May 18, 2016

Live blogging from the Michigan Microbial Meeting, microbiomes of Tibetan macaques and Pika, climate gases from SAR11, mycobiome of stored peanuts, and the deep biosphere.

Events

Ongoing now, with live written coverage: Michigan Meeting ““Unseen Partners: Manipulating Microbial Communities that Support Life on Earth.”

Bioinformatics for the Microbiome Symposium – Stanford Medicine – Friday May 27, 2016

Symposium: With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology – Jan 4-8 2017, New Orleans

General microbiome

Microbiome Data Science: Understanding Our Microbial Planet – Nikos C. Kyrpides – Trends in Microbiology

Animal experiments

Antiviral effect of vitamin A on norovirus infection via modulation of the gut microbiome
Heetae Lee – Scientific Reports

A single gene of a commensal microbe affects host susceptibility to enteric infection – Mi Young Yoon – Nature Communications

Conference abstract: The Impact of Dietary Soy on Gut Microbiome – India R Gill – The FASEB Journal

Animal microbiome

Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana) – Binghua Sun – Scientific Reports

Pika population density is associated with composition and diversity of gut microbiota – Huan Li – Frontiers in Microbiology

Review: The bovine milk microbiota: insights and perspectives from -omics studies – Mol Biosyst

Plant, root, and soil microbiome

Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale – Haichuan Cao – Scientific Reports

Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe – Joseph R. Jenkins – GCB Bioenergy

Biochar as a novel niche for culturing microbial communities in composting – Daquan Sun – Waste Management

Review: Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions –
Hezi Tenenboim – Trends in Plant Science

Temperature sensitivity of soil microbial communities: an application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Biogeosciences

Water and extremophile microbiome

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol – Jing Sun – Nature Microbiology

News coverage:
Story behind the paper: Climate gases from SAR11 – Stephen Giovannoni – Nature Microbiology Community Blog
Tiny organisms have huge effect on world’s atmosphere – Science Daily

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Depth-dependent and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific – Ryo Kaneko – Journal of Oceanography

Exploring the interaction patterns among taxa and environments from marine metagenomic data – Ze-Gang Wei – Quantitative Biology

Review: Analysis of Low-Biomass Microbial Communities in the Deep Biosphere – Y. Morono – Advances in Applied Microbiology

Undergraduate thesis: Oases of Microbial Life in the Highest Elevation Fumaroles on Earth – Adam Solon – University of Colorado-Boulder

Food microbiology

Variation in fungal microbiome (mycobiome) and aflatoxins during simulated storage of in-shell peanuts and peanut kernels – Fuguo Xing – Scientific Reports

Microbiology of death

Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates – Miguel Iniesto – Scientific Reports

Pollution and waste microbiology

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond – Enzong Xiao – Environmental Pollution

pH modulates arsenic toxicity in Bacillus licheniformis DAS-2 – K. Tripti – Ecotoxicology and Environmental Safety

News coverage: Bacteria discovered to remove arsenic from soil – BK Mishral – Times of India

More microbiology

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice – Stefan O. Reber – PNAS

News coverage: Immunization with bacteria promotes stress resilience, coping behaviors in mice, CU-Boulder study finds – University of Colorado Boulder

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation – Sudip Das – PNAS

Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population – Saurabh R. Gandhi – PNAS

Microbes and art

Creating art with bacteria at New England Biolabs – Jennie Oemig – Wicked Local Beverly

Microbes in the news

Interviewing the Founder of the World #1 Microbiome Investment fund: Isabelle De Cremoux – Labiotech

How Soil Microbes Fight Climate Change – They’re our microscopic allies in making dirt a major resource for storing excess carbon – Esther Ngumbi – Scientific American

Everything You Need to Know About Obama’s New Microbiome Initiative – Tiny organisms. Big budgets. – Kastalia Medrano – Inverse

Welcome To FiveThirtyEight’s Gut Science Week – Maggie Koerth-Baker – Five Thirty Eight
What Your Poop Says About You – Christine Laskowski – Five Thirty Eight

FAQ on Microbiology of Built Environments from the American Academy of Microbiology – Jonathan Eisen – MicroBEnet

At A Texas Body Farm, Studying The Decay Of Donated Corpses – Kai Kupferschmidt – World Crunch

Children with and without multiple sclerosis have differences in gut bacteria – EurekAlert

Bathroom Reader: A Brief History of the Toilet – Zack Fediay – uBiome Blog

Linfield Wine Lecture Series: Managing Expectations: The Microbiome in Agriculture – Jack Gilbert – Linfield College

Science, publishing, and career

Point of View: Avoiding a lost generation of scientists – Justin Q Taylor – eLIFE

Twitter won’t count links and photos as part of your 140 characters – Dave Gershgorn – PopSci

Bruno Lemaitre on Science and Narcissism – Leonid Schneider – For Better Science

Screen Shot 2016-05-17 at 10.58AM, May 17.jpg

Illustration by Leonid Schneider

May 12, 2016

Posted on May 12, 2016 by eliesbik

Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 11, 2016

Posted on May 11, 2016 by eliesbik

Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

May 10, 2016

Posted on May 10, 2016 by eliesbik

A very selective antibiotic that does not disturb the microbiota, metabolic pathways of the Deepwater Horizon spill, and GI microbiome role in acute myeloid leukemia.

Jobs and events

Postdoc funding opportunity “Microbiology of the built environment”, Alfred P. Sloan Foundation

The 4th Microbiome R&D and Business Collaboration Forum: USA – 3-4 October 2016, La Jolla, San Diego, USA

Human gut microbiome

The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Animal experiments

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model – Philipp Dirksen – BMC Biology

Editorial: Caenorhabditis microbiota: worm guts get populated – Laura C. Clark – BMC Biology

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome – Jiangwei Yao – Antimicrobial Agents and Chemotherapy

Waste, pollution, and water treatment microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states – I.B. Gomes – Science of the Total Environment

Microbes in the news

Gut Microbiome Startup CeMeT Aims to Build Reference Database from 10K Volunteers in Germany – Julia Karow – Genome Web

Microbiome linked to infectious complications in AML – Medical Xpress

Narrow-Spectrum Antibiotic Could Spare the Microbiome. A drug that singles out Staphylococcus aureus leaves gut-dwelling microbiota largely intact, a mouse study shows – Amanda B. Keener – The Scientist

Genetic potential of oil-eating bacteria from the BP oil spill decoded – University of Texas at Austin

Fooling the test: Antibiotic-resistant bacteria that look susceptible – Phys.org

A new industry that uses bacteria to remediate old mines? – Jonathan Migneault – Sudbury

The Mighty Microbes of Yellowstone – Scalding water is home to what microbiologists call extremophiles, heat-loving creatures that have figured in many scientific breakthroughs – David Quammen – National Geographic

Science, publishing, and career

John Oliver exposes how the media turns scientific studies into “morning show gossip”
– German Lopez – Vox

Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action – Elizabeth A. Silva – PLOS Biology

With quotes from me: Image manipulation in biomedical papers is commonplace – Maria Burke – Chemistry World

Open-access index delists thousands of journals. Many publications did not reapply after leading directory tightened its quality criteria – Monya Baker

May 4, 2016

Posted on May 4, 2016 by eliesbik

Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectiou s complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology

Bioinformatics

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research

Techniques

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review

May 1, 2016

Posted on May 1, 2016 by eliesbik

Events

Bioinformatics for the Microbiome – Stanford Center for Genomics and Personalized Medicine – May 27, 2016

General microbiome

Microbiome sequencing: challenges and opportunities for molecular medicine – Thomas Clavel – Expert Review of Molecular Diagnostics

Human skin microbiome

An In vitro Model for Bacterial Growth on Human Stratum Corneum – Danique A. van der Krieken – Acta Dermato-Venereologica

Human respiratory microbiome

Launching into the Deep: Does the Pulmonary Microbiota Promote Chronic Lung Inflammation and Chronic Obstructive Pulmonary Disease Pathogenesis? – Marc A. Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Targeting the gut to protect the bladder: Oral Phage therapy approaches against urinary Escherichia coli infections? – Harald Brüssow – Environmental Microbiology

Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease – Takuo Emoto – Heart and Vessels

Review: Gut microbiota: an Indicator to Gastrointestinal Tract Diseases – Trupti Patel – Journal of Gastrointestinal Cancer

Review: Gut microbiome and kidney disease: a bidirectional relationship – Souhaila Al Khodor – Pediatric Nephrology

Animal models

Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice – Jin Li – Circulation

The effects of maternal and post-weaning diet on gut microbiota and glucose metabolism in mice offspring – Jia Zheng – Bioscience Reports

Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota – Brittany E. Harlow – PLOS ONE

Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows – Marija Kaevska – Canadian Journal of Microbiology

Molecular exploration of fecal microbiome in quinoa-supplemented obese mice – Jose F. Garcia-Mazcorro – FEMS Microbiology Ecology

Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice – Lovisa Heyman-Lindén – Food and Nutrition Research

The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems – Victor Schmidt – Applied and Environmental Microbiology

Insights into the biodiversity of the gut microbiota of broiler chickens – Leonardo Mancabelli – Environmental Microbiology

Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups – Wilma T. Steegenga – Molecular Nutrition & Food Research

Animal microbiome

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan- Environmental Microbiology

Global microbialization of coral reefs – Andreas F. Haas – Nature Microbiology

Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria – Jan Hubert – Microbial Ecology

Review: Diagnosis and interpretation of intestinal dysbiosis in dogs and cats – Jan Suchodolski – The Veterinary Journal

Plant, root, and soil microbiome

Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea – Margrét Auður Sigurbjörnsdóttir – FEMS Microbiology Ecology

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites – Frederic Mahe – bioRxiv

Edaphic properties override the influence of crops on the composition of the soil bacterial community in a semiarid agroecosystem – Luke D. Bainard – Applied Soil Ecology

Effects of land use change on the composition of soil microbial communities in a managed subtropical forest – Xiaoping Guo – Forest Ecology and Management

Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach – Nathaniel A. Lyngwi – PLOS ONE

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems – Ian R Sanders – The ISME Journal

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter – Thea Whitman – The ISME Journal

Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa – I. Moroenyane – Microbial Ecology

Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance – Cécile E. Thion – FEMS Microbiology Ecology

Ecological restoration alters microbial communities in mine tailings profiles – Yang Li – Scientific Reports

Water and extremophile microbiome

Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton – Mathias Milici – Frontiers in Microbiology

Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench – Jonathan Tarn – Frontiers in Microbiology

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? – Mario Moreno-Pino – FEMS Microbiology Ecology

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring – Zhou Jiang – Scientific Reports

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – J. Goordial – Environmental Microbiology

Built environment microbiome

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Food microbiology

Overlap of spoilage microbiota between meat and meat processing environment in small-scale vs large-scale retail distribution – Giuseppina Stellato – Applied and Environmental Microbiology

Fermentative capabilities and volatile compounds produced by Kloeckera/Hanseniaspora and Saccharomyces yeast strains in pure and mixed cultures during Agave tequilana juice fermentation – Ivonne Wendolyne González-Robles – Antonie van Leeuwenhoek

Pollution and waste microbiology

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater – Scientific Reports – You-Wei Cui

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.– Alejandro Palomo – The ISME Journal

Bioinformatics and metagenomics

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2 – Johan Bengtsson-Palme – Ecological Informatics

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data – Mohamed Mysara – BMC Bioinformatics

Minireview: Tracking strains in the microbiome: insights from metagenomics and models – Ilana L. Brito – Frontiers in Microbiology

Viruses and phages

Review: Endogenized viral sequences in mammals – Nicholas F. Parrish – Current Opinion in Microbiology

Probiotics

Probiotic Cream: Viability of Probiotic Bacteria and Chemical Characterization – Lutfiye Yilmaz-Ersan – Journal of Food Processing and Preservation

Transcriptomics

Use of Metatranscriptomics in Microbiome Research – Stavros Bashiardes – Bioinform Biol Insights

More microbiology

Complex molecular mixtures under cycling gradients as basis for lifes origins – Bert Poolman – bioRxiv

Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ – Laura Villanueva – Environmental Microbiology

Review: Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits – Kai Hillman – Current Opinion in Microbiology

Microbes in the news

Findings from the Gut—New Insights into the Human Microbiome – Karen Weintraub – Scientific American

What our gut tells us about the ‘hygiene hypothesis’ – Veronica Meade-Kelly – MedicalXpress

Russian scientists prove Antarctic bacteria brought from other continents – TASS

Beer made from belly button fluff has a bit of the brewer in every glass – Jenni Ryal – Mashable @7centBrewery

Yep, This Brewery Makes Beer Using Bacteria From People’s Belly Buttons: “7 cent Brewery” – Alec MacDonald – Elite Daily

Bacteria from Burning Tree mastodon survived 13,000 years – Laura Arenschield – Dispatch

Echo Bay woman caught harvesting bacteria at gardening event – Jeff Klassen – Soo Today

Weakened coral reefs are facing the threat of algae colonisation – Kemal Atlay – SBS Australia

Junk Food Is Bad For Plants, Too – How a steady diet of fertilizers has turned crops into couch potatoes – Anne Biklé and David R. Montgomery – Nautilus

From running shoes to carbon sinks: four surprising uses for algae – ABC Future Tense

Science, publishing, and career

“Everyone” Downloads Research Papers Illegally – Science magazine just published a great piece on the utility of Sci-Hub. Unfortunately, its defense of its own business model is flawed – Justin Peters – Slate

April 29, 2016

Posted on April 29, 2016 by eliesbik

After Science’s Microbiome Issue yesterday, today’s digest features Genome Biology’s special Translational Microbiome issue. Papers on detecting colon cancer, Clostridium difficile infection, high-fat diets in mice. Also check out papers on H2 metabolism in the colon, no effects of temperature rise on soil microbiome of wet tropical forests, and ultra-basic springs.

Jobs and events

Nice speaker line-up: May 16-18, Michigan Meeting on Microbial Communities: a deep dive into the world of microbes – University of Michigan

Job opening in our lab: Life Science Research Professional – Stanford

Pregnancy and birth

Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study – Jason P. Bentley – BMC Pediatrics

Human gut microbiome

Special issue Genome Medicine: Translating the microbiome: health and disease, Guest Editor: Curtis Huttenhower

Editorial: A roadmap to translating the microbiome – Rabia Begum – Genome Medicine

Detecting colon cancer using microbiota: Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions – Nielson T. Baxter – Genome Medicine

Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection – Anna Maria Seekatz – Genome Medicine

Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children – Heidi Andersen – Journal of Clinical Microbiology

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection – Emmanuel Montassier – Genome Medicine

Impact of Helminth Infection on the Clinical and Microbiological Presentation of Chagas Diseases in Chronically Infected Patients – Fernando Salvador – PLOS Neglected Tropical Diseases

Malaria, helminths and malnutrition: a cross-sectional survey of school children in the South-Tongu district of Ghana – Patrick Ferdinand Ayeh-Kumi – BMC Research Notes

Review: The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan – Clinical Psychopharmacology and Neuroscience

Review: Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology – Mukesh Verma – Technology in Cancer Research & Treatment

Animal models
Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows – Jitka Kasparovska – PLOS ONE

Deep-fried oil consumption in rats impairs glycerolipid metabolism, gut histology and microbiota structure – Zhongkai Zhou – Lipids in Health and Disease

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations – Gabriella Cobellis – Journal of Animal Science and Biotechnology

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems – Raul Franzolin – BMC Research Notes

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet – Douglas Mahana – Genome Medicine

A fish, not the bird: Combined effects of dietary mannan- and fructo-oligosaccharide on growth indices, body composition, intestinal bacterial flora and digestive enzymes activity of regal peacock (Aulonocara stuartgranti) – S. S. Mirzapour-Rezaee – Aquaculture Nutrition

Plant, root, and soil microbiome

The composition, localization and function of low-temperature adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils – Yumei Dai – Journal of Applied Microbiology

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce – Jian-Gang Li – Scientific Reports

Pichia kudriavzevii as a representative yeast of North Patagonian winemaking terroir – Silvana M. del Mónaco – International Journal of Food Microbiology

Increases in mean annual temperature do not alter soil bacterial community structure in tropical montane wet forests – Paul C. Selmants – Ecosphere

Water and extremophile microbiome

A role for fungi as parasites in the black box of marine trophic interactions – Thomas A. Richards – Environmental Microbiology Reports

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis – Lukas Kohl – Journal of Geophysical Research

Viruses and phages

Minireview: Virus-host interplay in high salt environments – Nina S. Atanasova – Environmental Microbiology Reports

Metagenomics and bioinformatics

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques – Disha Tandon – PLOS ONE

Metabolomics

H2 metabolism is widespread and diverse among human colonic microbes – Patricia G. Wolf – Gut Microbes

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) – Katherine Louie – bioRxiv

Viruses and phages

The virome: a missing component of biological interaction networks in health and disease – Scott A. Handley – Genome Medicine

Microbial ecology

Commentary: Bacteriophages or bacteriovores – that is the question: variations on the theme of eating Stenotrophomonas maltophilia – Harald Brüssow – Environmental Microbiology Reports

Microbes in the news

Lots of press coverage for the Science and Genome Medicine special issues today!

Scientists think they’ve found the secret to better poop transplants – Rachel Feltman – The Washington Post

Why Are Your Gut Microbes Different From Mine? To find out, scientists collected poop from thousands of people—but they ended up with more questions than answers – Ed Yong – The Atlantic

Food you eat and medicines you take can alter your gut bacteria in both good and bad ways – Emma Tiller – NH Voice

Special microbiome issue – Science Codex

Gut Microbiome Makeup Influenced by Medication Use, Other Factors – Genome Web

In Dutch: Zijn koffie, rode wijn en chocola nou wel of niet goed voor je? – Sander Voormolen – NRC

Title fail: World’s first microbiome study reveals links between lifestyle and gut flora – EurekAlert

Lifestyle has a strong impact on intestinal bacteria – Medical Xpress

The “Friendly” Bacteria In Your Gut Isn’t As Set At Birth As We Thought – Tom Chivers – BuzzFeed

Gut bacteria may predict risk of life-threatening infections following chemotherapy – Science Daily

What Can Happen When You’re Way Too Clean – Alice Park – Time

10 Bizarre (and Wonderful) Facts About Microbes:truly amazing facts about the human microbiome – Dawn Field – TopTenz

Vancouver couple develops slime-free water dishes for dogs – Eric MacKenzie – Vancouver 24h

Podcast: Microbe Talk, April 2016, Can parasitic worms treat inflammatory diseases?

Some superbugs literally explode when they die, making them even more deadly
Ticking time bomb – Jacinta Bowler – Science Alert

Science, publishing, and career

Unconditional data sharing, plus peer review transparency, is key to research reproducibility – Leonid Schneider – The Winnower

Featuring our paper: Seeing double: Duplicated images plague research papers – Ivan Oransky and Adam Marcus – STAT News

Paper linking fecal transplants to obesity in rats retracted for faked data – Dalmeet Singh Chawla – Retraction Watch

April 28, 2016

Posted on April 28, 2016 by eliesbik

A special issue of Science with 2 papers on lifestyle factors that determine composition of the stool microbiome in large human cohorts, variation in microbiome LPS immunogenicity contributes to autoimmunity, SEM analysis of cave speleothem microbial communities, and saliva bacteria in Chicha (Ecuadorian beer).

Jobs and Events

Early Career Microbiome Meal, during European Respiratory Society Meeting 2016 London, September 2016

Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio – Greg Caporaso – MicroBEnet

General microbiome

A special Science Issue called The Microbiota At Work:

Introduction: Manipulating the Microbiota – Caroline Ash, Kristen Mueller – Science

Review: Cross-species comparisons of host genetic associations with the microbiome – Julia K. Goodrich – Science

Review: How colonization by microbiota in early life shapes the immune system – Thomas Gensollen – Science

Review: Antibiotic use and its consequences for the normal microbiome – Martin J. Blaser – Science

Review: The healthy human microbiome – Jason Lloyd-Price – Genome Medicine

Pregnancy and birth

Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants – T. Matsuki – Beneficial Microbes

Human oral microbiome

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

Human respiratory microbiome

[PDF] The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Human reproductive tract microbiome

[PDF] Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps – Rui-Li Fang – Am J Transl Res

Opinion: Cervicovaginal Microbiomes–Threats and Possibilities – Gregor Reid – Trends in Endocrinology & Metabolism

Review: Foodomics as part of the host-microbiota-exposome interplay – Lorenza Putignani – Journal of Proteomics

Human gut microbiome

Population-level analysis of gut microbiome variation – Gwen Falony – Science

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science

Durable coexistence of donor and recipient strains after fecal microbiota transplantation – Simone S. Li – Science

Review: Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens – Eric G. Pamer – Science

Associations between dietary flavonoid intake and gut microbiota in a group of adults with cystic fibrosis (CF) – L. Li – Journal of Nutrition & Intermediary Metabolism

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans – Tommi Vatanen – Cell

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals – Sergio Serrano-Villar – EBioMedicine

Serologic microbial associated markers can predict Crohn’s disease behaviour years before disease diagnosis – R. S. Choung – Alimentary Pharmacology & Therapeutics

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review: Human gut microbiota and healthy aging: Recent developments and future prospective – Manish Kumar – Nutrition an Healthy Aging

Animal and other models

Soluble and Insoluble Fiber Differentially Impact Canine Fecal Microbiome and Circulating Metabolome – Matthew Irick Jackson – The FASEB Journal

Germ-free and antibiotic-treated mice are highly susceptible to epithelial injury in DSS colitis – Cristina Hernández-Chirlaque – Journal of Crohn’s and Colitis

High intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity – Emmanuel Denou – American Journal of Physiology

Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium – Joshua C. Mccann – Frontiers in Microbiology

Review: Oral microbial biofilm models and their application to the testing of anticariogenic agents – Christina P.C. Sim – Journal of Dentistry

Animal microbiome

Patterns of bacteria-host associations suggest different ecological strategies between two reef building cold-water coral species – Anne-Leila Meistertzheim – Deep Sea Research Part I: Oceanographic Research Papers

Plant, root, and soil microbiome

Characterizing and handling different kinds of AM fungal spores in the rhizosphere – Xueguang Sun – World Journal of Microbiology and Biotechnology

Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field – Qianhan Shang – World Journal of Microbiology and Biotechnology

Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils – Xi-En Long – Environmental Science and Pollution Research

The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur) – S. Meaden – Environmental Microbiology Reports

Universal indicators for oil and gas prospecting based on bacterial communities shaped by light-hydrocarbon microseepage in China – Chunping Deng – Journal of Microbiology and Biotechnology

Performance of 16s rRNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies – Bram Beckers – Frontiers in Microbiology

Water and extremophiles

The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum – Fatima Foflonker – Algal Research

Microbial communities in a range of carbon dioxide fluxes from a natural volcanic vent in Campo de Calatrava, Spain – Irena Fernández-Montiel – International Journal of Greenhouse Gas Control

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats – Igor Stelmach Pessi – Journal of Phycology

Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean – Andreas Krupke – Frontier in Marine Science

Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment – Yung Mi Lee – Korean Journal of MIcrobiology

Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave – Cohord Mason – The Journal of Experimental Microbiology & Immunology

Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes – Gaston E. Small – Biogeochemistry

Built environment microbiome

Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air

Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Food microbiology

Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha) – Ana L. Freire – PeerJ

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics and metagenomics

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design – Christoph Mayer – Molecular Biology and Evolution

Microbial ecology

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship – Jonas Schluter – PLOS Computational Biology

Co-existence facilitates interspecific biofilm formation in complex microbial communities – Jonas S Madsen – Environmental Microbiology

Viruses and phages

Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints – W. C. Wilson – Virus Genes

Techniques

[Video Protocol] Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – Journal of Visualized Experiments

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Microbes in the news

Your gut bacteria are more than what you eat – Elizabeth Pennisi – Science

With quotes from me! New research confirms thriving gut bacteria is linked to a healthier body – Russell Brandom – The Verge

Want more good bugs in your gut? Try yogurt. And coffee – Patrick Skerrett – STAT News

This Bacteria Strain Offers a Curious Mix of Hope and Danger. The Elizabethkingia strain could cure malaria, but it’s also sickened dozens in Wisconsin – Lisa Margonelli – Slate

Bacteria beneficial to plants have spread across California – UC Riverside study shows spread of Bradyrhizobium has important implications for biofertilizers – EurekAlert

The Benefits of Slathering Your Newborn Baby with Vaginal Bacteria – Rebecca Schiller – Vice Broadly

A Timely Gut Check. At the American Museum of Natural History, meet your microbiome – Ralph Gardner – The Wall Street Journal

A Comprehensive Survey of Pre-Clinical Microbiology Curricula Among United States Medical Schools – Dora Melber – Clinical Infectious Diseases

Mayo Clinic Ventures Firm Explores Commercialization Of Gut Microbe Treatment – Don Jacobson – Twin City Business

Microbes and art

Quilting with soil: soil microorganisms had “painted” their efforts on the cloth in an unexpected variety of colors. – Martha Pings – Soils

Science, publishing, and career

Is most published research really false? – Jeffrey T Leek, Leah R Jager – bioRxiv

Who’s downloading pirated papers? Everyone. In rich and poor countries, researchers turn to the Sci-Hub website – John Bohannon – Science

The frustrated science student behind Sci-Hub – John Bohannon – Science

Plagiarism: A worm poking holes into the quality of our academic work – Christine Osae – The New Times

Bik’s Picks
Doctor ready to perform first human head transplant – Ross Kenneth Urken – News Week

April 27, 2016

Posted on April 27, 2016 by eliesbik

Cervical microbiome during cancer, distinct gut microbiome in kidney stone formers? (unclear due to vaguely formulated control group), culturing marine microbes in artificial seawater, codon usage to predict pathogenicity.

Events

Science Diplomats to present ‘Trust Your Gut: How Helpful Bacteria Impact Health’ – Free talk given 3 times at Yale in May

Pregnancy and birth

News & Views: Immunology: Mum’s microbes boost baby’s immunity – Mihir Pendse & Lora V. Hooper – Nature

Human respiratory microbiome

Culture based: Microbiology of peritonsillar abscess in the South Estonian population – Risto Vaikjärv – Microbial Ecology in Health and Disease

Human reproductive tract microbiome

Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study – Astride Audirac-Chalifour – PLOS ONE

Human gut microbiome

Note that the control group is poorly described: Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers – Joshua M. Stern – Urolithiasis

Review: Macrobiota — helminths as active participants and partners of the microbiota in host intestinal homeostasis – William C Gause – Current Opinion in Microbiology

Review: The possible mechanisms of the human microbiome in allergic diseases – Kagan Ipci – European Archives of Oto-Rhino-Laryngology

Review: Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Animal and bioreactor models

Biochar, Bentonite and Zeolite Supplemented Feeding of Layer Chickens Alters Intestinal Microbiota and Reduces Campylobacter Load – Tanka P. Prasai – PLOS ONE

Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state – Jutta Speda – Applied Microbiology and Biotechnology

A humanized microbiota mouse model of ovalbumin-induced lung inflammation – Marie-Claire Arrieta – Gut Microbes

Plant, root, and soil microbiome

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ Preprint

Water and extremophile microbiome

Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico – Michael W. Henson – mSphere

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes – Jian Yang – Scientific Reports

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations – Alexander J. Probst – Environmental Microbiology

Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes – J.M. Cook – Environmental Microbiology

Pollution and waste microbiology

Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency – Yang Zhang – Water Science & Technology

A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing – Lei Li – Microbial Cell Factories

Microbial ecology

Inhibitory interactions promote frequent bistability among competing bacteria –
Erik S. Wright – Nature Communications

Bioinformatics and metagenomics

Protocol: Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijani – Data Mining Techniques for the Life Sciences

Review: High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved – Dmitrij Turaev – Current Opinion in Biotechnology

Microbes in the news

Elizabethkingia: The bacteria strain that could kill you. Or cure malaria. Small Science: Genomic data is showing us how little we know – Lisa Margonelli – Houston Chronicle

New Anti-Biofilm Nano Coating Prevents Bacterial Growth on Metal Surfaces – Azo Nano

Quick mapping of our microbiomes and metabolomes – Science Daily

Viral Skin Infections – Tomislav Meštrović – News Medical

Bacteria pill is ‘better than statins’ in the war on cholesterol, say researchers – Joe Smith – Mirror UK

Bacterial virulence is stimulated by burns – EurekAlert

Science, publishing, and career

Meet The New CEO Of The $22 Billion Genomics Company You’ve Never Heard Of: Francis deSouza to lead Illumina – Christina Farr – Fast Company

What Happened When I Pushed Myself to Interview More Women: Increasing the breadth of sources in journalism – John R. Platt – Motherboard

The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life. The microbiologist spent years moving labs and relishing solitude. Then her work on gene-editing thrust her into the scientific spotlight – Alison Abbott – Nature

Speak up about subtle sexism in science: Female scientists face everyday, often-unintentional microaggression in the workplace, and it won’t stop unless we talk about it – Tricia Serio – Nature

Bik’s Picks

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station – Masahiro Terada – PLOS ONE

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Science – Career – Publishing

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