Author Archives: eliesbik

October 20, 2015

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Cohabitation of helminths, bacteria, and host in the gut, diurnal sampling bias in plankton biodiversity, contaminant influence on groundwater microbiome, volatile affairs, and new tools for metagenomics.

Events

Postdoc and grad student Summit — preceding the EMBO Symposium on Aquatic Microeukaryotes: Abstract deadline October 22 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Periodontal clinical and microbiological characteristics in healthy versus generalized aggressive periodontitis families – Mabelle de F. Monteiro – Journal of Clinical Periodontology

Masters Thesis: Caries and the Oral Microbiome of a Native American Population – Michael Tuan – Ohio State University

Human gut microbiome

Review: Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity – Lisa A. Reynolds – The Journal of Immunology

Review: Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases – Bidisha Paul – Clinical Epigenetics

Review: Intestinal Microbiota Metabolism and Atherosclerosis – Tian-Xing Liu – Chinese Medical Journal

Animal models

Colonic Lesions, Cytokine Profiles, and Gut Microbiota in Plasminogen-Deficient Mice – Bill Vestergaard – Comparative Medicine

Plant, root, and soil microbiomes

Cyanobacterial composition and spatial distribution based on pyrosequencing data in the Gurbantunggut Desert, Northwestern China – Bingchang Zhang – Journal of Basic Microbiology

Disease in apple orchards: Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth? – Bunlong Yim – Frontiers in Microbiology

A fragrant neighborhood: Volatile mediated bacterial interactions in soil – Kristin Schulz-Bohm – Frontiers in Microbiology

Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing – Lin Chen – Frontiers in Microbiology

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California – A. C. Hollowell – Plant Microbe Interactions

Water microbiome

Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique – Satoshi Nagai – Gene

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations – Xiaofen Wu – The ISME Journal

Viral impact on prokaryotic and microalgal activities in the microphytobenthic biofilm of an intertidal mudflat (French Atlantic coast) – Hélène Montanié – Frontiers in Microbiology

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes – Christopher L. Hemme – Frontiers in Microbiology

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir – Xiao Yang – Water

Extremophile microbiology

Review: Extremely Thermophilic Microorganisms as Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals – Benjamin M. Zeldes – Frontiers in Microbiology

Metagenomics and bioinformatics

Snowball: Strain aware gene assembly of Metagenomes – I. Gregor – ArXiv

PEPR: Pipelines for Evaluating Prokaryotic References – Nathan D. Olson – PeerJ preprint

cual­id: globally unique, correctable, and human­friendly sample identifiers for
comparative ­omics studies – John H Chase – PeerJ preprint

Why we need more algal metagenomes – Linda E. Graham – Journal of Phycology

Phages and viruses

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters – Jeremy J. Barr – PNAS

Microbial Ecology

Interspecies interactions are an integral determinant of microbial community dynamics –
Fatma A. A. Aziz – Frontiers in Microbiology

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity – Caroline M. Tucker – Oikos

Review: Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review – Patricia M. C. Huijbers – Environmental Science & Technology

More microbiology

Self-Protected Nitrate Reducing Culture for Intrinsic Repair of Concrete Cracks –
Yusuf C. Ersan – Frontiers in Microbiology

Metabolomics

Review: Volatile affairs in microbial interactions – Ruth Schmidt – The ISME Journal

Microbes in the news

Society for Neuroscience meeting in Chicago : Probiotic bacteria may aid against anxiety and memory problems – Ian Sample – The Guardian

ID Week: How Babies’ Gut Bacteria May Help Find Treatments for C. Diff – Rachael Rettner – Live Science

Video: Speaking of Chemistry: What is the Gut Microbiome? Matt Davenport – American Chemical Society

Study reveals a key role your gut bacteria play in body’s self-defense – David Callahan – Medical Xpress

Gut Microbiome Insights; Obesity and Digestive Health Risks; Delivery Options and Predictors of Failure for Fecal Microbiota Transplantation; among Featured Topics Presented at the American College of Gastroenterology’s 80th Annual Meeting – PR NewsWire

MS conference, Barcelona: Q&A With Helen Tremlett From the University of British Columbia: Gut Microbiome And Its Role In Multiple Sclerosis -HCP Live

Virginia Tech scientists reveal more about how body copes with common gut bacterium – Augusta Free Press

High Starch Diets’ Effects on Stress Response in Horses – Casie Bazay – The Horse

These Bacteria Could Live in Europa’s Ocean – Irene Klotz – Discovery

Local news: Dozens Sick With Shigella Bacteria After Eating At San Jose Restaurant – CBS Local

The Phage is a Lonely Hunter: New research reveals that bacteriophages use slow, staccato movements to hunt bacteria on cell surfaces – Michael Price – SDSU

Creating Healthier Microbiomes, from Conception to Childhood: A Clinical Conversation with Geeta Maker-Clark, MD, and Robert Rountree, MD -Alternative and Complementary Therapies

Microbes and art

Very cool: A Microbiologist Recreated ‘Starry Night’ With Bacteria In A Petri Dish And it’s not too shabby – Priscilla Frank – Huffington Post

Bik’s Picks

Poo turns naked mole rats into better babysitters – Oestrogen in queen mole rat’s faeces drives subordinates to care for her pups – Sara Reardon – Nature News
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October 19, 2015

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None of the Elsevier links from my PubMed alert worked today, and I could not find the articles through other searches. So just a short digest with polymicrobial DNA in sepsis patients and a collection of pre-antibiotic bacteria.

Infection microbiome

The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients – MMP Faria – BMC Microbiology

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis – Alexander L. Greninger – Genome Medicine

Microbiome models

The gut microbiota modulates host amino acid and glutathione metabolism in mice – Adil Mardinoglu – Molecular Systems Biology

Microbiome engineering could select for more virulent pathogens – Luke McNally – BioRxiv

Plant, root, and soil microbiome

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments – Özge Eyice – Archives of Microbiology

Other microbiology

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource – Kate S. Baker – Genome Medicine

Microbes in the news

Mac researcher eyes gut bacteria in preventing celiac disease: Elena Verdú – Joanna Frketich – Hamilton Spectator

This is of concern: No time to take safety training, says infected microbiology lab supervisor: report – Ruth Bonneville – Winnipeg Free Press

A super short microbial tour of Paris tombs – Rosin Cerate

How a 500-year experiment to revive dormant microbes could reveal the secrets to cheating time – Alex Riley – Aeon
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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 15, 2015

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Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyuan Fu – Circulation Research

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Mats Wedin – Environmental Microbiology

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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October 14, 2015

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Gut microbes and the brain, transgenic goats, Salmonella infection of pigs, viral infection in honey bees, and a catalogue of microbial culture media.

Human gut microbiome

Feature: The tantalizing links between gut microbes and the brain – Peter Andrey Smith – Nature

Animal models

Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella enterica and Lawsonia intracellularis – Klaudyna A. Borewicz – PLOS ONE

The Effects of GH Transgenic Goats on the Microflora of the Intestine, Feces and Surrounding Soil – Zekun Bao – PLOS ONE

Research highlight: Culinary traditions—revealing the effect of travel and diet on gut microbiota and motility – Gillian Patman – Nature Gastroenterology & Hepatology

Animal microbiome

No apparent correlation between honey bee forager gut microbiota and honey production – Melissa A. Horton – PeerJ

Four Categories of Viral Infection Describe the Health Status of Honey Bee Colonies – Esmaeil Amiri – PLOS ONE

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants – Clarissa S. Sit – PNAS

More microbes

Harnessing the landscape of microbial culture media to predict new organism–media pairings – Matthew A. Oberhardt – Nature Communications

Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units – Marine Combe – Cell Host & Microbe

Microbes in the news

What does your gut microbiome look like? – Katherine Harmon Courage – Popular Science

Microbiome May Predict Colon Cancer Tumor Mutational Status – Neil Osterweil – Medscape

“Studying sanitation is not always the sexiest topic” Stanford study on the effects of toilet facilities on child health in rural Africa – Stanford News

NDSU researcher, students study how bacteria adapts to survive – North Dakota State University

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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 12, 2015

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A nice and short digest today. Happy Columbus Day!

Human gut microbiome

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation – Gopanandan Parthasarathy – Gastroenterology

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa – Pål Trosvik and Eric Jacques de Muinck – Microbiome

Review: The Gut Microbiota as a Therapeutic Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors FXR and TGR5 – Annemarie Baars – Microorganisms

Review: Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy
Is It All About Diet? – Daniela Elena Serban – Nutrition in Clinical Practice

Review: Role of the Gut Microbiome in Obesity and Diabetes Mellitus – Gillian M. Barlow – Nutrition in Clinical Practice

Animal models

Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration – Hui-Xin Liu – Journal of Hepatology

Metagenomics and Bioinformatics

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data – Genivaldo Gueiros Z. Silva – Bioinformatics

Viruses and phages

Research Highlight: Phages’ box of tricks for CRISPR – Naomi Attar – Nature Reviews Microbiology

Microbes and art

Microbial masterpieces! Scientists ‘paint’ detailed works of art by growing bacteria from human skin and even faeces in petri dishes – Victoria Woollaston – Daily Mail
http://www.dailymail.co.uk/sciencetech/article-3269542/Microbial-masterpieces-Scientists-paint-detailed-works-art-growing-bacteria-petri-dishes.html

Microbes in the news

University of New Haven professor’s research focuses on ‘horrible’ Lyme disease – Mark Zaretsky – New Haven Register

Repeat from earlier podcast: The Bacterial Cloud We All Carry Could Be As Unique As A Fingerprint – Rob Stein – NPR

Antibiotics ban: California first state to outlaw routine use of bacteria-fighting drugs in livestock – Jessica Calefati – Mercury News

Desperate Families in Delhi as Dengue Overwhelms Hospitals – Nida Najar – New York Times

Novel mathematical method may help reduce development of antibiotic-resistant bacteria – News Medical

Bacteria Hysteria

Concerned about germs on shopping trolley handles? Cleaning gadget beats bacteria – Hannah Bouckley – BT

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October 10, 2015

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The Eukaryome of the human gut, core microbiome in rumen, overweight kitties, and viral metagenomics of a hot spring.

Human gut microbiome

Repertory of Eukaryotes (Eukaryome) in the Human Gastrointestinal Tract: Taxonomy and Detection Methods – Ibrahim Hamad – Parasite Immunology

Diversity of Duodenal and Rectal Microbiota in Biopsy Tissues and Luminal Contents in Healthy Volunteers – Gangping Li – Journal of Microbiology and Biotechnology

Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease – Bashar Aqel, John K. DiBaise – Nutrition in Clinical Practice

Review: Gut Microbiome: What We Do and Don’t Know – Gail A. Cresci and Emmy Bawden – Nutrition in Clinical Practice

Editorial: Contribution of Gut Bacteria to Lipid Levels Another Metabolic Role for Microbes? – Hooman Allayee, Stanley L. Hazen

Human vaginal microbiome

Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota – Kenetta L. Nunn – mBio

Models of microbiome research

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity
Denise Morais da Fonseca – Cell

Animal microbiome

Overweight and the feline gut microbiome – a pilot study – I. N. Kieler – Journal of Animal Physiology and Animal Nutrition

Bovine mastitis may be associated with the deprivation of gut Lactobacillus – C. Ma – Beneficial Microbes

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range – Gemma Henderson – Scientific Reports

Plant, root, and soil microbiome

Evaluating a multigene environmental DNA approach for biodiversity assessment
Alexei J. Drummond – GigaScience (via PMC)

Sheep grazing and soil bacterial diversity in shrublands of the Patagonian Monte, Argentina – Nelda L. Olivera – Journal of Arid Environments

Climatic conditions, soil fertility and atmospheric nitrogen deposition largely determine the structure and functioning of microbial communities in biocrust-dominated Mediterranean drylands – Raul Ochoa-Bon – Plant and Soil

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters – Amélia Bourceret – Microbial Ecology

Water and extremophile microbiome

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins – Dorina Seitaj – PNAS
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs – Sóley Ruth Gudbergsdóttir – Environmental Microbiology

Waste treatment microbiology

Characterization of microbial communities in water and biofilms along a large scale SWRO desalination facility: Site-specific prerequisite for biofouling treatments – Adi Levi – Desalination

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans – Massimo C Pernice – The ISME Journal

Metabolomics

A Global Metabolomic Analysis of a Mammalian Host Infected with Bacillus anthracis
Chinh T.Q. Nguyen – Infection and Immunity

Sequencing techniques

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
Tatsuya Unno – Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

Differential analysis of biological networks – Da Ruan – BMC Bioinformatics

SPINGO: a rapid species-classifier for microbial amplicon sequences – Guy Allard – BMC Bioinformatics

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection – Xiao Ding – BMC Bioinformatics

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology – Feng Ju and Tong Zhang – Environmental Science & Technology

A Comparison of Base-calling Algorithms for Illumina Sequencing Technology – Ashley Cacho – Briefings in Bioinformatics

Metabolomics

A Validated High Resolution Mass Spectrometry-based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype – Julie Vanden Bussche – Analytical Chemistry

Microbes in the news

Should We Bank Our Own Stool? – Moises Velasquez-Manoff – New York Times

Researchers use gut bacteria composition to genetically classify colorectal tumors – EurekAlert

Bacteria take on stinky problem in Kenner – Christie Walton – Fox8Live

MSU faculty member earns grant award for biofilm methodology research: Darla Goeres was recently awarded a Burroughs Wellcome Innovation in Regulatory Science Award. – Montana State University

Biotech of the week: Enterome, the Leading French Microbiome Start-up – LaBiotech

Conference Coverage: ID week: Drug Resistance: What Happens Inside the Nose? – HCP Live

Antibiotic use and cancer risk: Repeat exposure poses harm: interview with Ben Boursi – Healio

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October 9, 2015

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Microbes and midwives, gut-brain axis, gluten immunopathology, viruses from farm to fork, and handwashing in students.

Pregnancy and birth

Conference abstract: Seeding the infant microbiome: The midwife’s role – Asha McCurley – Women and Birth

Human skin microbiome

Poor hand hygiene by college students linked to more occurrences of infectious diseases, medical visits, and absence from classes – Kayla J. Prater – American Journal of Infection Control

Human gut microbiome

Gut microbiota interacts with brain microstructure and function – José-Manuel Fernandez-Real – The Journal of Clinical Endocrinology & Metabolism

Microbiota–Gut–Brain Axis: Yeast Species Isolated from Stool Samples of Children with Suspected or Diagnosed Autism Spectrum Disorders and In Vitro Susceptibility Against Nystatin and Fluconazole – A. Serda Kantarcioglu

Animal models

Intestinal Microbiota Modulates Gluten-Induced Immunopathology in Humanized Mice – Heather J. Galipeau – American Journal of Pathology

Animal microbiome

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation – Claudia Barelli – Scientific Reports

Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing – Michel Diouf – PLOS ONE

Built Environment microbiome

Microbial control of dental unit water: Feedback on different disinfection methods experience – Julie Lizon – American Journal of Infection Control

Food microbiology

Review: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce – Dan Li – Comprehensive Reviews in Food Science and Food Safety

Metagenomics

Strain recovery from metagenomes – C Titus Brown – Nature Biotechnology

Science, publishing, and career

Peer Review Resources: tips and suggestions from experienced reviewers as well as externally prepared resources for the beginning peer reviewer – Publons

Funny and informative: So you think you want to run an environmental conservation meeting? Advice on the slings and arrows of outrageous fortune that accompany academic conference planning – E. C. M. Parsons – Journal of Environmental Studies and Sciences

Microbes in the news

UNC-Chapel Hill researchers reveal type of vaginal bacteria that protects women from HIV – EurekAlert

When Evolution Is Infectious – How “probiotic epidemics” help wildlife—and us—survive – Moises Velasquez-Manoff – Nautilus
It takes a village of bacteria to help frogs fight deadly disease, Virginia Tech researchers say – Augusta Free Press

Dirty hospital equipment causes 11 people to become infected with bacteria that could lead to pneumonia – Daily Mail

Cat poop coffee goes biotech – Nature Biotechnology

Bad times for good bacteria: how modern life has damaged our internal ecosystems – The Conversation

Gut microorganisms cause gluten-induced pathology in mouse model of celiac disease – MedicalXpress

Bacteria Hysteria

Sponsored by Dettol: Most teddy bears are covered in food poisoning bacteria, tests reveal – Plymouth Herald
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