Category Archives: Human oral

March 31, 2015

Posted on by

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

Pregnancy and birth microbiome

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

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

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

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

Human oral microbiome

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

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

Human respiratory microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

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

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

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

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

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

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

Plant microbiome

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

Soil and plant root microbiome

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

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

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

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

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

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

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

Water microbiome

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

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

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

Extremophile microbiome

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

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

Built environment microbiome

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

Food microbiology

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

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

Metagenomics and bioinformatics

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

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

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

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

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

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

Metabolomics

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

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

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

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

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

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

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

Growing a Baby Microbiome – Kevin Bonham – Scientific American

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

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

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

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

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

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

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

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

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

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

Conferences

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

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

[hr]

March 28, 2015

Posted on by

Screen Shot 2015-03-28 at 1.00.33 AMFeatured video

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

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

 

Human oral microbiome

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

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

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

Human gut microbiome

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

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

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

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

Animal microbiome

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

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

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

Soil, rock, and marble microbiome

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

Water microbiome

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

Extremophile microbiome

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

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

Other microbiology

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

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

News

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

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

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

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

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

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

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

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

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

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

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

Science, publishing and career

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

Bik’s Picks

Crossing fingers can reduce feelings of pain – Science Daily

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

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

[hr]

March 23, 2015

Posted on by

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

[hr]

March 22, 2015

Posted on by

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 18, 2015

Posted on by

Human skin microbiome

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

Human oral microbiome

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

Human gut microbiome

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

Microbiome of pregnancy and birth

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

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

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

Animal and other models

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

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

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

Soil and plant root microbiome

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

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

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

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

Water microbiome

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

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

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

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

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

Bioreactor microbiome

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

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

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

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

Food microbiology

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

Phages and viruses

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

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

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

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

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

Metagenomics and bioinformatics

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

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

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

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

Metabolomics

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

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

Microbes in the news

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

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

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

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

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

Lab creates bioinformatics tool for metagenome analysis – Phys.org

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

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

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

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

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

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

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

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

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

Technology helps unlock secrets of rare bacteria – Phys.org

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

Video: Alexander Fleming – Inventor of Penicillin – Scientiflix

Bik’s Picks

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

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

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

[hr]

March 17, 2015

Posted on by

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

[hr]

March 9, 2015

Posted on by

Pregnancy and birth

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

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

Human oral microbiome

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

Human gut microbiome

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

Review: Collective unconscious: how gut microbes shape human behavior

Human microbiome after death

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

Animal models of microbiome research

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

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

Animal microbiome

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

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

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

Plant microbiome

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

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

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

Soil and plant root microbiome

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

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

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

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

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

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

Water (and ice) microbiome

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

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

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

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

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

Microbiome of the built environment

Urban microbiome – Orli G. Bahcall – Nature Review Genetics

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

Microbial evolution and ecology

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

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

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

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

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

Metagenomics and bioinformatics

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

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

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

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

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

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

Metabolomics

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

Techniques

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

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

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

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

Microbes in the news

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

20m podcast: The Straight Poop – Transistor

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

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

Drugging the gut microbiome – Ken Garber – Nature Biotechnology

Tummy Troubles? Your Microbiome Can Help – Isabel Smith

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

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

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

How Microbes Keep Us Healthy – Scientific American

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

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

Prediabetes Patients Have Fewer Gut Bugs – Parker Brown – MedPageToday

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

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

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

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

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

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

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

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

Fine Focus: Microbiology Research Journal for Undergraduate Students

Science and art

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

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

Science, publishing, and career

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

My Most Informative Error – Ami Schattner – JAMA Internal Medicine

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

Bik’s Picks: The science of aging edition

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

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

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

[hr]

March 6, 2015

Posted on by

Pregnancy and birth

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

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

Human respiratory microbiome

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

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

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

Plant microbiome

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

Soil and sediment microbiome

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

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

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

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

Water microbiome

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

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

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

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

Bioreactor microbiome

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

Microbiome of the built environment

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

Food microbiology

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

Metagenomics and bioinformatics

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

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

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

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

Proteomics

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

Microbial Ecology

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

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

Microbes in the news

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

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

Who owns my microbiome? – Gabrielle Morguelan – Transylvania Rambler

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

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

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

Science, publishing, and career

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

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

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

Bik’s Picks

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

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

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

[hr]

March 2, 2015

Posted on by

General microbiome papers

Review: The Microbiome: A Contributor to Health and Disease – Bailus Walker Jr. – Journal of the Health Care for the Poor and Underserved

Human oral microbiome

Transduction-mediated horizontal gene transfer in the oral microbiome – Roy H. Stevens – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Review: The lung mycobiome: an emerging field of the human respiratory microbiome – Linh D. N. Nguyen – Frontiers in Microbiology

Human gut microbiome

Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages – Se-Hoon Park – BMC Microbiology

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality – Yanfei Chen – Journal of Gastroenterology and Hepatology

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj – Abiola Olumuyiwa Olaitan – International Journal of Antimicrobial Agents

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Human vaginal microbiome

Correlates of the molecular vaginal microbiota composition of African women – Raju Gautam – BMC Infectious Diseases

Animal microbiome

In chickens: Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences – Dragana Stanley – BMC Microbiology

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh – Andrea M. Larsen – Microbial Ecology

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences – Sandra Pucciarelli – Microbial Ecology

Plant microbiome

Phenotypic and genetic characterization of rhizobia isolated from Hedysarum flexuosum in Northwest region of Morocco – Fatima Ezzakkioui – Journal of Basic Microbiology

Biotic and abiotic predictors of fungal colonization in grasses of the Colorado Rockies – Luciana B. Ranelli – Diversity and Distributions

Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Martina Köberl – Frontiers in Microbiology

Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. – Armin Erlacher – Frontiers in Microbiology

Soil and sediment microbiome

Agricultural intensification and the functional capacity of soil microbes on smallholder African farms – Stephen A. Wood – Journal of Applied Ecology

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees – Michaela Urbanová – Soil Biology and Biochemistry

Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia – Robert Duran – Environmental Science and Pollution Research

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation – Maria E. Hernandez – PeerJ

Water microbiome

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs – Peter Menzel – Microbial Ecology

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients – Jiwen Liu – Frontiers in Microbiology

Microbiome of the built environment

Thesis: Longitudinal and spatial characterization of microbial communities in offices – John Chase – Northern Arizona University

Bacterial transfer to beverages during drinking games: ‘beer pong’ – Paul L. Dawson – Int. J. Food Safety, Nutrition and Public Health

Food microbiology

High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia – Wenjun Liu – BMC Microbiology

Microbiological Changes and Biodiversity of Cultivable Indigenous Bacteria in Sanbao Larger Yellow Croaker (Pseudosciaena crocea), a Chinese Salted and Fermented Seafood – He Zhang – Journal of Food Sciences

Bioreactor microbiology

A methodological framework for linking bioreactor function to microbial communities and environmental conditions – Francis L de los Reyes III – Current Opinion in Biotechnology

Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing – Haihan Zhang – BMC Microbiology

Phages and viruses

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales – Uri Gophna – ISME Journal

Inactivation of an Enveloped Surrogate Virus in Human Sewage – Lisa M. Casanova – Environ. Sci. Technol. Lett.

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing – Friederike S. Rossmann – PLOS Pathogens

Archaea

Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing – Vanessa D. Nkamga – Current Microbiology

Bioinformatics and metagenomics

The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: Case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia – E. González-Tortuero – Molecular Ecology Resources

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics – Sandeep K Kushwaha – BMC Bioinformatics

Spaced seeds improve metagenomic classification – Karel Bˇrinda – ArXiv

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K – Naama M. Kopelman – Molecular Ecology Resources

PhD thesis: Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome – Sharon I. Greenblum – University of Washington

Masters thesis: MR-CUDASW – GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data – Amir Muhammadzadeh

Testing ecological theories with sequence similarity networks: marine ciliates
exhibit similar geographic dispersal patterns as multicellular organisms – Dominik Forster – BMC Biology

A Brief Review of Software Tools for Pangenomics – Jingfa Xiao – Genomics, Proteomics & Bioinformatics

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes – Xavier Didelot – PLOS Computational Biology

Ten years of pan-genome analyses – George Vernikos – Current Opinion in Microbiology

Metabolomics and proteomics

Towards further defining the proteome of mouse saliva – Anne A Blanchard – Proteome Science

Protein Complexes in Bacteria – J. Harry Caufield – PLOS Computational Biology

Review: Metabolomics and Diabetes: Analytical and Computational Approaches – Kelli M. Sas – Diabetes

Techniques

Inosine at Different Primer Positions to Study Structure and Diversity of Prokaryotic Populations – Eitan Ben-Dov and Ariel Kushmaro – Current Issues Molecular Biology

Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil – Hannes Schmidt – Soil Biology and Biochemistry

Microbes in the news

Diet, Location And Your Kid’s Gut Bacteria – Stefania Hartley – Asian Scientist Magazine

Killing off one Bacterium Can Lead to Obesity – Noel Angeles – SMN Weekly

The Human Microbiome Through an Oral Healthcare Lens – Natasha Singh – Oral Health Group

Yes Virginia, there is a paper on microbial transfer during beer pong – Jonathan Eisen

First detailed evidence of bacteria at the lower size limit of life – Science Codex

How Small Can Life Get? These Ultra-Small Bacteria May Be At The Limit – Science 2.0

Title Fail: Deadly bacteria outbreak linked to UCLA microscopes – Standard Examiner

The bioMASON Startup Grows Bricks from Bacteria – Annie Pilon – Small Biz Trends

Deadly bacteria release sparks concern at Louisiana lab – Alison Young – USA Today

Science, publishing and career

Riding Out Rejection: How to navigate the choppy waters of scientific publication – Kate Yandell – The Scientist

Medical Journals and Free Speech – Joel Bakan – Pediatrics

How to Write a Presubmission Inquiry – Thomas Lengauer, Ruth Nussinov – PLOS Computational Biology

Chill GPS: Keeping track of frozen biological samples – Jeffrey M. Perkel – The Scientist

Science and Art

Move over #TheDress and #LlamaDrama, this weekend’s Twitter storm was all about #SciArt – Twitter

Bik’s Picks

Scientists have created the perfect music for cats – Fiona MacDonald – Science Alert

Gulf of Mexico Turns Deadly for Dolphins – Rachel Nuwer – New York Times

‘Skeletorus’ and ‘Sparklemuffin’ the Newest Spiders – Agata Blaszczak Boxe – Live Science

[hr]

February 25, 2015

Posted on by

Nature and Scientific American have a joint Microbiome special: “Innovations in the Microbiome” with several overview papers from Rob Knight, Ruth Ley,  Justin Sonnenburg et al. Articles include:

The Microbes Within – David Grogan
Why Microbiome Treatments Could Pay Off Soon – Rob Knight
Your Microbes at Work: Fiber Fermenters Keep Us Healthy
Mental Health: Thinking from the Gut – Charles Schmidt
Gut Microbiome: The Peacekeepers – Moises Velasquez-Manoff
The Gene–Microbe Link – Ruth E. Ley
Microbiome Engineering – Justin L. Sonnenburg
The Diverse Microbiome of the Hunter-Gatherer – Stephanie L. Schnorr

Human oral microbiome

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci – Robert A. Whiley – PLOS ONE

Human skin microbiome

Malassezia Intra-Specific Diversity and Potentially New Species in the Skin Microbiota from Brazilian Healthy Subjects and Seborrheic Dermatitis Patients – Renan Cardoso Soares – PLOS ONE

Human gut microbiome

From the Gordon lab: Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans – Timothy Heisel – PLOS ONE

Animal models of microbiome research

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome – Benoit Chassaing – Nature

Animal microbiome

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole – Gordon M. Bennett and Nancy A. Moran

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider – Bram Vanthournout, Frederik Hendrickx – PLOS ONE

Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages – Yu Shi – Journal of Basic Microbiology

Plant microbiome

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations – Caio T. C. C. Rachid – PLOS ONE

Soil microbiome

Microbial dynamics in glacier forefield soils show succession is not just skin deep – Arwyn Edwards and Sophie Cook – Molecular Ecology

Microbial deposits in the aftermath of the end-Permian mass extinction: A diverging case from the Mineral Mountains (Utah, USA) – Emmanuelle Vennin – Sedimentology

Water microbiome

Characterizing variability in marine protist communities via ARISA fingerprints—a method evaluation – E.S. Kilias – Limnology and Oceanography: Methods

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System – Katherine E. Fish – PLOS ONE

Microbiome of the built environment

Sewage Reflects the Microbiomes of Human Populations – Ryan J. Newton – mBio

Phages and viruses

The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors – Orla McCabe – Molecular Microbiology

Bioinformatics

Tools for Bacterial Comparative Genomics – Kat Holt – Holt Lab

Techniques

Comparison of different methods for the recovery of DNA from spores of mycotoxin producing moulds in spiked food samples – Sabrina Grube – Letters in Applied Microbiology

Metabolomics

Nutritional stress induces exchange of cell material and energetic coupling between bacterial species – Saida Benomar – Nature Communications

Other papers of interest

Climate-driven introduction of the Black Death and successive plague reintroductions into Europe – Boris V. Schmid – PNAS USA

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs – Eric Londin – PNAS USA

Microbes in the news

Fishing For the Microbes Behind Malnutrition – Ed Yong – National Geographic

4th World Summit ‘Gut Microbiota For Health’ to be held in Barcelona – Phys.org

Indian scientist awarded 1.5 million euros grant to investigate the role of gut microbiota in autoimmune diseases – Economic Times India

Johnson & Johnson Bets On Alzheimer’s Vaccine, Disease Prediction, Human ‘Microbiome’ – Amy Nordrum – International Business Times

Altered microbiome may lead to liver disease in patients with cystic fibrosis – Healio

Cystic Fibrosis Liver Cirrhosis Associated with Intestinal Microbiome – Maureen Newmn – LungDiseaseNews

Linoleic acid role balanced by changes to gut microbiota: Study – Annie-Rose Harrison-Dunn – NutraIngredients

My Microbiome Experience from Start to Results – Alexandra Carmichael – uBiome Blog

Session Report: Citizen Microbiology at Citizen Science 2015 – David Coil – MicroBEnet

Bacteria pipe food to each other using tiny tubes – Francie Diep – Popular Science

CSU study finds that Leprosy bacteria can survive in unusual environments – Emily Vavra – Collegian

Science, publishing and career

Scientists are cautious about public outreach – Chris Woolston – Nature

It’s Time for More Racial Diversity in STEM Toys – Maia Weinstock – Scientific American

Science and art

Science and Culture: Data visualization nurtures an artistic movement – J. D. Talasek – PNAS USA

Bik’s Picks

Wanted: 80,000 British babies for massive study – Helen Pearson – Nature

28.8 million tons of Sahara desert fertilize the Amazon – Deborah Netburn – LA Times

Your Eyelashes Should Be This Long, Science Says – Megan Gannon – Scientific American [hr]