March 16, 2015

After a busy day showing three motivated high school students how to extract DNA and detect microbes from shoe soles, floor tiles, and mouths, finally time to catch up with the literature. Be sure to scroll down for the Microbiome Game.

Conferences and other events

March 19th, 2PM ET: Cheese Microbe Communities – Google Hangouts

29 June – 1 July 2015: Exploring Human Host-Microbiome Interactions in Health and Disease,  Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Human gut microbiome

A randomised, double- blind, cross-over study investigating the prebiotic effect of agave fructans in healthy human subjects – P. Ramnani – Journal of Nutritional Science

Water microbiome

Global dispersion and local diversification of the methane seep microbiome – S. Emil Ruff – PNAS USA

CRISPRs, phages, and viruses

Targeting Enterococcus faecalis biofilm using phage therapy – Leron Khalifa – Applied and Environmental Microbiology

Metagenomics

Quality control of microbiota metagenomics by k-mer analysis – Florian Plaza Onate – BMC Genomics

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes – Alastair Crisp – Genome Biology

Microbes in the news

Satire: Hipsterome – Pap Py – Megabiome

Satire: Hungry researchers have hard time replicating “Subway” microbiome study – Leaf E. Greens – Megabiome

Baby Microbiomes: Christi Investigates – Alexandra Carmichael – uBiome

Our viral companions – David Woodland – Summit Daily

Microbiome Editing with CRISPR/Cas9 Has Research, Diagnostic Potential – Andrew P. Han

Agave prebiotic significantly increases some faecal friendly bacteria, say researchers – Annie-Rose Harrison-Dunn – Nutraingredients

Horse dung has scientists on scent of antibiotic success – Jim Drury – Business Insider

Connection with bacteria found in sewage and weight gain – Tim Sandle – Digital Journal

Microbes and art

Gut Check: The Microbiome Game – David Coil – Microbe.net

“Gut Check is a game for 2-4 players where each player attempts to develop a healthy microbiome while interfering with the microbiomes of their opponents.”

Contaminant snowman – MicrobeWorld

Science, publishing, and career

Why you can’t always believe what you read in scientific journals – Julia Belluz – Vox

To Apply or Not to Apply: A Survey Analysis of Grant Writing Costs and Benefits – Ted von Hippel, Courtney von Hippel – PLOS ONE

Bik’s Picks

Your Eyes Are Wired Backwards: Here’s Why – Science 2.0

DNA is packaged like a yoyo, scientists find – Science Daily

Happy St. Patrick’s Day! Here’s the chemistry that makes your beer taste good (or bad) – Rachel Feltman – Washington Post

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March 15, 2015

Microbiome of pregnancy and birth

The vaginal microbiome during pregnancy and the postpartum period in a European population – David A. MacIntyre – Scientific Reports

Probiotic potential of Enterococcus faecalis strains isolated from meconium – Ahmed Khassaf Al Atyaa – Frontiers in Microbiology

Review: The human neonatal gut microbiome: a brief review – Emily C. Gritz and Vineet Bhandari – Frontiers in Pediatrics

Human gut microbiome

Gut microbiome of the Hadza hunter-gatherers – Stephanie L. Schnorr – Nature Communications

Gut microbiome variations during hematopoietic stem cell transplant in severe combined immunodeficiency – Jonathan P. Lane – Journal of Allergy and Clinical Immunology

Despite the title, this is 16S rRNA gene-based analysis: Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota – Jascha Vervoort – Journal of Antimicrobial Chemotherapy

Literature review: Mast Cell Activation Disease and Microbiotic Interactions – Lawrence B. Afrin, Alexander Khoruts- Clinical Therapeutics

Review: Autoimmune host–microbiota interactions at barrier sites and beyond – William E. Ruff, Martin A. Kriegel – Trends in Molecular Medicine

Review: Microbiota Regulation of the Mammalian Gut–Brain Axis – Aurelijus Buroka – Advances in Applied Microbiology

Review: IBD and the Gut Microbiota—from Bench to Personalized Medicine – Emanuelle Bellaguarda, Eugene B. Chang – Current Gastroenterology Reports

Review: Mutualistic presence of normal Flora in Human Intestine: A review – Karishma Kabir Nipa- Journal of Bio-Science

Animal models

Monosodium L-Glutamate and Dietary Fat Differently Modify the Composition of the Intestinal Microbiota in Growing Pigs – Feng Z-M – Obesity Facts

Altered profile of gut microbiota after subchronic exposure to neochamaejasmin A in rats – Lifeng Yan – Environmental Toxicology and Pharmacology

Effects of mulberry (Morus alba L.) leaf polysaccharides on growth performance, diarrhea, blood parameters, and gut microbiota of early-weanling pigs – Xiangjie Zhao – Livestock Science

Effect of grinding or pelleting high grain maize- or barley-based concentrates on rumen environment and microbiota of beef cattle – A. Gimeno – Animal Feed Science and Technology

Animal microbiome

Earthworms: Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus – Arjun Singh – Microbiological Research

Plant microbiome

Diversity and community ecology of forest epiphyte testate amoebae from European Russia – Richard J. Payne – European Journal of Protistology

Soil and plant root microbiome

Effects of single-root-grafting, double-root-grafting and compost application on microbial properties of rhizosphere soils in Chinese protected cucumber (Cucumis sativus L.) production systems – Yinan Gao – Scientia Horticulturae

Response of belowground communities to short-term phosphorus addition in a phosphorus-limited woodland – Uffe N. Nielsen – Plant and Soil

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia – Muhammad Yasir – BMC Microbiology

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas – Chen Hong – Environmental Science and Pollution Research

Geomicrobiology of Iron Layers in the Sediment of Lake Superior – M. Dittrich – Aquatic Geochemistry

Water and ice microbiome

Microbial abundance in surface ice on the Greenland Ice Sheet – Marek Stibal – Frontiers in Microbiology

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing – Chia Sing Chan – Frontiers in Microbiology

Review: New perspectives in benthic deep-sea microbial ecology – Cinzia Corinaldesi – Frontiers in Marine Science

Bioreactor microbiome

The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage – Susan Anne Baldwin – Frontiers in Bioengineering and Biotechnology

Food microbiology

Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities – María Sánchez Mainar, Frédéric Leroy – International Journal of Food Microbiology

Metagenomics and Bioinformatics

Modelling Computational Resources for Next Generation Sequencing Bioinformatics Analysis of 16S rRNA Samples – Matthew J. Wade – ArXiv

Accurate multiplexing and filtering for high-throughput amplicon-sequencing – Philippe Esling – Nucleic Acids Research

Transmission and Microevolution of USA300 MRSA in U.S. Households: Evidence from Whole-Genome Sequencing – Md Tauqeer Alam – mBio

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population – Jessica Labonté – Frontiers in Microbiology

ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data – Jane Hawkey – BioRXiv

Perspective: Wiretapping into microbial interactions by single cell genomics – Ramunas Stepanauskas – Frontiers in Microbiology

Perspective: Bridging the knowledge gap: from microbiome composition to function – Jeremiah J Faith – Molecular Systems Biology

Metabolomics and Transcriptomics

Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses – David Rojo – ISME Journal

Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children – S. Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia – Yu-Wei Wu – BioEnergy Research

Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Fish: Proteomic profile of the skin mucus of farmed gilthead seabream (Sparus aurata) – Juan Jurado – Journal of Proteomics

Transcriptomic analysis of three Veillonella spp. present in carious dentine and in the saliva of caries-free individuals – Thuy Do – Frontiers in Cellular and Infection Microbiology

The transcriptional response of microbial communities in thawing Alaskan permafrost soils – M J. Coolen and William D. Orsi – Frontiers in Microbiology

Review: Mucin glycan foraging in the human gut microbiome – Louise Tailford – Frontiers in Genetics

More microbial science

Untangling the origin of viruses and their impact on cellular evolution – Arshan Nasir – Annals of the New York Academy of Sciences

The Great Escape: Pathogen Versus Host – Eric Kong, Mary Ann Jabra-Rizk – PLOS Pathogens

A fantastic voyage for sliding bacteria – Joshua D. Shrout – Trends in Microbiology

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity – Roger A. Garrett – Life

Etiology of Pericarditis in a prospective cohort of 1162 cases – Frédérique Gouriet – The American Journal of Medicine

Microbes in the news

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen – Jonathan Eisen – The Tree of Life
belongs to:
Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight – Dr. Raphael Kellman – MindBodyGreen

The Era of the Microbiome – SXSW Session on Monday March 16

Mind Altering Microbes: How your gut microbiome may influence your mood – Jill Carnahan

CDC: Misuse of garments may have led to release of bacteria at Tulane lab – Debra Goldschmidt and Ed Payne – CNN

The dawn of the cyborg bacteria is here – Robert Boos – PRI

Famous Microbiologists – Paul Ehrlich – Today we honor Paul Ehrlich who was born on March 14 in 1912 – LumiByte

Science and art – microbial edition

Bacterial Paintings? New Art Uses Tiny Life Forms – Tia Ghose – LiveScience

How microbes inspire art (Video) – BBC

Fungi on Tea – Microbe World

Louis Pasteur T-shirt – The Strange company

Bik’s Picks

Five research papers that revolutionised health – Deborah Cohen – BBC News Health

Folic acid plus blood pressure drug lowers stroke risk: study – Daily Mail

Man Credits Hot Chili Sauce Challenge for Brain Cancer Diagnosis – Youth Health Magazine

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March 13, 2015

Pregnancy and birth

Comparative proteomics of human and macaque milk reveals species-specific nutrition during post-natal development – Kristen Lina Beck – Journal of Proteome Research

Human gut microbiome
Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index – Shih-Wen Lin – Obesity

Diversity of duodenal and rectal microbiota in biopsy tissues and luminal contents in healthy volunteers – Journal of Microbiology and Biotechnology

Perspective: Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients – Daniel McDonald – Microbial Ecology in Health & Disease

Review: Gut microbiota: a key player in health and disease. A review focused on obesity
M. J. Villanueva-Millán – Journal of Physiology and Biochemistry

Review: Being human is a gut feeling – Thiago Hutter

Review: Hirschsprung’s Disease and the Intestinal Microbiome
Li Hong and Valeriy Poroyko

Animal and other models of microbiome research

Microbial communities and nutrient dynamics in experimental microcosms are altered after application of a high dose of Bti – Dagne Duguma – Journal of Applied Ecology

Animal microbiome

Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology

Soil and plant root microbiome

ReviewPlant-endophyte symbiosis, an ecological perspective – Zahoor Ahmed Wani – Applied Microbiology and Biotechnology

Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and non-serpentine habitats – Petr Kohout – Molecular Ecology

Effects of Forest Management Practices in Temperate Beech Forests on Bacterial and Fungal Communities Involved in Leaf Litter Degradation – Witoon Purahong – Microbial Ecology

Water microbiome

Antibiotics, Antibiotic Resistance Genes, and Bacterial Community Composition in Fresh Water Aquaculture Environment in China – Wenguang Xiong – Microbial Ecology

Grazer and viral impacts on microbial growth and mortality in the southern California Current Ecosystem – Alexis L. Pasulka – Journal of Plankton Research

Microstructure and cyanobacterial composition of microbial mats from the High Arctic – Asunción de los Ríos – Biodiversity and Conservation

Cyanobacterial diversity in benthic mats of the McMurdo Dry Valley lakes, Antarctica – L. Zhang – Polar Biology

Bioreactor microbiome
Responses of Microbial Communities to Single-Walled Carbon Nanotubes in Phenol Wastewater Treatment Systems – Yuanyuan Qu – Environmental Science & Technology

Microbiome of the built environment
Evolution of the indoor biome – NESCent Working Group on the Evolutionary Biology of the Built Environment – Trends in Ecology & Evolution

Metabolomics and proteomics

Metabolic Phenotyping of an Adoptive Transfer Mouse Model of Experimental Colitis and Impact of Dietary Fish Oil Intake – Francois-Pierre J. Martin – Journal of Proteome Research

Comparative proteomics of human and macaque milk reveals species-specific nutrition during post-natal development – Kristen Lina Beck – Journal of Proteome Research

Techniques

Flow cytometry of microbial communities: Facilitated gate setting by sequential dot plot scanning – Susanne Günther and Susann Müller – Cytometry Part A

Microbes in the news

Some genes ‘foreign’ in origin and not from our ancestors – Science Daily

MoBio Laboratories giving Research Package awards of microbiome analysis

Evotec, Second Genome To Collaborate In Microbiome Discovery And Development – Nasdaq

Why you shouldn’t be freaked out by the bacteria in public bathrooms – Megan Thielking – Vox

Bringing together science and design: Can changing how we wash change our skins microbiome? (2m video) – Experiment – Vimeo

Study: How microbiome affects liver’s response to medication – Samuel Million-Weaver – HS NewsBeat

New study may lead to microbiome-based colon cancer diagnostic – American Microbiome Institute

Nature’s inbuilt immune defense could protect industrial bacteria from viruses – Phys.org

Bacteria do the work at water reclamation plant – Lee Shearer – OnlineAthens

Paleo Cookbook Tells Moms to Swap Breast Milk for Bone Broth – Josh Scherer – TakePart

#BacteriaHysteria: NZ pre-schoolers carry potentially harmful bacteria – TVNZ

Science, publishing, and career

Why Science Fairs Aren’t So Fair – These K-12 events are hardly more than a competition among over-involved parents – Hana Schank – The Atlantic

Springer journal on hold for “pattern of inappropriate and compromised peer review” – Ivan Oransky – RetractionWatch

Bik’s Picks

American Pi: Why the Day Belongs to the U.S. (and Belize) – Philip Yam – Scientific American

How the Penguin Got Its Waddle – Ed Yong – New Yorker

How to make powdered booze at home – Paul Adams – Popular Science

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The Beard Microbiome

A discussion today on Twitter led me to investigate researchers on a very specific part of the human microbiome: The Beard. Having no opportunity to grow one myself, I was curious to see how much is already known about this habitat. As it turns out, not a lot. Here are some articles I found on this topic, including the ones that came out today. They are mainly popular science articles, but not a lot of peer-reviewed papers, unfortunately.

Update, May 2015

New Beards_sometimes_as_dirty_as_toiletsshocking science was published the first weekend of May. Well, it was not science, and it was not published in a scientific journal. But shocking indeed.

A real microbiologist puts the dirty-beard theory to the test. He swabs several beards, inoculates petridishes….. and finds bacteria. OMG. The reporter is so shocked, she slaps her gloved hands (which probably just touched a beard or a petridish) to her face.

Some beards as dirty as toilets–  Microbiologist tests beards for germs (and is surprised when he finds them?!) – Royale Da – KOAT

This unintentionally funny video led to a whole new set of popular science articles. A selection:

Bearded men have poop on their faces – Michael Morrow – New York Post

Microbiologist John Golobic, of Quest Diagnostics, swabbed a number of beards searching for bacteria for the study and found that some of the bacteria “are the kind of things that you find in feces.” .. “Try to keep your hands away from your face, as much as possible,” Golobic added.

Poo in Beard: Study shows beards full of bacteria. How to wash my beard and avoid a face of faeces – MK Web

“Bad news ladies, you encouraged your man to grow it, watched it slowly bloom and marvelled as the boyish youth of your BF turned brutish male.”

Hey Guys, Toilet Bacteria Is Probably Lurking In Your Beards – Amy Capetta – Yahoo

“Some men believe that freedom from shaving is freedom from hygiene and maintenance yet nothing could be further from the truth, both for health and aesthetic reasons.”

So It Turns Out Men’s Beards Are Covered In Poop – Julie Gerstein – BuzzFeed

Albuquerque’s ABC affiliate swabbed and tested several men’s beards and found that while some beards contained normal bacteria, others’ beards contained bacteria similar to those found in fecal matter.

Your Beard Is Covered In Shit: According To New Study Beards Are Crawling In Poop Particles – Cass Anderson – BroBible

At some point every bro will need to make this decision: beard or poop face. ..There’s dung on your chin, there’s crap on your cheeks, there’s shit on your lip. Why haven’t you shaved yet?!?

Even The Atlantic is participating in the craze. How Filthy Is Your Beard? – Olga Khazan – The Atlantic

“There is more crap in these stories about poo in beards than there is in beards.”

Luckily, Rachel Feltman provides a scientific perspective: No, your beard isn’t full of poop (probably) – Rachel Feltman – The Washington Post

I have bad news for y’all: You’re covered in poo bacteria. COVERED. .. It’s okay. It’s really fine. Embrace the poo bacteria, it is a part of you because you are a multitude of microorganisms, each more special than the last.

David Coil also wrote a piece on Slate to debunk the story: Your Beard Is Covered in Bacteria: So is everything else. Don’t fall for the latest viral freak-out – David Coil – Slate

“We found germs on X” is pointless unless you’re talking about Mars, the moon, or something sterilized.

But I am afraid that the popsci articles on “dirty beards” will be around for a while. The general audience seems to love stories like this. Science stories, not so much.

The real science

Microbiological Laboratory Hazard of Bearded Men – Manuel S. Barbeito – Applied Microbiology 1967 (HT: James Meadow  ‏@JamesMeadow)

This is a must-read paper with very instructive images featuring men taking showers and baby chickens (peeps?).

The effect of facial hair and sex on the dispersal of bacteria below a masked subject – H. A. McLure – Anaesthesia – 2000

We investigated the effect of mask wiggling in 10 bearded and 10 clean-shaven male subjects, and 10 female subjects. Wiggling the mask significantly increased the degree of bacterial shedding onto agar plates 15 cm below the lips in bearded males (p = 0.03) and females (p = 0.03), but not in clean-shaven males. At rest without mask wiggling the bearded subjects shed significantly more bacteria than clean-shaven males (p = 0.01) or females (p = 0.001). To reduce the risks of contamination of the sterile field when face masks are worn females and bearded males should avoid wiggling the face mask. Bearded males may also consider removing their beards.

Bacterial ecology of hospital workers’ facial hair: a cross-sectional study – E. Wakeam – Journal of Hospital Infection – 2014

Workers with facial hair were less likely to be colonized with Staphylococcus aureus (41.2% vs 52.6%, P ¼ 0.02) and meticillin-resistant coagulase-negative staphylococci (2.0% vs 7.0%, P ¼ 0.01). Colonization rates with Gram-negative organisms were low for all healthcare workers, and Gram-negative colonization rates did not differ
by facial hair type.

News articles, March 2015

Beards Are Unhygienic As They Carry Bacteria And Spread Infection Claims Trichologist – Inquisitr

Are hipster beards unhygienic? Facial hair is riddled with bacteria which may spread germs and trigger infections, experts claim – Madlen Davies – Daily Mail

Experts say beards breed disease – Stephen Morgan – Digital Journal

Your Beard is a Disgusting Bacteria Breeding Ground – Jake Woolf – GQ

Older popular press articles

Better Beer Through Beards – Yeast Genome

Beard Yeast Beer – Christina Agapakis – Scientific American

Beard Beer – Rogue.com, with 6 ingredients: Munich, C15 and pilsner malts; Sterling hops; free-range coastal water; Beard Yeast (HT: Matthew Barber, @bioBarber)

The Beard-ome project by Hydrocalypse Industries (YouTube video)

The microbiome and the future of artisanal gastronomy – Jason Tetro – PopSci

Featuring UC Davis based feminist Jonathan Ricin: Researcher reveals microbiome involved in everything; wishes everyone would shut up about it – The Science Web

If this is all there is, I am calling out to all microbiome researchers with some free time and some money to spare (ha!) to fill this gap in our knowledge. A comparison of all the hairy surfaces of our bodies would be best, but I will take a small beard microbiome student project too!

I’d be more than happy to add more hairy papers, in case I missed one.

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March 12, 2015

Human gut microbiome

Gut microbiome development along the colorectal adenoma–carcinoma sequence – Qiang Feng – Nature Communications

In Vivo Selection To Identify Bacterial Strains with Enhanced Ecological Performance in Synbiotic Applications – Janina A. Krumbeck – Applied Environmental Microbiology

Animal models of microbiome research

Adipose tissue ​NAPE-PLD controls fat mass development by altering the browning process and gut microbiota – Lucie Geurts – Nature Communications

Animal microbiome

Phylogeny of Intestinal Ciliates, Including Charonina ventriculi, and Comparison of Microscopy and 18S rRNA Gene Pyrosequencing for Rumen Ciliate Community Structure Analysis – Sandra Kittelmann – – Applied Environmental Microbiology

Female-Specific Specialization of a Posterior End Region of the Midgut Symbiotic Organ in Plautia splendens and Allied Stinkbugs – Toshinari Hayashi – Applied Environmental Microbiology

Plant microbiome

Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity – Navid Bazghaleh – Applied Environmental Microbiology

Soil microbiome

Fungal Communities Respond to Long-Term CO2 Elevation by Community Reassembly
Qichao Tu – Applied Environmental Microbiology

Water microbiome

Natural Hot Spots for Gain of Multiple Resistances: Arsenic and Antibiotic Resistances in Heterotrophic, Aerobic Bacteria from Marine Hydrothermal Vent Fields – Pedro Farias – Applied Environmental Microbiology

Food microbiology

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese – Daniel J. O’Sullivan – Applied Environmental Microbiology

Metabolomics

Another FartAlyzer? Human intestinal gas measurement systems: in vitro fermentation and gas capsules – Jian Zhen Ou – Trends in Biotechnology

Metagenomics and bioinformatics

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells – Manu V. Tamminen and Marko P. J. Virta – Frontiers in Microbiology

BioMiCo: a supervised Bayesian model for inference of microbial community structure
Mahdi Shafiei – Microbiome

Microbes in the news

Interview with Les Dethlefsen from our lab: What’s in My Gut? An Access Conversation with Dr. Les Dethlefsen – Ernesto Ramirez – Medium
Microbiome study allows participants access to own data – Ernesto Ramirez – Genetic Literacy Project

Study proves all humans have a little microorganism DNA – Paul Hamaker – Examiner
Humans may harbor more than 100 genes from other organisms – Sarah CP Williams – Science

Before The Gas Is Passed, Researchers Aim To Measure It In The Gut – Angus Chen – NPR
Your farts could tell your doctor about your digestive health – Alexandra Ossola – Popular Science
Fecal Fermentation and Electronic Pills May Help Decipher Gut Gases – Li Zhou – Smithsonian

Researchers develop tool to understand how the gut microbiome works – EurekAlert

The Life Of A Queen: Worker Bees And Queen Bees Have Vastly Different Microbiomes – Jim Algar – TechTimes

Does your microbiome make you unique? – Sergio Laínez – Mapping Ignorance

Science and art

Dancing the Microbiome: Et si on dansait le microbiote ? – YouTube

Science, career, and publishing

Advice for PhD Students: Tips From Professors, Startup Founders, and Industry Professionals – Nick Mordwinkin – The Winnower

Indecent advances: Surveys of sexual harassment and assault during field research and on campus reveal a hitherto secret problem – Virginia Gewin – Nature

Bik’s Picks

Nearly 200,000 ‘new’ marine species turn out to be duplicates – Rachel Feltman – Washington Post

Neanderthals Had Fashion Too, Unearthed Jewelry Implies – Brian Stallard – Nature World News

Antarctic Octopus Is a True Blue Blood – Jennifer Viegas – Discovery

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March 11, 2015

Animal models of microbiome research

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics – Stephanie J Yaung – Molecular Systems Biology

Animal microbiome

Bacterial Diversity Associated with Wild Caught Anopheles Mosquitoes from Dak Nong Province, Vietnam Using Culture and DNA Fingerprint – Chung Thuy Ngo – PLOS ONE

Soil and sediment microbiome

Selective pressure of antibiotics on ARGs and bacterial communities in manure-polluted freshwater-sediment microcosms – Wenguang Xiong – Frontiers in Microbiology

Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica – Bradley M. Tebo – Frontiers in Microbiology

Microbiome of the built environment

High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes – Alison L. Ling – PLOS ONE

Metagenomics and bioinformatics

Metassembler: Merging and optimizing de novo genome assemblies – Alejandro Hernandez Wences , Michael Schatz – BioRxiv

Metabolomics

Introducing the FartAlyzer? Alcohol Induced Alterations to the Human Fecal VOC Metabolome – Robin D. Couch – PLOS ONE

More microbiology

Generation of Influenza Virus from Avian Cells Infected by Salmonella Carrying the Viral Genome – Xiangmin Zhang – PLOS ONE

Review: Archaeal Extrachromosomal Genetic Elements – Haina Wang – Microbiology and Molecular Biology Reviews

Viable Bacteria Associated with Red Blood Cells and Plasma in Freshly Drawn Blood Donations – Christian Damgaard – PLOS ONE

Microbes in the news

Predicting oral vs. gut microbiomes – Alexandra Carmichael – uBiome

Video: Guts and Genius with Joi Ito, Kevin Slavin, and David Kong – Media at MIT

The gut microbiome: how does it affect our health? – Honor Whiteman – Medical New Today

Researchers develop tool to understand how the gut microbiome works – Medical XPress

uBiome Analysis: Microbiome Hacking to Improve Gluten Intolerance and Acne – Animal Pharm

Bedlam excavation to examine 3,000 skeletons for plague bacteria strain – Marie Singer – Market Business News

Science and art

Dancing bacteria to invade the Eden Project – LeeTrewhela – Cornish Guardian

The egg
– S.B. Divya – Nature

Science, publishing, and career

Software: Career detective – Nature

Subscription Publisher Awkwardly Experiments with Open-Access – Jeffrey Beall – ScholarlyOA

Bik’s Picks

Gigantic ancient arthropod was really ‘a very peaceful guy’ – Will Dunham – Reuters

World’s whaling slaughter tallied – Commercial hunting wiped out almost three million animals last century – Daniel Cressey – Nature

High levels of vitamin D is suspected of increasing mortality rates – Science Daily
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March 10, 2015

Human microbiome, general

Abstract: Targeted Genomic Characterization, Uncultured Bacteria from Human Microbiota, Project – Mircea Podar – Environmental Metagenomics

Review: The Emerging Role of Metagenomics in the Diagnosis of Infectious Diseases – Jun Li and Qiang Feng – SOJ Microbiology & Infectious Diseases

Review: Chapter 4 – Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome – Philip Chuang – Comprehensive Analytical Chemistry

Microbiome of pregnancy and birth

In vitro impact of human milk oligosaccharides on Enterobacteriaceae growth – Jennifer L Hoeflinger – Journal of Agricultural and Food Chemistry

Human oral microbiome

Review: Distribution of Genes Related to Antimicrobial Resistance in Different Oral Environments: A Systematic Review – Ludmila Coutinho Moraes

Human gastric and gut microbiome

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia – Dariush Nasrollahzadeh – Scientific Reports

Review: Autism and Our Intestinal Microbiota – Reddy B.L. and Saier M.H – Journal of Molecular Microbial Biotechnology

Human reproductive organ microbiome

The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in Korea – Hea Young Oh – Clinical Microbiology and Infection

Animal models of microbiome research

Helicobacter pylori infection can affect energy modulating hormones and body weight in germ free mice – Yalda Khosravi – Scientific Reports

Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases – Huang, Edmond Y. – Inflammatory Bowel Diseases

Animal microbiome

Characterization of intestinal bacterial communities of western lowland gorillas (Gorilla gorilla gorilla), central chimpanzees (Pan troglodytes troglodytes), and a forest elephant (Loxodonta africana cyclotis) living in Moukalaba-Doudou National Park in Gabon – Sayaka Tsuchida – Tropics

Editorial: Phylogeny: Are arthropods at the heart of virus evolution? – Gytis Dudas, Darren J Obbard – eLIFE

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses – Ci-Xiu Li – eLIFE

Review: Marsupial oral cavity microbiome – Philip S Bird – Microbiology Australia

Review: The marine mammal microbiome: current knowledge and future directions – Tiffanie M Nelson – Microbiology Australia

Review: Mammalian microbiomes – Linda L Blackall – Microbiology Australia

Plant microbiome

Analysis of the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in phosphate solubilization – Margrét Auður Sigurbjörnsdóttir – Microbiology

The response of root-associated bacterial community to the grafting of watermelon –
Ning Ling – Plant and Soil

Soil and sediment microbiome

Call for papers: BIODESERT: Exploring and Exploiting the Microbial Resource of Hot and Cold Deserts – BioMed Research International

Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment – Patrícia S. Costa – PLOS ONE

Establishing microbial diversity and functions in weathered and neutral Cu–Pb–Zn tailings with native soil addition – Xiaofang Li – Geoderma

A novel sub-phylum method discriminates better the impact of crop management on soil microbial community – Florine Degrune – Agronomy for Sustainable Development

Grazing intensity in subarctic tundra affects the temperature adaptation of soil microbial communities – Sari Stark – Soil Biology and Biochemistry

Phytoremediation Using Microbial Communities: I – Mohammad Miransari – Phytoremediation

Effects of soil management practices on soil microbial communities and development of southern blight in vegetable production – Tiehang Wu – Applied Soil Ecology

Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem – Alena K. Oliver – Forest Ecology and Management

Short-term effects of simulated below-ground carbon dioxide leakage on a soil microbial community – I. Fernández-Montiel – International Journal of Greenhouse Gas Control
Review: Microbial communities and their primary to early diagenetic mineral phases; the record from Neoproterozoic microbialites of Qarn Alam, Oman – M. Mettraux – Microbial Carbonates in Space and Time: Implications for Global Exploration and Production

Water microbiome

Review: Halophilic microbial communities and their environments – Aharon Oren – Current Opinion in Biotechnology

Bioreactor microbiome

Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater – Yu Miao – Water Research

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples – Boonfei Tan – ISME Journal

Microbiome of the built environment

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin – Environmental Science & Technology

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance – Nicholas A Bokulich – eLIFE

Metabolomics and transcriptomics

Microbial community transcriptional networks are conserved in three domains at ocean basin scales – Frank O. Aylward – PNAS USA

Review: The use of evolutionary approaches to understand single cell genomes – Haiwei Luo – Frontiers in Microbiology

Book: Encyclopedia of Metagenomics – Genes, Genomes and Metagenomes – Basics, Methods, Databases and Tools – Nelson, Karen E. Some interesting book chapters include:

  • MEMOSys: Platform for GenomeScale Metabolic Models – Stephan Pabinger and Zlatko Trajanoski – Genes, Genomes and Metagenomes
  • Insights into Environmental Microbial Denitrification from Integrated Metagenomic, Cultivation, and Genomic Analyses – Stefan J. Green
  • Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences -Weizhong Li
  • Use of Bacterial Artificial Chromosomes in Metagenomics Studies, Overview – Lingling Wang
  • A 123 of Metagenomics – Torsten Thomas

Viruses and phages

The Importance of Virology at a Time of Great Need and Great Jeopardy – Michael J. Imperiale and Arturo Casadevall – mBio

A metagenomics and case-control study to identify viruses associated with bovine respiratory disease – Terry Fei Fan Ng – Journal of Virology

Techniques

Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species – Morgane Rossi-Tamisier – International Journal of Systematic and Evolutionary Microbiology

A single protocol for extraction of gDNA from bacteria and yeast – Laurie Vingataramin and Eric H. Frost – BioTechniques

Microbes in the news

Are you overweight? The clue’s in your poo – Robert Pickup – The Conversation

New research finds queen bee microbiomes are starkly distinct from worker bees – Indiana University Bloomington

Queen Bee Microbiomes Are not Like Those of Worker Bees – Entomology Today

Launch of the AMI Microbiome Podcast – American Microbiome Insitute

Dog bacteria might benefit human health – Kalli Ricka Wolf – Tucson Sentinel

A Short History of the Discovery of Viruses – MicrobiologyBytes

How Bacteria Work – Marianne Spoon – How Stuff Works

Resistance: The Film, a documentary on antibiotic resistance.

Science and art

Science and Culture: High concept art and experiments – Calla Cofield – PNAS USA

Science, publishing, and career

The postdoc series: What is a postdoc? – Julie Gould – Nature

Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida and M. Àngels Colomer – PNAS USA

A Second Chance for Fraudsters? What’s behind paper retractions? – Adam Marcus and Ivan Oransky – Labtimes

Bik’s Picks

Chameleons’ Color-Changing Secret Revealed – Laura Geggel – LiveScience

This plant can feel bugs eating it alive. Can scientists improve its self defense? – Darryl Fears – Washington Post

Picture of the Week: Plastiglomerate – Chau Tu – ScienceFriday

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March 9, 2015

Pregnancy and birth

Association between caesarean section and childhood obesity: a systematic review and meta-analysis – S. Kuhle – Obesity Reviews

Editorial: Metabolomics, milk-oriented microbiota (MOM) and multipotent stem cells: the future of research on breast milk – Vassilios Fanos – Journal of Pediatric and Neonatal Individualized Medicine

Human oral microbiome

Detection of Mycobacterium tuberculosis DNA on the oral mucosa of tuberculosis patients – Rachel C. Wood – Scientific Reports

Human gut microbiome

Microbes-Gut-Brain Axis: A Possible Future Therapeutics Target for Gastrointestinal and Behavioral Disorder – Amit Ghosh – International Journal of Health Sciences and Research

Review: Collective unconscious: how gut microbes shape human behavior

Human microbiome after death

Seasonal variation of postmortem microbial communities – David O. Carter – Forensic Science, Medicine, and Pathology

Animal models of microbiome research

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure – Adrienne B Narrowe – Microbiome

Responses in gut microbiota and fat metabolism to a halogenated methane analogue in Sprague Dawley rats – Yong Su – Microbial Biotechnology

Animal microbiome

The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection – Scott J Weese – Veterinary Research

Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis – Matthew H. Becker – Molecular Ecology

Microbial ecology in Hydra: Why viruses matter – Thomas C.G. Bosch – Journal of Microbiology

Plant microbiome

Microbial communities on flower surfaces act as signatures of pollinator visitation – Masayuki Ushio – Scientific Reports

Review: The Ecology and Natural History of Foliar Bacteria with a Focus on Tropical Forests and Agroecosystems – Eric A. Griffin, Walter P. Carson – Botanical Review

Review: Chemical diversity of microbial volatiles and their potential for plant growth and productivity – Chidananda N. Kanchiswamy – Frontiers in Plant Science

Soil and plant root microbiome

Metagenomic Assessment of the Potential Microbial Nitrogen Pathways in the Rhizosphere of a Mediterranean Forest After a Wildfire – José F. Cobo-Díaz – Microbial Ecology

Evaluation of Methyl Bromide Alternatives Efficacy against Soil-Borne Pathogens, Nematodes and Soil Microbial Community – Hongwei Xie – PLOS ONE

Relative importance of soil physico-chemical characteristics and plant species identity to the determination of soil microbial community structure – André M. Massenssini – Applied Soil Ecology

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria – Angus Angermeyer – Environmental Microbiology

Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils – Jing Li – Environmental Science and Pollution Research

Extreme plagiarism alert: Influence of heavy metals on earthworms, soil microbial community and mammals – Ahmad Gholamalizadeh Ahangar and Abbas Keshtehgar – Journal of Novel Applied Sciences

Water (and ice) microbiome

Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida – Alexandra M. Campbell – MicrobiologyOpen

Temperature affects the size-structure of phytoplankton communities in the ocean – Ángel López-Urrutia – Limnology and Oceanography

Stable microbial community composition on the Greenland Ice Sheet – Michaela Musilova – Frontiers in Microbiology

Diversity and spatial distribution of autotrophic communities within and between ice-covered Antarctic lakes (McMurdo Dry Valleys) – Jenna M. Dolhi – Limnology and Oceanography

Book chapter: Microbial Life in Volcanic Lakes – Francesca Mapelli – Volcanic Lakes

Microbiome of the built environment

Urban microbiome – Orli G. Bahcall – Nature Review Genetics

Our interface with the built environment: immunity and the indoor microbiota – Simon Lax – Trends in Immunology

Microbial evolution and ecology

Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life – Céline Petitjean – Molecular Biology and Evolution

The community ecology of pathogens: coinfection, coexistence and community composition – Eric W. Seabloom – Ecology Letters

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data – Sylvie Schulze – Frontiers in Microbiology

Genetic isolation between two recently diverged populations of a symbiotic fungus
Sara Branco – Molecular Ecology

Review: Ecology and exploration of the rare biosphere – Michael D. J. Lynch & Josh D. Neufeld – Nature Reviews Microbiology

Metagenomics and bioinformatics

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data – Johan Bengtsson-Palme – Molecular Ecology Resources

RITA: Rapid Identification of HighConfidence Taxonomic Assignments for Metagenomic Data – Norman J. MacDonald – Genes, Genomes and Metagenomes

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets – Matthias Scheuch – BMC Bioinformatics

Poster: Possibilities and obstacles in recovery of genomes from elusive microbes in complex metagenomes – Søren M. Karst

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic – Richard J. Hall – Frontiers in Microbiology

Whole genome sequencing in clinical and public health microbiology – Kwong, J. C – Pathology

Metabolomics

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links – Rico Rueedi – PLOS Genetics

Techniques

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons – Nathan D. Olson – Biomolecular Detection and Quantification

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations – Fiona Fouhy – PLOS ONE

Parallel DNA polymerase chain reaction: Synthesis of two different PCR products from a DNA template – Vikash Bhardwaj1, Kulbhushan Sharma2 – F1000 Research

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton- Nature Biotechnology

Microbes in the news

1h podcast with Jonathan Eisen: The Tiny World of Microbes Inside You – Inquiring Minds at Soundcloud

20m podcast: The Straight Poop – Transistor

Beyond Probiotics: Can You “Hack” Your Microbiome? – Beth Skwarecki – Vitals

The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’ – Nick Lane – Royal Society

Drugging the gut microbiome – Ken Garber – Nature Biotechnology

Tummy Troubles? Your Microbiome Can Help – Isabel Smith

Sewage Bacteria Reveal Cities’ Obesity Rates – Brian Owens – Inside Science

Trend of colon cleansing generally unnecessary – Denise Cedar and Marilyn Bacon – Statesman Journal

Health focus shifts to gut microbiome and nurturing ‘good’ bacteria – Peg Moline – LA Times

How Microbes Keep Us Healthy – Scientific American

Understanding psychobiotics: John F. Cryan – Catherine Lawson – Wired

“Thinking from the Gut” – Rob Wipond – Mad In America

Prediabetes Patients Have Fewer Gut Bugs – Parker Brown – MedPageToday

Fecal microbiota present target for glucose tolerance assessment – Elena Barengolts – Healio

How gut microbiota could play a key role in protecting the brain – Nina Weisbroth – Translational Microbiome

Hand-Wringing Over Bacteria – C. Claiborne Ray – New York Times

Beer Makers To Produce Beer Replicas of 170-Year-Old Brews – Jenny Michelle Panganiban – International Business News

Gut check: With bacteria in us and all over us, researchers are finding ways to take advantage of them – Kyle Peveto – The Advocate

First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life – Lab Manager

Autism’s bacteria link gains credence – Jonathan Sher – LF Press

Nestlé’s research on nutrition and the human gut microbiome – Enea Rezzonico – Scientific American

Fine Focus: Microbiology Research Journal for Undergraduate Students

Science and art

New Drawings Show the Strange Beauty of Phages, the Bacteria Slayers – Brian Handwerk – Smithsonian’

Cosmos: Abstract Images Created by Destroying Star Photo Film Slides with Bacteria – Michael Zhang – Peta Pixel

Science, publishing, and career

Keys to the kingdom (academic bioentrepreneurs) – Sybil C K Wong- Nature Biotechnology

My Most Informative Error – Ami Schattner – JAMA Internal Medicine

We need post-publication peer review of journals – Lenny Teytelman – The Spectroscope

Bik’s Picks: The science of aging edition

Cavers Find Ancient Hoard of Coins and Jewelry in Israel – Megan Gannon – Live Science

Book Review: Rust’ Offers an Engrossing Look at Corrosion – Gregory Cowles – New York Times

Achieving Immortality: How Science Seeks to End Aging – Josh Nilaya – WNPR

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March 6, 2015

Pregnancy and birth

Longitudinal Analysis of the Premature Infant Intestinal Microbiome Prior to Necrotizing Enterocolitis: A Case-Control Study – Yanjiao Zhou – PLOS ONE

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota – Tadao Enomoto – Allergology International

Human oral microbiome

Subgingival Microbial Communities in Leukocyte Adhesion Deficiency and Their Relationship with Local Immunopathology – Niki M. Moutsopoulos – PLOS Pathogens

Human gut microbiome

What is missing from this title? 16S gut community of the Cameron County Hispanic Cohort – Matthew C Ross – Microbiome

Review: The role of intestinal microbiota in acute graft-versus-host disease – Yuanyuan Chen – Journal of Immunology Research

Review: Type 1 diabetes and gut microbiota: Friend or foe? – Changyun Hu – Pharmacological Research

Review: Collective unconscious: how gut microbes shape human behavior
Timothy G. Dinan- Journal of Psychiatric Research

Human respiratory microbiome

2013 Workshop summary: Host–microbe interactions in distal airways: relevance to chronic airway diseases – Clémence Martin – European Respiratory Review

Review: Microbial Exposure and Onset of Allergic Diseases – Potential Prevention Strategies? – Petra Ina Pfefferle, Harald Renz – Allergology International

Animal models of microbiome research

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome – Jun Wang – Nature Communications

Disturbance of the intestinal microbial community by ursolic acid contributes to its function as a regulator of fat deposition – Zemeng Feng – Journal of Functional Foods

Helicobacter hepaticus infection in BALB/c mice abolishes subunit-vaccine-induced protection against M. tuberculosis – Isabelle C. Arnold – Vaccine

Animal microbiome

Early life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

In cattle: Characterization of mucosa-associated bacterial communities in abomasal ulcers by pyrosequencing – Alexandra Hund- Veterinary Microbiology

Baby marmosets (Do a Google Image search)! Isolation and identification of cultivable Bifidobacterium spp. from the faeces of 5 baby common marmosets (Callithrix jacchus L.) – Samanta Michelini – Anaerobe

A Kazal-type inhibitor is modulated by Trypanosoma cruzi to control microbiota inside the anterior midgut of Rhodnius prolixus – Tatiane S. Soares – Biochimie

Plant microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Soil and sediment microbiome

A Method for Determining Community Level Physiological Profiles of Organic Soil Horizons – Mathew J.B. Swallow and Sylvie A. Quideau – Soil Science Society of America Journal

Influence of elevated ozone concentration on methanotrophic bacterial communities in soil under field condition – Y.Z. Huang – Atmospheric Environment

Disruption of photoautotrophic intertidal mats by filamentous fungi – Cátia Carreira – Environmental Microbiology

Phylogenetically distinct phylotypes modulate nitrification in a paddy soil – Jun Zhao – Applied and Environmental Microbiology

Water microbiome

Metagenomic analysis of a high CO2 subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla – Joanne B. Emerson – Environmental Microbiology

Effect of historical residual hexachlorocyclohexanes and dichlorodiphenyltrichloroethane on bacterial communities in sediment core collected from an estuary in northeastern China by next-generation sequencing – Jianguo Guo – Marine Pollution Bulletin

Understanding diversity patterns in bacterioplankton communities from a Sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria (“Candidatus Thiopilula spp.”) from abyssal cold seeps of the Barbados Accretionary Prism – Daniel S. Jones – Applied and Environmental Microbiology

Bioreactor microbiome

Long-term dynamics of the microbial community in a full-scale wastewater treatment plant – A. Muszyński – International Biodeterioration & Biodegradation

Microbiome of the built environment

Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities – Tamar Dickerson – Online Journal of Public Health Informatics

Food microbiology

Yeast strains as potential aroma enhancers in dry fermented sausages – Mónica Flores – International Journal of Food Microbiology

Metagenomics and bioinformatics

IVA: accurate de novo assembly of RNA virus genomes – Martin Hunt – Bioinformatics

Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels – Rika A. Furuta – Transfusion

Review: Fungal genome sequencing: basic biology to biotechnology – Krishna Kant Sharma – Critical Reviews in Biotechnology

Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis – Qizhi Cao – Gut

Proteomics

Review: Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Microbial Ecology

Predicting ecosystem emergent properties at multiple scales – Jack A. Gilbert and Chris Henry – Environmental Microbiology Reports

Perspective: Re-defining microbial diversity from its single-celled building blocks – Ramunas Stepanauskas – Environmental Microbiology Reports

Microbes in the news

Not Even Science Could Explain the Bacteria In My Apartment – Sarah Zhang – Gizmodo

Gut microbial mix relates to stages of blood sugar control – Medical Xpress
Gut bacteria may contribute to diabetes in black males – Sharon Parmet – University of Illinois at Chicago

Who owns my microbiome? – Gabrielle Morguelan – Transylvania Rambler

Bill Gates Foundation backs microbiome engineering to boost infant health – Shane Starling – Nutraingredients

Antarctic lakes are full of small surprises – Sarah Payne – Australian Antarctic Magazine

Long list of food items in alphabetical order, but not much science: The human microbiome: How to feed your gut – Mindy Athas – Baltimore Sun

Science, publishing, and career

Need registration to read: It starts with a poster: Most researchers learn how to talk about science at meetings – Marcia McNutt – Science

Why has the scholarly journal endured? – Alice Meadows – Exchanges at Wiley

Reflecting on Fifty Years of Progress for Women in Science – Nancy Hopkins – DNA and Cell Biology

Bik’s Picks

Video: Giant Octopus makes slippery escape from tank in Seattle aquarium – Ben Axelson – Syracuse

CCTV unexpectedly catches rare wild giant panda on midnight stroll – Rose Troup Buchanan – Independent

Turning yogurt waste into new products – University of Wisconsin-Madison – Science Daily

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March 5, 2015

Human skin microbiome

Malassezia species and their associated skin diseases – Kazutoshi Harada – The Journal of Dermatology

Animal and other models for microbiome research

Plant identity drives the expression of biocontrol factors in a rhizosphere bacterium across a plant diversity gradient – Ellen Latz – Functional Ecology

Soil and sediment microbiome

Hydrogen export from intertidal cyanobacterial mats: sources, fluxes and the influence of community composition – Dörte Hoffmann – Environmental Microbiology

Discovery and microbial content of the driest site of the hyperarid Atacama Desert, Chile – Armando Azua-Bustos – Environmental Microbiology Reports

Community composition and population genetics of insect pathogenic fungi in the genus Metarhizium from soils of a long-term agricultural research system – Ryan M. Kepler – Environmental Microbiology

Characterization of wheat straw-degrading anaerobic alkali-tolerant mixed cultures from soda lake sediments by molecular and cultivation techniques – Katharina Porsch – Microbial Biotechnology

Microbes of the built environment

Modeling environmental contamination in hospital single- and four-bed rooms – M-F. King – Indoor Air

Metabolomics

Letter: volatile metabolomics of exhaled breath or faecal gas? – E. F. J. de Groot – Alimentary Pharmacology & Therapeutics

Microbes in the news

Gut Reaction: Study implicates bacteria in maternal stress and infant illnesses – Josie Glausiusz – The American Scholar

Scientists study the microbiome – the bacteria, viruses and fungi – living in an Alabama high school – Lee Roop – AL.com

Infant Gut Bacteria Linked To Later Food Sensitization – Interview with Anita Kozyrskyj – Medical Research

Podcast: SciCafe: Mapping the Urban Microbiome, Genome, Metagenome – American Museum of Natural History

Satire (but probably true): U.S. Children Getting Majority Of Antibiotics From McDonald’s Meat – The Onion

Science, publishing, and career

Movie science vs real life – People in White Coats

The Juggling Scientist: Tips for not Letting Things Fall – Black Science Blog

Developing world: The minority minority – Katia Moskvitch – Nature

Study: At ‘Rate My Professor,’ A Foreign Accent Can Hurt A Teacher’s Score – Kat Chow – NPR

Making Scientific Blogging “Count” – Joshua Nicholson – The Winnower

Bik’s Picks

Video reveals the incredible acrobatic feats (and occasional face plants) of a pouncing praying mantis – Rachel Feltman – Washington Post

After Menopause, Female Killer Whales Help Pod Survive – Jane J. Lee – National Geographic

170-Year-Old Shipwreck Beer Smells Gross – Megan Gannon – Live Science

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