Category Archives: Metagenomics & Bioinformatics

April 29, 2016

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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

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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: Screen Shot 2016-04-28 at 12.42PM, Apr 28 1.jpg

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

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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

April 26, 2016

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Gut microbiome in preterm infants, the bee microbiome, monitoring of surfaces in the ISS, and a database-independent approach to OTU picking.

Jobs and events

Assistant/Associate Professor in Microbiome Studies – University of Arizona

I am one of the judges! 2016 MoBio Microbiome Awards – Deadline May 31

General microbiome

Comment: A multi-omic future for microbiome studies – Janet K. Jansson – Nature Microbiology

Pregnancy and birth

Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender – Xiaomei Cong – PLOS ONE

Human oral microbiome

Microbiota-based Signature of Gingivitis Treatments: A Randomized Study – Shi Huang – Scientific Reports

Complementary clinical effects of red complex bacteria on generalized periodontitis in a caucasian population – E Lanza – Oral Diseases

Human blood ‘microbiome’

(also stool microbiome) Alteration of the serum microbiome composition in cirrhotic patients with ascites – Alba Santiago – Scientific Reports

Human gut microbiome

Lactobacillus rhamnosus GG Intake Modifies Preschool Children’s Intestinal Microbiota, Alleviates Penicillin-Associated Changes, and Reduces Antibiotic Use – Katri Korpela – PLOS ONE

Fecal Microbiota Transplantation Using Upper Gastrointestinal Tract for the Treatment of Refractory or Severe Complicated Clostridium difficile Infection in Elderly Patients in Poor Medical Condition: The First Study in an Asian Country – Tae-Geun Gweon – Gastroenterology Research and Practice

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman – Molecular Metabolism

Review: Mediterranean diet and faecal microbiota: a transversal study – Isabel Gutiérrez-Díaz – Food & Function

Editorial to a special Issue: Gut Microbiota and Metagenomic Advancement in Digestive Disease – Jinsheng Yu – Gastroenterology Research and Practice

Review: Efficacy and Mechanisms of Action of Fecal Microbiota Transplantation in Ulcerative Colitis: Pitfalls and Promises From a First Meta-Analysis – F. Scaldaferri – Transplantation Proceedings

Animal and other models

Sex steroid deficiency–associated bone loss is microbiota dependent and prevented by probiotics – Jau-Yi Li – the Journal of Clinical Investigation

Commentary: From the gut to the strut: where inflammation reigns, bone abstains – Jameel Iqbal – The Journal of Clinical Investigation

Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice – Peris Mumbi Munyaka – Journal of Basic Microbiology

Effects of low-level dietary microalgae supplementation on the distal intestinal microbiome of farmed rainbow trout Oncorhynchus mykiss (Walbaum) – Philip P Lyons – Aquaculture Research

The evolution of cooperation within the gut microbiota – Seth Rakoff-Nahoum – Nature

Gut microbiota-associated bile acid deconjugation accelerates hepatic steatosis in ob/ob mice – Mi-Young Park – Journal of Applied Microbiology

Effect of in ovo administration of an adult-derived microbiota on establishment of the intestinal microbiome in chickens – Adriana A. Pedroso – American Journal of Veterinary Research

Animal microbiome

First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough – Qing-lei Sun – PLOS ONE

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions – Philipp Engel – mBio

Masters thesis, pdf: Geographic influences on the skin microbiome of humpback whales – Kevin Charles Bierlch – Duke University

Plant, root, and soil microbiome

Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England – Melanie Sapp – MDPI Forests

Conservation tillage increases soil bacterial diversity in the dryland of northern China – Ziting Wang – Agronomy for Sustainable Development

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community – Ana Mellado – New Phytologist

A watering manipulation in a semiarid grassland induced changes in fungal but not bacterial community composition – Theresa A. McHugh – Pedobiologia

Vertical micro-distribution of microbial communities living in Sphagnum fallax – Lihong Song – Inter-Research Aquatic Microbial Ecology

Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia – Jorge R. Osman – The Open Conference Proceedings Journal

Water microbiome

Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current – Martina A. Doblin – PeerJ

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton – Samuel Bryson – mSystems

Phylogenetic structure of bacterial assemblages co-occurring with Ostreopsis cf. ovata bloom – Silvana Vanucci – Harmful Algae

Persistence, loss and appearance of bacteria upstream and downstream – Lisa Dann – Marine and Freshwater Research

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake – Yuyin Yang – Environmental Science and Pollution Research

Doctoral thesis: Characterization and comparison of microbial communities from different tourist ports in Mediterranean Sea and evaluation of applicability of bioremediation treatments – Enrica Bullita – Università di Cagliari

Built environment microbiome

Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach – Tomoaki Ichijo – MPJ Microgravity

Food microbiology

The microbiological quality of pasteurized milk sold by automatic vending machines – Apostolos S. Angelidis – Letters in Applied Microbiology

Waste and pollution microbiology

Seasonal monitoring of bacteria and archaea in a full-scale thermophilic anaerobic digester treating food waste-recycling wastewater: correlations between microbial community characteristics and process variables – Joonyeob Lee – Chemical Engineering Journal

Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure – Hyun Min Jang – Water Research

Performance of a new suspended filler biofilter for removal of nitrogen oxides under thermophilic conditions and microbial community analysis – Li Han – Science of The Total Environment

Viruses and phages

Deciphering the virus-to-prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems – Kaarle J. Parikka – Biological Reviews

Metagenomics, phylogeny, and bioinformatics

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods – Patrick D. Schloss – mSystems

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) – Matthew Z. DeMaere – PeerJ Preprint

From Sample to Multi-Omics Conclusions in under 48 Hours – Robert A. Quinn – mSystems

Microbes in the news

An emerging fungal disease is killing snakes in the US – Anand Jagatia – Microbe Post

Gut feeling: Research examines link between stomach bacteria, PTSD – Science Daily

Converting perchlorate into oxygen: Students colonise Mars with E. coli bacteria – Alpha Galileo

Are multidrug-resistant bacteria spread through sewage water? – Universität Bonn

Fermentation festival leads to rapid response system at Center for Microbiome Innovation – Science Codex

Changes in ‘microbiome’ during canine atopic dermatitis could lead to antibiotic-free therapies for human and canine disease – EurekAlert

More Than A Gut Feeling: Can Gut Microbiome Be Used To Treat Mental Disorders? – Catherine Cabral-Isabedra – Tech Times

Gut microbiome alteration may improve survival in graft-versus-host disease – Corinne Foley – 2MinuteMedicine

Your lungs are full of microorganisms … and that’s a good thing – Ian Hall – The Conversation

The new trillion-dollar market opportunity: Video with Jessica Richman – Anne Stych – BizJournals

Malaria, mosquitoes, and microbiota control – Jason Tetro – PopSci

Some Nonantibiotics Disrupt Biofilms in Endometritis Cases – Alexandra Beckstett – The Horse

A serious stomach bug: Norovirus costs billions of dollars of lost productivity – Ike Swetlitz – STAT News

April 20, 2016

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Posting from SJC: The reproductive tract microbiome from heterosexual couples, olfactory epithelium changes in GF mice, and life in the twilight zone.

Jobs

Post doc positions in human microbiome research in the Lynch Lab at #UCSF – Jonathan Eisen – MicroBEnet

Human respiratory microbiome

Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples – Lindsay J. Caverly – PLOS ONE

Human reproductive tract microbiome

Rationale and Safety Assessment of a Novel Intravaginal Drug-Delivery System with Sustained DL-Lactic Acid Release, Intended for Long-Term Protection of the Vaginal Microbiome – Hans Verstraelen – PLOS ONE

Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis – Marcela Zozaya – Microbiome

Human gut microbiome

Review: Antibiotics, obesity and the link to microbes – what are we doing to our children? – Olli Turta – BMC Medicine

Review: Microbiome mediation of infections in the cancer setting – Ying Taur – Genome Medicine

Review: Moody microbes or fecal phrenology: what do we know about the microbiota-gut-brain axis? – Paul Forsythe – BMC Medicine

Animal models

Olfactory epithelium changes in germfree mice – Adrien François – Scientific Reports

Association between Polycystic Ovary Syndrome and Gut Microbiota – Yanjie Guo – PLOS ONE

Effect of fidaxomicin versus vancomycin on susceptibility to intestinal colonization with vancomycin-resistant enterococci and Klebsiella pneumoniae in mice – Abhishek Deshpande – Antimicrobial Agents and Chemotherapy

Intestinal microbiota and oral administration of Enterococcus faecium associated with the growth performance of new-born piglets – Y.B. Wang – Beneficial Microbes

Animal microbiome

Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster – Johanna Sebald – PLOS ONE

Minireview: Lower Termite Associations with Microbes: Synergy, Protection, and Interplay – Brittany F. Peterson – Frontiers in Microbiology

Plant, root, and soil microbiome

Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action – Ángela María Sánchez-López – Plant, Cell & Environment

Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife (Lythrum salicaria L.) – Aaron S David – Mycologia

Effect of CaMSRB2-Expressing Transgenic Rice Cultivation on Soil Microbial Community – Soo-In Sohn – Journal of Microbiology and Biotechnology

Water microbiome

Marine protist associations and environmental impacts across trophic levels in the twilight zone and below – VP Edgcomb – Current Opinion in Microbiology

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters – Stefano Fazi – Microbial Ecology

Probiotics

Review: Probiotic approach to prevent antibiotic resistance – Arthur C. Ouwehand – Annals of Medicine

Infection microbiology

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology – Sarah K. Hilton – Frontiers in Microbiology

More microbiology
A Generalized Spatial Measure for Resilience of Microbial Systems – Ryan S. Renslow – Frontiers in Microbiology

Community assembly and coexistence in communities of arbuscular mycorrhizal fungi – Kriszta Vályi – The ISME Journal

Microbes in the news

Exploding bacteria could help in our battle against superbugs: Aussie researchers have discovered that some bacteria explode to share useful resources with others, causing the whole group to become nastier. – Signe Dean – SBS

Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web – Oscar Robinson – Molecular Biology and Evolution

April 19, 2016

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A review about breastmilk with a great name, skin microbiome in different populations, a mouse model for Sjögren’s, the office microbiome, Guam reef sponges, the Alaska tundra ecosystem, and taxonomic classification. Note that I will be traveling internationally in the next couple of days due to (another) tragic family situation, so posting will be irregular. But I will try my best!

Pregnancy and birth

Review: Breastfed at Tiffany’s – Thierry Hennet – Trends in Biochemical Sciences

Human skin microbiome

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome – Guillermo I. Perez Perez – PLOS ONE

Pathogenic bacteria profile and antimicrobial susceptibility patterns of ear infection at Bahir Dar Regional Health Research Laboratory Center, Ethiopia – Derese Hailu – SpringerPlus

Human oral microbiome (also see Animal models, below)

Comparison of the Oral Microbiome of Siblings Using Next-generation Sequencing: a Pilot Study – Hyo-Seol Lee – Oral Diseases

Human gastric microbiome

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures – E. R. Shanahan – Alimentary Pharmacology & Therapeutics

Human gut microbiome

Conference Abstract: Walnut Consumption Influences the Human Gut Microbiome – Heather M Guetterman – The FASEB Journal

Conference Abstract: Anemia and Iron Status are Predictors of Gut Microbiome Composition and Metabolites in Infants and Children in Rural Kenya – Daniela Paganini – The FASEB Journal

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles – J. R. Allegretti – Alimentary Pharmacology & Therapeutics

Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial – Mariona Balfegó – Lipids in Health and Disease

Review: From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways – G B Rogers – Molecular Psychiatry

Review: Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? – Jodi E. Nettleton – Physiology & Behavior

Book chapter, some plagiarism: Impact of Probiotics and Gut Microbiota on Host Behavior – Sarabjit Singh Kanwar – Microbes in Food and Health

Animal models of microbiome research

Mouse model: Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome – Cintia S. de Paiva – Scientific Reports

Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions – Jutarop Phetcharaburanin – Journal of Proteome Research

Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model – Imran Khan – Frontiers in Pharmacology

Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition – M-L Wong – Molecular Psychiatry

Animal microbiome

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers – Nicola Segata – Scientific Reports

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity – Georg Steinert – PeerJ

Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali – Vincensius S.P. Oetama – Marine Pollution Bulletin

Diversity of endosymbiont bacteria associated with a non-filarial nematode group – Stela S. Lazarova – Nematology

Master thesis: Effects of Roundup (glyphosate) on gut microorganisms of farm animals – Charlotte Lynggaard Katholm – Aarhus University

Plant, root, and soil microbiome

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China – Yao Zhao – Scientific Reports

Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe – Cancan Zhao – Scientific Reports

Bioaerosol Deposition to Food Crops near Manure Application: Quantitative Microbial Risk Assessment – Michael A. Jahne – Journal of Environmental Quality

Effects of biofumigation using Brassica juncea and Raphanus sativus in comparison to disinfection using Basamid on apple plant growth and soil microbial communities at three field sites with replant disease – Bunlong Yim – Plant and Soil

Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts – Claudia Rojas – Applied Soil Ecology

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation – Lin Chen – Microbial Ecology

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China – Wei Li – Journal of Soils and Sediments

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem – Eric R. Johnston – Frontiers in Microbiology

Water microbiome

Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship – Mathias Milici – Frontiers in Microbiology

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities – Jeffrey Marlow – Frontiers in Microbiology

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean – Tallita Cruz Lopes Tavares – Science of The Total Environment

Dissolution Tests and Microbial Community Analysis Using the Bottom Sediment before and after a Heavy Storm – Ikuo Tsushima – Journal of Water and Environment Technology

Carbohydrate production by microbial mats communities in tidal flat from Bahía Blanca Estuary (Argentina) – E. M. Fernández – Environmental Earth Sciences

Built environment microbiome

Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems

Waste and pollution microbiology

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years – Xiao-Tao Jiang – Scientific Reports

Quantification of microbial load in diesel storage tanks using culture- and qPCR-based approaches – Pedro M. Martin-Sanchez – International Biodeterioration & Biodegradation

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns – Shuo Jiao – Soil Biology and Biochemistry

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates – Okoro Chuma Conlette – Microbial Ecology

Phages and viruses

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system – Alex Betts – Evolution

Research highlight: More of the world’s a phage – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomics

Fast and sensitive taxonomic classification for metagenomics with Kaiju – Peter Menzel – Nature Communications

META-pipe – Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data – Espen Mikal Robertsen – ArXiv

Fast and sensitive mapping of nanopore sequencing reads with GraphMap – Ivan Sović – Nature Communications

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity – Beverly E. Flood – Frontiers in Microbiology

Editorial: A tale of two tardigrades – Thomas A. Richards – PNAS

Review: A guide through a family of phylogenetic dissimilarity measures among sites – Sandrine Pavoine – Oikos

Review: Compositional analysis: a valid approach to analyze microbiome high throughput sequencing data – Gregory B Gloor – Canadian Journal of Microbiology

More microbiology

Accessing Nature’s diversity through metabolic engineering and synthetic biology – Jason R. King – F1000 Research

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories – Vinoth Wigneswaran – F1000 Research

Microbes in the news

Your Invisible Neighbors: Each City Has Unique Microbes – Katherine Du – NPR

Can the bacteria on your skin reveal where you are from? Floors, walls and people in different cities have distinct microbial ‘signatures’ – Abigail Beall – Daily Mail

6 surprising facts about sugar-laden, virus-fighting breast milk – Megan Thielking – STAT News

Gut microbiota development driven by specific enzyme in breast milk – Yvette Brazier – Medical News Today

Mothers’ milk and the infant gut microbiota: An ancient symbiosis – Science Daily

Microbiome-Brain Research to Get $2.8M Boost from NIDA, NCCIH – Genome Web

Earth Day: New insights into coral health hidden in reefs’ microbiomes – National Science Foundation

Downwind safety on the farm. Manure application research aims to improve food safety – American Society of Agronomy

Heartburn Meds Alter the Gut. Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble – Melinda Wenner Moyer – Scientific American

Bacteria that ‘breathes’ iron: Microbes that might change our search for life in space – Dawn Papple – Inquisitr

Microbes and art
This artist uses bacteria as paint: Paint by Microbes – Steph Yin – PopSci

Science, publishing, and career

From #realtimechem to #whywedoresearch: Who are the Tweeting scientists? – Andrew Marsh – Piirus

Tips for Using Social Media to Promote Your Research – Emma Hedington – NPJ Biofilms and Microbiomes

About Joseph Mercola: Known Quack Forced to Refund Customers for Lying About Effects of Tanning Beds – Bryan Menegus – Gizmodo

Bik’s Picks

Meet the woman who makes fake fingers for Japan’s reformed gangsters – Justin McCurry – The Guardian

April 17, 2016

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General microbiome

Review: The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation – Amy Langdon – Genome Medicine

Human oral microbiome

The predictive value of microbiological findings on teeth, internal and external implant portions in clinical decision making – Luigi Canullo – Clinical Oral Implants Research

Human respiratory microbiome

Airway Microbiota in Severe Asthma and Relationship to Asthma Severity and Phenotypes – Qingling Zhang – PLOS ONE

Effects of a honeybee lactic acid bacterial microbiome on human nasal symptoms, commensals, and biomarkers – Anders Mårtensson – International Forum of Allergy & Rhinology

Human gut microbiome

Consistent Prebiotic Effect on Gut Microbiota With Altered FODMAP Intake in Patients with Crohn’s Disease: A Randomised, Controlled Cross-Over Trial of Well-Defined Diets – Emma P Halmos – Clinical and Translational Gastroenterology

Review: Role of the microbiome in non-gastrointestinal cancers – Meirav Pevsner-Fischer – World Journal of Clinical Oncology

Animal models

Thymol and Carvacrol Affect Hybrid Tilapia through the Combination of Direct Stimulation and an Intestinal Microbiota-Mediated Effect: Insights from a Germ-Free Zebrafish Model – Chao Ra – The Journal of Nutrition

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

The Microbiome of the Uropygial Secretion in Hoopoes Is Shaped Along the Nesting Phase – Ángela Martínez-García – Microbial Ecology

The microbiome associated with equine periodontitis and oral health – Rebekah Kennedy – Veterinary Research

Plant, root, and soil microbiome

Diversity and Composition of the Leaf Mycobiome of Beech (Fagus sylvatica) Are Affected by Local Habitat Conditions and Leaf Biochemistry – Martin Unterseher – PLOS ONE

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization – Da Cheng Hao – Scientific Reports

High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – Journal of Eukaryotic Microbiology

Temporal and spatial assessment of microbial communities in commercial silages from bunker silos– J. Kraut-Cohen – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Aquatic fungi: targeting the forgotten in microbial ecology – Hans-Peter Grossart – Current Opinion in MIcrobiology

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr’s Lake, the Bahamas – Varun G. Paul – Astrobiology

Microbial–meiofaunal interrelationships in coastal sediments of the Red Sea – Hamed A. El-Serehy – Saudi Journal of Biological Sciences

Waste and pollution microbiology

Biological Activity of Autochthonic Bacterial Community in Oil-Contaminated Soil – Agnieszka Wolińska – Water Air Soil Pollution

Bioinformatics

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0 – Brian R. Granger – PLOS Computational Biology

More microbiology

Antimicrobial activity of extracts from macroalgae Ulva lactuca against clinically important Staphylococci is impacted by lunar phase of macroalgae harvest – A.M. Deveau – Letters in Applied Microbiology

Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control – Suzanne A. Ford – PLOS Pathogens

Microbes in the news

The Wood Wide Web. A new study shows that trees of different species can exchange large amounts of carbon via the fungal internet that connects their roots. – Ed Yong – The Atlantic

Antibiotics may have lasting impact on the immune system of children – MedicalXpress

Drugs for your gut bugs are on the horizon – Elizabeth Preston – STAT News

A Gut Feeling. See profilee Hans Clevers discuss his work with stem cells and cancer in the small intestine – The Scientist

Qiime2 will revolutionize microbiome bioinformatics – Greg Caporaso – American Gut

Bik’s Picks

Pepper-sprayed students outraged as UC Davis tried to scrub incident from web – Anita Chabria – The Guardian

April 12, 2016, the late one

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Events

Standards for Microbiome Measurements Workshop – August 9-10, NIST, Gaithersburg, Md

General microbiome

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Moving microbiota research towards establishing causal associations that represent viable targets for effective public health interventions – Volker Mai – Annals of Epidemiology

Evolution of Koch’s postulates: towards a twenty-first century understanding of microbial infection – Guido Antonelli – Clinical Microbiology and Infection

Thematic Issue: Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology

Human oral microbiome

http://www.sciencedirect.com/science/article/pii/S104727971630076XThe Effects of Family, Dentition and Dental Caries on the Salivary Microbiome – Betsy Foxman – Annals of Epidemiology

Red fluorescent biofilm: the thick, the old, and the cariogenic – Catherine M.C. Volgenant – Journal of Oral Microbiology

Human gut microbiome

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening – Nielson T Baxter – BioRxiv Preprint

Changes in Korean Adult Females’ Intestinal Microbiota Resulting from Kimchi Intake – Kim JY – Omics Journal of Nutrition & Food Sciences

Review: The Fiber Gap and the Disappearing Gut Microbiome: Implications for Human Nutrition – Edward C. Deehan – Trends in Endocrinology & Metabolism

Animal model microbiome

Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism – P Zheng – Molecular Psychiatry

Temperate phages enhance pathogen fitness in chronic lung infection – Emily V Davies – The ISME Journal

Bacteraemia before during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal

Animal microbiome

Population and individual level dynamics of intestinal microbiota of a small primate – Tuomas Aivelo – Applied and Environmental Microbiology

The nasopharyngeal microbiota in feedlot cattle and its role in respiratory health – Edouard Timsit – Animal Frontiers

Review: Gut microbiome and omics: a new definition to ruminant production and health – Nilusha Malmuthuge – Animal Frontiers

Plant, root, and soil microbiome

Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass – Lin Chen – Soil Biology and Biochemistry

Assessing microbial activities in metal contaminated agricultural volcanic soils – An integrative approach – C. Parelho – Ecotoxicology and Environmental Safety

Review: The role of locally adapted mycorrhizas and rhizobacteria in plant-soil feedback systems – Daniel Revillini – Functional Ecology

Water microbiome

Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone – Claudia Lüke – PeerJ

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms – Hanno Teeling

Transporting Ocean Viromes: Invasion of the Aquatic Biosphere – Yiseul Kim – PLOS ONE

Seasonal changes in microbial community composition in river water studied using 454-pyrosequencing – Marija Kaevska – SpringerPlus

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets – Lukáš Falteisek – Microbial Ecology

Bioinformatics and metagenomics

Chapter: Improving Bloom Filter Performance on Sequence Data Using kk-mer Bloom Filters – David Pellow – Research in Computational Molecular Biology

Microbial ecology

A Game Theoretical Approach to Microbial Coexistence – Monica Abrudan – Advances in Dynamic and Evolutionary Games

The ecologist’s field guide to sequence-based identification of biodiversity –
Simon Creer – Methods in Ecology and Evolution

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

Mind the fibre gap: The case of the vanishing gut microbiome – Will Chu – NutraIngredients

uBiome Opens Voting to all Citizen Scientists to Select $100k Microbiome Research Grant Winner – uBiome

Here’s the mounting evidence against using antibacterial soaps; Few pros, but cons include upped risk of infection, microbiome changes, drug resistance – Beth Mole – Ars Technica

Six-step hand-washing technique most effective for reducing bacteria in hospitals – Glasgow Chamber of Commerce

Hacking Gut Bacteria Could Be The Future Of Medicine. MIT biologists are reprogramming gut bacteria as “live therapeutics.” – Carolyn Gregoire – Huffington Post

Feeding Bacteria to Livestock Could Cut Antibiotic Use – Amy Mayer – Iowa Public Radio

Drug-resistant bacteria found scattered in soil – V. Nilesh – Deccan Chronicle

Sweet Siren call of surface lures bacteria to their death – Anthony King – Chemistry World

New Tree of Life Beautifully Illustrates the Enormous World of Bacteria – Kate Horowitz – Mental Floss

April 12, 2016, part 1

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Too many alerts to go through after taking one day off, so here is part one. An updated tree of life, acute appendicitis, rhizosphere of a living fossil plant, Antarctic surface snow, and effects of Superstorm Sandy on creek water.

Jobs and events

Senior Scientist with significant track record in microbiome research – The National Institute for Biological Standards and Control, South Mimms, UK

General microbiome

A new view of the tree of life – Laura A. Hug – Nature Microbiology

Pregnancy and birth

The Gestational Vaginal Microbiome and Spontaneous Preterm Birth among Nulliparous African American Women – Deborah B. Nelson – American Journal of Perinatology

Early colonization of functional groups of microbes in the infant gut – Van T. Pham – Environmental Microbiology

The gut resistome is highly dynamic during the first months of life – Christian JH von Wintersdorff – Future Medicine

Human skin microbiome

Review: Skin Biomes – N. Fyhrquist – Current Allergy and Asthma Reports

Human respiratory microbiome

Review: Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis – A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions – Jake Jervis Bardy – Ann Otol Rhinol Laryngol

Human oral microbiome

The salivary microbiome for differentiating individuals: proof of principle – Sarah L. Leake – Microbes and Infection

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples – Jean-Luc C. Mougeot – Journal of Oral Microbiology

Human gut microbiome

There are no Enterotypes: Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome

Experiment with n=1: Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota – Blanca S. Noriega – Case Reports in Medicine

First Occurrence of Severe Extraintestinal Manifestations of Crohn’s Disease Following Faecal Microbiota Transplantation – Niels Teich – Journal of Crohn’s and Colitis

Acute appendicitis in children is associated with a local expansion of Fusobacteria – Matthew B. Rogers – Clinical Infectious Diseases

Hypothesis: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? – Alexis Mosca – Frontiers in Microbiology

Not endorsing, because highly controversial and not well founded: Bread and Other Edible Agents of Mental Disease – Paola Bressan and Peter Kramer – Frontiers in Human Neuroscience

Review: The human gut microbiome in health: establishment and resilience of microbiota over a lifetime – Kacy Greenhalgh – Environmental Microbiology

Review: Cytotoxicity of Nanoparticles Contained in Food on Intestinal Cells and the Gut Microbiota – Esther E. Fröhlich – MDPI International Journal of Molecular Sciences

Review: The Role of the Gut Microbiota in Childhood Obesity – Pihl Andreas Friis – Childhood Obesity

Animal models

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions – Rebeca Martín – Frontiers in Microbiology

Depletion of Cultivatable Gut Microbiota by Broad-Spectrum Antibiotic Pretreatment Worsens Outcome After Murine Stroke – Katarzyna Winek – Stroke

Plant, root, and soil microbiome

Common mycorrhizal networks and their effect on the bargaining power of the fungal partner in the arbuscular mycorrhizal symbiosis – Heike Bückinga – Communicative & Integrative Biology

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific – Catarina Cúcio – Frontiers in Microbiology

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil – Angel Valverde – PLOS ONE

Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents – Antonio Gazol – FEMS Microbiology Ecology

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms – Samir Rezki – PeerJ

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function – Jennifer E. Schmidt – Frontiers in Plant Science

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima – Daniel F R Cleary – Plant Biology

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists – Stefan Geisen – Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status – Yuyin Yang – Frontiers in Microbiology

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow – Anna Lopatina – Frontiers in Microbiology

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Impact of an intense water column mixing (0-1500m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea – T. Severin – Environmental Microbiology

Aquatic bacterial community is restructured by hydric dynamics associated with Superstorm Sandy – Nikea Ulrich – Applied and Environmental Microbiology

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula – Daniel Aguirre de Cárcer – FEMS Microbiology Ecology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Partitioning of Viruses in Wastewater Systems and Potential for Aerosolization – Mari Titcombe Lee – Environmental Science & Technology Letters

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow – Serena Caucci – FEMS Microbiology Ecology

Spatial and temporal variability of bacterial communities within a combined sewer system – Henriette Stokbro Jensen – MicrobiologyOpen

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters – Rasmus Hansen Kirkegaard – The ISME Journal

Bioinformatics

Not endorsing: Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification – Yin Wang – BioMed Research International

More microbiology

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo – Nathan D. McDonald – mBio

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota – Si Ming Man – Pathogens and Disease

Microbes in the news

Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there – Ed Yong – The Atlantic

Wealth of unsuspected new microbes expands tree of life – Science Daily

Can more fiber restore microbiome diversity? – Science Daily

Science, publishing, and career

Research Funding: the Case for a Modified Lottery – Ferric C. Fang and Arturo Casadevall – mBio

 

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

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 [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

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

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester