Category Archives: Animal experiments

February 9, 2015

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Human oral microbiome

Pulp and plaque microbiotas of children with severe early childhood caries – Natalia I. Chalmers – Journal of Oral Microbiology

Analysis of oral microbial community and Th17-associated cytokines in saliva of patients with oral lichen planus – Kun Wang – Microbiology and Immunology

Human gut microbiome

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities – Jiachao Zhang – The ISME Journal

Distinct gut microbiota of healthy children from two different geographic regions of Thailand – Orawan La-ongkham – Archives of Microbiology

An Appropriate Cutoff Value for Determining the Colonization of Helicobacter pylori by the Pyrosequencing Method: Comparison with Conventional Methods – Jaeyeon Kim – Helicobacter

Review: Dysbiosis of the gut microbiota in disease – Simon Carding – Microbial Ecology in Health and Disease

Review: Manipulating the gut microbiota to maintain health and treat disease – Karen P. Scott – Microbial Ecology in Health and Disease

Fecal Transplants

Successful treatment of severe sepsis and diarrhea after vagotomy utilizing fecal microbiota transplantation: a case report – Qiurong Li – Critical Care

Animal models of microbiome research

Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs – Marcio C Costa – BMC Veterinary Research

Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract – Jyoti Shankar – Scientific Reports

Gut microbial markers are associated with diabetes onset, regulatory imbalance, and IFN-γ level in NOD Mice – Ł. Krych – Gut Microbes

Defective NOD2 peptidoglycan sensing promotes diet-induced inflammation, dysbiosis, and insulin resistance – Emmanuel Denou – EMBO Journal

Animal Microbiome

Internal Extracellular Bacteria of Diaphorina citri Kuwayama (Hemiptera: Psyllidae), the Asian Citrus Psyllid – Lakshmi D. Kolora – Current Microbiology

Soil Microbiome

Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem – Jun-Tao Wang- Journal of Soils and Sediments

Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics – Dini Nurdiani – Journal of Bioscience and Bioengineering

Microbial diversity of mangrove sediment in Shenzhen Bay and gene cloning, characterization of an isolated phytase-producing strain of SPC09 B. cereus – Shengpeng Zhang – Applied Microbiology and Biotechnology

Food Microbiology

Zooming into food-associated microbial consortia: A “cultural” evolution
Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Review: Emerging DNA-based technologies to characterize food ecosystems – Andrea Galimberti – Food Research International

Bioreactor microbiology

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities – Wuttichai Mhuantong – Biotechnology for Biofuels

Metabolomics

Defining the Microbial Effluxome in the content of the Host-Microbiome Interaction – Anastasios Ioannidis – Frontiers in Pharmacology

Reference-free comparison of microbial communities via de Bruijn graphs – Serghei Mangul and David Koslicki – preprint

A systematic evaluation of high-dimensional, ensemble-based regression for
exploring large model spaces in microbiome analyses – Jyoti Shankar – BMC Bioinformatics

Microbial Ecology

Opinion: Landscape community genomics: understanding eco-evolutionary processes in complex environments – Brian K. Hand – Trends in Ecology & Evolution

Techniques

Accurate, multi-kb reads resolve complex populations and detect rare
microorganisms – Itai Sharon – Genome Research

A simple separation method for downstream biochemical analysis of aquatic microbes – Cody E. Garrison, Alexander B. Bochdansky – Journal of Microbiological Methods

Microbes in the News

How to Make Breakfast With Your Vagina – Janet Jay – Motherboard

Breast IS best: Researchers say babies get microbes from mother’s milk that makes them ‘more ready’ to digest solid food – Mark Prigg – Daily Mail

Common antibiotics trigger significant changes in equine gut bacteria – study – Horsetalk

The Hungry Microbiome Part 4: The colon, colon cancer, and butyrate – Jesse Hawley – CSIRO

Google Maps for bacteria? How NYC subway swab could change public health (Podcast) – PBS Newshour

Investigation into possible spread of bacteria found in local primate center – Ashley Rodrigue – WWLTV

What friendly bacteria really CAN do for you… but probiotic makers are banned from telling us about – Sadie Nicholas – DailyMail UK

Bacteria Hysteria: ‘Bacteria and mold will accumulate’: Expert weighs in on bath towel use – Fox8.com

Gut Bacteria Differs in Gluten-free Celiac Patients with Persistent Symptoms – Jefferson Adams – Celiac.com

Bacterial DNA from the Black Death found in teeth – Yngve Vogt – MedicalXpress

UC Merced graduate student to continue oral bacteria research in Brazil – Ana B. Ibarra – Mercedsunstar

Meet the Poop-Sniffing Dogs That Are Saving Endangered Wildlife – Charyn Pfeuffer – Wired

Experimental drug containing tiny fragments of teenage acne bacteria trialled on MS patients – Lucie van den Berg – Herald Sun

Bacteria’s hidden traffic control – Phys.org

Science, publishing, career

How not to write a sequence assembly comparison paper – Keith Robison – Omics!Omics!

Research Misconduct Identified by the US Food and Drug Administration
Out of Sight, Out of Mind, Out of the Peer-Reviewed Literature – Charles Seiffe – JAMA Internal Medicine

Are Your Medications Safe? The FDA buries evidence of fraud in medical trials. My students and I dug it up. – Charles Seife – Slate

Bik’s Picks

The Champion Egg-Layers of the Bird World – Emma Bryce – Audubon

Enzyme rapidly reduces sulfites in wine – Tim Sandle – Digital Journal

NASA Mars Curiosity Rover Collects Soil Samples – Deborah Grace – Pierce Pioneer

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February 6, 2015

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Pregnancy and birth microbiome

The composition of the gut microbiota throughout life, with an emphasis on early life – Juan Miguel Rodríguez – Microbial Ecology in Health and Disease

Review: Antenatal lower genital tract infection screening and treatment programs for preventing preterm delivery – Ussanee S Sangkomkamhang – Cochrane Library

Animal models of microbiome research

Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation – Edward Alain B. Pajarillo – Applied Microbiology and Biotechnology

Animal microbiome

Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae –
Timothy K. O’Connor – Frontiers in Microbiology

Plant microbiome

Agricultural probiotics enter spotlight – Jeffrey L Fox – Nature

Soil microbiome

Inorganic fungicides as routinely applied in organic and conventional agriculture can increase palatability but reduce microbial decomposition of leaf litter – Jochen P. Zubrod – Journal of Applied Ecology

Effect of diesel-oil addition on soil microbiological parameters in systems with and without plants – MC Petenello – Terra Latinoamericana

Does long-term use of mineral fertilizers affect the soil microbial biomass? – D Geisseler – Better Crops with Plant Food

News and views: Microbes: The chief ecological engineers in reinstating equilibrium in degraded ecosystems – Jay Shankar Singh – Agriculture, Ecosystems & Environment

Review: Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review – Marie Simonin, Agnès Richaume – Environmental Science and Pollution Research

Water microbiome

Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya – Tom O. Delmont – Frontiers in Microbiology

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait) – Pier Luigi Buttigieg – Frontiers in Microbiology

Aquifer environment selects for microbial species cohorts in sediment and groundwater – Laura A Hug – The ISME Journal

Fate of the Herbicide Alachlor Exposed to Different Microbial Consortia in Aquatic Systems – Armelle Paule – Water, Air, & Soil Pollution

Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi canyon 118 before the Deepwater Horizon disaster – Sarah Underwood – Deep Sea Research Part II: Topical Studies in Oceanography

Air microbiome

Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR – Min Wei – Journal of Environmental Sciences

Bioreactor and wastewater microbiology

Processing barley grain with lactic acid and tannic acid ameliorates rumen microbial fermentation and degradation of dietary fibre in vitro – Kathrin Deckardt – Journal of the Science of Food and Agriculture

Microbial community dynamics associated with veterinary antibiotics removal in constructed wetlands microcosms – Joana P. Fernandes – Bioresource Technology

Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing – Thorsten Köchling – Applied Microbiology and Biotechnology

Metabolomics and proteomics

Review: Nutriproteomics: Facts, concepts, and perspectives – Sascha Sauer and Toni Luge – Proteomics

Microbial Ecology

Dispersal among local communities does not reduce historical contingencies during metacommunity assembly – Zhichao Pu and Lin Jiang – Oikos

Functional dissimilarity across trophic levels as a driver of soil processes in a Mediterranean decomposer system exposed to two moisture levels – Mathieu Coulis – Oikos

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor – Alexandra Igorevna Klimenko – BMC Evolutionary Biology

Immunology

Recent infections are associated with decreased risk of rheumatoid arthritis: a population-based case-control study – Maria EC Sandberg – Annals of the Rheumatic Diseases

Viruses and phages

Assembly of viral genomes from metagenomes – Saskia L. Smits – Frontiers in Microbiology

Sorting of small infectious virus particles by flow virometry reveals distinct infectivity profiles – Raphaël Gaudin & Natasha S Barteneva – Nature Communications

Metagenomics and chromosomal organization

Novel assay to measure the plasmid mobilizing potential of mixed microbial communities – Uli Klümper – Frontiers in Microbiology

Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria – Ryan C. Lynch – Frontiers in Microbiology

Review: Evolution of small prokaryotic genomes – David J. Martínez-Cano – Frontiers in Microbiology

Bioinformatics

A Quick Guide for Building a Successful Bioinformatics Community – Aidan Budd – PLOS Computational Biology

Microbes in the news

Bacteria help breastfed babies digest solid food – Mark Derewicz – Futurity

From fourth-century soup to 21st-century procedure, fecal transplantation proves its worth against stubborn bacteria – VA Research Currents (HT: Inder Perkash)

Mapping the Microbes of the New York City Subway – Marcus Woo – Wired.com

Age-related hepatitis B infection and the gut microbiome – Heather Zeiger – Medical Xpress

Researchers Uncover Infant Gut Microbiome Alterations Linked to Type 1 Diabetes – GenomeWeb

Gut Bacteria Link Between Heart and Kidney Disease Strengthened – WH Wilson Tang – MedicalResearch.com

Nine ways your gut can protect your heart – Giovanni Campanile – Mens Fitness

New clinical study to focus on gut, autism connection (with James Versalovic) – Baylor College of Medicine

Science, publishing, and career

Frontiers for Young Minds – non-profit scientific journal for 8-15 year olds – Frontiers

A classroom experiment – Jeffrey Mervis – Science

Undergraduate research experiences: Impacts and opportunities – Marcia C. Linn – Science

Science by any means necessary (interview with Erich Jarvis) – Rachel Bernstein – Science

The Scientist’s Toolbox: Last Call – Name and describe a currently nonexistent invention that would make you a more effective scientist – Science

Breaking bad science – Joel Best – Science

Science and art

Cute pathology pictures – Seriously Science – Discover Magazine

Bik’s Picks

This college student is eating bugs for 30 days so you will too – Rachel Feltman – Washington Post

Where is Silicon Valley? – Jorge Guzman, Scott Stern – Science

Fire Department Saves Woman From Robot Vacuum Attack. It Begins. – Dan Van Winkle – The Mary Sue

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February 5, 2015

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Microbiome of pregnancy and birth

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes – Aleksandar D. Kostic – Cell Host & Microbe

Meeting abstracts in the Journal of Allergy and Clinical Immunology:
Influence of Infant Gut Microbiome on Development of Infant Regulatory T Cells – Kevin Bobbitt
The Infant Gut Microbiome Mediates the Association Between Breastfeeding and Allergic-like Response to Pets in Children – Alexandra R. Sitarik
Association of the Infant Gastrointestinal Microbiome with Nocturnal Symptoms in Children with Asthma – Albert M. Levin
Decrease in Diversity of Nasal Microbiota during Wheezing Episodes in Preschool Children – Gorka Alkorta-Aranburu

Maternal influences on fetal microbial colonization and immune development – Joann Romano-Keeler & Jörn-Hendrik Weitkamp – Pediatric Research

Human oral microbiome

Evaluation of human and microbial DNA content in subgingival plaque samples collected by paper points or curette – P.J. Pérez-Chaparro – Journal of Microbiological Methods

Human vaginal microbiome

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR – Takashi Kurakawa – Journal of Microbiological Methods

Human gut microbiome

Weight Gain After Fecal Microbiota Transplantation – Neha Alang and Colleen R. Kelly – Open Forum Infectious Diseases

The Gut Microbiota, Intestinal Permeability, Bacterial Translocation, and Nonalcoholic Fatty Liver Disease: What Comes First? – Erin Spengler, Rohit loomba – CMGH Cellular and Molecular Gastroenterology and Hepatology

$70 to read this one: Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy – Xiaobo Feng – The American Surgeon

Review: Gut Microbiota: Association with NAFLD and Metabolic Disturbances – E. Lau – BioMed Research International

Review: Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry – Eva M Selhub – Journal of Physiological Anthropology

Animal models of microbiome research

Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec – R. Khiaosa-ard – Journal of Dairy Science

Effect of feeding Jerusalem artichoke (Helianthus tuberosus) root as prebiotic on nutrient utilization, fecal characteristics and serum metabolite profile of captive Indian leopard (Panthera pardus fusca) fed a meat-on-bone diet – S.K. Pradhan – Zoo Biology

Comparative Analysis of Gastrointestinal Microbiota Between Normal and Caudal-Related Homeobox 2 (Cdx2) Transgenic Mice – Hirotsugu Sakamoto – Intestinal Research

Plant microbiome

Impact of mycorrhizal inoculation on the development of Intsia bijuga grown on soil under exotic species Casuarina equisetifolia plantation – Dina Ratahiriarisoa – Journal of Plant Sciences

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient – Susan G. Jarvis – New Phytologist

Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii – David H. Green – BioMed Research International

Review: The importance of the microbiome of the plant holobiont – Philippe Vandenkoornhuyse – New Phytologist

Soil microbiome

Soil microbial response to waste potassium silicate drilling fluid – Linjun Yao – Journal of Environmental Sciences

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218O – Elizabeth A. Rettedal and Volker S. Brözel – MicrobiologyOpen

Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils – Shamsa Akbar – Journal of Basic Microbiology

Microbiome of the built environment
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics – Ebrahim Afshinnekoo – Cell Systems

Food microbiology

Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos – Junichiro Marui – Bioscience of Microbiota, Food and Health

Review: Zooming into food-associated microbial consortia: A “cultural” evolution – Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Bioinformatics

Programming: Pick up Python – A powerful programming language with huge community support – Jeffrey M. Perkel – Nature

Microbes in the news

Podcast: What lived in ancient human intestines? Interview with Jessica Metcalf – The Naked Scientists

Woman becomes obese after fecal transplant from overweight donor – Brooks Hays – UPI

Microbiome linked to type 1 diabetes: Shift in microbiome species diversity prior to disease onset – Science Daily

Gut microbes are good for mood – Xanthe Hunt – LongevityLive

Satire: Five Dead As Pro- and Anti-Microbiome Demonstrators Clash – The Allium

Video: The role of gut bacteria in brain disease – Robert Friedland – YouTube

Book: I, Superorganism – Jon Turney – IconBooks

Big Data and Bacteria: Mapping the New York Subway’s DNA – Robert Lee Hotz – Wall Street Journal

Drug-resistant bacteria lurk in subway stations, high school students discover – Science Daily

Among New York Subway’s Millions of Riders, a Study Finds Many Mystery Microbes – Elizabeth A. Harris – New York Times

Environmental factors may affect how infants’ gut bacteria mature – News Medical

Could Genetically Engineered Bacteria in Your Colon Replace Vitamins? – Sarah Zhang – GizModo

Why Measles Is the Most Contagious Virus – Mandy Oaklander – Time

Busting the 5-second rule: Robot, Petri dishes of bacteria part of science fair – Leigh Guidry – The Town Talk

Not about microbiology, but a very good read: High throughput sequencing for neuroscience – Sean Eddy – Cryptogenomicon

No Bik’s Picks today, sorry guys.

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February 4, 2015

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Animal models of microbiome research

Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota – Han-Hsuan Chou – PNAS

Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-Yong Mao – Environmental Microbiology

Animal microbiome

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae) – Matteo Montagna – PLOS ONE

Plant microbiome

Editorial: Evolving insights to understanding mycorrhizas – Ian A. Dickie – New Phytologist

Soil and sediment microbiome

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Cyanobacteria drive community composition and functionality in rock–soil interface communities – Angel Valverde – Molecular Ecology

Water microbiome

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary – Erin M. Eggleston – Environmental Microbiology

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity – Matthieu Leray and Nancy Knowlton – PNAS USA

Bioinformatics

Phylogenomics with paralogs – Marc Hellmuth – PNAS USA

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets – Nikhil Chaudhary – PLOS ONE

DNA extraction and sequencing techniques

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform – Lucas Sinclair – PLOS ONE

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples – Androniki Psifidi – PLOS ONE

Metabolomics

Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD – Vicky De Preter – Gut

Probiotics

Review: The effects of consuming probiotic-fermented milk on the immune system: A review of scientific evidence – Lourdes Santiago-López – International Journal of Dairy Technology

Microbes in the News

Aquarium Microbiome Project – Shedd Aquarium

Video: Aquarium Microbiome Project – YouTube

A plea to stop ignoring microbial ecosystem effects of antimicrobial agents – Jonathan Eisen – MicroBEnet

Why you should embrace bacteria – Jody Berger – Deseret News

Infant Microbiota Influenced By Mother’s Birth Delivery, Gestation Period – Chris Weller – Medical Daily

Birth method, gestation duration may alter infants’ gut microbiota and influence later health – ASM

A warm (surprise!) welcome to the microbiome community – Alexandra Carmichael – uBiome

A Bacteria That Hasn’t Had To Evolve In More Than Two Billion Years – George Dvorsky – io9.com

Bik’s Picks

Cigarette Butt Decomposition and Associated Chemical Changes Assessed by 13C CPMAS NMR – Giuliano Bonanomi – PLOS ONE

What’s Up With That: Why Do Cats Love Boxes So Much? – Bryan Gardiner – Wired.com

Satire: Genome Study Finds Gene For Believing Genome Studies – The Allium

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February 3, 2015

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Pregnancy and birth

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio

Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE

Human oral microbiome

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports

Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology

Human respiratory microbiome

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE

Human gut microbiome

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Animal microbiome

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE

Plant microbiome

Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils

Soil microbiome

Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology

Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry

Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments

Water microbiome

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography

Microbiome of the built environment

Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment

Bioreactor microbiome

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports

Food microbiology

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology

Techniques

PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE

Bioinformatics, metagenomics

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE

In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research

SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics

A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Book: Biocode: The New Age of Genomics

Phages and viruses

Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE

Microbes in the news

The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio

The Human Microbiome and Media Confusion – Science in the News – Harvard

Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos

Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome

Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio

Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients

Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes

Science, publishing, and career

From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog

Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI

A Future Segregated by Science? – Charles M. Blow – New York Times

Bik’s Picks

Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily

Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs

Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press

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February 1, 2015

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Ah, the revenge of being away from work: my in-box was bursting out of the seams with new papers. Today I am quickly catching up after being offline for just 3 days, and I will skip most formatting to save some time (e.g. I will only do the bare essentials, and won’t add the hyperlinks). Enjoy.

General microbiome

Review? Discovering Emergent Behavior of Host-Microbiome Interactions with Biomimetic Robotics – Keith C. Heyde, Warren C. Ruder – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514046268

Book: Microbiome Community Ecology – Muhammad Saleem – Springer Briefs in Ecology
http://link.springer.com/book/10.1007/978-3-319-11665-5

Human oral microbiome

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis – Nursen Topcuoglu, Guven Kulekci – Anaerobe
http://www.sciencedirect.com/science/article/pii/S1075996415000128

Human respiratory microbiome

Dynamics of the nasal microbiota in infancy: A prospective cohort study – Moana Mika – Journal of Allergy and Clinical Immunology
http://www.sciencedirect.com/science/article/pii/S0091674914037099

Review: The microbiome of the upper airways: focus on chronic rhinosinusitis – Thanit Chalermwatanachai – World Allergy Organization Journal
http://link.springer.com/article/10.1186/s40413-014-0048-6/fulltext.html

Human skin microbiome

Mapping axillary microbiota responsible for body odours using a culture-independent approach – Myriam Troccaz – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/3/abstract

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites – Ana M Misic – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/2/abstract

Insights into bacterial colonization of intensive care patients’ skin: the effect of chlorhexidine daily bathing – N. Cassir – European Journal of Clinical Microbiology & Infectious Diseases
http://link.springer.com/article/10.1007/s10096-015-2316-y

Human gut microbiome

(see also Metagenomics) Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Gut microbiota composition correlates with changes in body fat content due to weight loss – M. Remely – Beneficial Microbes
http://wageningenacademic.metapress.com/content/ewq1620085607927/#.VM5HCVWJOuY

Genetic Modifier of the Gut Microbiome, GvHD and Bacterial Translocation Following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114008350

A Pilot Study of Donor Enteral Human Milk to Modulate the Gut Microbiome in Children Receiving Stem Cell Transplant – Stella M. Davies – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114010441

This might be review (no access from my location): Microbiome, peptide autoantibodies, and eating disorders: a missing link between gut and brain – Akio Inui – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000386

Oral Supplementation with L-Glutamine Alters Gut Microbiota of Obese and Overweight Human Adults: A Pilot Study – Alessandra Zanin Zambom de Souza – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000350

Review: Growth Promotion and Gut Microbiota: Insights from Antibiotic Use – Harald Brüssow – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12786/abstract

Hypothesis: An Agent-Based Modeling Framework for Evaluating Hypotheses on Risks for Developing Autism: Effects of the Gut Microbial Environment – Bronson Weston – Medical Hypotheses
http://www.sciencedirect.com/science/article/pii/S0306987715000481

Hypothesis: Gut feelings: A role for the intestinal microbiota in anorexia nervosa? – Susan C. Kleiman – International Journal of Eating Disorders
http://onlinelibrary.wiley.com/doi/10.1002/eat.22394/abstract

Review??? Beyond Model Systems: Super-Resolving the Subcellular Dynamics of Starch Digestion in the Human Gut Microbiome – Krishanthi S. Karunatilaka – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514023030

Review: Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena? – Mirjana Rajilić-Stojanović – American Journal of Gastroenterology
http://www.nature.com/ajg/journal/vaop/ncurrent/full/ajg2014427a.html

Review: H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases
http://onlinelibrary.wiley.com/doi/10.1111/1751-2980.12233/abstract

Review: Implication of Gut Microbiota in Nonalcoholic Fatty Liver Disease
Jerome Boursier – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004559

Review: The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts – Michael C. Toh and Emma Allen-Vercoe – Microbial Ecology in Health and Disease
http://www.microbecolhealthdis.net/index.php/mehd/article/view/26309

Review: The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity – Ningwen Tai – Reviews in Endocrine and Metabolic Disorders
http://link.springer.com/article/10.1007/s11154-015-9309-0

Review: Diet, Gut Microbiome, and Bone Health – Connie M. Weaver – Current Osteoporosis Reports
http://link.springer.com/article/10.1007/s11914-015-0257-0

Review: Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota – I. A. Fedorova, V. N. Danilenko – Biology Bulletin Reviews
http://link.springer.com/article/10.1134/S2079086414060036

Animal models of microbiome

Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain – Fabiola Gutierrez-Orozco – Nutrients
http://www.mdpi.com/2072-6643/7/2/764/htm

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis
Lauren E. Ritchie – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/14/femsec.fiv008.abstract

Effects of chronic exposure to environmentally relevant concentrations of waterborne depleted uranium on the digestive tract of zebrafish, Danio rerio – Starrlight Augustine – Journal of Environmental Radioactivity
http://www.sciencedirect.com/science/article/pii/S0265931X15000041

Cross-Differentiation from the CD8 Lineage to CD4 T Cells in the Gut-Associated Microenvironment with a Nonessential Role of Microbiota – Jen Bon Lui – Cell Reports
http://www.sciencedirect.com/science/article/pii/S2211124714011061

Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota – P. Treven- Journal of Dairy Science
http://www.sciencedirect.com/science/article/pii/S0022030215000417

Animal microbiome

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing – Shuai Peng – Journal of Applied Genetics
http://link.springer.com/article/10.1007/s13353-014-0258-1/fulltext.html

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows – Fabio S. Lima – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1327.abstract

Relationship between honeybee nutrition and their microbial communities – Miriane Acosta Saraiva – Antonie van Leeuwenhoek
http://link.springer.com/article/10.1007/s10482-015-0384-8

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation – Gang Yang – Biochemical and Biophysical Research Communications
http://www.sciencedirect.com/science/article/pii/S0006291X15001047

Microbiome affects egg carotenoid investment, nestling development and adult oxidative costs of reproduction in Great tits – Staffan Jacob – Functional Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12404/abstract

Review: Dietary fibre and the importance of the gut microbiota in feline nutrition: a review
Kristel Rochus – Nutrition Research Reviews
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9534845&fileId=S0954422414000213

Plant microbiome

T Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time – Merete Wiken Dees – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1530.abstract

Soil, rock, and sediment microbiome

Long-term forest soil warming alters microbial communities in temperate forest soils – Kristen M. DeAngelis – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00104/abstract

This one was submitted in June 2013, but just published: Soil microbial community structure and activity in a 100-year-old fertilization and crop rotation experiment – Cancan Zhao – Journal of Plant Ecology
http://jpe.oxfordjournals.org/content/early/2015/01/28/jpe.rtv007.abstract

Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions – Jamie M. Johnson – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2014/12/24/femsec.fiu035.abstract

Short-term effects of soil amendment with meadowfoam seed meal on soil microbial composition and function – Suphannika Intanon – Applied Soil Ecology
http://www.sciencedirect.com/science/article/pii/S0929139315000104

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China – Yuan Wei – Journal of Environmental Sciences
http://www.sciencedirect.com/science/article/pii/S100107421500008X

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing – Michael Joe Vaughan – Microbial Ecology
http://link.springer.com/article/10.1007/s00248-014-0560-9

Effects of increasing precipitation on soil microbial community composition and soil respiration in a temperate desert, Northwestern China – Gang Huang – Soil Biology and Biochemistry
http://www.sciencedirect.com/science/article/pii/S003807171500019X

Review: Microbial ecology of hot desert edaphic systems – Thulani P. Makhalanyane – FEMS Microbiology Reviews
http://femsre.oxfordjournals.org/content/early/2015/01/23/femsre.fuu011.abstract

Water microbiome

Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-driven phytoplankton bloom – Emma K. Wear – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10042/abstract

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina) – María Sofía Urbieta – Extremophiles
http://link.springer.com/article/10.1007/s00792-015-0729-2

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) – Cassandre Sara Lazar – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12659/abstract

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10035/abstract

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton – Heba El-Swais – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12629/abstract

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America – Caroline Souffreau – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12692/abstract

Microbial Contamination of Drinking Water and Human Health from Community Water Systems
Nicholas J. Ashbolt – Current Environmental Health Reports
http://link.springer.com/article/10.1007/s40572-014-0037-5

Book Chapter: Microbial Bioprospecting in Marine Environments – Mariana Lozada, Hebe M. Dionisi – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_11

Bioreactor microbiome

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops – Rico Lucas – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/11/femsec.fiv004.abstract

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology
http://onlinelibrary.wiley.com/doi/10.1002/jctb.4649/abstract

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants – Qiao Ma – Microbiological Research
http://www.sciencedirect.com/science/article/pii/S0944501315000105

New steady-state microbial community compositions and process performances in
biogas reactors induced by temperature disturbances – Gang Luo – Biotechnology for Biofuels

Click to access s13068-014-0182-y.pdf

Archaea

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers – Mark A. Lever and Andreas P. Teske – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1426.abstract

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter – WIlliam D Orsi – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014260a.html

Bioinformatics

Integrating Multi-omic features exploiting Chromosome Conformation Capture data – Ivan Merelli – Frontiers in Genetics
http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00040/abstract

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach – Philippe Rocca-Serra – Database
http://database.oxfordjournals.org/content/2015/bau132.full

Koonkie: An Automated Software Tool for Processing Environmental
Sequence Information using Hadoop – Dongjae Kim – ASE360
http://www.ase360.org/bitstream/handle/123456789/164/P9.pdf?sequence=1&isAllowed=y

MetAmp: combining amplicon data from multiple markers for OTU analysis – Ilya Y. Zhbannikov,, James A. Foster – Bioinformatics

Click to access bioinformatics.btv049.full.pdf

MetaAB – A Novel Abundance-Based Binning Approach for Metagenomic Sequences
Van-Vinh Le – Nature of Computation and Communication
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
http://link.springer.com/chapter/10.1007/978-3-319-15392-6_13

NCBI BLAST+ integrated into Galaxy – Peter J. A. Cock – BioRxiv

Click to access 014043.full.pdf

Metagenomics

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Integrated metagenomics and network analysis of soil microbial community of the forest timberline – Junjun Ding – Scientific Reports
http://www.nature.com/srep/2015/150123/srep07994/full/srep07994.html

Book Chapter: Marine Sponge Metagenomics – Valliappan Karuppiah, Zhiyong Li – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_17

Ecological and genetic interactions between cyanobacteria and viruses in a low-O2 mat community inferred through metagenomics and metatranscriptomics – Alexander A. Voorhies – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12756/abstract

Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream – Maria Liljeqvist – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/27/femsec.fiv011.abstract

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics

Click to access s12864-014-1207-4.pdf

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking – Yuji Sekiguchi – PeerJ
https://peerj.com/articles/740/

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12668/abstract

Review: Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism – Sang Sun Yoon – Current Opinion in Microbiology
http://www.sciencedirect.com/science/article/pii/S1369527415000089

Book Chapter: Marine Metagenome and Supporting Technology – Tetsushi Mori – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_19

Transcriptomics, metabolomics

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen – Xin Dai – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1375.abstract

Genomic Potential for Polysaccharide Deconstruction in Bacteria – Renaud Berlemont and Adam C. Martiny – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1513.abstract

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor – Masaru K Nobu – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014256a.html

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways – Philipp Engel – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1502.abstract

Transcriptome analyses to investigate symbiotic relationships between marine – Sergio Balzano – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00098/abstract

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Human metabolic, mineral, and microbiota fluctuations across daily nutritional intake visualized by a data-driven approach – Takuma Misawa – Journal of Proteome Research
http://pubs.acs.org/doi/abs/10.1021/pr501194k

Review: Prospects and challenges for fungal metatranscriptomics of complex communities – Cheryl R. Kuske – Fungal Ecology

Microbial Ecology

Disturbance opens recruitment sites for bacterial colonization – David Vuono – BioRxiv
http://biorxiv.org/content/early/2015/01/27/014456

Review: High-throughput DNA barcoding for ecological network studies – Hirokazu Toju – Population Ecology
http://link.springer.com/article/10.1007/s10144-014-0472-z

Book Chapter: For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
Jean-Claude Bertrand – Environmental Microbiology: Fundamentals and Applications
http://link.springer.com/chapter/10.1007/978-94-017-9118-2_4

Book Chapter: Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem- Muhammad Saleem – Microbiome Community Ecology
http://link.springer.com/chapter/10.1007/978-3-319-11665-5_1

More microbes

Introduction to a special issue of PLOS Pathogens: The Importance of Pathogen Load – Aubrey J. Cunnington – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004563

Microbes in the news

Satire: Secret Microbiome Forensic Study Reveals DeflateGate Culprit – Megabiome.net

Secret microbiome forensic study reveals #deflategate culprit

Among gut microbes, strains, not just species, matter – MedicalXpress
http://medicalxpress.com/news/2015-01-gut-microbes-strains-species.html

Analysis Highlights Strain Diversity in Gut Microbiome – GenomeWeb
https://www.genomeweb.com/genetic-research/analysis-highlights-strain-diversity-gut-microbiome

Jonathan Eisen and Jessica Richman on the Microbiome – Kevin Bonham – Scientific American
http://blogs.scientificamerican.com/food-matters/2015/01/30/jonathan-eisen-and-jessica-richman-on-the-microbiome/

Part-Time Pooping: A New Way to Make an Extra $13,000 a Year – Everyday Health
http://www.everydayhealth.com/columns/daily-checkup/part-time-pooping-new-way-make-extra-money-year/

OpenBiome will pay for poo – Helen Clark – GizMag
http://www.gizmag.com/openbiome-fecal-transplant/35845/

January 2015 Update on American Gut, British Gut and Australian Gut Human Microbiome Projects – IBS Impact
https://ibsimpact.wordpress.com/2015/01/30/january-2015-update-on-american-gut-british-gut-and-australian-gut-human-microbiome-projects/

The Microbiome – New Research On Inflammatory Bowel Disease May Foreshadow Autism? – Teresa Conrick – Age of Autism
http://www.ageofautism.com/2015/01/the-microbiome-new-research-on-inflammatory-bowel-disease-may-foreshadow-autism.html

The microbiome of the upper airways: focus on chronic rhinosinusitis – 7th Space
http://7thspace.com/headlines/503056/the_microbiome_of_the_upper_airways_focus_on_chronic_rhinosinusitis.html

Germ Theory: What You May Not Know About The Bacteria Crawling Around Your Bathroom – Justin Caba – Medical Daily
http://www.medicaldaily.com/pulse/germ-theory-what-you-may-not-know-about-bacteria-crawling-around-your-bathroom-319884

Altered gut microbiota seen in patients with psoriatic arthritis – Healio.com
http://www.healio.com/rheumatology/psoriatic-arthritis/news/online/%7B0dd6068d-11b8-4e05-82f2-7713d4f28749%7D/altered-gut-microbiota-seen-in-patients-with-psoriatic-arthritis

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – PRNewsWIre
http://www.prnewswire.co.uk/news-releases/the-human-microbiome-biomedical-implications-and-birth-of-a-market—overview-290212581.html

Meet Dr. Armpit, changing body odor with bacteria – Fast Company
http://www.fastcompany.com/3041388/body-week/meet-dr-armpit-changing-body-odor-with-bacteria

Gut bacteria byproduct linked to chronic kidney disease for the first time – Medical Xpress
http://medicalxpress.com/news/2015-01-gut-bacteria-byproduct-linked-chronic.html

Does draft beer give you a worse hangover? We came across people from the beer industry and beer drinkers who claimed the bacteria in those lines contributes to a hangover. – Jace Larson – Click 2 Houston
http://www.click2houston.com/news/does-draft-beer-give-you-a-worse-hangover/31037044

Bik’s Picks

Face blindness predicted by structural differences in the brain, Stanford neuroscientists discover – Leslie Willoughby – Stanford News
http://news.stanford.edu/news/2015/january/face-blind-brain-013015.html

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January 28, 2015

Posted on by

I will be traveling to visit family in the upcoming week, so there might not be a post every day. But I will do my best to keep y’all up to date with the microbiome literature. In today’s installment, there are articles about skin microbiome around abscesses, misclassifications of bacteria in Genbank, archaea and rice plant roots. Also, if you like chicken wings with Campylobacter, you should have put some sauce on it.

General microbiome

Crystal Ball: Human microbiota: ‘The philosophers have only interpreted the world in various ways. The point, however, is to change it’ – Harald Brüssow – Microbial Biotechnology

Human skin microbiome

The cutaneous microbiome in out-patients presenting acutely with skin abscesses – James M. Horton – Journal of Infectious Diseases

Animal and other models for microbiome research

In Vitro Investigation of the Effect of Oral Bacteria in the Surface Oxidation of Dental Implants – Sathyanarayanan Sridhar – Clinical Implant Dentistry and Related Research

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice – Xiaofei Xu – PLOS ONE

Animal microbiome

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description of Escovopsis kreiselii sp. nov. – Lucas A. Meirelles – PLOS ONE

Plant microbiome

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols– Sarah Croes – Environmental Microbiology

Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission – Judith Pump – Environmental Microbiology

Soil and rock microbiome

Formation of iron-rich shelled structures by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Water microbiome

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling– Markus V. Lindh – Environmental Microbiology

Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities – Mercè Berga – Environmental Microbiology

Review: Marine Snow: A Brief Historical Sketch – Mary Silver – Limnology and Oceanography Bulletin

Food microbiology

Just in time for the Superbowl: The Antimicrobial Effect of Spice-Based Marinades against Campylobacter jejuni on Contaminated Fresh Broiler Wings – Gintarė Zakarienė – Journal of Food Science

Metagenomics

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database – Roxana Beaz-Hidalgo – PLOS ONE

Metabolomics

Dominant components of the Thoroughbred metabolome characterised by 1H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids – E. E. Escalona – Equine Veterinary Journal

New Techniques

DNA sequencing using ​polymerase substrate-binding kinetics – Michael John Robert Previte – Nature Communications

Single cell biotechnology to shed a light on biological ‘dark matter’ in nature – Wei E. Huang – Microbial Biotechnology

Ecology

Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff – Jue Wang – PLOS Biology

Review: Is successional research nearing its climax? New approaches for understanding dynamic communities – Scott J. Meiners – Functional Ecology

Editorial: Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies – Gabriele Berg – Microbial Biotechnology

Microbes in the news

Skin abscesses displayed distinct cutaneous microbiota – Healio

Stress during pregnancy related to infant gut microbiota – HealthCanal

Fatal peanut allergies could be cured by probiotic bacteria, say Australian doctors – Jonathan Pearlman – The Telegraph

UF researcher gets grant to study probiotics’ effects – Jeff Schweers – Gainesville

Science, publishing and career

Not your average technician: Research relies on unsung heroes working behind the scenes — and some of them have rather unusual jobs – Michael Hopkin – Nature

Career counselling: Pick a path – Neil Savage – Nature

Inclusivity: Mentor matters – Nature

FactChecking Science-based Claims – FactCheck.org
http://www.factcheck.org/2015/01/factchecking-science-based-claims/

Bik’s Picks

Did genetic links to modern maladies provide ancient benefits? – Science Daily

Skull discovery suggests location where humans first had sex with Neanderthals – The Guardian

Spiders Spin Electrically Charged Silk To Make It Sticky – Marissa Fessenden – Smithsonian

[hr]

January 23, 2015

Posted on by

Several papers on the effect of functional foods on the microbiome, fecal bacteria of the blue tit, and finding an old vial of bacteria.

Human gut microbiome

Toll-like receptor 5 in obesity: The role of gut microbiota and adipose tissue inflammation – Satu Pekkala – Obesity

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone – Dae-Wook Kang – Anaerobe

Review: New aspects on the metabolic role of intestinal microbiota in the development of atherosclerosis – Ioannis Drosos – Metabolism

Review: The influence of diet on the gut microbiota and its consequences for health – Joël Doré, Hervé Blottière – Current Opinion in Biotechnology

Animal and other models of microbiome research

Effects of Probiotic Enterococcus faecium NCIMB 11181 Administration on Swine Fecal Microbiota Diversity and Composition using Barcoded Pyrosequencing – Edward Alain B. Pajarillo – Animal Feed Science and Technology

Influences of structures of galactooligosaccharides and fructooligosaccharides on the fermentation in vitro by human intestinal microbiota – Wei Li – Journal of Functional Foods

Differential effects of probiotics, prebiotics, and synbiotics on gut microbiota and gene expression in rats – Gunaranjan Paturi – Journal of Functional Foods

Animal microbiome

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota – Mansooreh Jami – Microbiological Research

Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus – Clare McW. H. Benskin – Ecology and Evolution

Review (could also be filed under plant microbiome): Is there a role for symbiotic bacteria in plant virus transmission by insects? – Patricia V. Pinheiro – Current Opinion in Insect Science

Plant microbiome

Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity – L.L. Gonzaga – Journal of Applied Microbiology

Bioreactor microbiome

Effect of hygienization treatment on the recovery and/or regrowth of microbial indicators in sewage sludge – M. Pascual-Benito – Journal of Applied Microbiology

Metabolomics and Proteomics

Review: New aspects on the metabolic role of intestinal microbiota in the development of atherosclerosis – Ioannis Drosos – Metabolism

Not in microbes, but of note: Tissue-based map of the human proteome – Mathias Uhlén – Science

Microbial detection general

First Experience of a Multicenter External Quality Assessment of Molecular 16S rRNA Gene Detection in Bone and Joint Infections – Chloé Plouzeau – Journal of Clinical Microbiology

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus – David Triest – Journal of Clinical Microbiology

A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens – R.P. Baker – Journal of Microscopy

Infection and Immunity

Twin study @Stanford: Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences – Petter Brodin – Cell

Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds – M. Asghar – Science

Review: Advances in Laboratory Methods for Detection and Typing of Norovirus – Jan Vinjé – Journal of Clinical Microbiology

Combating the emerging viral infectious diseases – Shibo Jiang, Peter J. Hotez – Microbes and Infection

Phages, viruses, CRISPRs

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition – Tao Liu – Nucleic Acids Research

Microbes in the news
Breathing in Bacteria – The healthy lung receives microbes from the mouth, a new model suggests – Jenny Rood – The Scientist

Viruses may play unexpected role in inflammatory bowel diseases – Science Daily

Researchers See IBD-related Shifts in Individuals’ Gut Viromes – GenomeWeb

How gut bacteria may affect brain health – ScienceCodex

New microbiome drug candidate licensed by major manufacturer – Healio.com

When the Microbiome Stages a Coup – GenomeWeb

Environment, not genes, plays starring role in human immune variation, study finds – Stanford Medicine

Dirty Mouth? Chewing Gum Removes Millions Of Bacteria, But With One Catch – Philip Ross – International Business Times

We’ve found a strange box at our student microbiology lab… – AwesomeScience – Imgur

Immune system promotes digestive health by fostering community of ‘good’ bacteria – EurekAlert

The New Measles – One of the most infectious viruses on the planet is making a comeback in the United States, and many doctors have never even seen it – Adrienne Lafrance – The Atlantic

Science, publishing, and career

Intel Science Talent Search finalists: 9 of 40 from Bay Area – James Urton and Sharon Noguchi – Mercury News

Should Teachers be Allowed to Touch Students? – Jessica Lahey – The Atlantic

Science and art

100 Years of National Geographic Maps: The Art and Science of Where – Cathy Newman – National Geographic

Kitty Microbiome – Artologica – Etsy

Bik’s Picks

Major breakthrough in reading ancient scrolls – Science Daily

The geometry of their shells keeps turtles from getting stuck on their back – Seriously Science – Discover Magazine

Scottish scientists slow down speed of light – Robert Ferris – CNBC

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January 22, 2015

Posted on by

The enteric virome is more diverse in patients with Crohn’s Disease and ulcerative colitis, measuring how fecal transplants are portrayed in Canadian media, and bacteria and archaea in sugarcane soils.

Human gut microbiome

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease – Jason M. Norman – Cell

Media Discourse on the Social Acceptability of Fecal Transplants – Kim H. Chuong – Qualitative Health Research

Perspective: Cancer and the gut microbiota: An unexpected link – Laurence Zitvogel – Science Translational Medicine

Editorial: Bugs, Guts, and Glia: How Microbiota Influence Enteric Gliogenesis and Migration – Meenakshi Rao – Neuron

Animal models

MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health – Jason L. Kubinak – Cell Host & Microbe

Soil microbiome

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil – Kanako Tago – Microbes and Environments

Metabolomics

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLIFE

Ecology

Perspective: The physiology and ecological implications of efficient growth – Benjamin RK Roller and Thomas M Schmidt – ISME Journal

Metagenomics and bioinformatics

Pollux: platform independent error correction of single and mixed genomes – Eric Marinier – BMC Bioinformatics

Microbes in the news

When bacteria-killing viruses take over, it’s bad news for the gut – Tina Hesman Saey – ScienceNews

Immune system promotes digestive health by fostering community of ‘good’ bacteria – NewsWise

Gut microbes may trigger autoimmune disease later in life – PuneMirror

Scientists claim breakthrough in taming genetically modified E.coli bacteria – Joel Achenbach – Washington Post

Have we found alien life? Microbes that eat and breath electricity have forced scientists to reimagine how life works – on this planet and others – Corey S. Powell – Popular Science

Science, publishing, and career

Origin stories of the scientists – Adam Ruben – Science

Bik’s Picks

The Science of Mmm – How food and drink tickle the brain’s pleasure centers – John McQuaid – Slate

Will this put an end to a very old discussion? Is glass a true solid? New research suggests it is – Science Daily

Which state f*cking loves science the most? – Phil Edwards – Vox

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January 21, 2015

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Today’s digest features the microbiome of chewing gum, infants of stressed-out moms, growing segmented filamentous bacteria, and a YouTube video with Jack Gilbert.

Chewing gum microbiome

Quantification and Qualification of Bacteria Trapped in Chewed Gum – Stefan W. Wessel – PLOS ONE

Human gut microbiome

Review: Gut microbial metabolism and colon cancer: Can manipulations of the microbiota be useful in the management of gastrointestinal health? – Antoaneta Belcheva – BioEssays

Microbiome of pregnancy and birth

Maternal Prenatal Stress is Associated with the Infant Intestinal Microbiota – Maartje A.C. Zijlmans – Psychoneuroendocrinology (which is a nice word for Scrabble or Hangman)

Animal and other models of microbiome research

Growth and host interaction of mouse segmented filamentous bacteria in vitro – Pamela Schnupf – Nature

Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology

Soil microbiome

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea – Jong-Shik Kim – Microbiology Open

Water microbiome

Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek’s watershed – A.L. Barkovskii – Journal of Applied Microbiology

Immunology

Reduced neonatal regulatory T cell response to microbial stimuli associates with subsequent eczema in high-risk infants – Intan H. Ismail – Pediatric Allergy and Immunology

Metagenomics

Biological interpretation of genome-wide association studies using predicted gene functions – Tune H. Pers – Nature Communications

Microbes in the news

YouTube video with Jack Gilbert: Invisible Influence: A Bacterial Guide to Your Health – Argonne OutLoud on YouTube

Commensal Defense: Beneficial gut bacteria have evolved resistance to antimicrobial peptides that hosts release to fight pathogens – Kate Yandell – The Scientist

GM microbes created that can’t escape the lab – Engineered bacteria kept in check with a designer diet – Elie Dolgin – Nature

SDSU Hosts the “Year of the Phage” – Jeneene Chatowsky and Michael Price – San Diego State University

Novel IBD microbiome drug advanced to phase 1 trial – Healio

Optibiotix unlocking the mysteries of the human microbiome – Ian Lyall – Proactive Investors

New bacterial ‘language’ discovered: Previously unknown communication pathway – Science Daily

Science, publishing and career

Turning point: Swati Padmaraj – Scott Kraft – Nature

Time management: Seize the moment – Jeffrey M. Perkel – Nature

How to recruit a good bioinformatician – Opiniomics

Science and Art

Micro Masterpiece: The artful science of Tom Deerinck, a micrographer who consistently places in Nikon’s Small World competition – Jef Akst – The Scientist

Bik’s Picks

The Science Behind Deflated Footballs – Erin Blakemore – Smithsonian

Science gets its moment in Obama’s 2015 State of the Union – David Malakoff – Science

The Namer: Carl Linnaeus’s lasting impact on biological science – Kerry Grens – The Scientist

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