Category Archives: Animal microbiome

March 31, 2015

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For today’s digest, I screened over 500 papers, and thousands of Tweets for you. Here is my selection:

Pregnancy and birth microbiome

PhD thesis [PDF]: Dynamics of co-existing Escherichia coli lineages in situ of the infant gut – Heidi Kira Gumpert – Technical University of Denmark

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis – Anne G Hoen – The Journal of Pediatrics

Review: Probiotics for Preterm Infants: A Premature or Overdue Necrotizing Enterocolitis Prevention Strategy? – Sharon Anderson – Neonatal Network

Review: Preterm infant nutrition, gut bacteria, and necrotizing enterocolitis – Josef Neu –  Current Opinion in Clinical Nutrition & Metabolic Care

Human oral microbiome

Periodontal Therapy Effects on Nitrite Related to Oral Bacteria: A 6-Month Randomized Clinical Trial – Sheila C Cortelli – Journal of Periodontology

Perspective: Mouthguards: Does the indigenous microbiome play a role in maintaining oral health? – Purnima S. Kumar and Matthew R. Mason – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Nasal Inoculation of the Commensal Neisseria lactamica Inhibits Carriage of Neisseria meningitidis by Young Adults: A Controlled Human Infection Study – Alice M. Deasy – Clinical Infectious Diseases

Human skin microbiome

Molecular cartography of the human skin surface in 3D – Amina Bouslimani – PNAS USA

Human gut microbiome

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection – Alexa Weingarden – Microbiome Journal

Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization – Zhang Lihua – Anaerobe

Review: The microbiota in inflammatory bowel disease – Donal Sheehan – Journal of Gastroenterology

Review: Promoting Health and Longevity through Diet: From Model Organisms to Humans – Luigi Fontana, Linda Partridge – Cell

Review: TLR4 at the crossroads of nutrients, gut microbiota and metabolic inflammation
Licio A. Velloso – Endocrine Reviews

Review: Cultivating Healthy Growth and Nutrition through the Gut Microbiota – Sathish Subramanian – Cell

Review: The human gut microbiome, a taxonomic conundrum – Senthil Alias Sankar – Systematic and Applied Microbiology

Review: The Role of Infectious Mediators and Gut Microbiome in the Pathogenesis of Celiac Disease – Mohammad Rostami-Nejad – Archives of Iranian Medicine

Review: Exercise and the microbiota – Orla O’Sullivan – Gut Microbes

Animal models of microbiome research

Abnormal Pregnancy Outcomes in Mice Using an Induced Periodontitis Model and the Haematogenous Migration of Fusobacterium nucleatum Sub-Species to the Murine Placenta – Sara Stockham – PLOS ONE

Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism – Silvia Falcinelli – Scientific Reports

Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats – Nina L. Cluny – Obesity

Animal microbiome

Editorial to Baboon microbiome paper: Metagenomics: Social behavior and the microbiome – Jack A Gilbert – eLIFE

More baboons: Development, diet, and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons – Tiantian Ren – Environmental Microbiology

Spider monkey: Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks – Vanessa L. Hale – Journal of Microbiological Methods

Cats: Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease – L. Pérez-Salcedo – Journal of Small Animal Practice

Desert wool rat: Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida) – Journal of Mammalogy

Tortoise: Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise – Michael L. Yuan – Molecular Ecology

Trout: Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes
Miray Etyemez, José Luis Balcázar – Research in Veterinary Science

Fruit fly: Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis – Awawing A. Andongma – Scientific Reports

Aphids: Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA – Jean-Pierre Gauthier – PLOS ONE

Plant microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Soil and plant root microbiome

A novel pathway producing ​dimethylsulphide in bacteria is widespread in soil environments – O. Carrión – Nature Communications

Metabolic characteristics of microbial communities of Aeolian sandy soils induced by saline water drip irrigation in shelter forests – Z. Jin – European Journal of Soil Science

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization – Jie Zhao – European Journal of Soil Biology

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus – Jean H. Burns – AoB Plants

Long-term oil contamination causes similar changes in microbial communities of two distinct soils – Jingqiu Liao – Frontiers in Environmental Science

Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments – Sadikshya R. Dangi – Applied and Environmental Soil Science

Water microbiome

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification – C. Harwood Theisen – Geobiology

The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth – Stephen M. Techtmann – PLOS ONE

Planktonic eukaryote molecular diversity: discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina) – Enrique Lara – J. Plankton Research

Extremophile microbiome

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate – B. F. N. Beall – Environmental Microbiology

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep – Stephanie D. Mendes – Journal of Geophysical Research: Oceans

Built environment microbiome

Are microbial communities in green roof substrates comparable to those in post-industrial sites?—a preliminary study – Chloe J. Molineux – Urban Ecosystems

Food microbiology

Some journals just have great titles: Microbial community changes in Makgeolli during brewing – Changhoon Chai – Journal of the Institute of Brewing

Review: Fermented Foods as Experimentally Tractable Microbial Ecosystems – Benjamin E. Wolfe, Rachel J. Dutton – Cell

Metagenomics and bioinformatics

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains
Marie Trussart – Nucleic Acids Research

CRISPR Detection from Short Reads Using Partial Overlap Graphs – Ilan Ben-Bassat, Benny Chor – Research in Computational Molecular Biology

CLARK: fast and accurate classification of metagenomic and genomic sequences using
discriminative k-mers – Rachid Ounit – BMC Genomics

FlowClus: efficiently filtering and denoising pyrosequenced amplicons – John M Gaspar and W Kelley Thomas – BMC Bioinformatics

Review: 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions – Feng Ju, Dr. Tong Zhang – Applied Microbiology and Biotechnology

Book Chapter: Single-Cell Sequencing of Microorganisms – Ying Chen – Single Cell Sequencing and Systems Immunology

Metabolomics

Review: Rumen Nutrition Symposium How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J. L. Firkins and Z. Yu – Journal of Animal Science

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

Body Maps Expose the Chemical Residue That Coats Our Skin – Marcus Woo – Wired.com
Crazy maps reveal colonies of bacteria and chemicals all over the human body – Kevin Loria – Business Insider
3D Human Skin Maps Aid Study of Relationships Between Molecules, Microbes and Environment – Heather Buschman – UC San Diego

Advancing the understanding of the dental microbiome – Maria Perno Goldie – Dentistry IQ

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria – Daniella Lowenberg – PLOS blogs

Antibiotic-resistant bacteria are not match for medieval potion – Alexandra Ossola – Popular Science

Antibiotic-Resistant Bacteria From Texan Cattle Yards Are Now Airborne, Study Finds
Kevin McSpadden – Time

Growing a Baby Microbiome – Kevin Bonham – Scientific American

Poop Transplants Can Treat Severe Infection In Patients – FPJ Bureau – The Free Press Journal

Poo transplants could save thousands – Geoff Egan – Range News
Healthy Microbiome Changes Last After Fecal Transplant in New Research – Elizabeth Gough-Gordon – MPR

With sample collection videos: GoViral – collecting nasal and saliva samples from sick people – Boston Children’s Hospital

Northwestern leads research on effects of long-term stay in space – Peter Kotecki – The Daily Northwestern
Conference paper: Research from the NASA Twins Study and Omics in Support of Mars Missions – NASA Technical Reports

Podcast (1min30): Donate Your Health Data To Medical Science – Cynthia Graber – Scientific American – American Gut, GoViral

You Act What You Eat: How Gut Microbes Modify Our Behavior – Monica Thunder – ResetMe

Meet The Bacteria That Make A Stink In Your Pits – Poncie Rutsch – NPR
Bacterial genetic pathway involved in body odor production discovered – Science Daily

Should Gut Bugs Influence the 2015 Dietary Guidelines? – Cameron Wells – US News

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

Nearly half of hospital uniforms are washed in temperatures too cool to kill bacteria, says DMU research – De Montfort University
Egyptians Brewed Beer in Tel Aviv 5,000 Years Ago – Megan Gannon – Live Science

Conferences

#IHMC2015: 5th International Human Microbiome Congress, March 31-April 2, 2015, Luxembourg (6/23 plenary speakers are women)

The 2nd Microbiome R&D and Business Collaboration Forum Europe, May 07 – 08, 2015, London, UK (10/36 listed speakers are women)

1st Annual Translational Microbiome Conference, 13–14 May 2015, Boston, United States (5/11 speakers are women)

ASM General Meeting, May 30 – June 2, 2015, New Orleans, LA, USA

Symbiomes: Systems Biology of Host-Microbiome Interactions, 5-10 June 2015, Pultusk, Poland (5/17 speakers are women)

The Human Microbiome, 10-12 Jun 2015, EMBL Heidelberg, Germany (8/23 confirmed speakers are women)

Exploring Human Host-Microbiome Interactions in Health and Disease, June 29 – July 1, 2015 , Cambridge, UK (7/17 speakers are women)

Science, publishing, and career

How Articles Get Noticed and Advance the Scientific Conversation – Victoria Costello – PLOS Blogs

Writing a Good Peer Review to Improve Scholarship: What Editors Value and Authors Find Helpful – H. McLaughlin – Social Work Education: The International Journal

Discussion: Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida – PNAS USA

What if you could replace performance evaluations with four simple questions? – Jena McGregor – Washington Post

Bik’s Picks

What 60 Minutes Got Right And Wrong On Duke’s Polio Virus Trial Against Glioblastoma – David Kroll – Forbes.com

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

What Elephants and Whales Look Like From Space – Robinson Meyer – The Atlantic

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March 30, 2015

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Microbiome in rhinosinusitis patients, microbes in permafrost, and responses of soil to deforestation.

Meetings
London Microbiome Meeting 2015 (LMM2015), St. Thomas’ Hospital, 28 May 2015

Human respiratory microbiome

Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome – Vijay R. Ramakrishnan – Journal of Allergy and Clinical Immunology

Animal microbiome

Antimicrobial resistance in faecal samples from buffalo, wildebeest and zebra grazing together with and without cattle in Tanzania – A.A.S. Katakweba – Journal of Applied Microbiology

Soil and plant root microbiome

Soil microbiome responses to the short-term effects of Amazonian deforestation –
Acacio A. Navarrete – Molecular Ecology

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

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China – Yucheng Wu – Frontiers in Microbiology

Extremophile microbiome

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania – Cristian Coman – Frontiers in Microbiology

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost – Mette M. Svenning – Frontiers in Microbiology

Bioreactor microbiome

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Food microbiology

Diffusion of solutes inside bacterial colonies immobilized in model cheese depends on their physicochemical properties: a time-lapse microscopy study – Juliane Floury – Frontiers in Microbiology

Metagenomics

It’s a dirty job — A robust method for the purification and de novo genome assembly of Cryptosporidium from clinical material – Sofia Andersson – Journal of Microbiological Methods

Bioinformatics and statistics

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA – Brendan J. Kelly – Bioinformatics

More microbe papers

Review: Tackling antibiotic resistance: the environmental framework – Thomas U. Berendonk – Nature Reviews Microbiology

Microbes in the news

You Should Know: Kristina Campbell and The Intestinal Gardener – DNLee – Scientific American
Link to blog: The Intestinal Gardener – Kristina Campbell

Video of the February VLAB meeting at Stanford: Gut-Feeling — Ventures into the Microbiome – Colleen Cutcliffe – VLAB videos

Chronic Rhinosinusitis Varies By Bacterial Microbiome – Vijay R. Ramakrishnan – Medical Research

Doctors: How gut bacteria affects obesity, diabetes, child health – Jondi Gumz – Santa Cruz Sentinel

The bacteria that could make your blue jeans greener – Michael Keller – Green Biz

Bacteria power up by using magnets as batteries – Catherine Brahic – New Scientist

Antibiotics from the medieval medicine cabinet: Could medieval medicine provide new antibiotics to treat deadly modern infections? – CrowdFunder

Science, publishing and career

These scientists studied journalists covering science. Whoa, meta. – Suzanne Jacobs – Grist

Let’s compare the backgrounds of science writers for Fox and NPR – Boing Boing

Mind the (gender) gap: Kew’s records show fewer than 3% of land plant species published by women – Lauren Gardiner – Kew Royal Botanical Gardens

I’m an engineer, not a cheerleader. Let’s abandon silly rules about gender roles. – Sara Sakowitz – Washington Post

Bik’s Picks

Velvet Worms, Squirting Slime – James Gorman – New York Times

An apple a day may not keep the doctor away, study says – Lindsey Tanner – Big Story AP

Family income, parental education related to brain structure in children, adolescents – Science Daily

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March 28, 2015

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Screen Shot 2015-03-28 at 1.00.33 AMFeatured video

I had hoped that this would have been a better video. The opening text/visuals are very confusing, and the cartoon human looks like a sad penguin. Is it supposed to be a human? Or human cells inside the human? Or a bacterium? And why is it looking so sad? #SadPenguin

Video (2014): Microbes: The Residents Living On And Inside You – Carl R. Woese Institute for Genomic Biology

 

Human oral microbiome

Acetaldehyde production by major oral microbes – Keisuke Moritani – Oral Diseases

Prelude to oral microbes and chronic diseases: Past, present and future – Kalina R. Atanasova – Microbes and Infection

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human gut microbiome

Common occurrence of antibacterial agents in human intestinal microbiota – Fatima Drissi – Frontiers in Microbiology

Maintaining gut ecosystems for health: Are transitory food bugs stowaways or part of the crew? – Coline Plé – International Journal of Food Microbiology

Size does not matter: commensal microorganisms forge tumorpromoting inflammation and anti-tumor immunity – Melanie R. Rutkowski – Oncoscience

Review: Time for Food: The Intimate Interplay between Nutrition, Metabolism, and the Circadian Clock – Gad Asher – Cell

Animal microbiome

Horses: Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses – M.C. Costa – The Veterinary Journal

Fish: Declining diversity of egg-associated bacteria during development of naturally spawned whitefish embryos (Coregonus spp.) – Laetitia G. E. Wilkins – Aquatic Sciences

Bees (see also under “Other microbiology” below): Characterization of gut bacteria at different developmental stages of Asian honey bees, Apis cerana – Jun Guo – Journal of Invertebrate Pathology

Soil, rock, and marble microbiome

Biofouling of marbles by oxygenic photosynthetic microorganisms – Zeki Karaca – Environmental Science and Pollution Research

Water microbiome

Bacterial diversity of polluted surface sediments in the northern Adriatic Sea determined by pyrosequencing – Marino Korlević – Systematic and Applied Microbiology

Extremophile microbiome

Genomics in a changing Arctic: Critical questions await the molecular ecologist – Stan D. Wullschleger – Molecular Ecology

Microbial diversity on Icelandic glaciers and ice caps – Stefanie Lutz – Frontiers in Microbiology

Other microbiology

Antimicrobial-Induced DNA Damage and Genomic Instability in Microbial Pathogens –
Rebecca S. Shapiro – PLOS Pathogens

Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera) – David A. Galbraith – PLOS Pathogens

News

Planetary Protection Workshop (Forward Contamination) – Jenna Lang – MicroBEnet

How to keep up with microbial ecology and the built environment: microBEnet is your place – Jonathan Eisen – The Tree of Life

Italian Researchers Publish Array Method to Profile Vaginal Microbiome, Gauge Treatment Response – Molika Ashford – Genome Web

Social constructs and behaviors can predict microbiome composition – American Microbiome Institute

Not a good title: Hunter-Gatherers Have Better Guts Than We Do – Cody Brooks – Clapway

The tiny intruders in YOUR home: Researchers reveal the average house has 8,000 different types of bacteria and bugs – Mark Prigg

Drug metabolism: manipulating the microbiome – Sarah DeWeerdt – Pharmaceutical Journal

A High-Fat Diet May Alter Your Behavior and Your Brain with Changed Gut Bacteria – Catherine Griffin – Science World Report

Surfwear founder’s charity backs UQ researcher in superbug war – University of Queensland

Paywalled: Bacteria: Master Microbial Colonizers – Marcia Stone – BioScience

A Farmer Drilled For Water, But What Came Up Turned This Desert Into An Oasis! – OffGridQuest

Science, publishing and career

BioMed Central retracting 43 papers for fake peer review – Cat Ferguson – Retraction Watch

Bik’s Picks

Crossing fingers can reduce feelings of pain – Science Daily

Giant pandas’ secret social life revealed – Bob Holmes – New Scientist

Watch Scientists Try Everything to Put a Camera on a Manatee – Jane J. Lee – National Geographic

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March 26, 2015

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General microbiome

Note: not about metagenomics but 16S rRNA gene: The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies – J Paul Brooks – BMC Microbiology

Human respiratory microbiome

Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography – Robert P. Dickson – Annals ATS

A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients – Mohammad A. Tariq – Frontiers in Microbiology

Perspective: Meningitis in adolescents: the role of commensal microbiota – James W.B. Moir – Trends in Microbiology

Human gut microbiome

An n=1 case report of a child with autism improving on antibiotics and a father’s quest to understand what it may mean – John Rodakis – Microbial Ecology of Health and Disease

Animal microbiome

Sponges: Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations – Ray Keren – Frontiers in Microbiology

Soil, sediment, and plant root microbiome

Community Dynamics of Arbuscular Mycorrhizal Fungi in High-Input and Intensively Irrigated Rice Cultivation Systems – Yutao Wang – Applied and Environmental Microbiology

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes – Zhichao Zhou – Frontiers in Microbiology

Isolation and characterization of culturable bacteria from bulk soil samples and the rhizosphere of arid-adapted Tylosema esculentum (Burchell). A. Schreiber (Marama bean) in Namibia – Olaf S. Kandjimi – African Journal of Biotechnology

Water microbiome

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea – Ching-Hung Tseng – BMC Genomics

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China – Xia Ding- Frontiers in Microbiology

Review: Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes – Kurt P. Kowalski – Frontiers in Microbiology

Extremophile microbiome (by special request!)

Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria – Kamil M. Szafranski – Frontiers in Microbiology

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines) – Kristin M. Woycheese – Frontiers in Microbiology

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China – Brian P. Hedlund – Frontiers in Microbiology

Fatty Acids Profile of Microbial Populations in a Mining Reclaimed Region Contaminated with Metals: Relation with Ecological Characteristics and Soil Respiration – Ramya Narendrula and Kabwe K. Nkongolo – Journal of Bioremediation & Biodegradation

Bioreactor microbiome

Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities – Anthony S. Amend – Frontiers in Microbiology

Food microbiology

Lipidomics as an important key for identification of beer-spoilage bacteria – Tomáš Řezanka – Letters in Applied Microbiology

Metabolomics

Combining reverse genetics and NMR-based metabolomics unravels trypanosome-specific metabolic pathways – Frédéric Bringaud – Molecular Microbiology

Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms – Ellard R. Hunting – Frontiers in Microbiology

Techniques

Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes – Shiue-Lin Li and Kenneth H. Nealson – Frontiers in Microbiology

Microbes in presentations

Video: Dissertation seminar for Suzanne Ishaq – comparative analysis of the moose rumen microbiota

Video: Vance Kramer of Syngenta discussing microbiome research and comparing soil microbe communities across the US, Europe, and Brazil.

Video: Dr. Jan Jones from AgBiome discussing the plant-soil microbiome

Microbes in the news
Hidden Life Forms: Investigating Microbial Diversity on Our Bodies and in Our Homes – Jennifer Cutraro – New York Times

My uBiome Sleep Hacking Update – Alexandra Carmichael – uBiome

Antimicrobial CRISPR-Cas systems may be better weapons against bacteria than antibiotics – The Conversation

Secret Science Club Post-Lecture Recap: Big Data, Genomics and Urban Microbiomes – Big Bad Bald Bastard

Antibiotics For Gut Bacteria Show Surprising Results In Treating Autism – Dianne Depra – Tech Times

Harmless bacteria may be helpful against meningococcal outbreaks – Eureka Alert

New Software Offers Improved Read-based Identification in Metagenome Studies – Andrew P. Han – Genome Web

Not sure which one, but here it is: I am the bacterium that lives in your intestine – MicrobeWorld

FMT: Update on OpenBiome – Paul Levy – Not Running A Hospital

Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro) – Jenna Lang – Microbe.net

Microbes and art

A Dress Made From Beer And Bacteria: C’est Chic Or C’est Ick? – Charles Poladian – IB Times

Science, publishing, and career

Developing microbiological learning materials for schools: best practice – James Redfern – FEMS Microbiology Letters

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights – Claire Bertelli – Frontiers in Microbiology

Calling attention to poor speaker gender ratio – even when it hurts – Jonathan Eisen – The Tree of Life

The 5 Biases Pushing Women Out of STEM – Joan C. Williams – Harvard Business Review

Bik’s Picks

Jurrassic Park, but then with more fur: Woolly mammoth could be revived after scientists paste DNA into elephant’s genetic code – Andrew Griffin – The Independent

The Fitness Guru of the Trucking Industry – The Atlantic

On Friday, half a pair of twins leaves for a year in space. Here’s why that’s awesome. – Rachel Feltman – Washington Post

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March 25, 2015

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General microbiome

Introducing npj Biofilms and Microbiomes – Staffan Normark – NPJ Biofilms and Microbiomes – includes:

Clinical Implications of Basic Science Discoveries: Immune Homeostasis and the Microbiome—Dietary and Therapeutic Modulation and Implications for Transplantation – J. A. Fishman, and A. W. Thomson – American Journal of Transplantation

Human respiratory microbiome

Clinical Outcomes and Microbiological Characteristics of Severe Pneumonia in Cancer Patients: A Prospective Cohort Study – Ligia S. C. F. Rabello – PLOS ONE

Human gut microbiome

Subsistence strategies in traditional societies distinguish gut microbiomes – Alexandra J. Obregon-Tito – Nature Communications

Variation in rural African gut microbiomes is strongly shaped by parasitism and diet – Elise R Morton – BioRxiv

Some problems with JAMA website, not sure if link works: Association of Gastrointestinal Symptoms With Autism – JAMA Psychiatry

Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women – Kyungsun Han – Molecular Nutrition & Food Research

Review: Alcohol and gut microbiota – the possible role of gut microbiota modulation in the treatment of alcoholic liver disease – G. Vassallo – Alimentary Pharmacology & Therapeutics

Perspective: Studies of the Gut: Overhyped or Underappreciated? – Tom Bartlett – The Chronicle of Higher Education

Review: Microbial biofilms and the human intestinal microbiome – Willem M de Vos – NPJ Biofilms and Microbiomes

Review: Microbial endocrinology: host-bacteria communication within the gut microbiome – Sara Sandrini – Journal of Endocrinology

Dead body microbiome

Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval – Franklin E. Damann – Journal of Forensic Sciences

Life after death: shallow-water Mediterranean invertebrate communities associated with mammal bones – Sergi Taboada – Marine Ecology

Animal microbiome

Monkeys: Adenovirus and Herpesvirus Diversity in Free-Ranging Great Apes in the Sangha Region of the Republic of Congo – Tracie A. Seimon – PLOS ONE

Birds (not birds and bees): Pathogenic bacteria and timing of laying – Anders Pape Møller – Ecology and Evolution

Arthropods: Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan, China – Han Xia – PLOS ONE

Nematodes: Associated bacteria of different life stages of Meloidogyne incognita using pyrosequencing-based analysis – Yi Cao – Journal of Basic Microbiology

Corals: Microbial Communities Associated with Healthy and White Syndrome-Affected Echinopora lamellosa in Aquaria and Experimental Treatment with the Antibiotic Ampicillin – David Smith – PLOS ONE

Water microbiome

Plant pathogenic bacteria in open irrigation systems: what risk for crop health? – J. R. Lamichhane and C. Bartoli – Plant Pathology

Elements of metacommunity structure and community-environment relationships in stream organisms – Jani Heino – Freshwater Biology

Opportunistic Pathogens and Elements of the Resistome that Are Common in Bottled Mineral Water Support the Need for Continuous Surveillance – Maria Fernanda Falcone-Dias – PLOS ONE

Bioinformatics

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome – Ohad Manor and Elhanan Borenstein – Genome Biology

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome – Stephen Nayfach and Katherine S Pollard – Genome Biology

Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data – Minna Vehkala – PLOS ONE

Ecology

Probabilistic Models to Describe the Dynamics of Migrating Microbial Communities – Joanna L Schroeder – PLOS ONE

Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals Extensive Population Genetic Diversity – Carol Chapman – PLOS ONE

Archaea

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis – Guanghong Zuo – Life

Techniques

Open Labware: 3-D Printing Your Own Lab Equipment – Tom Baden – PLOS Biology

Microbes in the news

Treponema are not “ancient” but absence from some human’s guts is very interesting – Jonathan Eisen – Tree of Life
Refers to:
Ancient bacteria found in hunter-gatherer guts – Ann Gibbons – Science

With recipes: Upcoming book by Justin and Erica Sonnenburg: “The Good Gut” – Amazon

The ‘intraterrestrials’: New viruses discovered in ocean depths – National Science Foundation

Martian Microbes Could Be Eating Carbon Monoxide From the Atmosphere – Popular Mechanics

Kids with Autism Are More Likely to Have Gastrointestinal Problems – Rachael Rettner – LiveScience

Examining the connection between infant gut bacteria and food allergies – HealthCanal

Repeated Use of Antibiotics May Raise Diabetes Risk – Agata Blaszczak-Boxe – LiveScience

Bacteria in bud prompts B.C. medical marijuana firm to recall product – Canadian Press

Twin astronauts provide Earth-bound control for orbital health study – Phys.org

Baylor College of Medicine: Certain makeup can cause bacterial infections – John Brannen – Click2Houston

The Bathroom Blast Radius (And Your Toothbrush) – Dollar Shave Club

The Antibiotics Problem in Meat – Olga Khazan – The Atlantic

Satire: Biotechnology pressure group calls for an end to Saccharomyces abuse – The Allium

Science, publishing, and career

The 2015 Salary Survey Is Here – The Scientist

Women still find it tough to reach the top in science – Sharon Bell – The Conversation

Bik’s Picks

Ancient Egyptian skeleton shows signs of breast cancer – Elahe Izadi – Washington Post

Unravelling the hidden ancestry of American admixed populations – Francesco Montinaro – Nature Communications

Short Circuit in Magnets Postpone Re-Launch of CERN Collider – InsightTicker

Why the world needs biodiversity – Scientists have engineered the food that will help save a starving, warming planet – Jack Aldwinckle – Quartz

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March 24, 2015

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General microbiome

Review: Biomarkers for the 21st Century: Listening to the Microbiome – Rodney Reynolds Dietert* and Ellen Kovner Silbergeld – Toxicological Sciences

Nice overview [PDF]: FASEB Releases “The Human Microbiome: Your Own Personal Ecosystem” – FASEB

Microbiome of pregnancy and birth

Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis – Valarie E McMurtry – Microbiome

Human vaginal microbiome

Vaginal Microbiota of Adolescent Girls Prior to the Onset of Menarche Resemble Those of Reproductive-Age Women – Roxana J. Hickey – mBio

Human gut microbiome

The detection of vector-borne-disease-related DNA in human stool paves the way to large epidemiological studies – Alpha Kabinet Keita – European Journal of Epidemiology

Animal and other models

A Modified R-Type Bacteriocin Specifically Targeting Clostridium difficile Prevents Colonization of Mice without Affecting Gut Microbiota Diversity – Dana Gebhart – mBio

Effects of Irradiation on Epithelial Wound Healing and Microbial Diversity in an
in-vitro Oral Mucosa Model – Tine De Ryck – Nuclear Medicine & Radiation
Therapy

Microbes on Mars? Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith – Gary M. King – PNAS USA

Animal microbiome

Rabbit: The bacterial communities associated with fecal types and body weight of rex rabbits – Bo Zeng – Scientific Reports

Plant microbiome

Lots of omics words in this book: Microbiomics: An Approach to Community Microbiology – Pankaj Sharma – In: PlantOmics

Soil and plant root microbiome

The Soil Microbiome Influences Grapevine-Associated Microbiota – Iratxe Zarraonaindia – mBio

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem – Jinbo Xiong – Scientific Reports

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust – Ulisses Nunes da Rocha – Frontiers in Microbiology

Nucleotide Sequences of Giant Viruses Found in Soil Samples of the Mojave Desert, the Prairie, the Tundra and the Antarctic Dry Valleys – Csaba Kerepesi – ArXiv

Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays – Matthew G. Bakker – Plant and Soil

Pyrosequencing Reveals Changes in Soil Bacterial Communities after Conversion of Yungas Forests to Agriculture – Marcela S. Montecchia – PLOS ONE

Priority effects during fungal community establishment in beech wood – Jennifer Hiscox – The ISME Journal

Water microbiome

Very cool, with longitudinal plots: The Source of the River as a Nursery for Microbial Diversity – Luiz Felipe Valter de Oliveira, Rogério Margis – PLOS ONE

Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps – Adrien Vigneron – Applied and Environmental Microbiology

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance – Silvia Pajares – PLOS ONE

Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic approach – Frédéric Gaboyer – FEMS Microbiology Ecology

Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source – Eleftheria Antoniou – Frontiers in Microbiology

Built environment microbiome

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments – Christine Moissl-Eichinger – Scientific Reports

Effect of Monochloramine Treatment on the Microbial Ecology of Legionella and Associated Bacterial Populations in a Hospital Hot Water System – Julianne L. Baron – Systematic and Applied Microbiology

Non-culturable bioaerosols in indoor settings: impact on health and molecular approaches for detection – Pascale Blais-Lecours – Atmospheric Environment

Probiotics

Development and Utility of the FDA “GutProbe” DNA Microarray for Identification, Genotyping, and Metagenomic Analysis of Commercially Available Probiotics – Jennifer N. Patro – Journal of Applied Microbiology

Antibiotics

Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Metagenomics and bioinformatics

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly – Tarini Shankar Ghosh – Journal of Bioinformatics and Computational Biology

Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors – Jeremy G. Owen – PNAS USA

Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis – Pushpendra Singh – PNAS USA

Metabolomics / Ecology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Microbes in the news

With a picture you will never forget: Acne and the Microbiome: Christi Investigates – Alexandra Carmichael

Vineyard’s soil microbes shape grapes’ microbial community – Science Daily

Crohn’s Disease: Gut Microbial Collaborations Trigger Inflammatory Diseases – PR NewsWire

Feed the microbes so they don’t feed on you: Fiber-Famished Gut Microbes Linked to Poor Health – Katherine Harmon Courage – Scientific American

Harnessing The Microbiome To Curb Hunger – Chemical and Engineering News

New Research On Appetite-Suppressing Bacteria Could Help Fight Obesity – Anna Almendrala

The MinION Access Programme (MAP) for portable DNA sequencing – Science Daily

Viruses, Archaea Self-mutate to Survive – Laboratory Equipment

Engineering and waterborne bacteria in building water systems – Colum Ó Bric -EngineersJournal

Gut and Mood: The Microbiome in Anxiety and Depression – Nina Weisbroth – Translational Microbiome

Not so fast, FastTree – Darling lab

Satire: Each bioinformatician to have their own personal short-read aligner by 2016 – The Science Web

Not about Dr. Who: The Doctor Who Tested Infectious Bacteria On Himself, And Won A Nobel – Ria Misra

Comparing the genomes of the leprosy bacteria – Phys.org

#BacteriaHysteria: “Beer Pong” Associated with Frequent Bacterial Transmissions – Jacquelyn Gray – HCPlive

#BacteriaHysteria: Clean machines: how to look after your tech and avoid bacteria bombs – David Howell – TechRadar

Science and art

Workshop, April 6, 2015: Paint with Bacteria – GenSpace, New York City’s Community Biolab

Science, publishing, and career

Opinion: Lay summaries needed to enhance science communication – Lauren M. Kuehne and Julian D. Olden – PNAS USA

50 min podcast: Women in Oceanography: Lots of Students, Not So Many Professors – Heather Goldstone – Capeandislands.com

This is why you shouldn’t believe that exciting new medical study – Julia Belluz – Vox.com

Stubborn Pay Gap Is Found in Nursing – Catherine Saint Louis – Catherine Saint Louis – New York Times

It’s time to reboot bioinformatics education – Todd Harris

Bik’s Picks

Macaques Exhibit a Naturally-Occurring Depression Similar to Humans – Fan Xu – Scientific Reports

Earth’s most powerful physics machine gets back in action – Marcus Woo – Wired.com

Scientists want museums to cut their ties with David Koch – Science Recorder

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March 22, 2015

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Human oral microbiome

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human vaginal microbiome

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. – Helena Mendes-Soares – Pathogens and Disease

Human gut microbiome

Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis – Ratnakar Shukla – Digestive Diseases and Sciences

Review: Psychobiotics and the gut–brain axis: in the pursuit of happiness – Zhou L – Neuropsychiatric Disease and Treatment

Microbiome of pregnancy and birth

The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Colonisation of the gut by bifidobacteria is much more common in vaginal deliveries than Caesarean sections – Sarka Musilova – Acta Paediatrica

Review: The Birth of the Holobiont: Multi-species Birthing Through Mutual Scaffolding and Niche Construction – Lynn Chiu, Scott F. Gilbert – Biosemiotics

Animal models

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota – Jessica Ann Thompson – Cell Reports

Vagotomy prevents the effect of probiotics on caspase activity in a model of postmyocardial infarction depression – M. Malick – Neurogastroenterology & Motility

Faecalibacterium prausnitzii prevents physiological damage in a chronic low-grade inflammation murine model – Rebeca Martín – BMC Microbiology

Peyer’s patch innate lymphoid cells regulate commensal bacteria expansion – Masaaki Hashiguchi – Immunology Letters

Animal microbiome

Review: A Review of Infectious Agents in Polar Bears (Ursus maritimus) and Their Long-Term Ecological Relevance – Anna C. Fagre – EcoHealth

Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH – Neeti Pandey andRaman Rajagopal – Insect Science

Genetic diversity of cyanophages of the myoviridae family as a constituent of the associated community of the Baikal sponge Lubomirskia baicalensis – T. V. Butina – Russian Journal of Genetics

Soil and plant root microbiome

Effects of Thinning and Induced Drought on Microbiological Soil Properties and Plant Species Diversity at Dry and Semiarid Locations – Javier Hedo de Santiago – Land Degradation & Development

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN-Soil, Air, Water

Water microbiome

Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China – Yongming Wang – Environmental Science and Pollution Research

Spatial distribution of marine airborne bacterial communities – Jasmin S. Seifried – Microbiology Open

Microbiome of the built environment

Interphase microbial community characteristics in the fermentation cellar of Chinese Luzhou-flavor liquor determined by PLFA and DGGE profiles – Xiaofei Ding – Food Research International

Bioreactor microbiology

Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing – Duntao Shu – Bioresource Technology

Cu and Cr enhanced the effect of various carbon nanotubes on microbial communities in an aquatic environment – Fei Wang – Journal of Hazardous Materials

Review: Utilization of microbial community potential for removal of chlorpyrifos: a review – Maya Yadav – Critical Reviews in Biotechnology

Metagenomics and Bioinformatics

A robust approach for identifying differentially abundant features in metagenomic samples – Michael B. Sohn – Bioinformatics

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe – Tianmin Wang – BMC Bioinformatics

The impact of quality filter for RNA-Seq – Pablo H.C.G. de Sáa – Gene

Poster: MetaGenSense: a web application for analysis and visualization of high throughput sequencing metagenomic data – Damien Correia – F1000 posters

SISPA-Seq for rapid whole genome surveys of bacterial isolates – Meredith S. Wright – Infection, Genetics and Evolution

Metabolomics

The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Deep metabotyping of the murine gastro-intestinal tract for visualization of digestion and microbial metabolism – Silke S Heinzmann and Philippe Schmitt-Kopplin – Journal of Proteome Research

Application of a new Dynamic Gastrointestinal Simulator (SIMGI) to study the impact of red wine in colonic metabolism – C. Cueva – Food Research International

Isolation of dextran-hydrolyzing intestinal bacteria and characterization of their dextranolytic activities – Jin Kyoung Kim – Biopolymers

Diet-induced obesity causes metabolic impairment independent of alterations in gut barrier integrity – Caroline Kless – Molecular Nutrition & Food Research

Other microbial science papers

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals – Thomas Obadia – PLOS Computational Biology

How bacterial pathogens colonize their hosts and invade deeper tissues – David Ribet, Pascale Cossart – Microbes and Infection

Antimicrobial stewardship: the role of scientists? – Laura Bowater – Journal of Antimicrobial Chemotherapy

Cyanobacteria: the bright and dark sides of a charming group – Katia Sciuto, Isabella Moro – Biodiversity and Conservation

Microbes in the news
The ChuckNorrisMicrobiome will get you, and you, and you … – Jonathan Eisen – The Tree of Life

The Oral Microbiota Affects More Than Just the Mouth – Lily Berrin – PLOS blog

This Week in Microbiology #100: Omnis cellula e cellula – MicrobeWorld

Wisconsin Longitudinal Study: Decades later, benchmark study yields data on human condition – Pamela Herd – Madison.com

Special microbes make anti-obesity molecule in the gut – American Chemical Society – Eureka Alert

About the baboon microbiome study: Are our gut bacteria swapped when we snuggle up? – Tim Sandle – Digital Journal

Wireless Sensors Help Scientists Map Staph Spread Inside Hospital – Scott Hensley – NPR

Science spreads antibiotic resistance by genetic experimentation – Karen Hardison – Digital Journal
Great #openaccess collection of papers on RNA – Jonathan Eisen – MicroBEnet

Visualizing the deadly threat of meningitis on campuses – Jamie Lampros – Standard Examiner

Epidemic Predicted by Bill Gates Who Pleads: Microbes Not Missiles – Jeanette Smith – Guardian LV

Science, publishing, and career

Forget Harvard and Stanford. It really doesn’t matter where you go to college – Jeffrey J. Selingo

Wolf Prize for Agricultural Science for Linda Saif: Award shines light on Ohio State scientist – Laura Arenschield – The Columbus Dispatch

Michigan judge asks PubPeer to turn over anonymous user information – Kelly Servick – Science Insider

In science, irreproducible research is a quiet crisis – Carolyn Johnson – Boston Globe

Bik’s Picks

Copy Cat: Someone Keeps Photocopying Their Cat at the University of Wisconsin Library – Samantha Grossman – Time.com

First fine-scale genetic map of the British Isles – Science Daily

Dude, why is my mushroom glowing? Scientists have the answer – Will Dunham – Reuters

March 20, 2015

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General microbiome

Ribosomal RNA, the lens into life – Daniel McDonald, Zhenjiang Xu, Embriette R. Hyde and Rob Knight – RNA

Upcoming event: Cell Symposium: Human Immunity and the Microbiome in Health and Disease – September 27-29, 2015, Montreal, Canada

Human gut microbiome

Review: Firmicutes and Bacteroidetes involved in insulin resistance by mediating levels of glucagon-like peptide 1 – Claire Greenhill – Nature Reviews Endocrinology

Review: The impact of phytochemicals present in the diet on microbial signalling in the human gut – R.R. McCarthy – Journal of Functional Foods

Review: Targeting gut microbiota as a possible therapy for diabetes – Canxia He – Nutrition Research

Human oral microbiome

Guest editorial for special oral microbes edition – Robert Dwayne Lunsford – Microbes and Infection

Animal microbiome

Cattle: Microbial diversity analysis of subclinical mastitis in dairy cattle in Northeast China – Qingyu Jiang – African Journal of Microbiology Research

Worms: The effects of earthworms Eisenia spp. on microbial community are habitat dependent – Anna Koubová – European Journal of Soil Biology

Review: Insect Behaviour and the Microbiome – Zenobia Lewis, Anne Lizé – Current Opinion in Insect Science

Soil, sediments, and plant root microbiome

Carnivory does not change the rhizosphere bacterial community of the plant Drosera intermedia – Manuel Aira – Applied Soil Ecology

Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night – Franz Hölker – Philosophical Transactions B
and
The biological impacts of artificial light at night: the research challenge – Kevin J. Gaston – Philosophical Transactions B

Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence – Qian Wang – Environmental Science and Pollution Research

Analysis of a population of magnetotactic bacteria of the Gulf of Gabès, Tunisia – Nathalie Pradel – Environmental Science and Pollution Research

Review: Linkages of plant-soil feedbacks and underlying invasion mechanisms – Inderjit and James F. Cahill Jr. – AoB Plants

Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China – Ying Ma – Marine Pollution Bulletin

Water and snow microbiome

Microbial abundance and community structure in a melting alpine snowpack – Anna Lazzaro – Extremophiles

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh – Zahid Hassan – FEMS Microbiology Ecology

Metagenomics, proteomics, bioinformatics

Editorial: Microbial Diversity: A Bonanza of Phyla – Laura Eme, W. Ford Doolittle – Current Biology
belongs to study reconstructing Archaea genomes from metagenomic data: Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling – Cindy J. Castelle – Current Biology

Book Chapter: Evaluation of Combined Genome Assemblies: A Case Study with Fungal Genomes – Mostafa M. Abbas – Bioinformatics and Biomedical Engineering

Navigating through metaproteomics data – a logbook of database searching – Thilo Muth – Proteomics

Microbes in the news

Quorum-Sensing Molecule Modifies Gut Microbiota – Anna Azvolinsky – The Scientist

Functional Metagenomics Enables First Study of Bacterial Fitness in the Gut Microbiome – Chris Williams – Columbia Systems Biology

How to Study a Complex Microbial World- Part 1: DNA sequencing – Kevin Bonham -Scientific American

How to Study a Complex Microbial World – Part 2: Next Generation Sequencing Technology – Kevin Bonham -Scientific American

Biological oceanography: Life in the deepest depths – Beth N. Orcutt – Nature Geoscience

1h Podcast/article: Say Cheese! Cheese history and science – GastroPod

Jailbreaking yeast could amp up wine’s health benefits, reduce morning-after headaches – Phys.org

29 min podcast: Queen Bee Microbiome (starts at 8 min), Yams, Resistence To Organic Checkoff – PRX Earth Eats

The World’s First €100M Microbiome-focused Venture Fund opened in France – Labiotech

Bioinformatics tool for metagenome analysis – Nancy Ambrosiano – R&D Magazine

Andreessen-Backed uBiome Is Now Doing An Indiegogo Campaign To Check Out Dental Bacteria – Kim-Mai Cutler – TechCrunch

Science, publishing, and career

“Canadian” Open-Access Journal Doesn’t Look Very Canadian – Jeffrey Beall – ScholarlyOA

Science and art

Art project: What Bacteria And Smell Have To Do With Feminism Today – Katherine Brooks – Huffington Post

Bik’s Picks

Morphological Mutations: Lessons from the Cockscomb Major comb variants and their genetic basis – Denis Headon – PLOS GeneticsWhat’s that thing?

How to Google Something You Don’t Know How to Describe – Adrienne Lafrance – The Atlantic

New Breast Milk Products Are on the Rise, but Commercialization Troubles Many – Andrew Pollack – New York Times

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March 19, 2015

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Just a short digest today!

General microbiome

Review: The role of the microbiota in ageing: current state and perspectives – Denise B. Lynch – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Human gut microbiome / proteomics

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota – Alessandro Tanca – Proteomics

Animal microbiome

Abalone: Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1 year – Reiji Tanaka – Aquaculture Research

Soil microbiome

Native California soils are selective reservoirs for multidrug-resistant bacteria – Amanda C. Hollowell – Environmental Microbiology Reports

Techniques

Growing microbes in millifluidic droplets – Laurent Boitard – Engineering in Life Sciences

Other microbiology

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology – Stephen J. Salipante – Journal of Clinical Microbiology

Microbes in the news

Adventures in exploring the great indoors – Anne A. Madden – Fierer Lab

MO BIO Laboratories, Inc. presents the Second Annual MO BIO Microbiome Awards, offering more than $10,000 in prizes! – MoBio

uBiome — Explore Your Dental Microbiome – IndieGoGo
uBiome Launches World’s First Dental Citizen Science Campaign – Global Newswire

Humans Need ‘Stronger’ Breast-Milk Than Most Mammals – Brian Stallard – Nature World News

Interactive/videos: The good, the bad and the ugly in everyday bacteria – CBC news

Los Alamos scientists develop new method for metagenomic analysis – News Medical Net

This week’s  Google Plus Microbiology Journal club: Cheese Microbe Communities – GPlusMicroJC

Researchers have a gut feeling – could chronic pain be caused by bacteria? – Michael Brooks – New Statesman

MeMed’s blood test accurately distinguishes bacterial and viral infections, research shows – Medical Xpress

Turning the gut microbiome into a chat room – Tina Hesman Saey – ScienceNews

Science, publishing, and career

A grad school survival guide – Andrew Gaudet – Science

Bik’s Picks

The New York Times’ smartwatch cancer article is bad, and they should feel bad – Russell Brandom – The Verge

Unmasked: – What 10 million passwords reveal – about the people who choose them – WP engine

All other languages tired of Python’s sh!t – The Science Web
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March 18, 2015

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Human skin microbiome

Book (hopefully also covering women’s skin): The Epidermis of Man: Co-existing with Commensals – Eds. Peter J Heidt et al.

Human oral microbiome

Salivary Microbiota Associated with Immunoglobulin A Nephropathy – Maria Piccolo – Microbial Ecology

Human gut microbiome

Review: Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease – Rosa Krajmalnik-Brown – Microbial Ecology in Health and Disease

Microbiome of pregnancy and birth

The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome –
Prince AL – CSH Perspect Med (only NCBI link available as of now)

Association between breastfeeding and intelligence, educational attainment, and income at 30 years of age: a prospective birth cohort study from Brazil – Cesar G Victora – The Lancet

Review: Individualized medicine and the microbiome of the reproductive tract – Andrea G. Braundmeier – Frontiers in Physiology

Animal and other models

The Quorum Sensing Peptides PhrG, CSP and EDF Promote Angiogenesis and Invasion of Breast Cancer Cells In Vitro – Bart De Spiegeleer – PLOS ONE

Registered report of a replication study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kate Eaton – eLIFE

Ablation of Tumor Necrosis Factor Is Associated with Decreased Inflammation and Alterations of the Microbiota in a Mouse Model of Inflammatory Bowel Disease – Yava L. Jones-Hall – PLOS ONE

Phytase Modulates Ileal Microbiota and Enhances Growth Performance of the Broiler Chickens – Anna Ptak – PLOS ONE

Intestinal Microbiota Succession and Immunomodulatory Consequences after Introduction of Lactobacillus reuteri I5007 in Neonatal Piglets – Chengli Hou – PLOS ONE

Animal microbiome

Monkeys: Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation – Bo Xu – BMC Genomics

Frogs: Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus – Matthew H. Becker – Proceedings of the Royal Society B

Cows: Altered Microbiomes in Bovine Digital Dermatitis Lesions, and the Gut as a Pathogen Reservoir – Martin Zinicola – PLOS ONE

Culture based, horses: Occurrence of bacteria and polymorphonuclear leucocytes (PMNLs) in foetal compartments at parturition; relationships with foal and mare health in the peripartum period- E. Hemberg – Theriogenology

Bees: Variation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location – Zuzana Hroncova – PLOS ONE

Bees: Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species – Haw Chuan Lim – PLOS ONE

Sponges: Molecular investigation of the microbial community associated with the fire sponge, Tedania ignis, in Bermuda – Nicholas J Jouett – PeerJ

Millipedes: Microbial dynamics in food, intestine and fecal pellets of two endemic pill-millipedes (Arthrosphaera: Sphaerotheriida) of the Western Ghats [PDF] – C.N. Ambarish and K.R. Sridhar – Journal of Agricultural Technology

Mosquitoes: RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi – James Angus Chandler – Frontiers in Microbiology

Soil and plant root microbiome

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench) – Mapula Kgomotso Annah Maropola – Journal of Microbiological Methods

Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression – Zongzhuan Shen – Biology and Fertility of Soils

The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms – Olaf Tyc – PLOS ONE

Organic amendments in avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities – Nuria Bonilla – Applied and Environmental Microbiology

Water microbiome

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China – Lemian Liu – The ISME Journal

Marine Fungi from Deep Subseafloor Sediments: Species richness and Adaptation -Vanessa Rédou – Applied and Environmental Microbiology

Microbial Methane Potential for the South Sumatra Basin Coal: Formation Water Screening and Coal Substrate Bioavailability – Rita Susilawati – Energy Procedia

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Spatial variability of microbial assemblages associated with a dominant habitat-forming seaweed – Alexandra H. Campbell – Frontiers in Microbiology

Bioreactor microbiome

Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing – Jianhua Guo – Microbial Cell Factories

Anaerobic codigestion of pretreated wheat straw with cattle manure and analysis of the microbial community – Zilin Song – Bioresource Technology

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration – Jin-Feng Liu – Frontiers in Microbiology

Bacterial and archaeal guilds associated with electrogenesis and methanogenesis in paddy field soil – Bo Lin – Geoderma

Food microbiology

Comparing natural and selected starter cultures in meat and cheese fermentations – Daniela Bassi – Current Opinion in Food Science

Phages and viruses

Perspective: The Next Epidemic — Lessons from Ebola – Bill Gates – The New England Journal of Medicine

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages – Simon Roux – Frontiers in Microbiology

Isolation of Phages for Phage Therapy: A Comparison of Spot Tests and Efficiency of Plating Analyses for Determination of Host Range and Efficacy – Mohammadali Khan Mirzaei – PLOS ONE

Evaluation of a Viral Microarray Based on Simultaneous Extraction and Amplification of Viral Nucleotide Acid for Detecting Human Herpesviruses and Enteroviruses – Yi Liu – PLOS ONE

Review: Origins and evolution of viruses of eukaryotes: The ultimate modularity – Eugene V. Koonin – Virology

Metagenomics and bioinformatics

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures – Tracey Allen K. Freitas – Nucleic Acid Research

k-mer analysis: Crossing the streams: a framework for streaming analysis of short DNA sequencing reads – Qingpeng Zhang – PeerJ

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum – Keith H. Turner – PNAS USA

Hypothesis: Systems modeling approaches for microbial community studies: From metagenomics to inference of the community structure – Mark Hanemaaijer – Frontiers in Microbiology

Metabolomics

Review: Role of Resistant Starch in Improving Gut Health, Adiposity, and Insulin Resistance – Michael J Keenan – Advances in Nutrition

Microbial Degradation of Whole-Grain Complex Carbohydrates and Impact on Short-Chain Fatty Acids and Health – Knud Erik Bach Knudsen – Advances in Nutrition

Microbes in the news

Pet Peeves on 16S rRNA gene sequencing – Noah Fierer – Fierer lab

Can Probiotic Bacteria Save An Endangered Frog? – Ed Yong – National Geographic

New paper examines social effects on the gut microbiome of wild baboons – William G. Gilroy – Notre Dame News

Breast-Feeding Boosts Chances Of Success, Study In Brazil Finds – Rob Stein – NPR

Breast-Feeding May Have Benefits Decades Later – Nicholas Bakalar – New York Times

Lab creates bioinformatics tool for metagenome analysis – Phys.org

Could Man’s Best Friend Be Man’s Best Medicine? – Alexis Blue – University of Arizona

Dog germs may be good for you – Bradley J. Fikes – UT San Diego

The vaginal microbiome changes during and after pregnancy – American Microbiome Institute

Can the bacteria in your bowels increase your cancer risk? – Amy Yurkanin – AL.com

Your microbiome: groundbreaking research about our gut bacteria shows it could be the key to health – Jacqui Gibbons – High 50 Health

From human gut to the smartphone, new health monitoring – Tim Sandle – Digital Journal

Parasite turns shrimp into voracious cannibals – Chris Bunting – University of Leeds

Gut Bacteria, ASD, and Probiotics: Exploring the Relationship – Elizabeth Gough-Gordon – EMPR

New Molecular Tool Assesses Vaginal Microbiome Health, Diagnosis Infections-Fast – ASM

Technology helps unlock secrets of rare bacteria – Phys.org

Stanford researchers unravel secrets of shape-shifting bacteria – Tom Abate and Chris Cesare – Stanford News

Video: Alexander Fleming – Inventor of Penicillin – Scientiflix

Bik’s Picks

Ultrasoundings: monitoring a pregnant dolphin – Bill Van Bonn – Shedd Aquarium

Why are there so many freaking beetles? Science may finally have the answer. – Rachel Feltman – Washington Post

The myopia boom: Short-sightedness is reaching epidemic proportions. Some scientists think they have found a reason why – Elie Dolgin – Nature

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