Health & Management

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease – Ermanno Federici – Microbes and Environments

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression –
Jia Y. Har – Frontiers in Microbiology

Plant, root, and soil microbiome

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage – Natalia Pimentel Esposito-Polesi – World Journal of Microbiology and Biotechnology

Endospores, prokaryotes, and microbial indicators in arable soils from three long-term experiments – Paulina Tamez-Hidalgo – Biology and Fertility of Soils

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities – Sandra Ronca – Frontiers in Microbiology

Responses of aromatic-degrading microbial communities to elevated nitrate in sediments –
Meiying Xu – Environmental Science & Technology

Climate change and physical disturbance cause similar community shifts in biological soil crusts – Scott Ferrenberg – PNAS

Water / Extremophile microbiome

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing – Jae-Ho Jung – Animal Cells and Systems

Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing – H. Jing – Biogeosciences Discussions

Built environment microbiome

Humans differ in their personal microbial cloud – James F. Meadow – PeerJ

Waste microbiology

Relationship between bacterial diversity and environmental parameters during composting of different raw materials – Xueqin Wang – Bioresource Technology

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination – Siobhan O’Brien, Angus Buckling – EMBO Reports

Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation – Marc A. Demeter – Frontiers in Microbiology

Microbial Ecology

Predicting microbial traits with phylogenies – Marta Goberna and Miguel Verdú – The ISME Journal

Bioinformatics and metagenomics

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories – Christine L Sun – The ISME Journal

CCLasso: correlation inference for compositional data through Lasso – Huaying Fang – Bioinformatics

Computational methodology for predicting the landscape of the human–microbial interactome region level influence – Edgar D. Coelho – Journal of Bioinformatics and Computational Biology

Techniques

Targeted single molecule mutation detection with massively parallel sequencing – Mark T. Gregory – Nucleic Acids Research

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures – Stefan A. Boers – Scientific Reports

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis – Thomas Briese – mBio

Microbes in the news

Wherever You Go, Your Personal Cloud Of Microbes Follows – Rob Stein – NPR

Former CEO knew about contamination, wrote “Just ship it”: 28 years for salmonella: Peanut exec gets groundbreaking sentence – Moni Basu – CNN

UGA microbiology researchers identify potential mechanism for neurodegenerative diseases – News Medical

Researchers find novel signature in the brains of children with cerebral malaria – EurekAlert

Science, publishing, and career

About annoying invitations to write papers in questionable journals and strategies how to handle those: You are invited to submit… – David Moher and Anubhav Srivastava – BMC Medicine

Bik’s Picks

8 trillion microbeads pollute U.S. aquatic habitats daily – Jareen Imam – CNN

Science Says This Is the Sound Giraffes Make – Alexandra Sifferlin – Time

I Am the Walrus: What 35,000 Walruses Tell Us About Our Future in Warming World – Miyoko Sakashita – Huffington Post

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September 21, 2015

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Microbiome Digest is back!

Today’s digest features nasal microbiomes of infants, oral microbiome of denture wearers, skin microbiome composition and outcome of infection, Atacama desert soil microbiome, and a comprehensive tree of life.

General microbiome

Viewpoint: The Human Microbiome and the Future Practice of Medicine – David A. Relman – JAMA

Review: Understanding Microbiome Data: A Primer for Clinicians – Seksik P. – Digestive Diseases

Pregnancy and birth microbiome

Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery – Meghan H. Shilts – Host Microbe Interactions

Review: Microbiome and pediatric atopic dermatitis – Claire E. Powers – The Journal of Dermatology

Editorial: Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant’s GI – Joshua E. Elias – Proteomics

Human oral microbiome

The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition – Lindsay E. O’Donnell – PLOS ONE

Forensic Identification in Teeth with Caries – Esther Alia-García – Forensic Science International

Review: Oral Microbiome Metabolism: From “Who Are They?” to “What Are They Doing?” – N. Takahashi – Journal of Dental Research

Review: Polymicrobial Candida biofilms: friends and foe in the oral cavity – Lindsay E. O’Donnell – FEMS Yeast Research
Review: Defining periodontal health – Angelo Mariotti and Arthur F Hefti – BMC Oral Health

Review: Can oral infection be a risk factor for Alzheimer’s disease? – Ingar Olsen and Sim K. Singhrao – Journal of Oral Microbiology

Review: The commensal microbiota and the development of human disease – an introduction – Philip D. Marsh – Journal of Oral Microbiology

Human skin microbiome

The Human Skin Microbiome Associates with the Outcome of and Is Influenced by Bacterial Infection – Julia J. van Rensburg – mBio

Review: Turning the inside out: The microbiology of atopic dermatitis – Harald Brüssow – Environmental Microbiology

Review: Microbiome and pediatric atopic dermatitis – Claire E. Powers – The Journal of Dermatology

Human gut microbiome

Decompensated cirrhosis and microbiome interpretation – Jasmohan S. Bajaj – Nature

The role of whole-grain barley on human fecal microbiota and metabolome – Maria De Angelis – Applied and Environmental Microbiology

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Intestinal microbiota and anastomotic leakage of stapled colorectal anastomoses: a pilot study – Jasper B. van Praagh – Surgical Endoscopy

Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters – Sachiko Miyake – PLOS ONE

Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population – Silan Gu- Microbes and Infection

Long Term Development of Gut Microbiota Composition in Atopic Children: Impact of Probiotics – N. B. M. M. Rutten – PLOS ONE

Review: Does the buck stop with the bugs?: an overview of microbial dysbiosis in rheumatoid arthritis – Pulukool Sandhya – International Journal of Rheumatic Diseases

Review: Potential role of gut microbiota and tissue barriers in Parkinson’s disease and amyotrophic lateral sclerosis – Xin Fang – International Journal of Neuroscience

Editorial: Did you know that your cravings might be microbes controlling your mind? –
A. Zakrisson – Acta Physiologica

Human reproductive tract microbiome

Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis –
B. Vitali – European Journal of Clinical Microbiology & Infectious Diseases

Plant, root, and soil microbiome

In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert – Alfonso F. Davila – Frontiers in Microbiology

Pervasive Effects of Wildfire on Foliar Endophyte Communities in Montane Forest Trees –
Yu-Ling Huang – Plant Microbe Interactions

Interrelated effects of mycorrhiza and free-living nitrogen fixers cascade up to aboveground herbivores – Botir Khaitov – Ecology and Evolution

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences – M. Jeanbille – Soil Microbiology

Composition of fungal soil communities varies with plant abundance and geographic origin – Vanessa Reininger – AoB Plants

Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities – Maria Cristiana Papaleo – The Open Microbiology Journal

Water microbiome

Influence of streambed substratum composition on stream microbial communities exposed to the fungicide tebuconazole – Florence Donnadieu – Freshwater Biology

Built environment microbiome

Microbial Density on Electronic Devices – Sulan Kith – Int.J.Curr.Microbiol.App.Sci

Food microbiology

The microbiota of high-moisture mozzarella cheese produced with different acidification methods – Angela Guidone – International Journal of Food Microbiology

Review: Metagenomic insights into the dynamics of microbial communities in food –
Gilles Kergourlay – International Journal of Food Microbiology

Bioinformatics and metagenomics

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – Jeremy A. Frank – BioRxiv

More microbes

Synthesis of phylogeny and taxonomy into a comprehensive tree of life – Cody E. Hinchliff – PNAS

Single cell activity reveals direct electron transfer in methanotrophic consortia –
Shawn E. McGlynn – Nature

Linking microbial community structure and microbial processes: an empirical and conceptual overview – Raven L. Bier – FEMS Microbial Ecology

Microbes in the news

Russian scientists make progress on secret of eternal life: Living bacteria found in permafrost – ‘3.5 million years old’ – is ‘scientific sensation’ which allows ‘mice grannies’ to reproduce. – The Siberian Times

Bacteria light up Rome’s Colosseum in ‘message of peace’ – Isla Binnie – Reuters

Son takes up fight against bacteria that took father’s leg – Daphne Chen – Washington Times

The frightening spread of antibiotic resistance around the world, visualized- Amy X. Wang – Quartz

Electron transport between species discovered in deep-sea research – Marilyn Malara – UPI

Feeding the world with microbacterial agriculture – Wendy Zukerman – The Saturday Paper
The bacteria-fighting super element that’s making a comeback in hospitals: copper – Lena H. Sun – Washington Post

St. Petersburg home brewer pushes the limits with wild bacteria beers – Michelle Stark – Tampa Bay

Scientists Create 1st ‘Tree of Life’ for Around 2.3 mn Species – TV Newsroom

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