Category Archives: Food Microbiology

June 3, 2015

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Microbiomes of seahorses, diet and human stool, gut microbes influencing CNS, lichen-associated bacteria, sequencing beer, and news from #ASM2015.

Human gut microbiome

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling – Ilario Ferrocino – PLOS ONE

Animal models of microbiome research

Host microbiota constantly control maturation and function of microglia in the CNS – Daniel Erny – Nature Neuroscience

Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community, Composition, and Diversity in Yanbian Yellow Cattle – Xiang Z. Li – PLOS ONE

Animal microbiome

A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province – Chenyan Shi – PLOS ONE

Comparison of the Intestinal Bacterial Flora in Healthy and Intestinal-diseased Seahorses Hippocampus trimaculatus, Hippocampus erectus, and Hippocampus spinosissimus – Feng Li – Journal of the World Aquaculture Society

Plant and soil microbiome

Analysis of the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in phosphate solubilization – Margrét Auður Sigurbjörnsdóttir – Microbiology

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration – Ramasamy Krishnamoorthy – PLOS ONE

Built environment microbiome

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes – Rachel I. Adams – PLOS ONE

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing – Wuttichai Mhuantong – PLOS ONE

Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities – Su-Kyoung Shin – PLOS ONE

Food microbiology

PCR-DGGE assessment of the bacterial diversity in Spanish-style green table-olive fermentations – Helena Lucena-Padrós – International Journal of Food Microbiology

Microbial ecology

Perspectives on the context-dependency of stream community responses to contaminants – William H. Clements – Freshwater Biology

Metacommunity speciation models and their implications for diversification theory – Nicolas Hubert – Ecology Letters

The complex relationship between microbial growth rate and yield and its implications for ecosystem processes – David A. Lipson – Frontiers in Microbiology

Techniques

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects – Danyta I. Tedjo – PLOS ONE

Microbes in the news

Sequence your beer: BeerDeCoded: the 1,000 beer genomes

#ASM2015 – Soil microbes ally with plants to fight disease and tolerate stress – Phys.org

#ASM2015 video: A Critical Role of the Plant Microbiome for Immunocompetency – ASM

#ASM2015: Share a Bathroom With Other People? Here’s Something You May or May Not Want to Know About Your Toothbrush – Liz Klimas – The Blaze

All About Flora: How Important Gut Health Really Is. Don’t be grossed out – those little guys living in your guts are your friends – Lacie Glover – US News
Ancient algae found deep in tropical glacier – Biology News

Microbes, biodiversity and the benefits of getting dirty – David Suzuki – National Observer

Former COD Theater Major Researches Microbiology in South Africa – Mitchell11 – Chicago Tribune

Interview with Jessica Richman of uBiome – Tracy Mac – The Power of Poop

Bacteria study may curb antibiotics use – Jeremy Watson – The Times

Could remnants of the earliest life be preserved in volcanic glass? Controversy about microbial “biotextures” – Shalini Saxena – ArsTechnica

Science, publishing, and career

Why we should help people understand our scientific literature – R. W. Abrams – Conservation Biology

Announcing mSystems™: a new ASM open-access journal launching in early 2016 with Jack Gilbert as Founding Editor in Chief – ASM

Scientists Behaving Badly (On Social Media) – Brett Buttliere – PLOS Blogs

Publons and the American Society for Microbiology announce pilot partnership – ASM

Helpful websites for women scientists interested in fellowships, scholarships and funding opportunities – ASM

Bik’s Picks

Chimps Can’t Cook, But Maybe They’d Like To – Michael D. Lemonick – National Geographic

20-year-old invents ingenious system to rid ocean of trash – Olivia Solon – Mirror

Sea lions injured in chlorine attack return to ocean (video) – Chicago Tribune

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June 1, 2015

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Still catching up from my trip abroad – lots of new papers to share, so I will do two blog posts today.

General microbiome

Elucidating microbial codes to distinguish individuals – Allyson L. Byrd and Julia A. Segre – PNAS

Human oral microbiome

Periodontal status and pathogenic bacteria after gastric bypass: a cohort study – Sílvia Helena de Carvalho Sales-Peres – Journal of Clinical Periodontology

Inflammation-associated microbiota in pediatric eosinophilic esophagitis – Alain J Benitez – Microbiome

Global transcription of CRISPR loci in the human oral cavity – Andrew G Lum – BMC Genomics

Oral and Gastric Helicobacter Pylori: Effects and Associations – Nélio Veiga – PLOS ONE

Book Chapter: Obesity and Periodontal Disease – Simon D. Tran – Environmental Metagenomics

Human gut microbiome

Investigation of the Association Between the Fecal Microbiota and Breast Cancer in Postmenopausal Women: a Population-Based Case-Control Pilot Study – James J. Goedert – Journal of the National Cancer Institute

Review: The art of targeting gut microbiota for tackling human obesity – Marisol Aguirre, Koen Venema – Genes and Nutrition

Review article: dietary fibre–microbiota interactions – H. L. Simpson and B. J. Campbell – Alimentary Pharmacology & Therapeutics

Animal and other microbiome models

Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet – Sailendharan Sudakaran – ISME Journal

Fecal Microbial Transplant After Ileocolic Resection Reduces Ileitis but Restores Colitis in IL-102/2 Mice – Troy Perry – IBD Journal

Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity – Injae Hwang – The FASEB Journal

Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains – Michael S. Gilmore – PNAS

Human Microbiota-Associated Swine: Current Progress and Future Opportunities – Mei Wang and Sharon M. Donovan – ILAR Journal

Animal microbiome

Marked seasonal variation in the wild mouse gut microbiota – Corinne F Maurice – ISME Journal

Evolution of host specialization in gut microbes: the bee gut as a model – Waidan K Kwong – Gut Microbes

Soil microbiome

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China – Yuguang Zhang – Microbial Biotechnology

High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil – Ronald Ragudo Navarro – Environmental Science & Technology

Study and assessment of microbial communities in natural and commercial bioleaching – Arevik Vardanyan – Minerals Engineering

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient – S. Hortal – Soil Biology and Biochemistry

Evaluation of soil microbial communities as influenced by crude oil pollution – Eucharia Oluchi Nwaichi and Magdalena Frac – African Journal of Biotechnology

Water microbiome

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management – William Van Bonn – Zoo Biology

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations – Sergio Pulido-Tamayo – Nucleic Acids Research

Manganese and iron as structuring parameters of microbial communities in Arctic marine sediments from the Baffin Bay – Camelia Algora – FEMS Microbial Ecology

Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level – Mounira Smati – Microbiology Open

Manganese cycling microbial communities inside deep-sea manganese nodules – Marco Blöthe – Environmental Science & Technology

Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands – Pengfei Li – Water

Thesis: Evaluating changes in diversity and functional gene abundance of denitrifying microbe communities and nutrient concentrations in runoff following the implementation of low-grade weirs in agricultural drainage systems – Beth Baker – Mississippi State University/ Gradworks

Bioreactor microbiome

Lipid hydrolysis products affect the composition of infant gut microbial communities in vitro – Rikke G. Nejrup – British Journal of Nutrition

Effect of phospholipid on pyrite oxidation and microbial communities under simulated acid mine drainage (AMD) conditions – Andro-Marc Pierre-Louis – Environmental Science & Technology

Antibiotic resistome and its association with bacterial communities during sewage sludge composting – Jianqiang Su – Environmental Science & Technology

Food microbiology

Microbiota dynamics associated with environmental conditions and potential roles of cellulolytic communities in traditional Chinese cereal starter solid-state fermentation – Pan Li- Applied and Environmental Microbiology

Bioinformatics and metagenomics

Note: not metagenomics but Single Locus Sequencing / OTU defining: MICCA: a complete and accurate software for taxonomic profiling of metagenomic data – Davide Albanese – Scientific Reports

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data: GotCloud – Goo Jun – Genome Research

GITIRBio: A Semantic and Distributed Service OrientedArchitecture for Bioinformatics Pipeline – Luis F. Castillo – Journal of Integrative Bioinformatics

mmnet: an R package for metagenomics systems biology analysis: community-level metabolic network reconstruction – Yang Cao – BioMed Research International

Techniques

How to evaluate PCR assays for the detection of low-level DNA – Frederik Banch Clausen – APMIS
http://onlinelibrary.wiley.com/doi/10.1111/apm.12405/full

A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems – Xiang Li – Environmental Science & Technology

Functional Foods

Programmable probiotics for detection of cancer in urine – Tal Danino – Science Translational Medicine

Microbes in the news

Alterations to the eye microbiome of contact lens wearers may increase infections – Medical News Today

U.S. defense chief monitoring military anthrax investigation – Reuters

Deadly Bacteria Now a Proven Cancer Detector? – Samantha Solomon – Wall Street Daily’

Gut Bacteria Impacts Toddlers’ Behavior, Particularly Boys – Traci Pederson – PsychCentral

Cervicovaginal Bacteria May Increase the risk of HIV Acquisition in Women – University of Kwazulu – Natal

DNA Genotek’s microbiome collection and stabilization blog: Microbiome learnings from the Weizmann Institute – Cindy MacCullough – DNA Genotek

Scientists probe mysterious wave of antelope deaths – Rory Galloway – BBC News

Bacteria may cause Type 2 diabetes – University of Iowa Now

Should we care about fungi? The mycobiome: an emerging field of the human microbiome research – Human Microbiome Club

Hardy bacteria thrive under hot desert rocks – Nola Taylor Redd – Phys.org

Colon Cancer Diagnosis With Lumninescent Bacteria: Modified Probiotics Can Successfully Detect Tumors In Liver – Colon Cancer News Today

Scientists Find Link Between Ocean Bacteria and Atmosphere – Simon Yu – UCSD Guardian

Woman goes blind after cat licks her and transmits rare bacteria that could affect the brain, eyes, heart, and internal organs – Daily Mail

Science, career, and publishing

This poor advice blog post was retracted from Science today, but the internet never forgets.

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May 29, 2015

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General microbiome

Perspective: The trendy microbes – VK Viswanathan – Gut Microbes

Review: Use of the Microbiome in the Practice of Epidemiology: A Primer on -Omic Technologies – Betsy Foxman – American Journal of Epidemiology

Review: Biological warfare: Microorganisms as drivers of host–parasite interactions – Nolwenn M. Dheilly – Infection, Genetics and Evolution

Microbiome of pregnancy and birth

Bacterial communities in neonatal feces are similar to mothers’ placentae – X-D Dong – Canadian Journal of Infectious Diseases and Medical Microbiology

Human oral microbiome

Maturation of Oral Microbiota in Children with or without Dental Caries – Pernilla Lif Holgerson – PLOS ONE

Exploring the variation of oral microbiota in supragingival plaque during and after head-and-neck radiotherapy using pyrosequencing – Li Gao – Archives of Oral Biology

Human genital microbiome

Sensitive Detection of Thirteen Bacterial Vaginosis-Associated Agents Using Multiplex Polymerase Chain Reaction – Natália Malaguti – BioMed Research International

Human gut microbiome

Esophageal Microbiome in Eosinophilic Esophagitis – J. Kirk Harris – PLOS ONE

Pyrosequencing Analysis Reveals Changes in Intestinal Microbiota of Healthy Adults Who Received a Daily Dose of Immunomodulatory Probiotic Strains – Julio Plaza-Díaz – Nutrients

Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota–targeted dietary intervention – J Philip Karl – American Journal of Clinical Nutrition

Pouch Inflammation is Associated with a Decrease in Specific Bacterial Taxa – Leah Reshef – Gastroenterology

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota – Jianjun Liu – Clinical Microbiology and Infection

Letter to the Editor: Mediterranean diet: the missing link between gut microbiota and inflammatory diseases – M Bifulco – European Journal of Clinical Nutrition

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: Not Just Yet – Ari M. Grinspan – Gastroenterology

Perspective: Rifaximin, gut microbes and mucosal inflammation: unraveling a complex relationship – Jun Gao – Gut Microbes

Review: Apples and Cardiovascular Health—Is the Gut Microbiota a Core Consideration? – Athanasios Koutsos  – Nutrients

Animal models of microbiome research

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats – Agnieszka Mika – PLOS ONE

Gut microbiota inhibit Asbt-dependent intestinal bile acid reabsorption via Gata4 – Carolien Out – Journal of Hepatology

Animal microbiome

RUMINANT NUTRITION SYMPOSIUM: The impact of the rumen microbiome on nutrition, health, and production – R.A. Kohn – Journal of Animal Science
How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J.L. Firkins – Journal of Animal Science

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas – I. De Barbieri – Livestock Science

The camel faecal metagenome under different systems of management: phylogenetic and gene-centric Approach – Suchitra S. Dande – Livestock Science

Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences – Cornelia Roder – Molecular Ecology

Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines – Dirkjan Schokker – BMC Genomics

Soil microbiome

Biodegradation kinetic rates of diesel-contaminated sandy soil samples by two different microbial consortia – Alejandro Ledezma-Villanueva – Annals of Microbiology

Temperature sensitivity of soil bacterial community along contrasting warming gradient – Jinfeng Wu – Applied Soil Ecology

Water microbiome

Heavy metals and TPH effects on microbial abundance and diversity in two estuarine areas of the southern-central coast of São Paulo State, Brazil – Aline Bartelochi Pinto – Marine Pollution Bulletin

Food microbiology

Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics – Mathilde H. Josefsen – Journal of Microbiological Methods

Metagenomics

Alarmingly high segregation frequencies of quinolone resistance alleles within human and animal microbiomes are not explained by direct clinical antibiotic exposure – Wesley Field – Genome Biology and Evolution

Bioinformatics

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – PeerJ PrePrints

Microbes in the news

The germ at the scene of the crime – Viviane Richter – Cosmos

Researchers combat bias in next-generation DNA sequencing – Eric Beidel – Phys.org

Microbiome research heralds new era of medical diagnosis – Aaron Krumins – Extreme Tech

Community Microbiomes: Chatting Cat Scat with Kittybiome’s Holly Ganz – Scott Edmunds – BioMedCentral Blog

Pheromones produced by gut bacteria found to kill resistant variants of its own kind – Bob Yirka – Phys.org

500 protesters chant in Santa Barbara as bacteria munch the oil spill – Chriss W. Street – Breitbart

Science, publishing, and career

Career Advice From an Oldish Not-Quite Geezer: You can’t count on your publications and awards to take care of you – Robert J. Sternberg – Chronicle

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May 19, 2015

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Two papers today on the microbiome of the Giant Panda – it’s not good at digesting bamboo!

Microbiome of pregnancy and birth

Bacterial community structure associated with elective cesarean section versus vaginal delivery in Chinese newborns – Liu D, et al. – J Pediatr Gastroenterol Nutr

The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of Moringa supplemented probiotic yogurt – Jordan E. Bisanz – Applied and Environmental Microbiology

Review: Gut microbiome and immunity: possible role in sudden infant death syndrome (SIDS) – Paul N. Goldwater – Frontiers in Immunology

Human oral microbiome

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics
Bo-Young Hong – PLOS ONE

Review: The human saliva proteome: overview and emerging methods for characterization
Timothy J. Griffin – SPIE Proceedings

Human gut microbiome

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology and Therapeutics

Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans – Lawrence A. David – mBio

Food Fight: Our gut microbes are no fans of junk food – Laura Beil – Science News

Human vaginal microbiome

Review: Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis – Muriel Aldunate – Frontiers in Physiology

Microbiome models

Composition and function of the undernourished neonatal mouse intestinal microbiome – Geoffrey A. Preidis – The Journal of Nutritional Biochemistry

Maternal microbiota regulate glucocorticoids levels and placental development in mice – Maha Al-Asmakh – Endocrine Abstracts

Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity – Jia Yin – PLOS ONE

Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility – K.R. Magnusson – Neuroscience

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition- and somatic growth in a standardized caprine animal model – Sina Fischer – Journal of Breath Research

Animal microbiome

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations – Zhengsheng Xue – mBio

The evolution of the gut microbiota in the giant and the red pandas – Ying Li – Scientific Reports

Patterns of Gut Bacterial Colonization in Three Primate Species – Erin A. McKenney – PLOS ONE

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis
Whitney M. Holden – Biological Conservation

Plant and Soil microbiome

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation – David R. Elliott – PLOS ONE

Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy – Gaidi Ren – Plant and Soil

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly
Fen-Guo Zhang – PLOS ONE

Time-dependent effect of graphene on the structure, abundance and function of the soil bacterial community – Wenjie Ren – Journal of Hazardous Materials

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions – Shaomei He – mBio

Nano titania aided clustering and adhesion of beneficial bacteria to plant roots to enhance crop growth and stress management – G. M. Palmqvist – Scientific Reports

Review: Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions – J. M. Barea – Journal of soil science and plant nutrition

Water microbiome

The influence of land-use, nutrients, and geography on microbial communities and fecal indicator abundance at Lake Michigan beaches – Danielle D. Cloutier – Applied and Environmental Microbiology

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison – Catherine M. Febria – Frontiers in Microbiology

Built environment microbiome

Distribution and population structure characteristics of microorganisms in urban sewage system – Yanchen Liu – Applied Microbiology and Biotechnology

Extremophile microbiome

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China – Ping Li – PLOS ONE

Microbial diversity in engineered haloalkaline environments shaped by shared geochemical drivers observed in natural analogues – Talitha C. Santini – Applied and Environmental Microbiology

Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan – O. V. Kutovaya – Eurasian Soil Science

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Food microbiology

An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea – Ming Zhao – Scientific Reports

Review: Foodomics in microbiological investigations – Yong-Jiang Xu – Current Opinion in Food Science

Metagenomics and Bioinformatics

Review: Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies – Anastasis Oulas – Bioinformatics and Biology Insights

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn – Ecology and Evolution

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? – Emily A. Brown – Ecology and Evolution

Sharing is caring – Claudio Nunes-Alves – Nature Reviews Microbiology

Microbes in the news

Kitty Kickstarter: See the Microbes That Live in Your Cat – Becky Oskin – Live Science

Eden unveils The Human Microbiome this week – West Briton

Bodyguards for precious seeds—without chemical mace – Phys.org

Panda poop reveals they’re bad at digesting bamboo – Laura Geggel – CBS News

Giant Panda Microbiome Ill-Suited for Bamboo Diet, Study Finds – Genome Web

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May 16, 2015

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Posting might be irregular in the coming days because of international travel, but I will try to keep you all updated as best as I can.

Human oral microbiome

Increased infection with key periodontal pathogens during gestational diabetes mellitus – Himabindu Gogeneni – Journal of Clinical Periodontology

Human respiratory microbiome

Airway microbiota and acute respiratory infection in children – Kohei Hasegawa – Expert Review of Clinical Immunology

Human gut microbiome

Microbiota—implications for immunity and transplantation – Jonathan S. Bromberg – Nature Reviews Nephrology

Poster: Association of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home (sic) – Rodriguez Diaz, Cristina – 5th International Human Microbiome Congres

Review: Probiotics, antibiotics and the immune responses to vaccines – Ira Praharaj – Philosophical Transactions B

Microbiome models

Exposure to soil, house dust, and decaying plants increases gut microbial diversity and decreases serum IgE levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Water microbiome

Metagenomics reveals the high PAH-degradation potential of abundant uncultured bacteria from chronically-polluted subantarctic and temperate coastal marine environments – Claudia L. Loviso – Journal of Applied Microbiology

Plant root and soil microbiome

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill – Terrence H. Bell – Environmental Microbiology

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa – S. Geisen – Molecular Ecology

Soil microbial communities vary as much over time as with chronic warming and nitrogen additions – Alexandra R. Contosta – Soil Biology and Biochemistry

Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia oxidizing bacteria – María C. Zabaloy – Pest Management Science

Changes in soil aggregation and microbial community structure control carbon sequestration after afforestation of semiarid shrublands – N. Garcia-Francoa – Soil Biology and Biochemistry

Air microbiome

Challenges and Opportunities of Airborne Metagenomics – Hayedeh Behzad – Genome Biology and Evolution

Food microbiology

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes– Amira Shousha – Applied and Environmental Microbiology

Techniques

A simple method of normalization of DNA extraction for improving the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR – M. Li – Letters in Applied Microbiology

Microbes in the news

The kittybiome Project – background and some plans – Jonathan Eisen – MicroBEnet

Science, publishing, and career

Why Medicine is Plagued with Fake Research – Chloe Della Costa – Business Cheat Sheet

Physics Paper on the Higgs Boson Has Record 5,154 Authors – Softpedia (link to actual pdf)

Bik’s Picks

Giant Squid Lore and Legends Date Back Centuries – Benjamin Radford – Discovery

Cocaine Use Could be Determined by a Fingerprint, New Study – Silvia Fernandez – Pierce Pioneer

New map shows most distinct causes of death by state – Marilyn Malara – UPI

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May 12, 2015

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Microbiome of pregnancy and birth

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women – Esther Jiménez – Journal of Human Lactation

Human oral microbiome

Abstract: Changes In The Oral Microbiome Of HIV-Infected Individuals May Alter Nitrogen Metabolism And The Enterosalivary Circulation Of Nitrate – Carl D. Koch – Am J Respir Crit Care Med

Human respiratory microbiome

Conference abstracts in Am J Respir Crit Care Med:

Human gut microbiome

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis – Caroline H. Johnson – Cell Metabolism

Review: The gut microbiome: What do we know? – Francisco Guarner – Clinical Liver Disease

Review: A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes – Austin G. Davis-Richardson – Diabetologia

Functional foods

Review: A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease – Takanori Kanai – Journal of Gastroenterology

Animal models of microbiome research

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure – Martin Kalmokoff – Nutrients

Animal microbiome

Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports

Plants and soil microbiome

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota – Mizue Naito – PNAS

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi – Caroline Gutjahr – PNAS
Reintroduction of locally extinct vertebrates impacts arid soil fungal communities –
Laurence J. Clarke – Molecular Ecology

Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain
Ana Rincón – Environmental Microbiology

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities – Valentyna Krashevska – Biology and Fertility of Soils

Masters Thesis: The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada – Paul Wartman – University of Guelph, Canada

Review: Plant growth promoting rhizobacteria and sustainable agriculture: A review –
Muhammad Arslan Ashraf – African Journal of Microbiology Research

Water microbiome

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells – Denise M. Akob – Applied Geochemistry

Perspective: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology

Not sure if these are small enough (20-500 um) to be classified as microbes: Metagenetic tools for the census of marine meiofaunal biodiversity: An overview – Laura Carugati – Marine Genomics

Extremophile microbiome

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes – Naseer Sangwan – Environmental Microbiology Reports

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA – Olivia U. Mason – Microbial Ecology

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hasan – PNAS

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Built environment microbiome

Forensic analysis of the microbiome of phones and shoes – Simon Lax – Microbiome

The Actinobacterial Colonization of Etruscan Paintings – Marta Diaz-Herraiz – Scientific Reports

Food microbiology

Molecular Analysis of Skin Bacterial Assemblages from Codfish and Pollock after Dry-Salted Fish Production – Natalia Pegoraro

Viruses and phages

Infection of phytoplankton by aerosolized marine viruses – Shlomit Sharoni – PNAS

Archaea

The two-domain tree of life is linked to a new root for the Archaea – Kasie Raymann – PNAS

Review: Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Hans-Peter Horz – Life

Review: The interplay between nucleoid organization and transcription in archaeal genomes – Eveline Peeters – Nature Reviews Microbiology

Metagenomics and bioinformatics

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data – Kathrin P. Aßhauer – Bioinformatics

ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling – Yiming Cheng – Nucleic Acids Research

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data – Adrian Baez-Ortega – Bioinformatics

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Manuscript: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant – Andreas Bremges

Review: The integration of sequencing and bioinformatics in metagenomics – Firouz Abbasian – Reviews in Environmental Science and Bio/Technology

Book Chapter: Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways – Luana Presta – Briefs in Molecular Science 2015

Book Chapter: Molecular Screening of Azurin-Like Anticancer Bacteriocins from Human Gut Microflora Using Bioinformatics – Van Duy Nguyen – Advanced Computational Methods for Knowledge Engineering

Other microbial papers of interest

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments – Alin Finkelshtein – mBio

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association – Gloria Torres-Cortés – PNAS

Perspective: Resilience vs. historical contingency in microbial responses to environmental change – Christine V. Hawkes – Ecology Letters

A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria – Joshua R. Nahum – PNAS

Microbes in the news
Can The Microbes You Leave Behind Be Used to Identify You? – Ed Yong – National Geographic

Forbidden Data: Wyoming wants to conceal the fact that many of its streams are contaminated by E. coli bacteria – Slate

UGSG looks at microbiology, chemistry of Pa. fracked wells – Bob Downing – Ohio.com

Chinese breast milk discovery strengthens case for probiotics in infant formula: Chr Hansen – By Mark Astley – Dairy Reporter

Researchers find metabolic link between bacterial ‘biofilms’, colon cancer – Medical Xpress

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences – NCBI Insights
#BacteriaHysteria

Germ City: Bacteria thriving at the makeup counter: 30% of used makeup samples in stores contain bacteria – PIX11

Tests found bacteria on popular single-serve coffeemakers – Your Central Valley

Bik’s Picks

De novo synthesis of a sunscreen compound in vertebrates – Andrew R Osborn – eLIFE

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past – Philippe Jeandet – PNAS

Unraveling ancient Egypt’s animal mummy mystery: Roughly a third of the animal mummies examined were completely empty – Michael E. Miller – Washington Post

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May 1, 2015

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A late post today – I was in meetings all day, and had no time to look at the 474 papers in my inbox until late. But let’s catch up!

General microbiome

Editorial: Bacteria make us human – Mohsin Ali – The Lancet

Microbiome of pregnancy and birth

Spotlight: Gut bacteria and necrotizing enterocolitis: cause or effect? – Christopher James Stewart – Trends in Microbiology

Editorial Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis – Leopoldo N. Segal and Martin J. Blaser – The Journal of Pediatrics

Human oral microbiome

Review: Dental Chatter: Bacterial Cross-Talk in the Biofilm of the Oral Cavity – Doron Steinberg – Israel Journal of Chemistry

The interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation – Izumi Mashima – Journal of Bacteriology

Human gut microbiome

Antibiotic treatment of diarrhoea is associated with decreased time to the next diarrhoea episode among young children in Vellore, India – Elizabeth T Rogawski – International Journal of Epidemiology

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals – Yehuda Ringel – Gut Microbes

Gut Microbiota-Mediated Drug-Antibiotic Interactions – Dong-Hyun Kim – Drug Metabolism & Disposition

Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination – Nobuhiko Kamada – Cell Host & Microbe

MicroRNA-193a-3p Reduces Intestinal Inflammation in Response to Microbiota via Down-regulation of Colonic PepT1 – Xin Dai – The Journal of Biological Chemistry

Editorial: Some Reflections on the Microbiome and Obesity – Richard I. Shader – Clinical Therapeutics

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Review: Role of Intestinal Microbiome in Lipid and Glucose Metabolism in Diabetes Mellitus – Casper van Olden – Clinical Therapeutics

Review: Gut microbiome, gut function, and probiotics: Implications for health – Neerja Hajela – Indian Journal of Gastroenterology

Review: Gut microbiota and the development of pediatric diseases – Chun-Yi Lu – Journal of Gastroenterology

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Animal models

Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model – Lei Lu – PLOS ONE

Pharmaceuticals and personal care products alter the holobiome and development of a medically important mosquito – Marcus J. Pennington – Environmental Pollution

Differences in the faecal microbiome of non-diarrhoeic clinically healthy dogs and cats associated with Giardia duodenalis infection: impact of hookworms and coccidia – Jan Šlapeta – International Journal for Parasitology

Ezetimibe and simvastatin modulate gut microbiota and expression of genes related to cholesterol metabolism – Emilie Catry – Life Sciences

Animal microbiome

Review: Tick microbiome: the force within – Sukanya Narasimhan – Trends in Parasitology

16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris) Harbor a Core Subset of Bacteria Normally Associated with the Wild Host – Ivan Meeus – PLOS ONE

Plant microbiome

Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes – Dongfang Li – GCB Bioenergy

Soil microbiome

Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea – Oluwatobi Oni – Frontiers in Microbiology

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities – Jun Liu – Environmental Science & Technology

Water microbiome

Differences in organic matter and bacterioplankton between sections of the largest Arctic river: Mosaic or continuum? – Michail I. Gladyshev – Limnology and Oceanography

Extremophile microbiome

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment – Sarah Stewart Johnson – PLOS ONE

The microbial diversity, distribution, and ecology of permafrost in China: a review – Weigang Hu – Extremophiles

Bioreactor microbiology

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole – Xuwang Zhang – PLOS ONE

Effects of garlic oil, nitrate, saponin and their combinations supplemented to different substrates on in vitro fermentation, ruminal methanogenesis, and abundance and diversity of microbial populations – A.K. Patra – Journal of Applied Microbiology

Food microbiology

Technological implications of reducing nitrate and nitrite levels in dry-fermented sausages: typical microbiota, residual nitrate and nitrite and volatile profile – Xavier F. Hospital – Food Control

Review: New Approaches for Bacteriotherapy: Prebiotics, New-Generation Probiotics, and Synbiotics – Rachna Patel – Clinical Infectious Diseases

Metagenomics and bioinformatics

DIDA: Distributed Indexing Dispatched Alignment – Hamid Mohamadi – PLOS ONE

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data – Tsutomu Ikegami – PLOS ONE

Using populations of human and microbial genomes for organism detection in metagenomes – Sasha K Ames – Genome Research

Metabolomics

Systems biology of host–microbe metabolomics – Almut Heinken and Ines Thiele – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Microbes in the news

Don’t douche, and other lessons about the vaginal microbiome: Exploring the microscopic world between our legs – Susan Keown – Fred Hutch

Gut bacteria easy scapegoat to explain diseases, but connections hard to prove – Meredith Knight – Genetic Literacy Project

Find Out Just How Bacteria-Infested Houston Street Is During This Weekend of Walking Tours – Jaime Cone – Bedford and Bowery
and
The Artist & The Scientist: Microbial Maps – Festival Walk in New York City with Chris Mason – Jane’s Walk

Video: The Microbiome Project: Hospitals – Bacteria may actually be beneficial to hospitals – Argonne National Laboratory

Freshmen participate in huge research study on tiny viruses – University of Colorado Boulder

uBiome is launching an academic consortium to bring together researchers and industry teams with the hope of accelerating scientific understanding of the microbiome – uBiome

Each vineyard has a unique microbiome – Louise Lerner – Futurity

Science, publishing, and career

Ten Simple (Empirical) Rules for Writing Science – Cody J. Weinberger – PLOS Computational Biology

Honors Thesis: Students’ Knowledge and Opinions Concerning Genetically Modified Organisms: A Survey at University of Colorado Boulder – Connor Folkerth – University of Colorado at Boulder

Sexism in science: Peer editor tells female researchers their study needs a male author – Rachel Feltman – Washington Post

Bik’s Picks

How This Beetle Creates 500 Explosions Per Second In Its Bum – Ed Yong – National Geographic

Evidence that premature girls thrive more than premature boys – Science Daily

House GOP Wants to Eviscerate NASA Earth Sciences in New Budget – Phil Plait – Bad Astronomy – Slate
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April 28, 2015

Posted on by

Wow, this was a busy day with about 700 new articles for y’all to screen. Here we go:

Events

May 7th Webinar: George Weinstock Ph.D., will present “The Human Microbiome: Impact on Health and Disease.”

May 13th Webcast at 11am EDT – “Innovations in the microbiome” with Annick Mercenier and Enea Rezzonico – Nature Publishing Group

Human oral microbiome

Periodontal disease in a remote Asian population: association between clinical and microbiological parameters – Christine Kvarnvik – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Comparison of the gut microbiota of people in France and Saudi Arabia – M. Yasir – Nutrition and Diabetes

Fecal microbiota characteristics of patients with colorectal adenoma detected by screening: A population-based study – James J. Goedert – EBioMedicine

Review: Archaea associated with human surfaces: not to be underestimated – Corinna Bang , Ruth A. Schmitz – FEMS Microbiology Reviews

Review: Keeping bugs in check: The mucus layer as a critical component in maintaining intestinal homeostasis – Martin Faderl – IUBMB Life

Review: A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host – Christoph A Thaiss – Gut Microbes

Review: Effect of Helicobacter pylori Infection on the Composition of Gastric Microbiota in the Development of Gastric Cancer – Cao L. · Yu J. – GastroIntestinal Tumors

Review: Immunogenetic control of the Intestinal Microbiota – Eric Marietta – Immunology

Review: Type 2 diabetes and gut microbiome: at the intersection of known and unknown – Smitha Upadhyaya – Gut Microbes

Review: Host-Microbiota Interactions in the Intestine – Elson C.O. – Digestive Diseases

Review: Control of commensal microbiota by the adaptive immune system – Husen Zhang – Gut Microbes

Animal models of microbiome research

Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets – Zhen Luo – Archives of Animal Nutrition

Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum – Refaat Ras – International Journal of Parasitology

Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats – Michaela D. J. Blyton – Environmental Microbiology Reports

Regulation by gut commensal bacteria of carcinoembryonic antigen-related cell adhesion molecule expression in the intestinal epithelium – Yasuaki Kitamura – Genes to Cells

Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition – Elena Gorokhova – Environmental Science & Technology

Role of intestinal microbiota in the generation of polyphenol-derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research

Animal microbiome

Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts – Joanito Liberti – Molecular Ecology

Microbial and sponge loops modify fish production in phase-shifting coral reefs – Cynthia B. Silveira – Environmental Microbiology

Coral symbiotic algae calcify ex hospite in partnership with bacteria – Jörg C. Frommlet – PNAS USA

Plant, plant root and soil microbiome

Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy – Kosuke Shiraishi – Scientific Reports

Role of root microbiota in plant productivity – Andrzej Tkacz and Philip Poole – Journal of Experimental Botany

Seasonal variation of bacterial endophytes in urban trees – Shu Yi Shen – Frontiers in Microbiology

Plant polysaccharides initiate underground crosstalk with bacilli by inducing synthesis of the immunogenic lipopeptide surfactin – Delphine Debois – Environmental Microbiology Reports

Banana leaf and glucose mineralization and soil organic matter in microhabitats of banana plantations under long-term pesticide use – Elena Blume – Environmental Toxicology and Chemistry

Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria – Sebastian Lòpez-Fernàndez – Frontiers in Microbiology

Decreases in soil moisture and organic matter quality suppress microbial decomposition following a boreal forest fire – Sandra R. Holden – Soil Biology and Biochemistry

Soil bacterial community response to sulfadiazine in the soil–root zone – Rüdiger Reichel – Journal of Plant Nutrition and Soil Science

Three-dimensional structure and cyanobacterial activity within a desert biological soil crust – Hagai Raanan – Environmental Microbiology

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Microbial 16S gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements – Anna Lavecchia – Biology and Fertility of Soils

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils – David VanInsberghe – The ISME Journal

Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study – Felipe Bastida – Applied Soil Ecology

Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities – Daniel S. Read – Environmental Science and Pollution Research

Functional diversity of soil microbial communities under Scots pine, Norway spruce, silver birch and mixed boreal forests – Chodak Marcin – Pedobiologia

Water microbiome

Metabolic cascades in marine microbial communities – Andreas F. Haas and Forest Rohwer – PNAS USA

A Rickettsiales Symbiont of Amoebae with Ancient Features – Frederik Schulz – Environmental Microbiology

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene – Yu-Mei Wei – Environmental Science and Pollution Research

Cyanobacterial dynamics in shallow Lake Apopka (Florida, U.S.A.) before and after the shift from a macrophyte-dominated to a phytoplankton-dominated state – Matthew N. Waters – Freshwater Biology

Extremophile microbiome

Open Access: Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming – Alexander Tøsdal Tveit – PNAS USA

Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil – Lori A. Phillips – Soil Biology and Biochemistry

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem – Karen Andrade – The ISME Journal

Microbiome of the built environment

From Lab to Field: The Influence of Urban Landscapes on the Invasive Potential of Wolbachia in Brazilian Aedes aegypti Mosquitoes – Heverton Leandro Carneiro Dutra – PLOS Neglected Tropical Diseases

Bioreactor microbiology

Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome – Zhiping Wang – Microbial Ecology

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage – Matthew D. Porter – Microbial Ecology

Food microbiology

Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing – Qian Peng – Current Microbiology

Microbial Ecology

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effect of audible sound in form of music on microbial growth and production of certain important metabolites – Niral Sarvaiya, Vijay Kothari – Microbiology

Techniques

Optimized DNA extraction and metagenomic sequencing of airborne microbial communities – Wenjun Jiang – Nature Protocols
http://www.nature.com/nprot/journal/v10/n5/full/nprot.2015.046.html

Bioinformatics

phylogeo: an R package for geographic analysis and visualization of microbiome data –
Zachary Charlop-Powers and Sean F. Brady – Bioinformatics

PhD thesis: Statistical models for large-scale comparative metagenome analysis – Kathrin Petra Aßhauer – Georg-August-Universität Göttingen

Metagenomics

Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe – Irena I. Artamonova – Environmental Microbiology

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes – Bing Li – The ISME Journal

Metabolomics and proteomics

Review: Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota – Weili Xiong – Proteomics

Fate of microbial metabolites of dietary polyphenols in rats: is the brain their target destination? – Mattia Gasperotti – ACS Chemical Neuroscience

Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders – Colin Heberling – International Journal of Molecular Sciences

Navigating through metaproteomics data: A logbook of database searching –
Thilo Muth – Proteomics

Phages and viruses

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity – Welkin H Pope – eLIFE

Linking environmental prokaryotic viruses and their host through CRISPRs
– Laura Sanguino – FEMS Microbiology Ecology

Microbes in the news

The Healthy Birth: Dyad or Triad? Exploring Birth and the Microbiome – Anne Estes – Science & Sensibility

Designing a Hospital to Better Fight Infection (about the Hospital Microbiome Project) – Robert Lee Hotz – Wall Street Journal
and
WSJ article on the Hospital Microbiome Project – Elisabeth Bik – MicroBEnet

Facts About Our Microbial Menagerie – Infection Control Today

Don’t Trust The Goats; Their Ticks Could Make You Sick – Poncie Rutsch – NPR

Tiny Creatures: The World of Microbes – Anne M. Estes – Mostly Microbes

Time-lapse movie of growth and death in bacterial communities – David Esteban – Experiment.com

Altered saliva shows increased risk for hospitalization in patients with cirrhosis, hepatic encephalopathy – Healio

An arms race of microbial proportions: A war between bacteria and bacteriophages is being fought at the genetic level – Jason Tetro – Popular Science

Microbes and money

uBiome Launches Clinical Laboratory: launch of their CLIA-regulated clinical laboratory to provide clinical tests based on its unique microbial assays – Globe News Wire

New report sheds light on the Global human microbiome market – size, share, segments analysis and outlook to 2020 – Whatech.com

Science, publishing and career

Five Non-Academic Careers for which Ph.D. Holders are Uniquely Qualified… – Colin White – Nature Careers

Study: Peer Review Predicts Success – Ruth Williams – The Scientist

Discussion paper: Appearance and Gender Bias in Academia – Tali Regev – Tel Aviv University

Bik’s Picks
Source of Antarctica’s Eerie ‘Bleeding Glacier’ Found – Becky Oskin – Live Science

Video: Watch an Algae Cell Turn Itself Inside Out – Douglas Main – NewsWeek

How do you find a Burmese python in the Everglades? – Michael Casey – CBS News

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April 27, 2015

Posted on by

Events:

Life Science Sunset Mixer and Protocols Hackathon – ZappyLab – Berkeley, CA – Thursday April 30 5:30 pm PDT

Microbiome webinar: can diet can modify GI bacteria? – May 6, 2015 at 1:00pm ET – American Society for Nutrition’s Nutritional Science Council

Microbiome of pregnancy and birth

The neonatal gut harbours distinct bifidobacterial strains – Eoin Barrett – Arch Dis Child Fetal Neonatal Ed

Doctoral thesis: Early Life Intestinal Microbiota in Health and in Atopic Eczema – Lotta Nylund – Turku, Finland

In mice: Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother – Joseph G Daft – Microbiome

Human gut microbiome

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT – E Biagi – Bone Marrow Transplantation

Review: Characterization of the intestinal microbiota and its interaction with probiotics and health impacts – Carine Nunes de Almada – Applied Microbiology and Biotechnology

Commentary: The Gut Microbiome: A New Frontier for Alcohol Investigation – Gail A. Cresci – Alcoholism: Clinical and Experimental Research

Review: The Microbiome for Gastroenterologists – Amit Dutta – Gastroenterology & Endoscopy News

Animal microbiome

Dynamic Distribution of the Gut Microbiota and the Relationship with Apparent Crude Fiber Digestibility and Growth Stages in Pigs – Qing Niu – Scientific Reports

Rumen: A new family of hybrid virophages from an animal gut metagenome – Natalya Yutin – Biology Direct

Rumen: Exploring the sheep rumen microbiome for carbohydrate-active enzymes – Lucas Dantas Lopes – Antonie van Leeuwenhoek

Fish: Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota – Chris CR Smith – The ISME Journal

Insects: Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods – Marcia Gumiel – Parasites and Vectors

Plant root and soil microbiome

Link to PDF on Fierer lab website (PNAS link still not working): Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition – Andrzej Tkacz – The ISME Journal

Forest harvesting reduces the soil metagenomic potential for biomass decomposition – Erick Cardenas – The ISME Journal

Peatland vascular plant functional types affect methane dynamics by altering microbial community structure – Bjorn JM Robroek – Journal of Ecology

Structure and function of rhizosphere and non-rhizosphere soil microbial community respond differently to elevated ozone in field-planted wheat – Zhan Chen – Journal of Environmental Sciences

Review: Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential – Shyamalina Haldar – The Open Microbiology Journal

Water microbiome

Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea – Paraskevi N. Polymenakou – Research in Microbiology

Characterization of the Relative Importance of Human- and Infrastructure-Associated Bacteria in Graywater: A Case Study – Scott P. Keely – Journal of Applied Microbiology

Extremophiles

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh – Verena Salman – The ISME Journal

Book: Microbial Evolution under Extreme Conditions – Corien Bakermans – Google Books/Nature

Microbiome of the built environment

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system – Li-Yang Hsu – Genome Biology

Food microbiology

Evolution of microbial counts and chemical and physico-chemical parameters in high-moisture Mozzarella cheese during refrigerated storage – Annamaria Ricciardi – LWT – Food Science and Technology

Phages, viruses, and CRISPRs

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus – David Paez-Espino – mBio

Perspective: Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans?
Fanny Balique – Viruses

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring – Hongming Wang – Springer Plus

Metagenomics and Bioinformatics

He’s alive! Elviz – exploration of metagenome assemblies with an interactive visualization tool – Michael Cantor – BMC Bioinformatics

Genome assembly using Nanopore-guided long and error-free DNA reads – Mohammed-Amin Madoui – BMC Genomics

Protocol: Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing – Carolina Grob – Springer Protocols Handbooks 2015

PhD thesis: MetaPathways : a modular pipeline for the analysis of environmental sequence information – Niels William Hanson – University of British Columbia

Metabolomics

Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii – Sylvie Miquel – mBio

MetaboAnalyst 3.0—making metabolomics more meaningful – Jianguo Xia – Nucleic Acids Research

Microbes in the news

Crowd funding: Stayin’ alive: how do microbes help corals recover from bleaching? The roles of bacteria in corals – Laura Núñez-Pons – Experiment.com

Building a better microbiome – Richard A. Marini – Express News

The Truth About C-Sections, Probiotics, and the Bacteria in Your Gut: Dr. Neil Stollman on fecal microbiota transplants

Your make-up could be a breeding ground for bacteria – Kimberley Hibbert – Jamaica Observer

Learning from Earth’s Smallest Ecosystems (Kavli Hangout) – Alan Brown – Live Science

Spoiled rotten: how breweries are trying to spot bad beer through DNA – Josh Lowensohn -The Verge

The Fecal Bacterium You’ll Learn to Love – Jason Tetro – Huffington Post

Pet Talk: Research reveals canine skin microbiome – Your Houston News

Physician-scientist cautions against indiscriminate use of antibiotics – Bob Kustra – Idaho Statesman

Waterproof bacteria inspire special coatings – Tim Sandle – Digital Journal

Metanome changes name to Diversigen – News Medical

Solving Real-World Problems With Unconventional Solutions: Using Bacteria To Heal Wounds – Texas A&M Today

Strike a healthy bacteria balance in your gut – Scott Scanlon – Buffalo News

How Safe is Your Shrimp? – Consumer Reports study finds 60% of frozen shrimp contaminated with bacteria – Food Safety News

Science, publishing, and career

Trove of VA reports reveals research misconduct, medical malpractice – Brendan Borrell – Retraction Watch

Lab Bloopers: Reddit users share the worst mishaps they’ve witnessed while working in the lab – Jenny Rood – The Scientist

Peer review, explained (cartoon) – Academia Obscura

Bik’s Picks

Why pregnant women in Mississippi keep dying – Danielle Paquette – Washington Post

Oil May Have Killed Gulf Dolphins – David Biello – Scientific American

Photos: 7-Year-Old Boy Discovers T. Rex Cousin – Live Science
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April 22, 2015

Posted on by

Happy Earth Day! Today, I screened 371 papers for you from ISME Journal, Nature, Applied and Environmental Microbiology, PLOS ONE, and others. Here is what I found:

Human oral microbiome

Quorum-Sensing Dysbiotic Shifts in the HIV-Infected Oral Metabiome – Robert E. Brown – PLOS ONE

Full mouth periodontal debridement with or without adjunctive metronidazole gel in smoking patients with chronic periodontitis: A pilot study – C. C. Bergamaschi – Journal of Periodontal Research

Human respiratory microbiome

Changes in Cystic Fibrosis Airway Microbial Community Associated with a Severe Decline in Lung Function – Patrizia Paganin – PLOS ONE

Bacteriological Assessment of Healthcare-Associated Pneumonia Using a Clone Library Analysis – Shingo Noguchi – PLOS ONE

Human gut microbiome

Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome – Christine Dominianni – PLOS ONE

Editorial: Gut Bacteria Combined With Poor Diet May Promote Childhood Malnutrition – M. J. Friedrich – JAMA

Animal models of microbiome research

Effects of dietary supplementation of selenium-enriched probiotics on production performance and intestinal microbiota of weanling piglets raised under high ambient temperature – C. H. Lv – Journal of Animal Physiology and Animal Nutrition

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation – A. Corrigan – Applied and Environmental Microbiology

Animal microbiome

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats – Jinzhen Jiao – Applied and Environmental Microbiology

Shifts in Bacterial Communities of Eggshells and Antimicrobial Activities in Eggs during Incubation in a Ground-Nesting Passerine – Stéphanie Grizard – PLOS ONE

Plant microbiome

Fungi on leaves: Host genotype is an important determinant of the cereal phyllosphere mycobiome – Rumakanta Sapkota – New Phytologist

Soil and plant soil microbiome

Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS USA

Missing forests: Soil microbiome responses to the short-term effects of Amazonian deforestation – Acacio A. Navarrete – Molecular Ecology

Distinct soil microbial diversity under long-term organic and conventional farming – Martin Hartmann – The ISME Journal

Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms – Maxime Bonhomme – Molecular Biology and Evolution

Differential Assemblage of Functional Units in Paddy Soil Microbiomes – Yongkyu Kim – PLOS ONE

The Effect of Biochar and Its Interaction with the Earthworm Pontoscolex corethrurus on Soil Microbial Community Structure in Tropical Soils – Jorge Paz-Ferreiro – PLOS ONE

Water microbiome

Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments – Vanessa Rédou – Applied and Environmental Microbiology

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems – Delphine Lallias – The ISME Journal

Food microbiology

Spoiler alert: Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage – Stéphane Chaillou – ISME Journal

Proteomics

“You produce while I clean up,” a strategy revealed by exoproteomics during Synechococcus–Roseobacter interactions – Joseph A. Christie-Oleza – Proteomics

Microbes in the news

How Modern Life Depletes Our Gut Microbes – Michaeleen Doucleff – NPR Goats and Soda

Great longread: Forensic science: The soil sleuth – Forensic geologist Lorna Dawson helps convict criminals using the dirt from their shoes – Chelsea Wald – Nature

A Microbiome Three-Conference Summary – Kristina Campbell – The Intestinal Gardener

University brews up artificial kopi luwak coffee with even more flavor using civet microbiome – Katherine Wei – China Post

Science, publishing, and career

The postdoc series: What comes next? A postdoc sets you up for a variety of careers, including academia, editing, working in industry, core laboratories and more – Julie Gould – Nature Jobs

Is it fair to evaluate Ph.D. students based on their personalities? Fallout from a gutless adviser – Alice Huang – Science

Minority Ph.D. students: Where do they go? – Beryl Lieff Benderly – Science

Bibliometrics: The Leiden Manifesto for research metrics – Diana Hicks – Nature

Rita Colwell: Women in science still battle bias – Mike McInally – Mid-Valley Health

Bik’s Picks

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop – Tina Kyndt – PNAS

How exactly do mosquitoes track us down – and what makes humans their meal of choice? – Biodetectives

Construction workers in China accidentally unearth dinosaur eggs – Sean O’Kane – The Verge
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