Category Archives: Pregnancy and birth

February 15, 2016

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Drosophila longevity, gut immunity in insects, metagenomics and beef production, secure computation, and mutualistic phages.

Pregnancy and birth

Research Highlight: Add the microbiota to your birth plan – Cláudio Nunes-Alves – Nature Reviews Microbiology

Human gut microbiome

Review: Gut microbiome and Metabolic Syndrome – Mohsen Mazidi – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Review: Role of microbes (probiotics and prebiotics) – D.M.A.E. Jonkers – Best Practice & Research Clinical Gastroenterology

Review: Intestinal Microbiota in Liver Disease – Tanvir R. Haque – Best Practice & Research Clinical Gastroenterology

Models of microbiome research

Folate Acts in E. coli to Accelerate C. elegans Aging Independently of Bacterial Biosynthesis – Bhupinder Virk – Cell Reports

Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – Biology Open

Bacterial successions in the gastrointestinal tract of broilers – Samir Ranjitkar – Applied and Environmental Microbiology

Triclosan Exposure is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A Gaulke – BioRxiv

Research Highlight: How to extend your stay – Cláudio Nunes-Alves – Nature Reviews Microbiology

Animal microbiome

Review: Gut immunity in Lepidopteran insects – Kai Wu – Developmental & Comparative Immunology

Editorial: Bears Arouse Interest in Microbiota’s Role in Health – Kimberly A. Dill-McFarland – Trends in Microbiology

Plant, root, and soil microbiome

Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome – Letícia Carlos Babujia – Transgenic Research

Food microbiology

Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain – Xiang Yang – Applied and Environmental Microbiology

Microbial dynamics in industrial Blue veined cheeses in different packaging –
P. Duval – International Dairy Journal

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing – Janja Trček – International Journal of Food Microbiology

Built environment microbiome

Air dispersed essential oils combined with standard sanitization procedures for environmental microbiota control in nosocomial hospitalization rooms – Fabrizio Gelmini – Complementary Therapies in Medicine

Waste and extremophile microbiology

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes – Simon Poirier – Bioresource Technology

Bioinformatics and metagenomics

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – Bioinformatics

Phages and viruses

Opinion: The Significance of Mutualistic Phages for Bacterial Ecology and Evolution – Nancy Obeng – Trends in Microbiology

Techniques

Unique sequence characteristics account for good DGGE separation of almost full-length 18S rDNAs – Zhiqing Huang – World Journal of Microbiology and Biotechnology

Microbes in the news

New appreciation for human microbiome leads to greater understanding of human health – University of Oklahoma – EurekAlert

From Huts to Cities: How Changes in Dwellings Have Impacted Microbe Exposure for the Human Immune System – New York University Langone

Researchers outline progress in turning bacteria into mini construction workers – The Construction Index

Can we outrun Zika? Walk this street in Colombia and you’ll see how tough it is – Andrew Joseph – STATnews

Cranberries help urinary tract infections, but not as juice – Yvette Brazier – Medical News Today

Biofilm Formation Hampers Removal of Dangerous Bacteria from Hospital Surfaces – Medical Research

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February 13, 2016

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Fungal communities of bark beetles, microbiome in rhinosinusitis, deep-sea chemolithoautotrophic communities, talking walls (microbes in houses), and, for Valentine’s Day: cocoa bean fermentation. 

Jobs and events

Postdoc opportunity, University of Notre Dame: 20,000 longitudinal gut microbiome samples from wild baboons

Pregnancy and birth

Review: Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant – Kannikar Vongbhavit – Clinical Therapeutics

Human oral microbiome

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing – Kwan Hee Yun – International Journal of Paediatric Dentistry

Human respiratory microbiome

Composition and dynamics of the respiratory tract microbiome in intubated patients – Brendan J. Kelly – Microbiome Journal

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity – Simon J. S. Cameron- PLOS ONE

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes – Edward John Cleland – American Journal of Rhinology & Allergy

Review: Microbiome of the paranasal sinuses: Update and literature review – Jivianne T. Lee – American Journal of Rhinology & Allergy

Editorial: The microbiome of the sinuses and its relevance in health and disease – Simon A. Carney

Human reproductive tract microbiome

Molecular detection of intrauterine microbial colonization in women with endometriosis – Khaleque N. Khan – European Journal of Obstetrics & Gynecology and Reproductive Biology

Review: The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine – Deepak S. Ipe – Frontiers in Cellular and Infection Microbiology

Review: The Human Microbiome during Bacterial Vaginosis – Andrew B. Onderdonk – Clinical Microbiology Reviews

Human gut microbiome

Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project – Xing Hua – EBioMedicine

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection – Vijay C. Antharam – PLOS ONE

Review: The Role of Probiotics on the Microbiota: Effect on Obesity – Esther Nova – Nutrition in Clinical Practice

Editorial: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Perspective: The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders? – Javier Ochoa-Repáraz – Current Obesity Reports

Review: Butyrate, Neuroepigenetics and the Gut Microbiome: Can a High Fiber Diet Improve Brain Health? – Megan W. Bourassa – Neuroscience Letters

Gut passage

Colonic response to laxative ingestion as assessed by MRI differs in constipated irritable bowel syndrome compared to functional constipation – C. Lam – Neurogastroenterology & Motility

How do primates affect seed germination? A meta-analysis of gut passage effects on neotropical plants – Lisieux F. Fuzessy – Oikos

Models of microbiome research

Drosophila: Effects of co-occurring Wolbachia and Spiroplasma endosymbionts on the Drosophila immune response against insect pathogenic and non-pathogenic bacteria – Upasana Shokal – BMC Microbiology

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Thesis, mice: The effects of nicotine on the gut microbiome and the serum metabolite profile of mice – Ridwan Amin Mahbub – University of Georgia

Contains several cases of image duplication (might be error): Dietary Fiber Intake Regulates Intestinal Microflora and Inhibits Ovalbumin-Induced Allergic Airway Inflammation in a Mouse Model – Zhiyu Zhang – PLOS ONE

Animal microbiome

Metabarcoding of fungal communities associated with bark beetles – Kirsten E. Miller – Ecology and Evolution

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue-green sharpshooter (Graphocephala atropunctata) – E. E. Rogers – Journal of Applied Entomology

A bacterial filter protects and structures the gut microbiome of an insect – Michele Caroline Lanan – The ISME Journal

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression – Shaikhul Islam – Frontiers in Microbiology

Microbial biomass and soil organic carbon accumulation on a former lakebed near Novosibirsk, Russia – Mikhail. V. Yakutin – Journal of Plant Nutrition and Soil Science

A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition – A.B. Siddique – Fungal Ecology

Primer: Networking in the Plant Microbiome – Marcel G. A. van der Heijden – PLOS Biology

Thesis: Next generation sequencing on soil samples from Etosha National Park: Diversity studies of an anthrax reservoir – Valseth, Karoline

Water and extremophile microbiome

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent – Caroline S Fortunato – The ISME Journal

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt – Sean P Jungbluth – The ISME Journal

Context dependency in biodiversity patterns of central German stream metacommunities – Jonathan D. Tonkin – Freshwater Biology

Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys – Heebok Choi – Journal of Microbiology and Biotechnology

Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community – Enrique Zozaya-Valdés – Frontiers in Microbiology

Using in situ bacterial communities to monitor contaminants in river sediments – Yuwei Xie – Environmental Pollution

DGGE: Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities – J. R. Lawrence – Environmental Science and Pollution Research

Built environment microbiome

Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances

Microbial communities affecting albumen photography heritage: a methodological survey – Andrea Puškárová – Scientific Reports

Food microbiology

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing –
Alessandra Dalmasso – LWT-Food Science and Technology

Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses – Tiong Gim Aw – International Journal of Food Microbiology

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment – Monika Dzieciol

Review: The cocoa bean fermentation process: from ecosystem analysis to starter culture development – L. De Vuyst – Journal of Applied Microbiology

Techniques

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis – Ahmad Paintdakhi – Molecular Microbiology

Viruses and phages

Perspective: A Virological Perspective on Cancer – Blossom Damania – PLOS Pathogens

Bioinformatics and metagenomics

Fast search of thousands of short-read sequencing experiments – Brad Solomon – Nature Biotechnology

Open-Source Sequence Clustering Methods Improve the State Of the Art – Evguenia Kopylova

Editorial: Bacterial Speciation: Genetic Sweeps in Bacterial Species -Frederick M. Cohan – Current Biology

Microbes in the news

Walls talk – or at least hold many secrets a wall whisperer can reveal – Jonathan Eisen – MicroBEnet

Country microbes, city microbes—where you live can change how you get sick – Annalee Newitz – Ars Technica

Urbanization Leads to Change in Type of Bacteria in the Home – Lauran Neergaard – ABC News

Fun list: Ranking the Top 10 Best Bacteria on Earth – Ben Guarino – Inverse

Science, publishing and career

The Research Pirates of the Dark Web – Kaveh Waddell  – The Atlantic

Researcher illegally shares millions of science papers free online to spread knowledge – Science Alert

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February 12, 2016

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Infant gut microbiota development and family foods, a paper on the “blood microbiome” that caused some discussion on Twitter, Penicillinum and pears, and community types in the human microbiome.

Jobs and events

Mothur and programming in R workshop, May 23-25, Detroit

Postdoctoral Research Assistant – Microbiome – University of Oxford – Department of Plant Sciences

Pregnancy and birth

Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity – Martin Frederik Laursen – mSphere

Human gut

A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection – Sahil Khanna – The Journal of Infectious Diseases

Microbiome of blood

No carefully designed controls, no deposit of sequence reads, misleading Y-axis in Figure S1. I don’t endorse this study: Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing – Sandrine Païssé – Transfusion

Animal models

Rearing room affects the non-dominant chicken caecum microbiota, while diet affects the dominant microbiota – Jane Ludvigsen – Frontiers in Veterinary Science

Extremophiles and water microbiome

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction – Silvan Scheller – Science

Perspective: A new diet for methane oxidizers – Amelia-Elena Rotaru – Science

The role of particle associated microbes in remineralization of fecal pellets in the upper mesopelagic of the Scotia Sea, Antarctica – Anna Belcher – Limnology and Oceanography

Growth dynamics of a laminated microbial mat in response to variable irradiance in an Antarctic lake – Ian Hawes – Freshwater Biology

Food microbiology

Profile of Penicillium species in the pear supply chain – I. Scholtz – Plant Pathology

More microbes

Survival games at the dinner table: regulation of Enterobacterial virulence through nutrient sensing and acquisition – Gaëlle Porcheron – Current Opinion in Microbiology

Bioinformatics and metagenomics

On the Origins and Control of Community Types in the Human Microbiome – Travis E. Gibson – PLOS Computational Biology

Microbes in the news

Forget chocolates. Give your sweetheart mushrooms this Valentine’s Day, says Stanford scientist – Rosemary Mena-Werth – Stanford News

Infant gut microbiome development not driven by maternal weight – Stephen Feller – UPI

Solid foods take over shaping of gut microbiota by 9 months – Yvette Brazier – Medical News Today

Why we might need to kill Australia’s koalas: Chlamydia infection is running rampant through their population, and a controlled cull might be their best hope- Katie Silver – BBC

Researchers Believe That Socialization Helps Spread Beneficial Gut Bacteria – Shariqua Ahmed – DogoNews

Novel microbiome therapy appears to prevent recurrent C. difficile infection – Healio

AbbVie Launches IBD Collaboration with Synlogic – GenEngNews

Bik’s Picks

Thursday’s massive gravitational wave news was broken by a sheet cake (really) – Rachel Feltman – Washington Post

Science and art

An Artist Asks: Whose Business Is Our DNA? – Short film on artwork by Heather Dewey-Hagborg who created masks of strangers based on genetic material left behind – The Atlantic

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February 10, 2016

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Socioeconomic status and microbiota diversity, metagenome of a carnivorous plant, microbiota of homes of CF patients, and high-resolution phylogenetic microbial community profiling.

Events

ASM Microbe 2016, June 16-20, Boston MA. With opening keynote lecture by Bill Gates

SC2: Microbiome: Sorting out the hype from the hope – March 6-11 2016, San Francisco

Probiotics and Prebiotics – June 21-23, Budapest

Pregnancy and birth

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome – Abdulkadir B. – Neonatology

Human oral microbiome

Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication – Sadia Ambreen Niazi – Clinical Oral Investigations

Human gut microbiome

Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach – Francesca Turroni – The ISME Journal

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults – Gregory E. Miller – PLOS ONE

The features of mucosa-associated microbiota in primary sclerosing cholangitis –
J. Torres – Alimentary Pharmacology & Therapeutics

Review: Physiological Role of Gut Microbiota for Maintaining Human Health – Andoh A. – Digestion

Editorial: You Are What You Feed Your Gut Microbiome – Joseph E. Scherger – Health Affairs

Review: Gastroenvironmental distress: metaphorical antecedents of the gut microbiome – Nitin K Ahuja – Medical Humanities

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Models of microbiome research

Drosophila: Preventing Age-Related Decline of Gut Compartmentalization Limits Microbiota Dysbiosis and Extends Lifespan – Hongjie Li – Cell Host & Microbe

Editorial: Microbes without Borders: Decompartmentalization of the Aging Gut – Erin S. Keebaugh – Cell Host & Microbe

Mice (and humans): Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation – Lirui Wang – Cell Host & Microbe

Editorial: Alcohol Lowers Your (Intestinal) Inhibitions – Namrata Iyer – Cell Host & Microbe

Mice: Daikenchuto (TU-100) shapes gut microbiota architecture and increases the production of ginsenoside metabolite compound K – Takumu Hasebe – Pharmacology Research & Perspectives

Editorial: Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Animal microbiome

Beetles: Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing – Julia Tiede – PLOS ONE

Plant, root, and soil microbiome

The Metagenome of Utricularia gibba’s Traps: Into the Microbial Input to a Carnivorous Plant – Luis David Alcaraz – PLOS ONE

Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria – Sai Shiva Krishna Prasad Vurukonda – Microbiological Research

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity –
Fatemeh Mohammadipanah – Frontiers in Microbiology

Organic Fertilization in Traditional Mediterranean Grapevine Orchards Mediates Changes in Soil Microbial Community Structure and Enhances Soil Fertility – Fuensanta García-Orenes – Land Degradation & Development

Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland – Dima Chen – Journal of Ecology

Water microbiome

Plankton networks driving carbon export in the oligotrophic ocean – Lionel Guidi – Nature

Built environment microbiome

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections – Alya Heirali – PLOS ONE

Metabolomics

Microbial metabolomics in open microscale platforms – Layla J. Barkal – Nature Communications

More microbiology

Open for discussion: Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients – Marina Manrique – bioRxiv

Ethanol Production by Selected Intestinal Microorganisms and Lactic Acid Bacteria Growing under Different Nutritional Conditions – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Rapid radiation in bacteria leads to a division of labour – Wook Kim – Nature Communications

Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli – Akira Nakagawa – Nature Communications

Bioinformatics and metagenomics

PhyloTags: High-resolution phylogenetic microbial community profiling – Esther Singer – The ISME Journal

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum – Karthik Anantharaman – PeerJ

Microbes in the news

The Good, the Bad and the Microbiome – Rachel Reisig – University of Minnesota

Unraveling the Mysterious Function of the Microbiome – by Mike Orcutt – MIT Technology Review

Wound-healing intestinal bacteria: Like shrubs after a forest fire
Akkermansia + other anaerobic bacteria temporarily bloom – EurekAlert

San Diego Scientists Find Data Brewing In Local Fermentation Culture – David Wagner – KPBS

Bacteria Have Ability to ‘See,’ Eye-Opening Study Finds – Maggie Fox – NBC News

A gut feeling about bacteria: Men are from Mars, women are from Venus – and their gut bacteria is just as different. – The Senior

How Your Gut Affects Your Bones. The surprising new science of how intestinal bacteria control bone strength – Rana Samadfam – Scientific American

Scientists Discover New Bacteria Responsible For Lyme Disease – David Beasly – Huffington Post

Overhyped: Sci-Q: The Science Of Love: The role of the microbiome in romantic attraction

Science, publishing, and career

Improving the peer-review process and editorial quality: key errors escaping the review and editorial process in top scientific journals – Antoni Margalida – PeerJ

Does it take too long to publish research? – Kendall Powell – Nature

The history of publishing delays – Daniel Himmelstein

The sexual misconduct case that has rocked anthropology – Michael Balter – Science
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February 9, 2016

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Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.

Events

2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA

Pregnancy and birth

Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports

Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology

Human skin microbiome

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio

Human urinary tract microbiome

Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology

Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology

Human respiratory microbiome

Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases

Human gut microbiome

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports

Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection

Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology

Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne

Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology

Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine

Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology

Models of microbiome research

Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS

Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio

Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports

More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports

Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition

Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract

Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology

Animal microbiome

Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports

Plant, root, and soil microbiome

Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology

Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports

Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology

Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography

Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology

Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science

Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science

Water and pollution microbiome

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences

Built environment microbiome

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology

Viruses and phages

Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology

Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters

Sequencing techniques

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ

Bioinformatics and metagenomics

Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ

Metabolomics

Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

More microbiology

Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE

Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports

Microbes in the news

Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News

Gut environment could reduce severity of malaria – EurekAlert

Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist

The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News

Plants trick bacteria into attacking too soon – Chris Samoray – Science News

Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine

Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire

Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert

Science, publishing, and career

Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews

I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science

Change the system to halt harassment – Joan Schmelz – Nature

Bik’s Picks

The peptidergic control circuit for sighing – Peng Li – Nature

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February 5, 2016

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Just a quick new Digest in the lunch break at the #GamingMetrics conference at UC Davis. Here is a Storify from Day 1 (yesterday) by Jonathan Eisen – more to follow soon.

Pregnancy and birth

Microbial transmission from mothers with obesity or diabetes to infants: an innovative opportunity to interrupt a vicious cycle – Taylor K. Soderborg – Diabetologia

Human urinary tract microbiome

16S rRNA gene-based metagenomic analysis reveals differences in bacteria-derived extracellular vesicles in the urine of pregnant and non-pregnant women – Jae Young Yoo – Experimental & Molecular Medicine

Human gut microbiome

Fungal microbiota dysbiosis in IBD – Harry Sokol – Gut

Animal models of microbiome research

Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model – Dorothee Tegtmeier – Applied and Environmental Microbiology

Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches – Aram Mikaelyan – Applied and Environmental Microbiology

Associations of microbiota and toll-like receptor signaling pathway in esophageal adenocarcinoma – Ali H. Zaidi – BMC Cancer

Comparison of fecal microbiota between German Holstein dairy cows with and without left-sided displacement of the abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Animal microbiome

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos – Felix Sommer – Cell Reports

Plant, root, and soil microbiome

Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India – Subramanya Rao – Indian Journal of Microbiology

Microbial communities play important roles in modulating paddy soil fertility
Xuesong Luo – Scientific Reports

Diversity of archaeal and bacterial communities on exfoliated sandstone from Portchester Castle (UK) – Elisabetta Zanardini – International Biodeterioration & Biodegradation

Distance from the sea as a driving force of microbial communities under water potential stresses in litters of two typical Mediterranean plant species – Anne Marie Farnet Da Silva – Geoderma

Opinion: Back to the future of soil metagenomics – Joseph Nesme – Frontiers in Microbiology

Waste and water treatment

Occurrence and enrichment of ‘bacterial sherpas’: climb to sustainability in wastewater treatment – M. Arnaldos – Water Science & Technology

Metagenomics

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs – Francy Jimenez-Infante – Applied and Environmental Micro

Microbial Ecology

Model-based media selection to minimize the cost of metabolic cooperation in microbial eco-systems – Mattia Zampieri – Bioinformatics

Microbes in the news

Savvy bacteria parents distribute damage unevenly among their children – Cara Giaimo – Atlas Obscura

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February 4, 2016

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A late digest today – Meetings and lab work kept me busy all day! Review about gut microbiota and malnutrition, Helicobacter infection affects local microbiome, salinity tolerance in corals, rhizosphere reviews, microbial mats in Shark Bay, and missing CRISPR regions in major bacterial lineages.

Jobs

Assistant, Associate or Senior Editor (Microbiology and Infectious Disease), Nature Communications, London, New York or Shanghai

Bioinformatics Scientist, Microbiome – Synthetic Genomics, Inc. – La Jolla CA

Pregnancy and birth
Routine Amoxicillin for Uncomplicated Severe Acute Malnutrition in Children – Sheila Isanaka – New England Journal of Medicine

Review: The case in favour of probiotics before, during and after pregnancy: insights from the first 1,500 days – G. Reid – Beneficial Microbes

Review: Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis – Timothy G. Elgin – Clinical Therapeutics

Human oral microbiome

Interesting choice of  journal: Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response – Vincent Blasco-Baque

Non-oral gram-negative facultative rods in chronic periodontitis microbiota – Arie J. van Winkelhoff – Microbial Pathogenesis

Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis – S. Bizzarro – Scientific Reports

Human respiratory microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome – Homer L Twigg III – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The emerging view of Firmicutes as key fibre degraders in the human gut – David Berry – Environmental Microbiology

Review: Gut Microbiota and Malnutrition – Matthieu Million – Microbial Pathogenesis

Review: Diet, Microbiota, And Dysbiosis: A ‘Recipe’ For Colorectal Cancer – Kishore Vipperla – Food & Function

Review: Microbiota, Immunity and the Liver – T. Vaikunthanathan – Immunology Letters

Animal and other models of microbiome research

Alterations of the Ileal and Colonic Mucosal Microbiota in Canine Chronic Enteropathies – Eric Cassmann – PLOS ONE

In a Neonatal Piglet Model of Intestinal Failure, Administration of Antibiotics and Lack of Enteral Nutrition Have a Greater Impact on Intestinal Microflora Than Surgical Resection Alone – Crystal L. Levesque – Journal of Parenteral & Enteral Nutrition

Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity – Anne L. Ballou – Frontiers in Veterinary Science

Gastric Helicobacter pylori Infection Affects Local and Distant Microbial Populations and Host Responses – Sabine Kienesberger – Cell Reports

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota – Rosanna Drumo – Frontiers in Cellular and Infection Microbiology

Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection – Qiuhong Niu – Scientific Reports

Chitosan lowers body weight through intestinal microbiota and reduces IL-17 expression via mTOR signalling – Dingfu Xiao – Journal of Functional Foods

The effect of agave fructan products on the activity and composition of the microbiota determined in a dynamic in vitro model of the human proximal large intestine – Marjorie E. Koenen – Journal of Functional Foods

Animal microbiome

Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome – Till Röthig – Molecular Ecology

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet – Wen Wang – Microbiology Open

Plant, root, and soil microbiome

Spatial Distribution of Fungal Communities in an Arable Soil – Julia Moll – PLOS ONE

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria – Paul C. A. Wintermans – Plant Molecular Biology

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition – Cheng Wang – Biotechnology for Biofuels

Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells – Carmen Vida – Frontiers in Microbiology

Editorial: How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities – Aurélie Deveau – Environmental Microbiology

Lots of reviews on the plant rhizosphere in Trends in Plant Science: 

Review: Impact of Bacterial–Fungal Interactions on the Colonization of the Endosphere – Leonard S. van Overbeek – Trends in Plant Science

Review: Signaling in the Rhizosphere – Vittorio Venturi – Trends in Plant Science

Review: Root–Root Interactions: Towards A Rhizosphere Framework – Liesje Mommer – Trends in Plant Science

Review: Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication – Nicole M. van Dam – Trends in Plant Science

Opinion: Mannitol in Plants, Fungi, and Plant–Fungal Interactions
Takshay K. Patel – Trends in Plant Science

Water and extremophile microbiome

Evolution of Chemical Characteristics of Technosols in an Afforested Coal Mine Dump over a 20-year Period – Ivana M. Rivas-Pérez – Land Degradation and Development

Microbial mats: New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia – E. P. Suosaari – Scientific Reports

Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China – Peike Gao – Scientific Reports

Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) – Christina Pavloudi – Marine Genomics

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Food microbiology

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species – Ignacio Belda – Frontiers in Microbiology

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness – Andrea Pitzschke – Frontiers in Microbiology

Viruses, phages, and CRISPRs

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems – David Burstein – Nature Communications

High-Throughput Isolation of Giant Viruses in Liquid Medium Using Automated Flow Cytometry and Fluorescence Staining – Jacques Y. B. Khalil – Frontiers in Microbiology

Review: Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems – Mart Krupovic – Current Opinion in Microbiology

Techniques

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

More microbiology

Elie Metchnikoff, the Man and the Myth – Gordon S. – Journal of Innate Immunology

Microbes in the news

What Your Low-Fiber Diet Does to Your Health – Mandy Oaklander – Time

Your beard doesn’t contain poop, but it could help develop new antibiotics – Sarah Kaplan – The Washington Post

Modern microbial ecosystems provide window to early life on Earth. UM Rosenstiel School-led team reveals new details on modern-day stromatolites – Science Daily

Two Santa Clara University Students Confirmed with Meningitis – ABC7

USDA Imposes Stricter Limit On Salmonella Bacteria In Poultry Products – NPR Morning Edition

Young scientists present intriguing and surprising research – Kristen Browning-Blas – Colorado State University

Meet the CEO of Europe’s Leading Microbiome Biotech, Pierre Belichard of Enterome – Labiotech

Podcast: As Arctic Permafrost Thaws, Microbes Kick Into Action – with Janet Jansson – Science Friday

Podcast: Bear Gut Microbes Help Prep Hibernation – Karen Hopkin – Scientific American

Podcast: The Good Side of Viruses – Medical Discovery News
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February 2, 2016

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Events

Note: website was working yesterday, but not this morning. I hope to fix this soon. SCDA Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis, Feb 25-26, New York

Pregnancy and birth microbiome

Not carefully worded, and not novel: New Insight into the Analysis of Amniotic Fluid Microflora using 16S rRNA Sequencing – Young-Ah You – JMM Case Reports

Human oral microbiome

Perspective: What Are We Learning and What Can We Learn from the Human Oral Microbiome Project? – Benjamin Cross – Current Oral Health Reports

Animal microbiome

Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium – Keren Ray – Microbial Ecology

Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows –
Jun-hua Liu – Microbial Biotechnology

Experimental exposure to trace metals affects plumage bacterial community in the feral pigeon – M. Chatelain – Journal of Avian Biology

Plant, root, and soil microbiome

Effects of biogas and raw slurries on grass growth and soil microbial indices – Stefanie Wentzel – Journal of Plant Nutrition and Soil Science

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression – Menno van der Voor – Ecology Letters

Impact of grassland management regimes on bacterial endophyte diversity differs with grass species – Franziska Wemheuer – Letters in Applied Microbiology

Novel soil fumigation method for suppressing cucumber Fusarium wilt disease associated with soil microflora alterations – Rong Li – Applied Soil Ecology

Water and extremophile microbiome

‘Candidatus Kryptonia’: Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs – Emiley A. Eloe-Fadrosh – Nature Communications

Novel Virophages Discovered in a Freshwater Lake in China – Chaowen Gong – Frontiers in Microbiology

Metagenomics and bioinformatics

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken) – Fabiola Valenzuela-González – Journal of Microbiological Methods

Opinion: From barcodes to genomes: extending the concept of DNA barcoding – Eric Coissac – Molecular Ecology

More microbes

Streptomyces thermoautotrophicus does not fix nitrogen – Drew MacKellar – Scientific Reports

Microbes in the news

How to (not) write a microbiome grant, Part I by David Baltrus

Does Having a C-Section Alter Baby’s First Microbiome? – Brian Handwerk – Smithsonian

Vaginal Microbes Can Be Partially Restored to C-Section Babies – Heather Buschman – UC San Diego Health

George Weinstock Discusses the Human Microbiome at Eastern – Michael Rouleau – Connecticut State University

‘Holy grail’ bacteria for crop farming debunked by scientists – Hayley Dunning – Imperial College London

Orange slime confirmed to be iron bacteria: Crenothrix polyspora – Herald Net

Iranian Researchers: Extraction of gold, copper from e-waste by two types of bacteria – The Iran Project

Microbes in an ancient mummy : We spoke to study author and microbiologist Dr Frank Maixner about the significance of this new research – MicrobePost
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February 1, 2016

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Vaginal microbiota transplant, temporal sampling of lung microbiota, skin microbiota of a cute frog, extreme CO2 exposure in soil, and microbial mats.

General human microbiome

Human Microbiota of the Argentine Population- A Pilot Study – Belén Carbonetto – Frontiers in Microbiology

Now officially published: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans – Ron Sender – Cell

Pregnancy and birth

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer – Maria G Dominguez-Bello – Nature Medicine

Chiba study of Mother and Children’s Health (C-MACH): cohort study with omics analyses – Kenichi Sakurai – BMJ Open

Human respiratory microbiome

Prevalence and antimicrobial susceptibility profiles of Staphylococcus aureus nasal carriage among pre-clinical and clinical medical students in a Tanzanian University
Benard Okamo – BMC Research Notes

A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus –
Yongfeng Hu – Journal of Clinical Virology

Human gut microbiome

Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis – Dmitry A. Ravcheev – Frontiers in Microbiology

Animal models of microbiome research

Research Highlight: Transgenerational missing taxa – Naomi Attar – Nature Reviews Microbiology

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Animal microbiome

Molecular evidence of vector-borne pathogens in dogs and cats and their ectoparasites in Algiers, Algeria – Amina Bessas – Comparative Immunology, Microbiology and Infectious Diseases

Manatees: Antifungal Resistance and Virulence Among Candida spp. from Captive Amazonian manatees and West Indian Manatees: Potential Impacts on Animal and Environmental Health – José Júlio Costa Sidrim – EcoHealth

Very cute frog: Assessing Antibacterial Potential of Components of Phyllomedusa distincta Skin and its Associated Dermal Microbiota – Ananda Brito de Assis – Journal of Chemical Ecology

Plant, root, and soil microbiome

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure – Felix Beulig – Nature Microbiology

Precipitation regime drives warming responses of microbial biomass and activity in temperate steppe soils – Weixing Liu- Biology and Fertility of Soils

The diversity of iron reducing bacteria communities in subtropical paddy soils of China – Qi-an Peng – Applied Soil Ecology

Water and extremophile microbiome

Editorial: Systems biology and ecology of microbial mat communities – Martin G. Klotz – Frontiers in Microbiology

Bioreactor microbiology

Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing – Claudia Etchebehere – Applied Microbiology and Biotechnology

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions – Man Jae Kwon – PLOS ONE

Performance and microbial community variations in thermophilic anaerobic digesters treating OTC medicated cow manure under different operational conditions – Çağrı Akyol – Bioresource Technology

More microbiology

Acanthamoeba and mimivirus interactions: the role of amoebal encystment and the expansion of the ‘Cheshire Cat’ theory – Ludmila Karen dos Santos Silva – Current Opinion in Microbiology

Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome – Rohan Maddamsetti – Mobile Genetic Elements

Microbes in the news

The Bacterium Disappearing From Our Stomachs – H. pylori is losing its foothold – Chau Tu – Science Friday

The Mycobiome: The largely overlooked resident fungal community plays a critical role in human health and disease – Mahmoud Ghannoum – The Scientist

Opportunities for Nanoscience and Nanotechnology in Studying Microbiomes – Paul S Weiss – ACS Nano

“Seeding” The Newborn’s Microbiome – Can We Do It? Should We Be Doing It? – Anne M. Estes – Science & Sensibility

Icy Worlds and their Analog Sites.Fieldwork on Earth provides insight into life’s potential on icy bodies – Keith Cooper – NASA Astrobiology

Bilingual Exhibition Explores the Human Microbiome – Alexandra Mendoza – La Prensa San Diego

Stalin May Have Studied Mao’s Poop in a Secret Lab – Erin Blakemore – Smithsonian

Mapping the Mouth Microbiome – GenEngNews

CosmosID raises $6M to advance microbiome bioinformatics offering – Nick Paul Taylor – Fierce BiotechIt

Science, publishing, and career

The Scientific 23 with Ed Yong: “Science takes us… to the entire natural world, to space, to molecules – things related to humans but not about us.”

How quality control could save your science. It may not be sexy, but quality assurance is becoming a crucial part of lab life – Monya Baker – Nature
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January 27, 2016 – second edition

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A call from the White House, synergy between Mycoplasma and Gardnerella, urinary microbiome, sarcoidosis, and a hiking guide to microbes on the seafloor.

Events

The White House wants feedback from “All Microbiome-Science Champions” – give it – give it now – Jonathan Eisen – MicroBEnet
and
Calling All Microbiome-Science Champions! – Jo Handelsman and Elizabeth Stulberg – The White House

General human microbiome

Review: Exploring and Understanding the Biochemical Diversity of the Human Microbiota – Nitzan Koppel – Cell Chemical Biology

Pregnancy and birth

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content – Zachery T. Lewis – PeerJ

The common vaginal commensal bacterium Ureaplasma parvum is associated with chorioamnionitis in extreme preterm labour – Ciara Cox – The Journal of Maternal-Fetal & Neonatal Medicine

Human vaginal microbiome

Mycoplasma hominis and Gardnerella vaginalis display a significant synergistic relationship in bacterial vaginosis – C. Cox – European Journal of Clinical Microbiology & Infectious Diseases
Human oral microbiome

The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology – Mohsen Sohrabi – Journal of Microbiological Methods

Human skin microbiome

Note: 1 person per study group: Skin microbiota of first cousins affected by psoriasis and atopic dermatitis – Lorenzo Drago – Clinical and Molecular Allergy

Human urinary tract microbiome

Review: The human urinary microbiome and how it relates to urogynecology – Jenifer Schneeweiss – International Urogynecology Journal

Human gut microbiome

Metabolomics connects aberrant bioenergetic, transmethylation, and gut microbiota in sarcoidosis – Andreea Geamanu – Metabolomics

Review: Role of antibiotics for treatment of inflammatory bowel disease – Orna Nitzan – World Journal of Gastroenterology

Review: Gut microbiota imbalance and colorectal cancer – Johan Gagnière – World Journal of Gastroenterology

Animal models

In mice: A detrimental role of immunosuppressive drug, dexamethasone, during Clostridium difficile infection in association with a gastrointestinal microbial shift – Hyeun Bum Kim – Journal of Microbiology and Biotechnology

Animal microbiome

Diversity of the gastric microbiota in Thoroughbred racehorses having gastric ulcer – Hee-Jin Dong – Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest – Ju-pei Shen – Scientific Reports

Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies – Wiebke Sickel – Microbial Ecology

Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia – Yuji Jiang – Soil Biology and Biochemistry

Emergence in mapping microbial diversity in tea (Camellia sinensis (L.) O. Kuntze) soil of Assam, North-East India: A novel approach – PN Bhattacharyya – European Journal of Biotechnology and Bioscience

High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea – Shuai Zhao – Current Microbiology

Water and waste microbiome

Use of matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant – Laura Sala-Comorera – International Journal of Hygiene and Environmental Health

Extremophile microbiome

The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation – Andreas Teske – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities – Boyu Ren – ArXiv

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets – Jai Ram Rideout – PeerJ Preprint

Characterization of sequence-specific errors in various next-generation sequencing systems – Sunguk Shin – Molecular Biosystems

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data – Claudia Sala – BMC Bioinformatics

Protocol: “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities – Lejla Pašić – Microbial Environmental Genomics (MEG)

Protocol: Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler – Microbial Environmental Genomics (MEG)

Science, publishing, and career

Funding: What stops women getting more grants? – David McAllister – Nature

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