Category Archives: Animal experiments

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

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

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 8, 2016

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Obesity and microbiome patterns, universality of human microbial dynamics, intestinal fungal dysbiosis, pre-eclampsia, seaweed ice-ice disease.

Pregnancy and birth

Review: A dormant microbial component in the development of pre-eclampsia – Douglas B Kell – bioRxiv

General human microbiome

Universality of human microbial dynamics – Amir Bashan – Nature

News and Views: Host-microbe interaction: Rules of the game for microbiota – Karoline Faust – Nature

Perspectives: Accounting for reciprocal host–microbiome interactions in experimental science – Thaddeus S. Stappenbeck – Nature

Human gut microbiome

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc Sze – bioRxiv

Animal and in vitro experiments

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & Microbe

Editorial: The Fungal Mycobiota: Small Numbers, Large Impacts – Carol A. Kumamoto – Cell Host & Microbe

Research Highlights: Love Thy Neighbor: Sharing and Cooperativity in the Gut Microbiota – Nathan T. Porter – Cell Host & Microbe

Animal microbiome

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales – Jesse R. Zaneveld – Nature Communications

Restructuring of the sponge microbiome favors tolerance to ocean acidification – M. Ribes – Environmental Microbiology Reports

Plant, root, and soil microbiome

Molecular identification of new bacterial causative agent of ice-ice disease on seaweed Kappaphycus alvarezii – Marlina Achmad – PeerJ Preprint

Effect of temperature (5 °C–25 °C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage – Yiqin Zhou – Journal of Applied Microbiology

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils – Yuanfeng Cai – Nature Communications

More microbiology

Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi – Stephen J. Mondo – Molecular Biology and Evolution

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics – Maria A. Spyrou – Cell Host & Microbe

Microbes in the news

Arlington native Alexandra Worden named American Academy of Microbiology fellow – Arlington Wicked Local

Disease Researcher Finds New Home at Valencia — in the Classroom, with Dr. Hemangi Patil – Linda Shrieves Beaty – Valencia College

From the Congress of the European Academy of Neurology in Copenhagen, Denmark: Scientists Gather to Discuss Novel Connections Between Gut Microbiome and Brain Disorders – Patricia Inacio – Multiple Sclerosis News Today

Cooperative and Combative Behaviour in the Human Gut: Probing the Microbiome, with Athena Aktipis – SciCasts

Speeding Up Drug Discovery to Fight Tuberculosis – Seattle researchers created a genetic blueprint of the cunning tuberculosis bacteria, then used it to predict and rank potential drug targets – SystemsBiology

Science, publishing, and career

What does research reproducibility mean? – Steven N. Goodman – Science Translational Medicine

Editorial: Second chances – The line between compliance and misconduct is finer than you might think – Nature

Misconduct: Lessons from researcher rehab – James M. DuBois – Nature

June 7, 2016

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Microbiomes of the lung, red coral, effect of invertebrates on water microbes, and bacteriophages are reservoirs of antibiotic resistance genes.

General microbiome

The vast unknown microbial biosphere – Carlos Pedrós-Alió – PNAS

Human respiratory microbiome

Review: The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease – David N. O’Dwyer – The Journal of Immunology

Review/Hypothesis: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? – Navena Navaneetharaja – MDPI Journal of Clinical Medicine

Human gut microbiome

Review: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions – Shahla Abdollahi-Roodsaz – Nature Reviews Rheumatology

Animal experiments

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium – Qianpeng Zhang – Scientific Reports

Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut – Cristiano G. Moreira – mBio

Animal microbiome

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale – Jeroen A. J. M. van de Water – Scientific Reports

Plant, root, and soil microbiome

Mangrove succession enriches the sediment microbial community in South China – Quan Chen – Scientific Reports

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions – Witoon Purahong – Fungal Ecology

History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates – Carolin Boeker – Limnologica – Ecology and Management of Inland Waters

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community – Adriana Novais – Science of The Total Environment

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria – Gregory K. Farrant – PNAS

Bacterial community composition and structure in an Urban River impacted by different pollutant sources – A. Mark Ibekwe – Science of The Total Environment

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill – Anne Bernhard – Frontiers in Microbiology

Review: Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities – V. Marie – International Journal of Environmental Science and Technology

Built environment microbiome

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine – Tairacan Augusto Pereira da Fonseca – Data in Brief

The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota – Noor-Azira Abdul-Mutalib – AIMS Microbiology

Metagenomics and viruses

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes – Jéssica Subirats – International Journal of Antimicrobial Agents

Bioinformatics

SMART: Statistical Metabolomics Analysis—An R Tool – Yu-Jen Liang – Analytical Chemistry

Techniques

Book: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing – Editors: Ana M. Aransay, José Luis Lavín Trueba – Springer Books

More microbiology

Coupling spatiotemporal community assembly processes to ecosystem function – Emily Graham – PeerJ Preprint

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease – Zhe Lyu – Cellular and Molecular Life Sciences

Species richness influences wine ecosystem function through a dominant species – Primrose J. Boynton – Fungal Ecology

Microbes in the news
New antimicrobial material joins fight against antibiotic-resistant bacteria – Michael Irving – GizMag

Note: PNAS paper not yet out: Distinguishing Deadly Staph Bacteria from Harmless Strains – Heather Buschman – UC San Diego

Scientists craft an artificial seawater concoction. New recipe facilitates marine microbe cultivation and characterization – EurekAlert

The man who can map the chemicals all over your body: Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world – Paul Tullis – Nature

Stockton Kimball Awardee is Noted Bacterial Pathogenesis Researcher – University of Buffalo

MSU doctoral student Jeffrey Simkins awarded National Science Foundation fellowship to research in Australia – Montana State University – KBZK

Vaccine watches bacteria, strikes only when trouble stirs – University of Buffalo

Bacteria hairs make excellent electrical wires – Science Daily

Science, publishing, and career

My paper got published: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio

June 6, 2016

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Human oral microbiome

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing – Fabiana de Melo – Clinical Oral Implants Research

Subgingival microbiota in individuals with severe chronic periodontitis – Chi-Ying Tsai – Journal of Microbiology, Immunology and Infection

Human gut microbiome

Gut to brain interaction in Autism Spectrum Disorders: a randomized controlled trial on the role of probiotics on clinical, biochemical and neurophysiological parameters – Elisa Santocchi – BMC Psychiatry

Review: Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health – Helen Wasielewski – Annals of the New York Academy of Sciences

Press: War and peace in the human gut: probing the microbiome -Biodesign

Animal and tissue culture experiments

Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience

Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection – Carla Bellinghausen – Respiratory Research

Animal microbiome

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae) – Maxi Snyman – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages – Shengjing Shi – Ecology Letters

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth – M. A. Soares – Microbial Ecology

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Water and extremophile microbiome

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap – Jarishma K. Gokul – Molecular Ecology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic – Sunil Mundra – MicrobiologyOpen

Microbial sedimentary imprint on the deep Dead Sea sediment – Camille Thomas – The Depositional Record

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand – Nick H. Secker – Journal of Phycology

Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea – Zahar Marziah – MicrobiologyOpen

Pollution and waste microbiology

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing – Lei Wang – Marine Pollution Bulletin

Effects of erythromycin, trimethoprim and clindamycin on attached microbial communities from an effluent dominated prairie stream – M.J. Waiser – Ecotoxicology and Environmental Safety

Metagenomics and bioinformatics

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data – Vladimir I. Ulyantsev – Bioinformatics

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology

Microbes in the news

New Bacterial Research May Help Reduce Excessive Amounts Of Phosphorus In Lakes –
Catherine Cabral-Isabedra – Tech Times

About Nicholas Muzyczka, microbiology professor at the University of Florida: Inventor says fame is fine, but best reward is helping others – Anthony Clark – Gainesville.com

Bacteria has potential to clean up oil spills – Zia Lyle – Daily Texan Online

Clif Bars join list of products recalled over listeria concern – Debra Goldschmidt – CNN

Microbes in Space: JPL Researcher Explores Tiny Life – NASA

Jason Tetro aims to rehabilitate microbes’ bad reputation with The Germ Files – Rebecca Tucker – National Post

Science, publishing, and career

Publishing for academic refugees: Paul Ostwald: The Journal of Interrupted Studies – Emma Christie – Oxford Student

Postdoc mysteries: three recent developments raise puzzling uncertainties about postdocs’ present and future lives – Beryl Lieff Benderly – Science

June 4, 2016

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A very late Saturday digest, after a fun day at the pool and dinner with family. Germ-free jewel wasps, tooth extraction in horses, dormancy in lakes, subways and urban biomes.

Pregnancy and birth

Review: Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior – Rochellys Diaz Heijtz – Seminars in Fetal and Neonatal Medicine

Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR – L. Qian – Beneficial Microbes

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants – Tali Raveh-Sadka – The ISME Journal

Human gut microbiome

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data – Patricio Jeraldo – Frontiers in Microbiology

Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract – Cedric C. Laczny – Frontiers in Microbiology

Cryptic functional variation in the human gut microbiome – Patrick H Bradley – bioRxiv Preprint

Review: The gut microbiome in human immunodeficiency virus infection – Gili Zilberman-Schapira – BMC Medicine

Review: The Gut Microbiome and Obesity – George Kunnackal John – Current Oncology Reports

Animal experiments

An optimized approach to germ-free rearing in the jewel wasp Nasonia – J. Dylan Shropshire – PeerJ Preprints

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

Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers – Yuhong Niu – PLOS ONE

Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness – Hui Yang – Scientific Reports

Animal microbiome

Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii – Eleni Mente

DGGE: A comparison of microbial profiles of different regions of the equine hindgut –
K. Fliegerova – Livestock Science

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – Elisa Lobato – Symbiosis

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Structure of Fungal Communities in Sub-Irrigated Agricultural Soil from Cerrado Floodplains – Elainy Cristina A. M. Oliveira – Diversity

Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils – Valentina Ciccolini – Biology and Fertility of Soils

The impact of pasture systems on soil microbial biomass and community-level physiological profiles – Francisco Marques Cardozo Junior – Land Degradation & Development

Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation – Yan Xie – Frontiers in Plant Science

Isolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island – G. Polizzotto – Letters in Applied Microbiology

Water and extremophile microbiome

Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Extremophiles

Bacterial dormancy is more prevalent in freshwater than hypersaline lakes – Zachary T. Aanderud – Frontiers in Microbiology

Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters – Andrea K. Borsodi – Environmental Science and Pollution Research

Responses of aquatic bacteria to terrestrial runoff: effects on community structure and key taxonomic groups – Huong T. Le – Frontiers in Microbiology

Metagenomics accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil – Milena Marcela D P Schettini – PeerJ Preprint

Built environment microbiome

Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts – Kerstin Schön – Food Control

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report – The MetaSUB International Consortium – Microbiome

Bioinformatics and metagenomics

The Pepsi Challenge, Metagenomics style? COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge – Yang Young Lu – Bioinformatics

Microbial Ecology

A stable genetic polymorphism underpinning microbial syntrophy – Tobias Großkopf – The ISME Journal

Microbes in the news

Two Stanford microbiology and immunology professors elected to National Academy of Sciences – Stanford Medicine

From the American Society of Clinical Oncology Annual Meeting in Chicago: Bacteria found in female upper reproductive tract, once thought sterile – Science Daily

Crowds of crows spread C. jejuni: Are humans vulnerable? – EurekAlert

Antimicrobial Kills E. Coli Within 30 Seconds – Greg Watry – RD Magazine

June 3, 2016

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Microbes around a methane seep that look like ancient ruins, microbial metabolites protecting intestinal stem cells, and human-derived microbes in a Mars-like simulator.

Jobs and events

For everyone anxious to see the videos of the Stanford Bioinformatics for the Microbiome Symposium (including me!), please be patient. The AV team is working hard to generate videos for each individual talk, but that will take some time. Check in at this blog under the “Jobs and Events” header where I will post them once they are ready.

Assistant Professor in the Department of Biology – Macalester College, St. Paul, MN

Human vaginal microbiome

Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora – Bingbing Xiao – Scientific Reports

Human gut microbiome

Review: Reframing the Teenage Wasteland: Adolescent Microbiota-Gut-Brain Axis – Karen-Anne McVey Neufeld – The Canadian Journal of Psychiatry
Editorial to their own paper (?): Stress and the Microbiota-Gut-Brain Axis. An Evolving Concept in Psychiatry – John F. Cryan – The Canadian Journal of Psychiatry

Review: Emerging evidence of the role of gut microbiota in the development of allergic diseases – Kotryna Simonyte Sjödin – Current Opinion Allergy Clinical Immunology

Review: Microbiota and pathogen ‘pas de deux’: setting up and breaking down barriers to intestinal infection – Elizabeth S. McKenney – Pathogens and Disease

Review: Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance – M. J. A. Saad – Physiology

Research Highlight: Sensing gene–microbiota signals in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Editorial: Probiotics and microbiota composition – Mary Ellen Sanders – BMC Medicine

Animal / tissue culture experiments

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko – Cell

Press: Gut microbes’ metabolite dampens proliferation of intestinal stem cells – Science Daily

Animal microbiome

Unfortunately no reference to our recent paper,  which included dolphin blowhole samples: Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises – Xiaoling Wan – Antonie van Leeuwenhoek

Plants, roots, and soil microbiome

Seeing is believing: cell biology at the plant–microbe interface: report from the 36th New Phytologist Symposium – Mike Deeks – New Phytologist

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities – Yuli Marcela Ordoñez – PLOS ONE

Water and extremophile microbiome

Exhumed hydrocarbon-seep authigenic carbonates from Zakynthos island (Greece): Concretions not archaeological remains – Julian E Andrews – Marine and Petroleum Geology

Press:
Ancient Civilization of Microbes, Not Greeks, Built ‘Lost City’ – Henry Fountain – The New York Times
The lost (microbe) colony: bacteria make underwater ‘ruins’ off Greek island – Alan Yuhas – The Guardian
This “Lost Underwater City” Was Actually Made by Microbes. Though these formations may not be evidence of a lost city, they show off some intriguing chemistry – Danny Lewis – Smithsonian
Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico – Patricia Velez – PeerJ

Built environment microbiome

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation – Teresa Mayer – Microbiome

In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria – Joyce M. McBeth – Frontiers in Microbiology

Ecology and bioinformatics

Applications of species accumulation curves in large-scale biological data analysis – Chao Deng – Quantitative Biology

Microbes in the news

See beautiful gif below: Educate Your Immune System. Our bodies are confused by this 21st-century world – Moises Velasquez-Manoff – NY Times

Will Microbes Save Agriculture? Experts Aim To Find Out – Geoffrey Mohan – Sci Tech Today

Alzheimer’s May Defend Against Microbes – Paul Rodgers – Forbes

Methane-producing microbes in California rocks – Science Daily

Science, publishing, and career

Science launches the 2016 ‘Dance Your Ph.D.’ contest – John Bohannon – Science Magazine

Let’s talk about preprint servers – Emilie Marcus – Crosstalk Cell

Bik’s Picks

A New Origin Story for Dogs. The first domesticated animals may have been tamed twice – Ed Yong – The Atlantic

The meteoritic origin of Tutankhamun’s iron dagger blade – Daniela Comelli – Meteoritics & Planetary Science

05valasquez-manoff-superJumbo.gif

Gif by Santtu Mustonen, New York Times

 

June 1, 2016

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Cystic fibrosis, microbial detoxification in the Sage Grouse, salinity gradient in the Baltic Sea, and testing different 16S rRNA gene primer pairs.

Human respiratory microbiome

Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients – H. Al-momani – Scientific Reports

The Dynamics of Disease Progression in Cystic Fibrosis – Frederick R. Adler – PLOS ONE

Human gut microbiome

Alterations and correlations of the gut microbiome, metabolism, and immunity in patients with primary biliary cirrhosis – Long-Xian Lv – Environmental Microbiology

Review: Analysis and Interpretation of the Human Microbiome – Ashton, James J. – Inflammatory Bowel Diseases

Review: Gut microbiota and colorectal cancer – Mayuko Yamamoto – Genes and Environment

Animal experiments

The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific – Busra Aktas – PLOS ONE

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat – D. W. Pitta – Frontiers in Microbiology

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens – Lingling Wang – Frontiers in Microbiology

Animal microbiome

Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean – Andrea Blanquer – Frontiers in Microbiology

Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse – Kevin D. Kohl – FEMS Microbiology Letters

Plant, root, and soil microbiome

Understory herb layer exerts strong controls on soil microbial communities in subtropical plantations – Kai Yin – Scientific Reports

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages – Grant L. Thompson – PLOS ONE

Water and extremophile microbiome

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea – Tue O. O. Hu – Frontiers in Microbiology

Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities – Ali Nawaz – Frontiers in Microbiology

Culture-independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments – Fernanda Abreu – Environmental Microbiology

Food microbiology

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine – Xutao Hong – Scientific Reports

Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar – Zong-Min Wang – Scientific Reports

Bioreactor microbiology

Mycoalgae biofilm: development of a novel platform technology using algae and fungal cultures – Aravindan Rajendran – Biotechnology for Biofuels

Techniques

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies – Bram Beckers – Frontiers in Microbiology

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases – Victor Satler Pylro – Journal of Microbiological Methods

Microbes in the news

Unlocking the secrets of bacterial biofilms – to use against them – Karin Sauer – The Conversation

CDC to set up network of labs to fight tough bacteria – Dale Shoemaker – The Morning Call

Stick insects produce bacterial enzymes themselves. In the course of evolution, genes of gut microbes ‘jumped’ to their insect host – EurekAlert

Tobacco Smoke Makes Germs More Resilient – University of Louisville – NewsWise

Malaria, Zika and Dengue Could Meet Their Match in Mosquito-Borne Bacteria. A common bacteria that infects mosquitoes seems to prevent them from carrying more deadly diseases – Brian Handwerk – Smithsonian

Wild Culture: The Wild Side of Beer Brewing – Anna Brones – Paste Magazine

Unlocking the Mysteries of the Microbiome – J Craig Venter Institute

Science, publishing, and career

Nondisclosure of Financial Interest in Clinical Practice Guideline Development: An Intractable Problem? – Hilda Bastian – PLOS Medicine

Financial Relationships between Organizations That Produce Clinical Practice Guidelines and the Biomedical Industry: A Cross-Sectional Study – Paul Campsall – PLOS Medicine

Pseudoscience

Why Is Big Naturopathy Afraid Of This Lone Whistleblower? – Kavin Senapathy – Forbes

May 26, 2016

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Bioinformatics Symposium tomorrow at Stanford with free live stream, development of upper respiratory tract microbiome in infants, coral microbiome in Hawaii, calcified red algae microbiome, and metagenomics pathogen detection tool.

Events

Tomorrow, starts at 8am Pacific Time: Bioinformatics for the Microbiome, Stanford University. Will also be live streamed (and recording will be kept here for a while too) at Stanford Webcast. Due to family circumstances I won’t be able to be there, unfortunately 😦

Targeting the Microbiome – September 19-22, Boston, MA

Report from meeting earlier this week: Frontiers in Human Microbiota Symbiotic Interactions” 3rd Annual Meeting of the Bridging Biomedical Worlds Series

Jobs

Postdoc position in Pat Schloss group – Department of Microbiology & Immunology at the University of Michigan

General microbiome

Bioengineering microbial communities: Their potential to help, hinder and disgust – Diane Sivasubramaniama – Bioengineered

Pregnancy and birth

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery – Astrid A.T.M. Bosch – EBioMedicine

Human respiratory microbiome

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection – Inês N. Silva – mSystems

Study shows how bacteria evolve in lungs of cystic fibrosis patients – Science Daily

Upper airway microbial colonization in patients with neuromuscular disorders – Florian Stehling – Respirology

Human gut microbiome

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study – Toshitaka Odamaki – BMC Microbiology

Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s Disease – Chandra Sekhar Pedamallu – CMGH Cellular and Molecular Gastroenterology and Hepatology

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium – Elizabeth R. Volkmann – Arthritis & Rheumatology

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice – Joseph D. Planer – Nature

Animal experiments

Impact of a High-Fat or High-Fiber Diet on Intestinal Microbiota and Metabolic Markers in a Pig Model – Sonja N. Heinritz – MDPI Nutrients

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & MIcrobe

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Editorial: Microbiome: Does the brain listen to the gut? – Thomas Kuntz – eLIFE

Animal microbiome

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago – Jennifer L. Salerno – FEMS Microbiology Ecology

Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts – Aidan A. G. Hall – Environmental Microbiology

An exploration of the fungal assemblage in each life history stage of the butterfly, Lycaeides melissa (Lycaenidae), as well as its host plant Astragalus canadensis (Fabaceae) – Joshua G. Harrison – Fungal Ecology

Comparison of the fecal microbiota in horses with Equine Metabolic Syndrome (EMS) and metabolically normal controls fed a similar all forage diet – S. Elzinga – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga – Juliet Brodie – FEMS Microbiology Ecology

Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment – Manuel Delgado-Baquerizo – Functional Ecology

Effect of agricultural practices and coastal constraints on soil microbial functional properties in Mediterranean olive orchards – N. Boukhdoud – European Journal of Soil Science

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicholas Fanin – Ecology

Book Chapter: Bacteria and Non-lichenized Fungi Within Biological Soil Crusts – Stefanie Maier – Biological Soil Crusts: An Organizing Principle in Drylands

Metagenomics, bioinformatics, and techniques

HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts – Patrick W. Laffy – Frontiers in Microbiology

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling – Steven Flygare – Genome Biology

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed – EurekAlert

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing – Matthew Thoendel – Journal of Microbiological Methods

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies – Victor S. Pylro – Microbial Ecology

Functional foods

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms – Christos Stefanis – Current Research in Nutrition and Food Science

Microbes in the news

Polio-free world? Not if scientists refuse to destroy their research specimens – Helen Branswell – STAT news

The secret history of ancient toilets. By scouring the remains of early loos and sewers, archaeologists are finding clues to what life was like in the Roman world and in other civilizations – Chelsea Wald – Nature

Using Gut Bacteria To Save The Planet – John Farrell – Forbes

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics – Jessica L. Miles and Anthony D. Sabatelli – Lexology

May 25, 2016

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The sinonasal microbiome in chronic rhinosinusitis, walnut consumption in a mouse model, and treatment of cows with antibiotics has effects on dung beetle microbiomes.

Jobs and Grants

Assistant professor of food science, microbial ecology – Penn State

American Gastroenterological Association Invites Applications for Gut Microbiome Award – Philanthropy news digest

Three Post-Doctoral Fellowships for Tropical Microbial Ecologists in Panama – Smithsonian Tropical Research Institute

Events

1st International Conference on the Marine Microbiome – Discovery & Innovation for science and industry, 27 June 2016 — 30 June 2016, Berlin, Germany

Pregnancy and birth

Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women – Luisa F Gomez-Arango – Diabetes

Human oral microbiome

Minireview: A practical guide to the oral microbiome and its relation to health and disease – K Krishnan – Oral Diseases

Human respiratory microbiome

Review: A systematic review of the sinonasal microbiome in chronic rhinosinusitis – Martin Anderson – American Journal of Rhinology & Allergy

Human gut microbiome

Letter: Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis – Malte Christoph Rühlemann – Gut

Review: Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children – Evalotte Decker – Gut Microbes

Human vaginal microbiome

Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis – Gary Ventolini – Women’s Health

Animal experiments

Pulmonary Th17 Antifungal Immunity Is Regulated by the Gut Microbiome – Jeremy P. McAleer – The Journal of Immunology

Microbial modulation of behavior and stress responses in zebrafish larvae – Daniel J. Davis – Behavioural Brain Research

Effects of walnut consumption on colon carcinogenesis and microbial community structure – Masako Nakanishi – Cancer Prevention Research

Animal microbiome

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata – Sonny T. M. Lee – Frontiers in Microbiology

Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus – Aneta Nowakiewicz – PLOS ONE

Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles – Tobin J. Hammer – Proceedings of the Royal Society B

Immune response and gut microbial community structure in bumblebees after microbiota transplants – Kathrin Näpflin – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing – Linkun Wu – Scientific Reports

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize – Giovanni Vigliotta – Journal of Environmental Management

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil – Stefano Covino – Science of the Total Environment

Water microbiome

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed – Liyan Song – Microbial Ecology

Built environment microbiome

Review: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review – Marcus H. Y. Leung – Microbiome

Review: Use of Homogeneously-Sized Carbon Steel Ball Bearings to Study Microbially-Influenced Corrosion in Oil Field Samples – Gerrit Voordouw – Frontiers in Microbiology

Food microbiology

Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective – Ileana Vigentini – Frontiers in Microbiology

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Bioinformatics

mockrobiota: a public resource for microbiome bioinformatics benchmarking – Nicholas A Bokulich – PeerJ Preprints

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals – Yevgeny Nikolaichik

Techniques

Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics – Linn Sgie – Nature Communications

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly – Christopher Huptas – BMC Research Notes

Microbes in the news

Inner Workings: Ancient teeth reveal clues about microbiome evolution – Jyoti Madhusoodanan – PNAS

Study shows cows on antibiotics produce dung with higher levels of greenhouse gases – DW

May 24, 2016

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Endophytes in Miscanthus seeds, the microbes of Blood Pond Hell, microbes in indoor dust, and Dada2 sample inference from Illumina data.

General microbiome

Moonshot or mania? – Sally Adee looks behind the hype – New Scientist

Human gut microbiome

Research Highlight: Microbiota trigger inflammation – Ellen F. Carney – Nature Reviews Nephrology

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies – Emmanouil Angelakis – Scientific Reports

Microbiome of HIV-infected people – Grégory Dubourg – Microbial Pathogenesis

Review: The microbiota and immune response during Clostridium difficile infection – Erica L. Buonomo – Anaerobe

Animal experiments

Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man – Coline Plé – Gastroenterology Research and Practice

Plant, root, and soil microbiome

The microbiomes and metagenomes of forest biochars – Genevieve L. Noyce – Scientific Reports

Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding – Naomi Cope-Selby – GCB Bioenergy

Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season – Anna Siczek – Int J Mol Sci

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research – Tim Richter-Heitmann – Frontiers in Microbiology

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time – Ngoc-Lan Nguyen – PLOS ONE

Water and extremophile microbiome

Estimating planktonic diversity through spatial dominance patterns in a model ocean – Alice Soccodato – Marine Genomics

Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1 – Yusei Masakia – Research in Microbiology

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea) – Peeter Laas – PLOS ONE

Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding – Wei Li – Scientific Reports

Built environment microbiology

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study – Blake Hanson – Environmental Science: Processes & Impact

Microbiome Profiling of Drinking Water in Relation to Incidence of Inflammatory Bowel Disease – Jessica D Forbes – Canadian Journal of Microbiology

Infection microbiology

The scanning electron microscope in microbiology and diagnosis of infectious disease – Christine G. Golding – Scientific Reports

Bioinformatics

DADA2: High-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods (OA by author)

MetaTrans: an open-source pipeline for metatranscriptomics – Xavier Martinez – Scientific Reports

An Introduction to Programming for Bioscientists: A Python-based Primer – Berk Ekmekci – Arxiv / PLOS

An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis – Md Sarwar Kamal – Classification and Clustering in Biomedical Signal Processing

Complex heatmaps reveal patterns and correlations in multidimensional genomic data – Zuguang Gu – Bioinformatics

Unsupervised random forest: a tutorial with case studies – Nelson Lee Afanador – Journal of Chemometrics

Metagenomics

Review: The bright side of microbial dark matter: lessons learned from the uncultivated majority – Lindsey Solden – Current Opinion in Microbiology

Metabolomics

Review: Metabolomics of fecal samples: a practical consideration – Silke Matysik – Trends in Food Science & Technology

Viruses and phages

Targeted virus detection in next-generation sequencing data using an automated e-probe based approach – Marike Visser – Virology

Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens – Shin-Yi Lee Marzano – Journal of Virology

Viruses and bacteria in Th2 biased allergic airway disease – Feng Lan – Allergy

More microbiology

Biofilms: Microbial Shelters Against Antibiotics – Skander Hathroubi – Microbial Drug Resistance

Microbes in the news

Building An Antibiotic To Kill Bad Microbes While Sparing Good Ones – Madeline K. Sofia – NPR

A rallying call for microbiome science national data management – A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data – EurekAlert

Could Gut Microbiome Be the Holy Grail for Diabetes Treatment? – An Expert Weighs In at International Endocrinology Congress – Business Wire

AOBiome and its Consumer Division, Mother Dirt, Founding members of the Microbiome Coalition, Helps Launch of the National Microbiome Initiative – PR Newswire

Painful pooping may stop panda sex. A gut-wrenching tummy ache can throw cold water on pandas’ love life. Amy Middleton reports. – Amy Middleton – Cosmos Magazine