Category Archives: Pregnancy and birth

March 31, 2015

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

Pregnancy and birth microbiome

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

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

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

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

Human oral microbiome

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

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

Human respiratory microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

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

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

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

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

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

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

Plant microbiome

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

Soil and plant root microbiome

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

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

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

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

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

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

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

Water microbiome

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

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

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

Extremophile microbiome

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

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

Built environment microbiome

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

Food microbiology

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

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

Metagenomics and bioinformatics

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

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

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

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

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

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

Metabolomics

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

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

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

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

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

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

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

Growing a Baby Microbiome – Kevin Bonham – Scientific American

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

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

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

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

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

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

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

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

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

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

Conferences

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

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

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March 27, 2015

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Science Direct is down today, and all links to their papers did not work. Hopefully they can fix that soon.

Pregnancy and birth

Does Breastfeeding Help to Reduce the Risk of Childhood Overweight and Obesity? A Propensity Score Analysis of Data from the KiGGS Study – Maike Miriam Grube – PLOS ONE

Human gut microbiome

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

Soil and sediment microbiome

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment – Özge Eyice – The ISME Journal

Water microbiome

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages – C Chénard – The ISME Journal

Transcriptomics

Metatranscriptomic census of active protists in soils – Stefan Geisen – The ISME Journal

Bioinformatics

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists – Marco D. Visser – PLOS Computational Biology

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees – Brad Solomon, Carleton Kingsford – BioRxiv

Techniques

Evaluation of four methods of assigning species and genus to medically important bacteria using 16S rRNA gene sequence analysis – Geon Park – Microbiology and Immunology

Microbes in the news

Surprises Emerge As More Hunter-Gatherer Microbiomes Come In – Ed Yong – National Geographic

Poo’s clues: what sewage can tell us about public health – Roger Pickup – Quartz

Our Plan to Combat and Prevent Antibiotic-Resistant Bacteria – Sylvia Mathews Burwell et al. – White House

Different takes on justice – Larry Forney’s microbial ecology work on the vaginal microbiome has given him a unique perspective on biological diversity and justice – UI Argonaut

On terroir, and the vine’s microbiome – Steve Heimoff

Advances in Genome Biology and Technology (AGBT2015) conference Roundup – Dale Yuzuki – Behind the Bench

Give Breast Milk Some women are computer programmers or impressive cooks. I’m good at producing breast milk. – Elizabeth Currid-Halkett – New York Times.

Science, publishing, and education

From start to finish: A guide to informational interviewing – Prital Patel – Nature Jobs

Stanford is investigating an ‘unusually high number’ of student cheating allegations – Business Insider

Bik’s Picks

30 Previously-Unknown Species of Fly Discovered in Los Angeles – Annalee Newitz – Gizmodo

Official Report: Nuclear Waste Accident Caused By Wrong Cat Litter – Geoff Brumfiel – NPR

The mysterious deaths of all but one bluefin tuna in Tokyo Sea Life Park – Lindsey Bever – Washington Post

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March 24, 2015

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General microbiome

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

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

Microbiome of pregnancy and birth

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

Human vaginal microbiome

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

Human gut microbiome

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

Animal and other models

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

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

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

Animal microbiome

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

Plant microbiome

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

Soil and plant root microbiome

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

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

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

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

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

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

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

Water microbiome

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

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

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

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

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

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

Built environment microbiome

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

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

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

Probiotics

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

Antibiotics

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

Metagenomics and bioinformatics

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

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

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

Metabolomics / Ecology

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

Microbes in the news

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

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

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

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

Harnessing The Microbiome To Curb Hunger – Chemical and Engineering News

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

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

Viruses, Archaea Self-mutate to Survive – Laboratory Equipment

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

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

Not so fast, FastTree – Darling lab

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

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

Comparing the genomes of the leprosy bacteria – Phys.org

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

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

Science and art

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

Science, publishing, and career

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

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

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

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

It’s time to reboot bioinformatics education – Todd Harris

Bik’s Picks

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

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

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

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March 22, 2015

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Human oral microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

Microbiome of pregnancy and birth

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

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

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

Animal models

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

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

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

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

Animal microbiome

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

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

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

Soil and plant root microbiome

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

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

Water microbiome

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

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

Microbiome of the built environment

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

Bioreactor microbiology

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

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

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

Metagenomics and Bioinformatics

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

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

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

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

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

Metabolomics

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

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

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

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

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

Other microbial science papers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

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

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

March 18, 2015

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Human skin microbiome

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

Human oral microbiome

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

Human gut microbiome

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

Microbiome of pregnancy and birth

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

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

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

Animal and other models

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

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

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

Soil and plant root microbiome

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

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

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

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

Water microbiome

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

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

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

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

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

Bioreactor microbiome

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

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

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

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

Food microbiology

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

Phages and viruses

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

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

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

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

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

Metagenomics and bioinformatics

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

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

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

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

Metabolomics

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

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

Microbes in the news

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

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

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

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

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

Lab creates bioinformatics tool for metagenome analysis – Phys.org

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

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

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

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

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

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

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

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

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

Technology helps unlock secrets of rare bacteria – Phys.org

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

Video: Alexander Fleming – Inventor of Penicillin – Scientiflix

Bik’s Picks

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

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

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

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March 15, 2015

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Microbiome of pregnancy and birth

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

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

Animal models

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

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

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

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

Animal microbiome

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

Plant microbiome

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

Soil and plant root microbiome

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

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

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

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

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

Water and ice microbiome

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

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

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

Bioreactor microbiome

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

Food microbiology

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

Metagenomics and Bioinformatics

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

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

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

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

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

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

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

Metabolomics and Transcriptomics

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

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

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

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

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

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

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

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

More microbial science

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

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

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

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

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

Microbes in the news

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

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

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

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

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

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

Science and art – microbial edition

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

How microbes inspire art (Video) – BBC

Fungi on Tea – Microbe World

Louis Pasteur T-shirt – The Strange company

Bik’s Picks

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

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

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

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March 9, 2015

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Pregnancy and birth

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

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

Human oral microbiome

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

Human gut microbiome

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

Review: Collective unconscious: how gut microbes shape human behavior

Human microbiome after death

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

Animal models of microbiome research

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

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

Animal microbiome

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

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

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

Plant microbiome

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

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

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

Soil and plant root microbiome

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

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

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

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

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

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

Water (and ice) microbiome

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

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

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

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

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

Microbiome of the built environment

Urban microbiome – Orli G. Bahcall – Nature Review Genetics

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

Microbial evolution and ecology

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

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

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

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

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

Metagenomics and bioinformatics

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

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

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

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

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

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

Metabolomics

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

Techniques

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

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

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

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

Microbes in the news

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

20m podcast: The Straight Poop – Transistor

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

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

Drugging the gut microbiome – Ken Garber – Nature Biotechnology

Tummy Troubles? Your Microbiome Can Help – Isabel Smith

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

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

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

How Microbes Keep Us Healthy – Scientific American

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

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

Prediabetes Patients Have Fewer Gut Bugs – Parker Brown – MedPageToday

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

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

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

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

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

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

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

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

Fine Focus: Microbiology Research Journal for Undergraduate Students

Science and art

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

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

Science, publishing, and career

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

My Most Informative Error – Ami Schattner – JAMA Internal Medicine

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

Bik’s Picks: The science of aging edition

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

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

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

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March 6, 2015

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Pregnancy and birth

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

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

Human respiratory microbiome

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

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

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

Plant microbiome

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

Soil and sediment microbiome

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

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

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

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

Water microbiome

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

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

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

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

Bioreactor microbiome

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

Microbiome of the built environment

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

Food microbiology

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

Metagenomics and bioinformatics

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

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

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

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

Proteomics

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

Microbial Ecology

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

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

Microbes in the news

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

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

Who owns my microbiome? – Gabrielle Morguelan – Transylvania Rambler

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

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

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

Science, publishing, and career

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

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

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

Bik’s Picks

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

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

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

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March 3, 2015

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Human microbiome general

Manuscript: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes and Other Selfish Entities Shape Our Behavior – Peter Kramer and Paola Bressan

Microbiome of pregnancy and birth

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development – Tali Raveh-Sadka – eLIFE

Human respiratory microbiome

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals – Christine M. Bassis – mBio

Human gut microbiome

The relevance of intestinal dysbiosis in liver transplant candidates – M. Grąt – Transplant Infectious Disease

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohn’s Disease – Suskind, David L. – Inflammatory Bowel Diseases

Review: The Guts of Obesity: Progress and Challenges in Linking Gut Microbes to Obesity  – Gabriel A. Al-Ghalith – Discovery Medicine

Animal models of microbiome research

Thesis: Exercise is more effective at producing robust, lasting changes in gut microbial composition in juvenile than in adult male F344 rats – Agnieszka Mika – University of Colorado at Boulder

The gut microbiome restores intrinsic and extrinsic nerve function in germ-free mice accompanied by changes in calbindin – K. A. McVey Neufeld – Neurogastroenterology & Motility

Cystic fibrosis mouse model-dependent intestinal structure and gut microbiome – Mark Bazett – Mammalian Genome

Use of bacteriocin-producing, probiotic strain Enterococcus faecium AL41 to control intestinal microbiota in farm ostriches – Andrea Lauková – Letters in Applied Microbiology

Animal microbiome

Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses – Shaufi M Mohd Asrore – Gut Pathogens

Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens – Douglas C. Woodhams – Ecological Archives

Diet shapes the gut microbiota of the omnivorous cockroach Blatella germanica – Ana Elena Pérez-Cobas – FEMS Microbiology Ecology

Characterization of the honey bee microbiome throughout the queen-rearing process – David R. Tarpy – Applied and Environmental Microbiology

Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand-islands reef complex, West-Java, Indonesia – Nicole J. de Voogd – FEMS Microbiology Ecology

Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf – B. C. C. Hume – Scientific Reports

Plant microbiome

Grazing livestock are exposed to terrestrial cyanobacteria – Bruce C McGorum – Veterinary Research

Soil and root microbiome

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere –
Chanyarat Paungfoo-Lonhienne – Scientific Reports

Changes in soil microbial community structure and activity in a cedar plantation invaded by moso bamboo – Ed-Haun Chang, Chih-Yu Chiu – Applied Soil Ecology

Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities – Kristin Aleklett – PeerJ

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site – Indumathy Jayamani, Alison M. Cupples – Environmental Science and Pollution Research

Impact of metal pollution on fungal diversity and community structures – Michiel Op De Beeck – Environmental Microbiology

Water microbiome

Diverse uncultivated ultra-small bacterial cells in groundwater – Birgit Luef – Nature Communications

Impacts of the Three Gorges Dam on microbial structure and potential function – Qingyun Yan – Scientific Reports

Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean – Rosemary E. Scavotto – Environmental Microbiology

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India) – Sheryl Oliveira Fernandes – Brazilian Journal of Microbiology

Bioreactor microbiology

Start-up strategies in manure-fed biogas reactors: Process parameters and methanogenic communities – M. Goberna – Biomass and Bioenergy

Microbiome of the built environment

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China – Huirong Lin – BioMed Research International

Observational scores of dampness and mold associated with measurements of microbial agents and moisture in three public schools – S. J. Cho – Indoor Air

Food microbiology

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome – Armin Erlacher – PLOS ONE

Phages and viruses

‘Ménage à trois’: a selfish genetic element uses a virus to propagate within Thermotogales – Julien Lossouarn – Environmental Microbiology

Microbial Ecology

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession – Francisco Dini-Andreote – PNAS USA

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

Tuberculosis: Fighting an old disease with next-generation sequencing – Anzaan Dippenaar, Robin M. Warren – eLIFE

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen – Braham Dhillon – PNAS USA

A tortoise-infecting picornavirus expands the host range of the family Picornaviridae
Terry Fei Fan Ng – Archives of Virology

Metagenomics and bioinformatics

Review: Insights from 20 years of bacterial genome sequencing – Miriam Land – Functional & Integrative Genomics

Review: The Current Status and Challenges in Computational Analysis of Genomic Big Data – Yiming Qin – Big Data Research

Metabolomics

Impact of storage conditions on metabolite profiles of sputum samples from persons with cystic fibrosis – Jiangchao Zhao – Journal of Cystic Fibrosis

Microbes in the news

Enter the Vaginome: Meet the Microbes that Live in Our Vaginas – A.V. Flox – Motherboard

New paper on diseased vs healthy infants in a NICU, possible impacts for future hospital microbiome work – Bubba Brooks – MicroBEnet

Archaea: Mysterious microbes hold big possibilities for Sloan Research Fellow Alyson Santoro – EurekaAlert

Genes & cells: Jet lag disrupts microbes in the gut: Mice with time-shifted bacteria develop metabolic problems – Tina Hesman Saey – Science News

The environment may change, but the microbiome of queen bees does not – Matt Shipman

Cheesey Microbial Communities – Daniel P. Haeusser – Small Things Considered

150,000 of these bacteria could fit on the tip of a hair (and that’s about as small as life can get) – Rachel Feltman – Washington Post

Unusual Bacteria Discovered In Deepest Ocean Trench – Ocean Leadership

Link Identified Between Virus Recognition, Destruction in Bacterial Immune System – Infection Control Today
Researchers Discover How Bacteria ‘Steal’ Genetic Information – Jim Algar – Tech Times

Science, publishing, and career

Different personal propensities among scientists relate to deeper vs. broader knowledge contributions – Thomas S. Bateman, and Andrew M. Hess – PNAS USA
Attention, All Scientists: Do Improv, With Alan Alda’s Help – Kenneth Chang – New York Times

Bik’s Picks

Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa –
Fabrice Lihoreau – Nature Communications

Termites: Guardians of the Soil – Natalie Angier – New York Times

A social chemosignaling function for human handshaking – Idan Frumin – eLIFE

Snip, Snap, Slurp: Misophonia Makes Them Unbearable – What sound most grates on your nerves? – Karen Barrow – New York Times
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February 23, 2015

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General human microbiome

Review: Human Microbiome: When a Friend Becomes an Enemy – Magdalena Muszer – Archivum Immunologiae et Therapiae Experimentalis

Microbiome of pregnancy and birth

Probiotics and gut health in infants: A preliminary case–control observational study about early treatment with Lactobacillus reuteri DSM 17938 – Francesco Savino – Clinica Chimica Acta

Review: Clinical impact of human breast milk metabolomics – Flaminia Cesare Marincola – Clinica Chimica Acta

Human oral microbiome

Review: A review on microbiological cause of periodontal disease: disease and treatment. – Durgesh, Bangalore H – Reviews in Medical Microbiology $$$

Human gut microbiome

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls – Aldona Dlugosz – Scientific Reports

Microbiota disbiosis is associated with colorectal cancer – Zhiguang Gao – Frontiers in Microbiology

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

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: Gut microbiota: Microbiota organisation—a key to understanding CRC development – Georgina L. Hold & Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Changing views on diverticular disease: impact of aging, obesity, diet, and microbiota – R. C. Spiller – Neurogastroenterology & Motility

Animal models of microbiome research

Oral microbiome composition changes in mouse models of colitis – Jaana Rautava – Journal of Gastroenterology and Hepatology

Animal microbiome

Diverse small circular DNA viruses circulating amongst estuarine molluscs – Anisha Dayaram – Infection, Genetics and Evolution

Plant microbiome

Moth Outbreaks Alter Root-Associated Fungal Communities in Subarctic Mountain Birch Forests – Karita Saravesi – Microbial Ecology

The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses – Nhu H. Nguyen, Thomas D. Bruns – Microbial Ecology

Soil microbiome

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill – Luis M Rodriguez-R – The ISME Journal

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands – Haowei Yue – The ISME Journal

Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles – Julia Moll – Microbial Ecology

Characteristic microbial communities in the continuous permafrost beside the bitumen in Qinghai-Tibetan Plateau – Nan Jiang – Environmental Earth Sciences

Effect of early dry season induced by the Three Gorges Dam on the soil microbial biomass and bacterial community structure in the Dongting Lake wetland – Haipeng Wu – Ecological Indicators

Disentangling plant and soil microbial controls on carbon and nitrogen loss in grassland mesocosms – Franciska T. De Vries – Journal of Ecology

Water microbiome

Evidence for an active rare biosphere within freshwater protists community – Didier Debroas – Molecular Ecology

Response of the microbial community to seasonal groundwater level fluctuations in petroleum hydrocarbon-contaminated groundwater – Ai-xia Zhou – Environmental Science

Microbiome of the built environment

Isolation of Vermamoeba vermiformis and associated bacteria in hospital water – Isabelle Pagnier – Microbial Pathogenesis

Dynamics of bacterial communities before and after distribution in a full-scale drinking water network – Joline El-Chakhtoura – Water Research

Marine bioerosion of lapideous archaeological artifacts found in the Grotta Azzurra (Capri, Naples, Italy): Role of microbiota and boring Porifera – Carlotta Sacco Perasso – International Biodeterioration & Biodegradation

Bioreactor microbiome

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities – Florian Centler and Martin Thullner – Frontiers in Microbiology

Review: Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus – Marta Carballa – Current Opinion in Biotechnology

Metagenomics, Sequencing and Bioinformatics

Improved detection of artifactual viral minority variants in high-throughput sequencing data – Matthijs R. A. Welkers – Frontiers in Microbiology

Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population – Walter Pirovano – Frontiers in Microbiology

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

Uploaded manuscript: Metagenomic Assembly Validation of an in vitro Mock Community [PDF] – Ino de Bruijn – Authorea

DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly – Guo Xuan – Journal of Computational Biology

Clustering of reads with alignment-free measures and quality values – Matteo Comin – Algorthms for Molecular Biology

Improved data analysis for the MinION nanopore sequencer – Miten Jain – Nature Methods

Genome-wide gene order distances support clustering the gram-positive bacteria – Christopher H. House – Frontiers in Microbiology

Perspective: Current strategies for mobilome research – Tue S. Jørgensen – Frontiers in Microbiology

Metabolomics

Species-specific dynamic responses of gut bacteria to a mammalian glycan – Varsha Raghavan and Eduardo A. Groisman – Journal of Bacteriology

Role of intestinal microbiota in the generation of polyphenol derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

Review: Does Our Gut Microbiome Predict Cardiovascular Risk? – A Review of the Evidence From Metabolomics – Julian L. Griffin – Circulation: Cardiovascular Genetics

http://intl-circgenetics.ahajournals.org/content/8/1/187.full

Other microbiology papers of interest

Review: Interactions of Salmonella with animals and plants – Agnès Wiedemann – Frontiers in Microbiology

Microbes in the news

Rob Knight awarded Vilcek Prize 2015 – Vilcek Foundation

AAAAI Annual Meeting Research Links Infants’ Microbiome to Development of Immune System, Allergic Diseases and Asthma – Our Midland

Examining the Hygiene Hypothesis and the Role of the Microbiome in Allergic Disease – Rodrigo Barros – HCP Live

The Role of the Skin Microbiome in Health and Disease – Rodrigo Barros – HCP Live

Facebook banned “Human Microbiome” artist picture for being ‘overly sexual’ – Hannah Parry – Mail Online

Campus bacteria: The whats and wheres of Columbia’s most infamous bacteria (e.g. the Sweatococcus @ Dodge Gym Equipment) – Sophia Hotung – Columbia Spectator

Bacteria connect to each other and exchange nutrients – Phys.org

Researchers explore influence of host organisms on bacterial metabolism – News Medical

Blood tests indicate scientist may not have been sickened at Tulane primate center – Kim Chatelain – Nola

We’re all hosts on a viral planet: E. coli O157 edition – Doug Powell – BarfBlog

Bik’s Picks

Surprise! 1,000-Year-Old Mummy Found in Buddha Statue – NBC News

Crews free humpback whale tangled in fishing line off Hawaii – Fox News

Satire: Collective Cleanliness: A Meta-Discursive Study of Academic Tearoom Culture – Lotta Washinup and Duya Dishez – Journal of Applied Elbow Grease

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