Category Archives: Plant Root Soil microbiome

October 16, 2015

Posted on by

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

[hr]

October 15, 2015

Posted on by

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

[hr]

October 13, 2015

Posted on by

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

[hr]

October 10, 2015

Posted on by

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

[hr]

October 8, 2015

Posted on by

Animal models

Impact of the gut microbiota on the neuroendocrine and behavioural responses to stress in rodents – Sylvie Rabot – OCL

Animal microbiome

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus – Jenifer B. Walke – PLOS ONE

Plant, root, and soil microbiome

Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands – Roberto A. Geremia – New Phytologist

Disentangling the ‘brown world’ faecal–detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Molecular Characterization and Assessment of Phylogenetic Relationship among Tomato Rhizospheric Bacterial Population – Rabaila Riaz – Biologia (Pakistan)

Metagenomic analysis of microbial community in uranium-contaminated soil – Xun Yan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Periphytic and planktonic bacterial community structure in turbid and clear shallow lakes of the Pampean Plain (Argentina): a CARD-FISH approach – Sánchez, Laura María – Latin American Journal of Aquatic Research

Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring – S. Chen – Biogeosciences Discussions

Waste treatment microbiology

Molecular Assessment of Microbial Species Involved in the Biodegradation of Crude Oil in Saline Niger Delta Sediments Using Bioreactors – Chioma Blaise Chikere – Bioremediation & Biodegradation

Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants – An-Dong Li – Frontiers in Microbiology

Metagenomics and bioinformatics

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers – Rachid Ounit, Stefano Lonardi – Algorithms in Bioinformatics

Microbes in the news

From Bacteria to Mold, Health Concerns Abound in Aftermath of South Carolina Flooding – Associated Press

Researchers team up with Illumina to speed-read your microbiome – Medical Xpress

I Sent a Sample of My Poop to uBiome – Sarah Scoles – Discover Magazine

Video: Where are The Most Bacteria-Filled Places In Your Life? – Discover

A ‘bacterial condom’ could help prevent HIV – Alexandra Ossola – Popular Science

Wrap up of talk by Norm Pace on “Metagenomics and the Tree of Life” – Jonathan Eisen – MicroBEnet

Frog Microbes May Help Fight Disease: Commensal skin bacteria adjusted their community structure when frogs were exposed to chytrid fungus in a recent study – Karen Zusi – The Scientist

[hr]

October 7, 2015

Posted on by

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
[hr]

October 6, 2015

Posted on by

Human gut microbiome

Intersections between Microbiome and Heart Failure: Revisiting the Gut Hypothesis –
Yuji Nagatomo – Journal of Cardiac Failure

Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects – Adriana Cuervo – Food and Function

Review: The Human Microbiota: Composition, Functions, and Therapeutic Potential – Rick Conrad, Alexander V. Vlassov – Medical Science Review

Models of microbiome research

Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection – Jason P. Mooney – Scientific Reports

Protocols for the Use of Gut Models to Study the Potential Contribution of the Gut Microbiota to Human Nutrition Through the Production of Short-Chain Fatty Acids –
Andrew J McBain – Springer Protocols Handbooks

Salami? Cecum microbial communities from steers differing in feed efficiency – P. R. Myer – Journal of Animal Science

Animal microbiome

Dholes are a species of wild dog: First report on the bacterial diversity in the distal gut of dholes (Cuon alpinus) by using 16S rRNA gene sequences analysis – Lei Chen – Journal of Applied Genetics

Plant, root, and soil microbiome

Diversity of fungi associated with plants growing in geothermal ecosystems and evaluation of their capacities to enhance thermotolerance of host plants – Wen-Na Zhou – Journal of Plant Interactions

Forage crops alter soil bacterial and fungal communities in an apple orchard – Sijun Qin – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Bacterial communities estimated by pyrosequencing in the soils of chinampa, a traditional sustainable agro-ecosystem in Mexico – Salvador Embarcadero-Jiménez – Journal of Soils and Sediments

Water microbiome

Bacterial diversity and community composition from seasurface to subseafloor – Emily A Walsh – The ISME Journal

Modelling the effects of hydrodynamic regimes on microbial communities within fluvial biofilms: combining deterministic and stochastic processes – Yi Li – Environmental Science & Technology

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect – Danny Ionescu – Scientific Reports

Book chapter: Protistan Diversity in Environmental Molecular Surveys – Ramon Massana – Marine Protists

Book chapter: Diversity of Microbial Eukaryotes in Deep Sea Chemosynthetic Ecosystems Illuminated by Molecular Techniques – Kiyotaka Takishita – Marine Protists

Extremophile microbiome

Metagenomic and metatranscriptomic analyses of Lake Vostok accretion ice – Yury M. Shtarkman – Bowling Green State University

Metabolic networks, proteomics

Gastrointestinal symptoms and altered intestinal permeability induced by combat-training are associated with distinct metabotypic changes – Lee Cheng Phua – Journal of Proteome Research

Review: Roles of Indole as an Interspecies and Interkingdom Signaling Molecule – Jin-Hyung Lee – Trends in Microbiology

Bioinformatics and metagenomics

Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ Preprints

MG-RAST, a Metagenomics Service for the Analysis of Microbial Community Structure and Function – Elizabeth M. Glass, Folker Meyer – Springer Protocols Handbook

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering – Oscar Franzén – Microbiome

Techniques

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms – Hooman Derakhshani – Journal of Basic Microbiology

More microbiology

This paper contains large amounts of plagiarism and confusing images, but here it is: Microbial Forensics in Legal Medicine – Pankaj Shrivastava – SAS Journal of Medicine

Microbes in the news

Georgia State Researcher Gets $1.35 Million to Study Effects of Common Food Additive on Body – Georgia State University
[hr]

October 5, 2015

Posted on by

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

[hr]

October 4, 2015

Posted on by

Pregnancy and birth

Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children – Jing Cheng – ISME Journal

Transplantation and infection microbiology

How’s your microbiota? Let’s check your urine. – Robert R. Jenq – Blood
Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome – Daniela Weber – Blood

Next-Generation Sequencing for Infectious Disease Diagnosis and Management : A Report of the Association for Molecular Pathology – Martina I. Lefterova – The Journal of Molecular Diagnostics

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Human gut microbiome

The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology – Kleiman, Susan C. – Psychosomatic Medicine

Interview: The Relationship Between the Gut Microbiota and Liver Disease – Jasmohan S. Bajaj – Gastroenterology & Hepatology

Animal models

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides – Meng Wu – Science

Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms: Part 2. Role of Gut Microorganisms – Yu Yang – Environmental Science & Technology

Animal microbiome

An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus – Joseph A. Hakim – Frontiers in Microbiology

Plant, root, and soil microbiome

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance – Hiromi Kato – DNA Research

Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica – Ying-wu Shi – Journal of Microbiology

Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan – Yu Fukasawa – Fungal Ecology

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities – Ye Deng – Global Change Biology

Waste microbiology

Contrasting microbial community composition and function perspective in sections of a full-scale coking wastewater treatment system – Shuang Zhu – Environmental Biotechnology

Microbial interactions and implications for oil biodegradation process in mangrove sediments – Adriana Daudt Grativol – PeerJ Preprint

Extremophiles

Subsurface Halophiles: An Analogue for Potential Life on Mars – Woolman, P. F – The Open University

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond – Addis Simachew – Microbiology of Aquatic Systems

Conference Abstract: Life on the frozen continent: diversity of RuBisCO, nifH and pufLM genes in soils around the Princess Elisabeth Station, Sør Rondane Mountains, Antarctica – Guillaume Tahon – Ghent University

Bioinformatics, mathematical models, metagenomics

Habitat Fluctuations Drive Species Covariation in the Human Microbiota – Charles K. Fisher – BioRxiv

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Metabolomics, Proteomics

Video: An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis – David Colatriano, David A. Walsh – JoVE

Rumen microbial communities influence metabolic phenotypes in lambs – Diego P. Morgavi – Frontiers in Microbiology

Phages and viruses

The Tailocin Tale: Peeling off Phage Tails – Maarten G.K. Ghequire and René De Mot- Trends in Microbiology

Functional foods

Review: Prebiotics: why definitions matter – Robert W Hutkins – Current Opinion in Biotechnology

Microbes in the news

Microbiome Meals: Researchers identify a handful of genes that help bacteria in the mouse gut adapt to dietary changes – By Rina Shaikh-Lesko – The Scientist

Signature dishes: As people pass through life they leave a trail of bacteria in their wake – Economist

Chronic kidney disease and its effect on microbiome metabolism – American Microbiome Institute

Recap: Gut microbiome conference September 2015, Huntington Beach – UNC Center of Excellence for Eating Disorders

Nominations sought for NAS Committee on Microbiomes of the Built Environment – Jonathan Eisen – MicroBEnet

Legionnaires’ Bacteria Regrew in Bronx Cooling Towers That Were Disinfected – Benjamin Mueller – New York Times

NYU professor to chair presidential council on antibiotic bacteria resistance – Farhin Lilywala – Washington Square News

You say microbiota, I say microbiome: The 8 word guide to the microbiota – James Vitale – Taconic

[hr]

October 2, 2015

Posted on by

Human gut microbiome

Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease – Mireia Lopez-Siles – Applied and Environmental Microbiology

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection – Joshua S. Son – PLOS ONE

Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC – Kathleen Machiels – Gut

Review: The Intestinal Microbiome in Bariatric Surgery Patients – Christine M. Peat – European Eating Disorders Review

Human urinary tract microbiome

Incontinence medication response relates to the female urinary microbiota – Krystal J. Thomas-White – International Urogynecology Journal

Animal models

In rats: N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota – Matteo M. Pusceddu – PLOS ONE

Table grape consumption reduces adiposity and markers of hepatic lipogenesis and alters gut microbiota in butter fat-fed mice – Jessie Baldwin – The Journal of Nutritional Biochemistry

In mice: Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut – Jinbao Yin – Ecotoxicology

Review: Changes to the Intestinal Microbiome With Parenteral Nutrition – Review of a Murine Model and Potential Clinical Implications – Farokh R. Demehri – Nutrition in Clinical Practice

Plant, root, and soil microbiology

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis – Chen-hua Li – PLOS ONE

Water microbiology

The Ocean as a Global Reservoir of Antibiotic Resistance Genes – Stephen M. Hatosy – Applied and Environmental Microbiology

Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats – Mireia Fillol – FEMS Microbiology Ecology

DGGE: Bacterial Diversity in Bohai Bay Solar Saltworks, China – Jiaojiao Zhang – Current Microbiology

Techniques

Quantitative Microbial Ecology through Stable Isotope Probing – Bruce A. Hungate – Applied and Environmental Microbiology

Bioinformatics

Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Science, publishing, and career

Predatory publishers earned $75 million last year, study finds – John Bohannon – Science

‘Predatory’ open access: a longitudinal study of article volumes and market characteristics – Cenyu Shen and Bo-Christer Björk – BMC Medicine

Ten Simple Rules for Protecting Research Integrity – David M. Shaw, Thomas C. Erren – PLOS Computational Biology

Microbes in the news

How gut health affects cycling performance – Cycling Weekly

Microbial sampling starts in Cherokee Homes – Jordan Peccia – MicroBEnet

Why It Was Easier to Be Skinny in the 1980s – Olga Khazan – The Atlantic

How do we protect ourselves from Martian bacteria? – Anjana Ahuja – World Economic Forum
[hr]