Category Archives: Microbes in the News

February 12, 2015

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Happy Darwin Day! To celebrate, I’ll start of with an older paper:

What did Darwin say about microbes, and how did microbiology respond? – Maureen A. O’Malley – Trends in Microbiology

Two San Francisco Bay Area events of interest

Sat/Sun Feb 14/15: Family Science Days. Free event. Join the LSA, NASA, Science is Elementary (where I volunteer) and more at #FamSciDays!

Tue Feb 17, VLAB forum discussion: Gut-Feeling — Ventures into the Microbiome. Will bacteria enable personalized medicine?

General human microbiome

Review: Microbial Diversity: Relevance and Relationship Between Environmental Conservation And Human Health – Jeremias Pakulski Panizzon – Brazilian Archives of Biology and Technology

Human skin microbiome

Editorial: S. epidermidis Influence on Host Immunity: More Than Skin Deep – Richard L. Gallo – Cell Host & Microbe

Human gut microbiome

What role do bacteria play in persisting fistula formation in idiopathic and Crohn’s anal fistula? – P. J. Tozer – Colorectal Disease

Review: Spondyloarthritis and the Microbiome: New Insights From an Ancient Hypothesis – Julia Manasson, Jose U. Scher – Current Rheumatology Reports

Animal models of microbiome research

Editorial: TFH-IgA Responses Keep Microbiota in Check – Kanya Honda – Cell Host & Microbe

Effects of rearing temperature and dietary short-chain fructooligosaccharides supplementation on allochthonous gut microbiota, digestive enzymes activities and intestine health of turbot (Scophthalmus maximus L.) juveniles – I. Guerreiro – Aquaculture Nutrition

Animal microbiome

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Catacombs microbiome

When in Rome: Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies – Lucia Krakova – Environmental Microbiology

Soil and sediment microbiome

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems – Jun Gong – Environmental Microbiology

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group – Travis B. Meador – Environmental Microbiology

Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica – Sean T. S. Wei – Polar Biology

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments – Anniet M. Laverman – Environmental Science and Pollution Research

Temperature Sensitivity of Microbial Respiration of Fine Root Litter in a Temperate Broad-Leaved Forest – Naoki Makita, Ayumi Kawamura – PLOS ONE

Water microbiome

Review: Marine microbial community dynamics and their ecological interpretation – Jed A. Fuhrman – Nature Reviews Microbiology

Bioreactor microbiome

Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater – Hyun Min Jang – Water Research

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus – Xiao-Mei Su – Microbial Biotechnology

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

Opinion/review: Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities – Shaman Narayanasamy – Microbial Biotechnology

Metabolomics and Proteomics

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities – Sandi Yen – Journal of Proteome Research

Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: a case-control study – Stephen J Fowler – Thorax

The Unipept metaproteomics analysis pipeline – Bart Mesuere – Proteomics

Review: A Biotechnological Approach to Microbial Based Perfumes and Flavours – Charu Gupta – Journal of Microbiology & Experimentation

Microbial Ecology

Ecological Perspectives on Synthetic Biology: Insights from Microbial Population Biology – Ana E. Escalante – Frontiers in Microbiology

Bioinformatics

A machine learning pipeline to improve De Bruijn graph metatranscriptomic assemblies – Hussein Mohsen – Bioinformatics

Techniques

Identification of response classes from heavy metal-tolerant soil microbial communities by highly resolved concentration-dependent screenings in a microfluidic system – Dana Kürsten – Methods in Ecology and Evolution

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria – Kelley A. Meinhardt – Environmental Microbiology Reports

Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples – Jan Mareš – Journal of Phycology

Other microbiology papers

Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack – Chamutal Gur – Immunity

Microbes in the news

Podcast on the NY Subway Microbiome paper (19 min): Listen To Our Conversation With The Microbe Map Man – Jody Avirgan – Five Thirty Eight

Another short Podcast: Subway DNA Survey Finds Microbes, Mozzarella and Mystery – Christopher Intagliata – Scientific American

What The Bacteria In Your Gut Have To Do With Your Physical And Mental Health – Carolyn Gregoire – The Huffington Post
Cecilia Westbrook Makes Yogurt With Her Own Vaginal Bacteria (NSFW) – David Moye – The Huffington Post

Bacteria, economics and our aging population – Julie Flaherty – MedicalXpress

Session Recap: Therapeutic Workshop “Trust Your Gut” with Martin Blaser et al. – BiotechNow

Is there a link between gut microbiota and Parkinson’s disease? – GutMicrobiotaWatch

Early microbiome development impacts later weight gain – Nathan Gray – NutraIngredients

Not all microbial strains are equally efficient – Kemin – All About Feed

The Nanotech View of the Microbiome (Kavli Roundtable) – Alan Brown – LiveScience

Bacteria protect intestinal tumor model from being killed by immune cells – Cell Press – Eureka Alert

A discussion of Casadevall and Pirofski’s Nature commentary: What’s The Damage? – Amesh Adalja – BifurcatedNeedle

New Non-Stick Coating Will Stop Bacteria Sticking to Medical Materials – Jamie Condliffe – GizModo

Science, publishing, and career

NIH proposal to create grant for aging scientists hits a nerve – Jocelyn Kaiser – Science

Social media: A network boost – How scientists can use Twitter to expand their social contacts and find jobs – Monya Baker – Nature

Elsevier Valentines – It all started with an innocent tweet. – Sylvain Deville – Storify

Bik’s Picks

U.S. Droughts Will Be the Worst in 1,000 Years – Mark Fischetti – Scientific American

Emaciated sea lion pup rescued from side of San Francisco highway – Reuters.com

Happy Darwin Day! Here are our favorite stories about evolution – Rachel Feltman – Washington Post

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February 11, 2015

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Human oral microbiome

Extensive Description and Comparison of Human Supra-Gingival Microbiome in Root Caries and Health – Lin Chen – PLOS ONE

Human gut microbiome

Characterization of the Gut Microbiota of Papua New Guineans Using Reverse Transcription Quantitative PCR – Andrew R. Greenhill – PLOS ONE

Animal models

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks – Andrey Morgun – Gut

Long-Lasting Effects of Early-Life Antibiotic Treatment and Routine Animal Handling on Gut Microbiota Composition and Immune System in Pigs – Dirkjan Schokker – PLOS ONE

Plant microbiome

A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey – Wayne Reeve – Standards in Genomics Sciences

More microbes

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens – Ramya Srinivasan – PLOS ONE

Mutualism Breakdown by Amplification of Wolbachia Genes – Ewa Chrostek – Luis Teixeira – PLOS Biology

Intranuclear bacteria: inside the cellular control center of eukaryotes – Frederik Schulz, Matthias Horn – Trends in Cell Biology

Microbes in the news

Satire: Fitbiotics: A secret supplements company, until now known only by high levels athletes, sells the fittest microbiome on Earth – The Megabiome

Must-read for anyone interested in the New York subway microbiome paper: There’s No Plague on the NYC Subway. No Platypuses Either – Ed Yong

Metagenomics best hit analysis: caveat emptor – Nick Loman – Github blog

Win a home microbiome analysis plus 50 giant microbes (if you subscribe to New Scientist) – New Scientist

Drs. Cardelli and Woolard Funded to Study Bacteria in the Intestine – LSU Health

From Solar Energy To Liquid Fuel: Scientists Use Bacteria The Way Plants Do – James Maynard – Tech Times

Science, publishing, and career

Science Communication in Less Than 140 Characters – Lauren Dobischok – Future Science Leaders

How Elementary School Teachers’ Biases Can Discourage Girls From Math and Science – Claire Cain Miller – New York Times

And the winner is: not science – Portrayals of science in the cinema are growing in sophistication — but not exactly at the speed of light – Colin Macilwain – Nature

Bik’s Picks

Chronic Fatigue Syndrome Gets a New Name – Karen Barrow – New York Times

Google Now Serving Fact-Checked Medical Search Results – Dan Van Winkle – The Mary Sue

Evolution of Darwin’s finches and their beaks revealed by genome sequencing – Sangeet Lamichhaney – Nature

Long read: The Food Babe: Enemy of Chemicals – James Hamblin – The Atlantic

Why Your Cat May Be More Human Than You Think – Karen Becker – Huffington Post

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February 10, 2015

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Microbiome of pregnancy and birth

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan (Sam) Ma – Scientific Reports

Human respiratory microbiome

The nasal microbiota in health and disease: variation within and between subjects – Kristi Biswas – Frontiers in Microbiology

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis – Won Hee Jung – Mycoses

Human oral microbiome

Review: Salivary Diagnostics and the Oral Microbiome – Jennifer E. Kerr – Advances in Salivary Diagnostics

Review: Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses – Georgios Charalampakis – Virulence

Review: On the dynamics of root canal infections – what we understand and what we don’t – Matthias Zehnder – Virulence

Human gut microbiome

See also Rojo paper under Metabolomics

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences – Brett Wagner Mackenzie – Frontiers in Microbiology

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease – Weiwei Jiang – Scientific Reports

Intestinal Lesions Are Associated with Altered Intestinal Microbiome and Are More Frequent in Children and Young Adults with Cystic Fibrosis and Cirrhosis – Thomas Flass – PLOS ONE

The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing – LY Kwok – Beneficial Microbes

Review: Contribution of diet to the composition of the human gut microbiota – Daniela Graf – Microbial Ecology in Health and Disease

Animal microbiome

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing – Edward Alain B. Pajarillo – Asian-Australasian Journal of Animal Sciences

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Abstract: Bugs in bats 2: Analysis of microbial communities in faecal samples obtained from bats in the Netherlands – JCM Wolkers-Rooijackers – 11th Conference of the Dutch Society for Wildlife Health

Plant microbiome

Rapid quantification of rice root-associated bacteria by flow cytometry – G. Valdameri – Letters in Applied Microbiology

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria – Kiwamu Minamisawa – Frontiers in Microbiology

Characterization of Leaf Blade- and Leaf Sheath-Associated Bacterial Communities and Assessment of Their Responses to Environmental Changes in CO2, Temperature, and Nitrogen Levels under Field Conditions – Seishi Ikeda – Microbes and Environments

Soil, sediment, and rock microbiome

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice – J. J. Elser – Applied and Environmental Microbiology

Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils – Ning Wang – FEMS Microbiology Ecology

Analysis of Sclerotia-Associated Fungal Communities in Cool-Temperate Forest Soils in North Japan – Anzilni F. Amasya – Microbes and Environments

Water microbiome

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year – M. Korlević – Applied and Environmental Microbiology

Viruses and phages

Traces of ATCV-1 associated with laboratory component contamination – Kristín Rós Kjartansdóttir – PNAS USA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination – Robert H. Yolken – PNAS USA

Microbial Ecology

Temporal patterns of rarity provide a more complete view of microbial diversity – Ashley Shade, Jack A. Gilbert – Trends in Microbiology

Metagenomics

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics – Carolina Megumi Mizuno – mBio

Metabolomics

Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases – David Rojo – Scientific Reports

Review: Animals in a bacterial world: opportunities for chemical ecology – Alexandra M. Cantley and Jon Clardy – Natural Product Reports

Bioinformatics

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies – Mohamed Mysara – Applied and Environmental Microbiology

Techniques

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – MicroBEnet

More microbes

Natural Green Coating Inhibits Adhesion of Clinically Important Bacteria – Danielle S. Trentin – Scientific Reports

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

Breastfeeding prepares a baby for solid food – Tim Sandle – Digital Journal

Gut microbiota reveal better ways of detecting (and preventing) colorectal cancer – Kristina Campbell – Microbiome Institute

Our Inner Viruses: Forty Million Years In the Making – Carl Zimmer – National Geographic

Our wine owes a debt to ancient viruses – Andrew Geering – Phys.org

Diet is the Chief Factor Behind Gut Microbiome Diversity, Study Shows – Patricia Inacio – IBD News Today

Citizen Oceanography Meets the Marine Microbiome – Rachelle Lauro – Mission Blue

Fecal Microbiota Transplants: An Insider’s Guide – Monica J. Smith

Science and Art

Researcher Determined to Play Piano Duet With Yellow Slime Mold – The Mary Sue

And the winners of the #spacemicrobes Microbial Playoffs are… – Arvind Suresh – Discover Magazine

A Beautiful Wallpaper Made With Smallpox Vaccine – Joseph Flaherty – Wired.com

Bik’s Picks
Stressed Young Bees Linked To Colony Collapse – Jim Algar – Tech Times

Meet Spot: New Breed of Robot Dog Climbs and Trots – Elizabeth Palermo – Live Science

Australia’s Shocking Rate Of Mammal Extinction Blamed On Cats And Red Foxes Brought Over By European Settlers – Rebekah Marcarelli – Headlines and Global News

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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

[hr]

February 1, 2015

Posted on by

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

[hr]

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

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January 27, 2015

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Human gut microbiome

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas – Chunguang Luan – Scientific Reports

Plant microbiome

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – Bin Ma – Journal of Applied Microbiology

Nostopeptolide plays a governing role during cellular differentiation of the symbiotic cyanobacterium Nostoc punctiforme – Anton Liaimer – PNAS USA

Air microbiome

Antibiotics, Bacteria, and Antibiotic Resistance Genes: Aerial Transport from Cattle Feed Yards via Particulate Matter – Andrew D. McEachran – Environmental Health Perspectives

Techniques

Review: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats – Jizhong Zhou – mBio

Bioinformatics

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline) – Murat Eren – Github

Why now is the time to learn R – David Smith – OpenSource

Other scientific papers of interest

Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses – Jennifer E. Cox – PNAS USA

Discussion: Mice are not men – H. Shaw Warren – PNAS USA
Reply to Warren et al. and Shay et al.: Commonalities across species do exist and are potentially important – Keizo Takao – PNAS USA

Microbes in the news

Dust From Factory Farms Carries Drugs, Poop Bacteria, and Antibiotic-Resistant Genes Far and Wide – Tom Philpott – Mother Jones

How does your gut garden grow? Feeding your intestinal bacteria in a positive way – Áilín Quinlan – Irish Independent

The expert’s view: Ted Dinan, Professor of Psychiatry at UCC, on microbiome and stool transplants – Irish Independent

Obama proposes sharp increase to fight drug-resistant bacteria – Amy R. Connolly – UPI

Antibiotics for travellers’ diarrhoea – super-bacteria as a souvenir – Päivi Lehtinen – University of Helsinki

Science, publishing, and career

Number of College Students Pursuing Science, Engineering Stagnates – Melissa Korn – Wall Street Journal

Baring it all: Some researchers believe that openness can promote constructive communication and enable science to move forward faster – Rachel Bernstein – Science Careers

Why women are ditching STEM careers-and how to change it – Vivian Giang – FastCompany

Science and art

“Blurred Bands”: 2015 Lab Grammys: 8 nominees for Lab Parody of the Year – Biotechniques.com

Science and Culture: Science on-screen and behind the scenes – Stephen Ornes – PNAS USA

Science And Art Need Each Other, And Here’s Why – Cheryl Eddy – io9.com

Winners of the British Heart Foundation’s annual Reflections of Research competition – Richard P Grant – The Guardian

Bik’s Picks

Science finds a new way to unboil an egg – Michelle Starr – CNET

Asteroid that flew past Earth has moon – Science Daily

The continental divide of 2014 temperature – Thomas Summer – Science News

Blizzard 2015: Science Experiments to Do With Snow – Alyssa Newcomb – ABC News

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