Category Archives: Plant Root Soil microbiome

June 7, 2016

Posted on by

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

Posted on by

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

Posted on by

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

Posted on by

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 2, 2016

Posted on by

Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

June 1, 2016

Posted on by

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 30, 2016

Posted on by

Blogging from AMS Airport, with just a couple of new papers that came out yesterday.

Pregnancy and birth

Randomized Control Trial of Human Recombinant Lactoferrin: A Substudy Reveals Effects on the Fecal Microbiome of Very Low Birth Weight Infants – Michael P. Sherman – The Journal of Pediatrics

Editorial: Clinical Benefits of Lactoferrin for Infants and Children – Paolo Manzoni – The Journal of Pediatrics

Human oral microbiome

Initial oral biofilm formation on titanium implants with different surface treatments: An in vivo study – Cyntia Ferreira Ribeiro – Archives of Oral Biology

Human gut microbiome

Research Highlight: Helminths and Intestinal Flora Team Up to Improve Gut Health – Paul Giacomin – Trends in Parasitology

Plant, root, and soil microbiome

How to live with phosphorus scarcity in soil and sediment: Lessons from bacteria.– Yunuen Tapia-Torres – Applied and Environmental Microbiology

Waste and pollution microbiology

Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge – Can Liu – Bioresource Technology

Is there a distance-decay relationship in biological wastewater treatment plants? – Xiaohui Wang – Applied and Environmental Microbiology

Microbes in the news

UCSB Professor Wins Bacteria-Killing Grant – Microbial Geneticist David Low Receives Award to Pinpoint BamA Protein – Santa Barbara Independent

Minnesota chief epidemiologist: No cause for concern after anthrax detection
An initial positive test was followed by negative ones, said Dr. Ruth Lynfield. The bacteria can occur naturally. – Beatrice Dupuy – Star Tribune

Master Gardener Explains Soil Nitrogen – Frank Rauchschwalbe – My Mother Lode

US reports first case of bacteria resistant to antibiotic of last resort – The Guardian

May 27, 2016

Posted on by

image1Just a short Microbiome Digest in between funeral ceremonies today. But today also brought good news: Microbiome Digest / Bik’s Picks received the “Microbiome Pioneer Award” today at Stanford’s Bioinformatics for the Microbiome Symposium. Professor Ami Bhatt handed out the prize, and Professor Christina Vandenbroucke-Grauls took the photo. I am very honored and thankful for this award, and I owe a big thank you for Tomer Altman for helping me start the blog and David Relman for helping me run it!

Human skin and hair microbiome

Physiological and microbiological verification of the benefit of hair washing in patients with skin conditions of the scalp – Miwa Kobayashi – Journal of Cosmetic Dermatology

Animal microbiome

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis) – Robert J. Gruninger – PLOS ONE

Beaver Gut Microbiome Provides Clues to Plant Material Breakdown – Genome Web

Plant, root, and soil microbiome

Rapid identification of bacteria associated with Acute Oak Decline by high resolution melt (HRM) analysis – Carrie Brady – Letters in Applied Microbiology

Sediment microbial communities rely on different dissolved organic matter sources along a Mediterranean river continuum – A. Freixa – Limnology and Oceanography

More Microbiology

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
Jason M. Peters – Cell

Survivability of bare, individual Bacillus subtilis spores to high-velocity surface impact: Implications for microbial transfer through space – Brandon L. Barney – Planetary and Space Science

Crash test bacteria study at BYU could shed light on outer space – Daniel Woodruff – KUTV

Microbes in the news

Bacterial diversity in soils was shaped by ice ages – Amanda Garris – Cornell

Superbugs for dummies: Explaining the battle between bacteria and antibiotics – Helen Branswell – STAT News

Goose Island identifies bacteria that caused tainted beer, but not source – Josh Noel – Chicago Tribune

Cork scientists win funding from Bill Gates’ foundation for Africa study – Gordon Hunt – Silicon Republic

High-dose vitamin D may boost diversity of the gut microbiome – Nutraingredients

 

UCSB receives Grand Challenges Explorations grant – EurekAlert

Science, publishing, and career

Should researchers publish their findings before peer review? – Ivan Oransky and Adam Marcus – STAT News

May 26, 2016

Posted on by

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

Posted on by

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