March 31, 2015

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

ReviewProbiotics 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


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 –
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


#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

DiscussionMistake 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 –

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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