Category Archives: Science – Career – Publishing

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 23, 2015

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General microbiome

Perspective: Separating the microbiome from the hyperbolome – Fergus Shanahan – Genome Medicine

Human oral microbiome

Interkingdom networking within the oral microbiome – Angela H. Nobbs, Howard F. Jenkinson – Microbes and Infection

Poster: Composition, Taxonomy And Functional Diversity Of The Oropharynx Microbiome In Individuals With Schizophrenia And Controls – Eduardo Castro Nallar – FigShare

Water microbiome

Targeted diversity generation by intraterrestrial archaea and archaeal viruses – Blair G. Paul – Nature Communications

Microbes in the News

Your poop could be a literal goldmine of precious metals – Rachel Feltman – Washington Post

Chlorine use in sewage treatment could promote antibiotic resistance – Science Daily

50 min podcast: Dr. Seth Bordenstein: Seeing Science and Symbiosis Through the Lens of an Evolutionary Microbiologist – People behind the science

New strategy to protect healthy gut microbes from antibiotics – Science Daily

Human parasites found in medieval cesspit reveal links between Middle East and Europe – Science Daily

Special Programmed Microbes May Help You Beat Obesity, Vanderbilt University Study – BioSpace

Skin microbiome may hold answers to protect threatened gold frogs from lethal fungus – Science Daily

Surviving in Hostile Territory: UCSB scientists discover a mechanism of self-mutation in mysterious viruses and microbes from within the Earth – Julie Cohen – UC Santa Barbara

Soaring antibiotic use in animals fuels ‘super bug’ fears – Chris Arsenault – Reuters

MRSA Is More Widespread Than You Think – Jason Tetro – Huffington Post Canada

Wolbachia Bacteria Can Control Mosquitoes with Fewer Chemicals – Erin Weeks – Entomology Today

Science, publishing and career

Social Media and Internet Driven Study Recruitment: Evaluating a New Model for Promoting Collaborator Engagement and Participation – Chetan Khatri – PLOS ONE

University of North Georgia apologized and agreed to stop distributing a course catalog with an denigrating picture – Travis Gettys – Raw Story

Bik’s Picks – Ancient rocks edition

When A Meteorite Hits Snow It Forms A “Snow Carrot” Instead Of A Crater – Mika McKinnon – Space io9

Telling stories from stone tools – Bruce Bower – Science News

Double Impact Crater in Canada Formed in Two Separate Impacts – Space Daily

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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 17, 2015

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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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March 16, 2015

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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 12, 2015

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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

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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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