Category Archives: Metagenomics & Bioinformatics

October 20, 2015

Posted on by

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
[hr]

October 17, 2015

Posted on by

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
[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 12, 2015

Posted on by

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

[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 9, 2015

Posted on by

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
[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 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]