March 19, 2015

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

AbaloneTemporal 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

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

ReviewGut 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

MonkeysMetagenomic 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

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

CowsAltered 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

BeesVariation 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

PerspectiveThe 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 analysisCrossing 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

VideoAlexander 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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March 17, 2015

Happy St. Patrick’s day! Enjoy the green microbial fermented fluids.

Human oral microbiome

Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage – Weiwei Zheng – Scientific Reports

A Filifactor alocis-centered co-occurrence group associates with periodontitis across different oral habitats – Hui Chen – Scientific Reports

Review: Polymicrobial nature of chronic oral disease – Stuart Dashper – Microbiology Australia

Animal models

Intestinal Microbiota Composition Modulates Choline Bioavailability from Diet and Accumulation of the Proatherogenic Metabolite Trimethylamine-N-Oxide – Kymberleigh A. Romano – mBio

Animal microbiome

Social networks predict gut microbiome composition in wild baboons – Jenny Tung – eLIFE

Unfolding the secrets of coral–algal symbiosis – Nedeljka Rosic – The ISME Journal

Water microbiome

Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments – Steven D’Hondt – Nature Geoscience

Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea – Mohd Ikram Ansari – Scientific Reports

Oceanographic structure drives the assembly processes of microbial eukaryotic communities – Adam Monier – The ISME Journal

Other microbial science

Microbial reflectance spectra: Surface biosignatures of exo-Earths: Remote detection of extraterrestrial life – Siddharth Hegde – PNAS USA

Viruses and phages

Membrane vesicles in natural environments: a major challenge in viral ecology – Nicolas Soler – The ISME Journal

Lytic phages obscure the cost of antibiotic resistance in Escherichia coli – Samuel J Tazzyman and Alex R Hall – The ISME Journal

Metagenomics

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy – Masaki Shintani – Frontiers in Microbiology

Bioinformatics

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences – A Murat Eren – The ISME Journal

Microbes in the news

Baboon friends swap gut germs – Science Daily

No limit to life in deep sediment of ocean’s “deadest” region – National Science Foundation

The microbiome of alcoholics may contribute to pathologies – American Microbiome Institute

Reflectance spectra from microbes: This Alien Color Catalog May Help Us Spot Life on Other Planets – Jesse Emspak – Smithsonian

New Data May Help Identify Extraterrestrial Life – William Large – Clapway

Science, publishing, and career

Competitive Science: Is Competition Ruining Science? – Ferric C. Fang and Arturo Casadevall – Infection and Immunity

Bik’s Picks – Marine Mammal Edition

Starving sea lion pups inundate Southern California rescue centers – Marty Graham – Reuters

Sciencespeak: Whale Pump. Whales can poop almost anywhere they want. – Brian Switek – National Geographic

Long-lost whale fossil sheds light on East Africa’s evolution – Bianca Nogrady – ABC Science

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The Vaginal Microbiome

An overview of large studies on the human vaginal microbiome. Please leave a comment if I missed an important paper, which is extremely likely. This is just a first draft, and this post is meant to be continuously updated.

Scientific papers, most recent first

The vaginal microbiome during pregnancy and the postpartum period in a European population – David A. MacIntyre – Scientific Reports – March 2015

  • Subjects: 42 British women with term delivery, sampled longitudinally, 3 ethnic groups
  • DNA extraction: bead-beating + QIAamp DNA Mini kit
  • Sequencing: V1-V2 region, MiSeq, 2,113,251 reads, 14088 reads/sample (rarefied to 1916?)

The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women – Roberto Romero – Microbiome – February 2014

  • Subjects: 32 non-pregnant women, 22 pregnant women who delivered on time
  • DNA extraction: Bead-beating, ZR Fecal DNA extraction kit (ZYMO Research)
  • Sequencing: V1-V2 region, 454 FLX Titanium, 2,946,507 reads, 2878 reads/sample

Diversity of the Vaginal Microbiome Correlates With Preterm Birth – Richard W. Hyman – Reproductive Sciences – January 2014

  • Subjects: 88 pregnant women (various ethnicities), 143 swabs
  • DNA extraction: QIAgen DNeasy Tissue and Blood Kit
  • Sequencing: 8F-1492R, clone library, Sanger sequencing, read from one end? not clear.
    Number of clones not clear?

Diverse Vaginal Microbiomes in Reproductive-Age Women with Vulvovaginal Candidiasis
Mu-Biao Liu – PLOS ONE – November 2013

  • Subjects: 95 women, some with BV or VVC, 226 swabs
  • DNA extraction: DNA Magnetic Sand Extract kit (BioEAsy,China)
  • Sequencing: V6 region, Illumina HiSeq 2000, 1,026,382 reads, 4,542 reads/sample

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy – Kjersti Aagaard – PLOS ONE – June 2012

  • Subjects: 24 pregnant women, 60 non-pregnant controls, multiple timepoints/subject
  • DNA extraction: PowerSoil DNA Isolation Kit
  • Sequencing: V3-V5 region, 454 FLX Titanium, 2.5 million reads, 6837 reads/sample

$$ Temporal Dynamics of the Human Vaginal Microbiota – Pawel Gajer – Science Translational Medicine – May 2012

  • Subjects: 32 women, 937 samples
  • DNA extraction: Bead-beating with ZR Fecal DNA extraction kit (Zymo Research)
  • Sequencing: V1-V2 region, 454 Titanium, 2,522,080 reads, 2692 sequences/sample

Vaginal Microbiome and Epithelial Gene Array in Post-Menopausal Women with Moderate to Severe Dryness – Ruben Hummelen – PLOS ONE – November 2011

  • Subjects: 32 post-menopausal women, some sampled over 10 weeks
  • DNA extraction: Instagene (Bio-Rad)
  • Sequencing: V6 region, Illumina, 1,758,430, 17,410 reads/sample

Vaginal microbiome of reproductive-age women – Jacques Ravel – PNAS USA – March 2011

  • Subjects: 396 North American women representing four ethnic groups
  • DNA extraction: Bead beating combined with QIAamp DNA mini kit
  • Sequencing: V1-V2 region, 454 FLX, 897,345 good-quality reads, 2200 reads/sample

Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women – Xia Zhou – The ISME Journal – May 2007

  • Subjects: 144 women, 2 ethnicities
  • DNA extraction: not listed
  • Sequencing: T-RFLP, clone library , 6000 clones, 90 clones/sample

Microbes on the human vaginal epithelium – Richard W. Hyman – PNAS USA – April 2005

  • Subjects: 20 women
  • DNA extraction: QIAgen DNAeasy
  • Sequencing: 8F x 1492R, ~1000-2000 clones per subject

Review papers

The vaginal microbiome: rethinking health and diseases – Bing Ma – Annual Reviews in Microbiology – September 2013

Understanding vaginal microbiome complexity from an ecological perspective – Roxana J. Hickey – Translational Research – October 2012

A New Era of the Vaginal Microbiome: Advances Using Next-Generation Sequencing – Jennifer M. Fettweis – Chemistry & Biodiversity – May 2012

The vaginal microbiome in health and disease – Bryan A. White – Trends in Endocrinology & Metabolism – October 2011

The vaginal microbiome: new information about genital tract flora using molecular based techniques – RF Lamont – BJOG: An International Journal of Obstetrics & Gynaecology
– April 2011

News articles

Sweet Peach won’t make vaginas smell like fruit or taste of Diet Coke – Hannah Jane Parkinson – The Guardian – November 2014

What’s in Your Vagina? A healthy microbiome, hopefully. Moises Velasquez-Manoff – Slate – January 2013

Characterizing the “Healthy” Vagina – Jef Akst – The Scientist – May 2014

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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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