Category Archives: Water microbiome

March 9, 2015

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Pregnancy and birth

Association between caesarean section and childhood obesity: a systematic review and meta-analysis – S. Kuhle – Obesity Reviews

Editorial: Metabolomics, milk-oriented microbiota (MOM) and multipotent stem cells: the future of research on breast milk – Vassilios Fanos – Journal of Pediatric and Neonatal Individualized Medicine

Human oral microbiome

Detection of Mycobacterium tuberculosis DNA on the oral mucosa of tuberculosis patients – Rachel C. Wood – Scientific Reports

Human gut microbiome

Microbes-Gut-Brain Axis: A Possible Future Therapeutics Target for Gastrointestinal and Behavioral Disorder – Amit Ghosh – International Journal of Health Sciences and Research

Review: Collective unconscious: how gut microbes shape human behavior

Human microbiome after death

Seasonal variation of postmortem microbial communities – David O. Carter – Forensic Science, Medicine, and Pathology

Animal models of microbiome research

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure – Adrienne B Narrowe – Microbiome

Responses in gut microbiota and fat metabolism to a halogenated methane analogue in Sprague Dawley rats – Yong Su – Microbial Biotechnology

Animal microbiome

The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection – Scott J Weese – Veterinary Research

Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis – Matthew H. Becker – Molecular Ecology

Microbial ecology in Hydra: Why viruses matter – Thomas C.G. Bosch – Journal of Microbiology

Plant microbiome

Microbial communities on flower surfaces act as signatures of pollinator visitation – Masayuki Ushio – Scientific Reports

Review: The Ecology and Natural History of Foliar Bacteria with a Focus on Tropical Forests and Agroecosystems – Eric A. Griffin, Walter P. Carson – Botanical Review

Review: Chemical diversity of microbial volatiles and their potential for plant growth and productivity – Chidananda N. Kanchiswamy – Frontiers in Plant Science

Soil and plant root microbiome

Metagenomic Assessment of the Potential Microbial Nitrogen Pathways in the Rhizosphere of a Mediterranean Forest After a Wildfire – José F. Cobo-Díaz – Microbial Ecology

Evaluation of Methyl Bromide Alternatives Efficacy against Soil-Borne Pathogens, Nematodes and Soil Microbial Community – Hongwei Xie – PLOS ONE

Relative importance of soil physico-chemical characteristics and plant species identity to the determination of soil microbial community structure – André M. Massenssini – Applied Soil Ecology

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria – Angus Angermeyer – Environmental Microbiology

Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils – Jing Li – Environmental Science and Pollution Research

Extreme plagiarism alert: Influence of heavy metals on earthworms, soil microbial community and mammals – Ahmad Gholamalizadeh Ahangar and Abbas Keshtehgar – Journal of Novel Applied Sciences

Water (and ice) microbiome

Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida – Alexandra M. Campbell – MicrobiologyOpen

Temperature affects the size-structure of phytoplankton communities in the ocean – Ángel López-Urrutia – Limnology and Oceanography

Stable microbial community composition on the Greenland Ice Sheet – Michaela Musilova – Frontiers in Microbiology

Diversity and spatial distribution of autotrophic communities within and between ice-covered Antarctic lakes (McMurdo Dry Valleys) – Jenna M. Dolhi – Limnology and Oceanography

Book chapter: Microbial Life in Volcanic Lakes – Francesca Mapelli – Volcanic Lakes

Microbiome of the built environment

Urban microbiome – Orli G. Bahcall – Nature Review Genetics

Our interface with the built environment: immunity and the indoor microbiota – Simon Lax – Trends in Immunology

Microbial evolution and ecology

Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life – Céline Petitjean – Molecular Biology and Evolution

The community ecology of pathogens: coinfection, coexistence and community composition – Eric W. Seabloom – Ecology Letters

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data – Sylvie Schulze – Frontiers in Microbiology

Genetic isolation between two recently diverged populations of a symbiotic fungus –
Sara Branco – Molecular Ecology

Review: Ecology and exploration of the rare biosphere – Michael D. J. Lynch & Josh D. Neufeld – Nature Reviews Microbiology

Metagenomics and bioinformatics

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data – Johan Bengtsson-Palme – Molecular Ecology Resources

RITA: Rapid Identification of HighConfidence Taxonomic Assignments for Metagenomic Data – Norman J. MacDonald – Genes, Genomes and Metagenomes

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets – Matthias Scheuch – BMC Bioinformatics

Poster: Possibilities and obstacles in recovery of genomes from elusive microbes in complex metagenomes – Søren M. Karst

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic – Richard J. Hall – Frontiers in Microbiology

Whole genome sequencing in clinical and public health microbiology – Kwong, J. C – Pathology

Metabolomics

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links – Rico Rueedi – PLOS Genetics

Techniques

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons – Nathan D. Olson – Biomolecular Detection and Quantification

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations – Fiona Fouhy – PLOS ONE

Parallel DNA polymerase chain reaction: Synthesis of two different PCR products from a DNA template – Vikash Bhardwaj1, Kulbhushan Sharma2 – F1000 Research

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton- Nature Biotechnology

Microbes in the news

1h podcast with Jonathan Eisen: The Tiny World of Microbes Inside You – Inquiring Minds at Soundcloud

20m podcast: The Straight Poop – Transistor

Beyond Probiotics: Can You “Hack” Your Microbiome? – Beth Skwarecki – Vitals

The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’ – Nick Lane – Royal Society

Drugging the gut microbiome – Ken Garber – Nature Biotechnology

Tummy Troubles? Your Microbiome Can Help – Isabel Smith

Sewage Bacteria Reveal Cities’ Obesity Rates – Brian Owens – Inside Science

Trend of colon cleansing generally unnecessary – Denise Cedar and Marilyn Bacon – Statesman Journal

Health focus shifts to gut microbiome and nurturing ‘good’ bacteria – Peg Moline – LA Times

How Microbes Keep Us Healthy – Scientific American

Understanding psychobiotics: John F. Cryan – Catherine Lawson – Wired

“Thinking from the Gut” – Rob Wipond – Mad In America

Prediabetes Patients Have Fewer Gut Bugs – Parker Brown – MedPageToday

Fecal microbiota present target for glucose tolerance assessment – Elena Barengolts – Healio

How gut microbiota could play a key role in protecting the brain – Nina Weisbroth – Translational Microbiome

Hand-Wringing Over Bacteria – C. Claiborne Ray – New York Times

Beer Makers To Produce Beer Replicas of 170-Year-Old Brews – Jenny Michelle Panganiban – International Business News

Gut check: With bacteria in us and all over us, researchers are finding ways to take advantage of them – Kyle Peveto – The Advocate

First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life – Lab Manager

Autism’s bacteria link gains credence – Jonathan Sher – LF Press

Nestlé’s research on nutrition and the human gut microbiome – Enea Rezzonico – Scientific American

Fine Focus: Microbiology Research Journal for Undergraduate Students

Science and art

New Drawings Show the Strange Beauty of Phages, the Bacteria Slayers – Brian Handwerk – Smithsonian’

Cosmos: Abstract Images Created by Destroying Star Photo Film Slides with Bacteria – Michael Zhang – Peta Pixel

Science, publishing, and career

Keys to the kingdom (academic bioentrepreneurs) – Sybil C K Wong- Nature Biotechnology

My Most Informative Error – Ami Schattner – JAMA Internal Medicine

We need post-publication peer review of journals – Lenny Teytelman – The Spectroscope

Bik’s Picks: The science of aging edition

Cavers Find Ancient Hoard of Coins and Jewelry in Israel – Megan Gannon – Live Science

Book Review: Rust’ Offers an Engrossing Look at Corrosion – Gregory Cowles – New York Times

Achieving Immortality: How Science Seeks to End Aging – Josh Nilaya – WNPR

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March 6, 2015

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Pregnancy and birth

Longitudinal Analysis of the Premature Infant Intestinal Microbiome Prior to Necrotizing Enterocolitis: A Case-Control Study – Yanjiao Zhou – PLOS ONE

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota – Tadao Enomoto – Allergology International

Human oral microbiome

Subgingival Microbial Communities in Leukocyte Adhesion Deficiency and Their Relationship with Local Immunopathology – Niki M. Moutsopoulos – PLOS Pathogens

Human gut microbiome

What is missing from this title? 16S gut community of the Cameron County Hispanic Cohort – Matthew C Ross – Microbiome

Review: The role of intestinal microbiota in acute graft-versus-host disease – Yuanyuan Chen – Journal of Immunology Research

Review: Type 1 diabetes and gut microbiota: Friend or foe? – Changyun Hu – Pharmacological Research

Review: Collective unconscious: how gut microbes shape human behavior
Timothy G. Dinan- Journal of Psychiatric Research

Human respiratory microbiome

2013 Workshop summary: Host–microbe interactions in distal airways: relevance to chronic airway diseases – Clémence Martin – European Respiratory Review

Review: Microbial Exposure and Onset of Allergic Diseases – Potential Prevention Strategies? – Petra Ina Pfefferle, Harald Renz – Allergology International

Animal models of microbiome research

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome – Jun Wang – Nature Communications

Disturbance of the intestinal microbial community by ursolic acid contributes to its function as a regulator of fat deposition – Zemeng Feng – Journal of Functional Foods

Helicobacter hepaticus infection in BALB/c mice abolishes subunit-vaccine-induced protection against M. tuberculosis – Isabelle C. Arnold – Vaccine

Animal microbiome

Early life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

In cattle: Characterization of mucosa-associated bacterial communities in abomasal ulcers by pyrosequencing – Alexandra Hund- Veterinary Microbiology

Baby marmosets (Do a Google Image search)! Isolation and identification of cultivable Bifidobacterium spp. from the faeces of 5 baby common marmosets (Callithrix jacchus L.) – Samanta Michelini – Anaerobe

A Kazal-type inhibitor is modulated by Trypanosoma cruzi to control microbiota inside the anterior midgut of Rhodnius prolixus – Tatiane S. Soares – Biochimie

Plant microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Soil and sediment microbiome

A Method for Determining Community Level Physiological Profiles of Organic Soil Horizons – Mathew J.B. Swallow and Sylvie A. Quideau – Soil Science Society of America Journal

Influence of elevated ozone concentration on methanotrophic bacterial communities in soil under field condition – Y.Z. Huang – Atmospheric Environment

Disruption of photoautotrophic intertidal mats by filamentous fungi – Cátia Carreira – Environmental Microbiology

Phylogenetically distinct phylotypes modulate nitrification in a paddy soil – Jun Zhao – Applied and Environmental Microbiology

Water microbiome

Metagenomic analysis of a high CO2 subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla – Joanne B. Emerson – Environmental Microbiology

Effect of historical residual hexachlorocyclohexanes and dichlorodiphenyltrichloroethane on bacterial communities in sediment core collected from an estuary in northeastern China by next-generation sequencing – Jianguo Guo – Marine Pollution Bulletin

Understanding diversity patterns in bacterioplankton communities from a Sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria (“Candidatus Thiopilula spp.”) from abyssal cold seeps of the Barbados Accretionary Prism – Daniel S. Jones – Applied and Environmental Microbiology

Bioreactor microbiome

Long-term dynamics of the microbial community in a full-scale wastewater treatment plant – A. Muszyński – International Biodeterioration & Biodegradation

Microbiome of the built environment

Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities – Tamar Dickerson – Online Journal of Public Health Informatics

Food microbiology

Yeast strains as potential aroma enhancers in dry fermented sausages – Mónica Flores – International Journal of Food Microbiology

Metagenomics and bioinformatics

IVA: accurate de novo assembly of RNA virus genomes – Martin Hunt – Bioinformatics

Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels – Rika A. Furuta – Transfusion

Review: Fungal genome sequencing: basic biology to biotechnology – Krishna Kant Sharma – Critical Reviews in Biotechnology

Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis – Qizhi Cao – Gut

Proteomics

Review: Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Microbial Ecology

Predicting ecosystem emergent properties at multiple scales – Jack A. Gilbert and Chris Henry – Environmental Microbiology Reports

Perspective: Re-defining microbial diversity from its single-celled building blocks – Ramunas Stepanauskas – Environmental Microbiology Reports

Microbes in the news

Not Even Science Could Explain the Bacteria In My Apartment – Sarah Zhang – Gizmodo

Gut microbial mix relates to stages of blood sugar control – Medical Xpress
Gut bacteria may contribute to diabetes in black males – Sharon Parmet – University of Illinois at Chicago

Who owns my microbiome? – Gabrielle Morguelan – Transylvania Rambler

Bill Gates Foundation backs microbiome engineering to boost infant health – Shane Starling – Nutraingredients

Antarctic lakes are full of small surprises – Sarah Payne – Australian Antarctic Magazine

Long list of food items in alphabetical order, but not much science: The human microbiome: How to feed your gut – Mindy Athas – Baltimore Sun

Science, publishing, and career

Need registration to read: It starts with a poster: Most researchers learn how to talk about science at meetings – Marcia McNutt – Science

Why has the scholarly journal endured? – Alice Meadows – Exchanges at Wiley

Reflecting on Fifty Years of Progress for Women in Science – Nancy Hopkins – DNA and Cell Biology

Bik’s Picks

Video: Giant Octopus makes slippery escape from tank in Seattle aquarium – Ben Axelson – Syracuse

CCTV unexpectedly catches rare wild giant panda on midnight stroll – Rose Troup Buchanan – Independent

Turning yogurt waste into new products – University of Wisconsin-Madison – Science Daily

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March 3, 2015

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Human microbiome general

Manuscript: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes and Other Selfish Entities Shape Our Behavior – Peter Kramer and Paola Bressan

Microbiome of pregnancy and birth

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development – Tali Raveh-Sadka – eLIFE

Human respiratory microbiome

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals – Christine M. Bassis – mBio

Human gut microbiome

The relevance of intestinal dysbiosis in liver transplant candidates – M. Grąt – Transplant Infectious Disease

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohn’s Disease – Suskind, David L. – Inflammatory Bowel Diseases

Review: The Guts of Obesity: Progress and Challenges in Linking Gut Microbes to Obesity  – Gabriel A. Al-Ghalith – Discovery Medicine

Animal models of microbiome research

Thesis: Exercise is more effective at producing robust, lasting changes in gut microbial composition in juvenile than in adult male F344 rats – Agnieszka Mika – University of Colorado at Boulder

The gut microbiome restores intrinsic and extrinsic nerve function in germ-free mice accompanied by changes in calbindin – K. A. McVey Neufeld – Neurogastroenterology & Motility

Cystic fibrosis mouse model-dependent intestinal structure and gut microbiome – Mark Bazett – Mammalian Genome

Use of bacteriocin-producing, probiotic strain Enterococcus faecium AL41 to control intestinal microbiota in farm ostriches – Andrea Lauková – Letters in Applied Microbiology

Animal microbiome

Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses – Shaufi M Mohd Asrore – Gut Pathogens

Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens – Douglas C. Woodhams – Ecological Archives

Diet shapes the gut microbiota of the omnivorous cockroach Blatella germanica – Ana Elena Pérez-Cobas – FEMS Microbiology Ecology

Characterization of the honey bee microbiome throughout the queen-rearing process – David R. Tarpy – Applied and Environmental Microbiology

Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand-islands reef complex, West-Java, Indonesia – Nicole J. de Voogd – FEMS Microbiology Ecology

Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf – B. C. C. Hume – Scientific Reports

Plant microbiome

Grazing livestock are exposed to terrestrial cyanobacteria – Bruce C McGorum – Veterinary Research

Soil and root microbiome

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere –
Chanyarat Paungfoo-Lonhienne – Scientific Reports

Changes in soil microbial community structure and activity in a cedar plantation invaded by moso bamboo – Ed-Haun Chang, Chih-Yu Chiu – Applied Soil Ecology

Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities – Kristin Aleklett – PeerJ

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site – Indumathy Jayamani, Alison M. Cupples – Environmental Science and Pollution Research

Impact of metal pollution on fungal diversity and community structures – Michiel Op De Beeck – Environmental Microbiology

Water microbiome

Diverse uncultivated ultra-small bacterial cells in groundwater – Birgit Luef – Nature Communications

Impacts of the Three Gorges Dam on microbial structure and potential function – Qingyun Yan – Scientific Reports

Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean – Rosemary E. Scavotto – Environmental Microbiology

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India) – Sheryl Oliveira Fernandes – Brazilian Journal of Microbiology

Bioreactor microbiology

Start-up strategies in manure-fed biogas reactors: Process parameters and methanogenic communities – M. Goberna – Biomass and Bioenergy

Microbiome of the built environment

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China – Huirong Lin – BioMed Research International

Observational scores of dampness and mold associated with measurements of microbial agents and moisture in three public schools – S. J. Cho – Indoor Air

Food microbiology

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome – Armin Erlacher – PLOS ONE

Phages and viruses

‘Ménage à trois’: a selfish genetic element uses a virus to propagate within Thermotogales – Julien Lossouarn – Environmental Microbiology

Microbial Ecology

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession – Francisco Dini-Andreote – PNAS USA

The community ecology of pathogens: coinfection, coexistence and community composition – Eric W. Seabloom – Ecology Letters

Tuberculosis: Fighting an old disease with next-generation sequencing – Anzaan Dippenaar, Robin M. Warren – eLIFE

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen – Braham Dhillon – PNAS USA

A tortoise-infecting picornavirus expands the host range of the family Picornaviridae
Terry Fei Fan Ng – Archives of Virology

Metagenomics and bioinformatics

Review: Insights from 20 years of bacterial genome sequencing – Miriam Land – Functional & Integrative Genomics

Review: The Current Status and Challenges in Computational Analysis of Genomic Big Data – Yiming Qin – Big Data Research

Metabolomics

Impact of storage conditions on metabolite profiles of sputum samples from persons with cystic fibrosis – Jiangchao Zhao – Journal of Cystic Fibrosis

Microbes in the news

Enter the Vaginome: Meet the Microbes that Live in Our Vaginas – A.V. Flox – Motherboard

New paper on diseased vs healthy infants in a NICU, possible impacts for future hospital microbiome work – Bubba Brooks – MicroBEnet

Archaea: Mysterious microbes hold big possibilities for Sloan Research Fellow Alyson Santoro – EurekaAlert

Genes & cells: Jet lag disrupts microbes in the gut: Mice with time-shifted bacteria develop metabolic problems – Tina Hesman Saey – Science News

The environment may change, but the microbiome of queen bees does not – Matt Shipman

Cheesey Microbial Communities – Daniel P. Haeusser – Small Things Considered

150,000 of these bacteria could fit on the tip of a hair (and that’s about as small as life can get) – Rachel Feltman – Washington Post

Unusual Bacteria Discovered In Deepest Ocean Trench – Ocean Leadership

Link Identified Between Virus Recognition, Destruction in Bacterial Immune System – Infection Control Today
Researchers Discover How Bacteria ‘Steal’ Genetic Information – Jim Algar – Tech Times

Science, publishing, and career

Different personal propensities among scientists relate to deeper vs. broader knowledge contributions – Thomas S. Bateman, and Andrew M. Hess – PNAS USA
Attention, All Scientists: Do Improv, With Alan Alda’s Help – Kenneth Chang – New York Times

Bik’s Picks

Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa –
Fabrice Lihoreau – Nature Communications

Termites: Guardians of the Soil – Natalie Angier – New York Times

A social chemosignaling function for human handshaking – Idan Frumin – eLIFE

Snip, Snap, Slurp: Misophonia Makes Them Unbearable – What sound most grates on your nerves? – Karen Barrow – New York Times
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March 2, 2015

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General microbiome papers

Review: The Microbiome: A Contributor to Health and Disease – Bailus Walker Jr. – Journal of the Health Care for the Poor and Underserved

Human oral microbiome

Transduction-mediated horizontal gene transfer in the oral microbiome – Roy H. Stevens – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Review: The lung mycobiome: an emerging field of the human respiratory microbiome – Linh D. N. Nguyen – Frontiers in Microbiology

Human gut microbiome

Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages – Se-Hoon Park – BMC Microbiology

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality – Yanfei Chen – Journal of Gastroenterology and Hepatology

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj – Abiola Olumuyiwa Olaitan – International Journal of Antimicrobial Agents

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Human vaginal microbiome

Correlates of the molecular vaginal microbiota composition of African women – Raju Gautam – BMC Infectious Diseases

Animal microbiome

In chickens: Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences – Dragana Stanley – BMC Microbiology

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh – Andrea M. Larsen – Microbial Ecology

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences – Sandra Pucciarelli – Microbial Ecology

Plant microbiome

Phenotypic and genetic characterization of rhizobia isolated from Hedysarum flexuosum in Northwest region of Morocco – Fatima Ezzakkioui – Journal of Basic Microbiology

Biotic and abiotic predictors of fungal colonization in grasses of the Colorado Rockies – Luciana B. Ranelli – Diversity and Distributions

Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Martina Köberl – Frontiers in Microbiology

Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. – Armin Erlacher – Frontiers in Microbiology

Soil and sediment microbiome

Agricultural intensification and the functional capacity of soil microbes on smallholder African farms – Stephen A. Wood – Journal of Applied Ecology

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees – Michaela Urbanová – Soil Biology and Biochemistry

Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia – Robert Duran – Environmental Science and Pollution Research

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation – Maria E. Hernandez – PeerJ

Water microbiome

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs – Peter Menzel – Microbial Ecology

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients – Jiwen Liu – Frontiers in Microbiology

Microbiome of the built environment

Thesis: Longitudinal and spatial characterization of microbial communities in offices – John Chase – Northern Arizona University

Bacterial transfer to beverages during drinking games: ‘beer pong’ – Paul L. Dawson – Int. J. Food Safety, Nutrition and Public Health

Food microbiology

High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia – Wenjun Liu – BMC Microbiology

Microbiological Changes and Biodiversity of Cultivable Indigenous Bacteria in Sanbao Larger Yellow Croaker (Pseudosciaena crocea), a Chinese Salted and Fermented Seafood – He Zhang – Journal of Food Sciences

Bioreactor microbiology

A methodological framework for linking bioreactor function to microbial communities and environmental conditions – Francis L de los Reyes III – Current Opinion in Biotechnology

Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing – Haihan Zhang – BMC Microbiology

Phages and viruses

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales – Uri Gophna – ISME Journal

Inactivation of an Enveloped Surrogate Virus in Human Sewage – Lisa M. Casanova – Environ. Sci. Technol. Lett.

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing – Friederike S. Rossmann – PLOS Pathogens

Archaea

Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing – Vanessa D. Nkamga – Current Microbiology

Bioinformatics and metagenomics

The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: Case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia – E. González-Tortuero – Molecular Ecology Resources

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics – Sandeep K Kushwaha – BMC Bioinformatics

Spaced seeds improve metagenomic classification – Karel Bˇrinda – ArXiv

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K – Naama M. Kopelman – Molecular Ecology Resources

PhD thesis: Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome – Sharon I. Greenblum – University of Washington

Masters thesis: MR-CUDASW – GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data – Amir Muhammadzadeh

Testing ecological theories with sequence similarity networks: marine ciliates
exhibit similar geographic dispersal patterns as multicellular organisms – Dominik Forster – BMC Biology

A Brief Review of Software Tools for Pangenomics – Jingfa Xiao – Genomics, Proteomics & Bioinformatics

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes – Xavier Didelot – PLOS Computational Biology

Ten years of pan-genome analyses – George Vernikos – Current Opinion in Microbiology

Metabolomics and proteomics

Towards further defining the proteome of mouse saliva – Anne A Blanchard – Proteome Science

Protein Complexes in Bacteria – J. Harry Caufield – PLOS Computational Biology

Review: Metabolomics and Diabetes: Analytical and Computational Approaches – Kelli M. Sas – Diabetes

Techniques

Inosine at Different Primer Positions to Study Structure and Diversity of Prokaryotic Populations – Eitan Ben-Dov and Ariel Kushmaro – Current Issues Molecular Biology

Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil – Hannes Schmidt – Soil Biology and Biochemistry

Microbes in the news

Diet, Location And Your Kid’s Gut Bacteria – Stefania Hartley – Asian Scientist Magazine

Killing off one Bacterium Can Lead to Obesity – Noel Angeles – SMN Weekly

The Human Microbiome Through an Oral Healthcare Lens – Natasha Singh – Oral Health Group

Yes Virginia, there is a paper on microbial transfer during beer pong – Jonathan Eisen

First detailed evidence of bacteria at the lower size limit of life – Science Codex

How Small Can Life Get? These Ultra-Small Bacteria May Be At The Limit – Science 2.0

Title Fail: Deadly bacteria outbreak linked to UCLA microscopes – Standard Examiner

The bioMASON Startup Grows Bricks from Bacteria – Annie Pilon – Small Biz Trends

Deadly bacteria release sparks concern at Louisiana lab – Alison Young – USA Today

Science, publishing and career

Riding Out Rejection: How to navigate the choppy waters of scientific publication – Kate Yandell – The Scientist

Medical Journals and Free Speech – Joel Bakan – Pediatrics

How to Write a Presubmission Inquiry – Thomas Lengauer, Ruth Nussinov – PLOS Computational Biology

Chill GPS: Keeping track of frozen biological samples – Jeffrey M. Perkel – The Scientist

Science and Art

Move over #TheDress and #LlamaDrama, this weekend’s Twitter storm was all about #SciArt – Twitter

Bik’s Picks

Scientists have created the perfect music for cats – Fiona MacDonald – Science Alert

Gulf of Mexico Turns Deadly for Dolphins – Rachel Nuwer – New York Times

‘Skeletorus’ and ‘Sparklemuffin’ the Newest Spiders – Agata Blaszczak Boxe – Live Science

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February 27, 2015

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Human skin microbiome

Poster abstract: The skin microbiome in psoriatic arthritis: methodology development and pilot data – Madhura Castelino – The Lancet

Human gut microbiome

Gut microbiota and obesity: Involvement of the adipose tissue – Sonia Guida, Koen Venema – Journal of Functional Foods

Review about Diabetes: T1DM and the gut microbiome – Jennifer Sargent – Nature Reviews Endocrinology

Review: The emerging influence of the intestinal microbiota during allogeneic hematopoietic cell transplantation: Control the gut and the body will follow – Melissa D. Docampo – Biology of Blood and Marrow Transplantation

Animal and bioreactor models

Reshaping Faecal Gut Microbiota Composition by the Intake of Trans-Resveratrol and Quercetin in High-Fat Sucrose Diet-Fed Rats – U. Etxeberria – The Journal of Nutritional Biochemistry

Quantification of symbiotic contributions to lower termite lignocellulose digestion using antimicrobial treatments – Brittany F. Peterson – Insect Biochemistry and Molecular Biology

Interactions of Salmonella enterica subspecies enterica serovar Typhimurium with gut bacteria – Gaspar Avendaño-Pérez – Anaerobe

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome – Jo De Vrieze – Water Research

Animal microbiome

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque
Koji Yasuda – Cell Host & Microbe

Prospects of host-associated microorganisms in fish and penaeids as probiotics with immunomodulatory functions – Carlo C. Lazado – Fish & Shellfish Immunology

A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes – Nurdyana Abdul Rahman – Microbiome

Pathogenicity of bacteria isolated from gut of Spodoptera litura (Lepidoptera: Noctuidae) and fitness costs of insect associated with consumption of bacteria – Abhinay Thakur – Journal of Invertebrate Pathology

Plant microbiome

Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon – Marcela Hernández – Applied and Environmental Microbiology

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley – Davide Bulgarelli – Cell Host & Microbe

Review: Greater than the sum of their parts: characterizing plant microbiomes at the community-level – Sarah L Lebeis – Current Opinion in Plant Biology

Soil microbiome

Review: Belowground environmental effects of transgenic crops: a soil microbial perspective – Alessandra Turrini – Research in Microbiology

Water microbiome

Counting Viruses and Bacteria in Photosynthetic Microbial Mats – Cátia Carreira – Applied and Environmental Microbiology

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota – Lauren M. Sassoubre – Applied and Environmental Microbiology

Microbiome of the built environment

Key determinants of the fungal and bacterial microbiomes in homes – Eric M. Kettleson – Environmental Research

Microbes in the news

The Case of the Curious Microbiome – Alexandra Carmichael – uBiomeBlog

Unlocking the Key to Immunological Memory in Bacteria – Lynn Yarris – Berkeley Lab News Center

Gut microbes targeted for diagnosis, treatment of childhood undernutrition – Caroline Arbanas – Medical Xpress

Virus or bacteria? Soon a test could tell you – Ben Deighton – Horizon

Science, publishing, and career

Why one science journal wants to publish failed studies – Julia Belluz – Vox
Table of Contents: The Missing Pieces: A Collection of Negative, Null and Inconclusive Results – PLOS ONE

Satire: Professor Delighted Grad Student Understands At Least 17% Of Advice – The Allium

Science and Art

Oregon man with rare disorder, Cadillac ties making art from medical imaging – Cadillac News

Bik’s Picks

In Short-Lived Fish, Secrets to Aging – Carl Zimmer – New York Times

What Happens When You Strap a Camera to a Sea Turtle’s Shell – Nicholas St. Fleur – The Atlantic

‘Big Brain’ Gene Found in Humans, But Not in Chimps – Tia Ghose – NBC News/LiveScience

#TheDress The Science of Why No One Agrees on the Color of This Dress – Adam Rogers – Wired

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February 25, 2015

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Nature and Scientific American have a joint Microbiome special: “Innovations in the Microbiome” with several overview papers from Rob Knight, Ruth Ley,  Justin Sonnenburg et al. Articles include:

The Microbes Within – David Grogan
Why Microbiome Treatments Could Pay Off Soon – Rob Knight
Your Microbes at Work: Fiber Fermenters Keep Us Healthy
Mental Health: Thinking from the Gut – Charles Schmidt
Gut Microbiome: The Peacekeepers – Moises Velasquez-Manoff
The Gene–Microbe Link – Ruth E. Ley
Microbiome Engineering – Justin L. Sonnenburg
The Diverse Microbiome of the Hunter-Gatherer – Stephanie L. Schnorr

Human oral microbiome

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci – Robert A. Whiley – PLOS ONE

Human skin microbiome

Malassezia Intra-Specific Diversity and Potentially New Species in the Skin Microbiota from Brazilian Healthy Subjects and Seborrheic Dermatitis Patients – Renan Cardoso Soares – PLOS ONE

Human gut microbiome

From the Gordon lab: Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans – Timothy Heisel – PLOS ONE

Animal models of microbiome research

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome – Benoit Chassaing – Nature

Animal microbiome

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole – Gordon M. Bennett and Nancy A. Moran

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider – Bram Vanthournout, Frederik Hendrickx – PLOS ONE

Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages – Yu Shi – Journal of Basic Microbiology

Plant microbiome

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations – Caio T. C. C. Rachid – PLOS ONE

Soil microbiome

Microbial dynamics in glacier forefield soils show succession is not just skin deep – Arwyn Edwards and Sophie Cook – Molecular Ecology

Microbial deposits in the aftermath of the end-Permian mass extinction: A diverging case from the Mineral Mountains (Utah, USA) – Emmanuelle Vennin – Sedimentology

Water microbiome

Characterizing variability in marine protist communities via ARISA fingerprints—a method evaluation – E.S. Kilias – Limnology and Oceanography: Methods

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System – Katherine E. Fish – PLOS ONE

Microbiome of the built environment

Sewage Reflects the Microbiomes of Human Populations – Ryan J. Newton – mBio

Phages and viruses

The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors – Orla McCabe – Molecular Microbiology

Bioinformatics

Tools for Bacterial Comparative Genomics – Kat Holt – Holt Lab

Techniques

Comparison of different methods for the recovery of DNA from spores of mycotoxin producing moulds in spiked food samples – Sabrina Grube – Letters in Applied Microbiology

Metabolomics

Nutritional stress induces exchange of cell material and energetic coupling between bacterial species – Saida Benomar – Nature Communications

Other papers of interest

Climate-driven introduction of the Black Death and successive plague reintroductions into Europe – Boris V. Schmid – PNAS USA

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs – Eric Londin – PNAS USA

Microbes in the news

Fishing For the Microbes Behind Malnutrition – Ed Yong – National Geographic

4th World Summit ‘Gut Microbiota For Health’ to be held in Barcelona – Phys.org

Indian scientist awarded 1.5 million euros grant to investigate the role of gut microbiota in autoimmune diseases – Economic Times India

Johnson & Johnson Bets On Alzheimer’s Vaccine, Disease Prediction, Human ‘Microbiome’ – Amy Nordrum – International Business Times

Altered microbiome may lead to liver disease in patients with cystic fibrosis – Healio

Cystic Fibrosis Liver Cirrhosis Associated with Intestinal Microbiome – Maureen Newmn – LungDiseaseNews

Linoleic acid role balanced by changes to gut microbiota: Study – Annie-Rose Harrison-Dunn – NutraIngredients

My Microbiome Experience from Start to Results – Alexandra Carmichael – uBiome Blog

Session Report: Citizen Microbiology at Citizen Science 2015 – David Coil – MicroBEnet

Bacteria pipe food to each other using tiny tubes – Francie Diep – Popular Science

CSU study finds that Leprosy bacteria can survive in unusual environments – Emily Vavra – Collegian

Science, publishing and career

Scientists are cautious about public outreach – Chris Woolston – Nature

It’s Time for More Racial Diversity in STEM Toys – Maia Weinstock – Scientific American

Science and art

Science and Culture: Data visualization nurtures an artistic movement – J. D. Talasek – PNAS USA

Bik’s Picks

Wanted: 80,000 British babies for massive study – Helen Pearson – Nature

28.8 million tons of Sahara desert fertilize the Amazon – Deborah Netburn – LA Times

Your Eyelashes Should Be This Long, Science Says – Megan Gannon – Scientific American [hr]

February 24, 2015

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Human oral microbiome

Review: The Oral Microbiome and Cancer – A. Ross Kerr – Journal of Dental Hygiene

Human esophageal/stomach microbiome

Association between tobacco use and the upper gastrointestinal microbiome among Chinese men – Emily Vogtmann – Cancer Causes & Control

Human gut microbiome

Diversity in gut bacterial community of school-age children in Asia – Jiro Nakayama – Scientific Reports

Characterization of the human gut microbiome during travelers’ diarrhea – Bonnie P. Youmans – Gut Microbes

Review: Interactive roles of gut microbiota and gastrointestinal motility in the
development of inflammatory disorders – Hirofumi Okubo – Macrophage

Review: Microbial endocrinology: the interplay between the microbiota and the endocrine system – Hadar Neuman – Microbiology Reviews

Review: Gut/brain axis and the microbiota – Emeran A. Mayer – The Journal of Clinical Investigation

Animal models of microbiome research

Exercise training modifies gut microbiota in normal and diabetic mice – Jennifer Elizabeth Lambert – Applied Physiology, Nutrition, and Metabolism

Impact of dietary deviation on disease progression and gut microbiome composition in lupus-prone SNF1 mice – Benjamin M. Johnson – Clinical & Experimental Immunology

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster – Adam J. Dobson – Nature Communications

Microbial community structure in the gut of the New Zealand insect Auckland tree weta (Hemideina thoracica) – David W. Waite – Archives of Microbiology

Animal microbiome

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing – Xufeng Han – PLOS ONE

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges – Fan Zhang – PNAS USA

Plant microbiome

Identification of novel Bromus- and Trifolium-associated circular DNA viruses – Simona Kraberger – Archives of Virology

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Review: Microbial Symbionts: A Potential Bio-Boom – Mustafa Morsy – Journal of Investigative Genomics

Water microbiome

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth – Takuro Nunoura – PNAS USA

Resilience and recovery: the effect of triclosan exposure timing during development, on the structure and function of river biofilm communities – J.R. Lawrence – Aquatic Toxicology

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm – Min Wang – Journal of Hazardous Materials

Metagenomics

Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool – Aurélia Caputo – Biology Direct

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage – Nicholas H. Putnam – ArXiv

Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information – Jan Zoll – Journal of Clinical Virology

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology – Lilian Pukk – Molecular Ecology Resources

AMAS: optimizing the partition and filtration of adaptive seeds to speed up read mapping – Ngoc Hieu Tran, Xin Chen – arXiv

The Genome 10K Project: A Way Forward – Klaus-Peter Koepfli – Annual Reviews of Animal Biosciences

Other papers of interest

Allergy in Children in Hand Versus Machine Dishwashing – Bill Hesselmar – Pediatrics

Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis – Rachel Bleich – PNAS USA

Microbes in the news

Were early seas transformed by sponge microbiome? – Catherine Brahic – New Scientist

Bacteria Thrive in the Ocean Depths of Challenger Deep – NBC News

Scientists discover bacteria in marine sponges harvest phosphorus for the reef community – Phys.org

Infant Gut Microbiome Linked to Allergic Predisposition (interview with Christine Cole Johnson) – Medical Research

Genetic variety in gut critters tied to disease – Max Green – Columbia Chronicle

Exposure to bacteria, good for a strong immune system? – Justin J Reyes – KGNS

After 8 centuries, rats exonerated in spread of Black Death. Gerbils implicated. – Sarah Kaplan – Washington Post

Your Soap Has Bacteria In It, But It Still Gets You Clean – Poncie Rutsch – NPR Shots

Antibiotics cause dangerous bacteria communities to appear, study says – Suzanne Plunkett – Reuters

Antibiotics give rise to new communities of harmful bacteria – Science Daily

Hand-wash your dishes to help protect kids from allergies – Jessica Firger – CBS News

The Problem With Dirty Money – Paul Rodgers – Forbes

Bik’s Picks

Peanut consumption in infancy prevents peanut allergy, study finds – Science Daily

Climate change is really bad news if you like oysters, scallops and clams – Puneet Kollipara – Washington Post

Space is cool, but NASA’s cheeseburgers look gross – Brian Koerber – Mashable

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February 23, 2015

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General human microbiome

Review: Human Microbiome: When a Friend Becomes an Enemy – Magdalena Muszer – Archivum Immunologiae et Therapiae Experimentalis

Microbiome of pregnancy and birth

Probiotics and gut health in infants: A preliminary case–control observational study about early treatment with Lactobacillus reuteri DSM 17938 – Francesco Savino – Clinica Chimica Acta

Review: Clinical impact of human breast milk metabolomics – Flaminia Cesare Marincola – Clinica Chimica Acta

Human oral microbiome

Review: A review on microbiological cause of periodontal disease: disease and treatment. – Durgesh, Bangalore H – Reviews in Medical Microbiology $$$

Human gut microbiome

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls – Aldona Dlugosz – Scientific Reports

Microbiota disbiosis is associated with colorectal cancer – Zhiguang Gao – Frontiers in Microbiology

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women
Kyungsun Han – Molecular Nutrition & Food Research

Review: Gut microbiota: Microbiota organisation—a key to understanding CRC development – Georgina L. Hold & Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Changing views on diverticular disease: impact of aging, obesity, diet, and microbiota – R. C. Spiller – Neurogastroenterology & Motility

Animal models of microbiome research

Oral microbiome composition changes in mouse models of colitis – Jaana Rautava – Journal of Gastroenterology and Hepatology

Animal microbiome

Diverse small circular DNA viruses circulating amongst estuarine molluscs – Anisha Dayaram – Infection, Genetics and Evolution

Plant microbiome

Moth Outbreaks Alter Root-Associated Fungal Communities in Subarctic Mountain Birch Forests – Karita Saravesi – Microbial Ecology

The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses – Nhu H. Nguyen, Thomas D. Bruns – Microbial Ecology

Soil microbiome

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill – Luis M Rodriguez-R – The ISME Journal

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands – Haowei Yue – The ISME Journal

Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles – Julia Moll – Microbial Ecology

Characteristic microbial communities in the continuous permafrost beside the bitumen in Qinghai-Tibetan Plateau – Nan Jiang – Environmental Earth Sciences

Effect of early dry season induced by the Three Gorges Dam on the soil microbial biomass and bacterial community structure in the Dongting Lake wetland – Haipeng Wu – Ecological Indicators

Disentangling plant and soil microbial controls on carbon and nitrogen loss in grassland mesocosms – Franciska T. De Vries – Journal of Ecology

Water microbiome

Evidence for an active rare biosphere within freshwater protists community – Didier Debroas – Molecular Ecology

Response of the microbial community to seasonal groundwater level fluctuations in petroleum hydrocarbon-contaminated groundwater – Ai-xia Zhou – Environmental Science

Microbiome of the built environment

Isolation of Vermamoeba vermiformis and associated bacteria in hospital water – Isabelle Pagnier – Microbial Pathogenesis

Dynamics of bacterial communities before and after distribution in a full-scale drinking water network – Joline El-Chakhtoura – Water Research

Marine bioerosion of lapideous archaeological artifacts found in the Grotta Azzurra (Capri, Naples, Italy): Role of microbiota and boring Porifera – Carlotta Sacco Perasso – International Biodeterioration & Biodegradation

Bioreactor microbiome

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities – Florian Centler and Martin Thullner – Frontiers in Microbiology

Review: Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus – Marta Carballa – Current Opinion in Biotechnology

Metagenomics, Sequencing and Bioinformatics

Improved detection of artifactual viral minority variants in high-throughput sequencing data – Matthijs R. A. Welkers – Frontiers in Microbiology

Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population – Walter Pirovano – Frontiers in Microbiology

Accurate multiplexing and filtering for high-throughput amplicon-sequencing – Esling Philippe – Nucleic Acids Research

Uploaded manuscript: Metagenomic Assembly Validation of an in vitro Mock Community [PDF] – Ino de Bruijn – Authorea

DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly – Guo Xuan – Journal of Computational Biology

Clustering of reads with alignment-free measures and quality values – Matteo Comin – Algorthms for Molecular Biology

Improved data analysis for the MinION nanopore sequencer – Miten Jain – Nature Methods

Genome-wide gene order distances support clustering the gram-positive bacteria – Christopher H. House – Frontiers in Microbiology

Perspective: Current strategies for mobilome research – Tue S. Jørgensen – Frontiers in Microbiology

Metabolomics

Species-specific dynamic responses of gut bacteria to a mammalian glycan – Varsha Raghavan and Eduardo A. Groisman – Journal of Bacteriology

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

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

Review: Does Our Gut Microbiome Predict Cardiovascular Risk? – A Review of the Evidence From Metabolomics – Julian L. Griffin – Circulation: Cardiovascular Genetics

http://intl-circgenetics.ahajournals.org/content/8/1/187.full

Other microbiology papers of interest

Review: Interactions of Salmonella with animals and plants – Agnès Wiedemann – Frontiers in Microbiology

Microbes in the news

Rob Knight awarded Vilcek Prize 2015 – Vilcek Foundation

AAAAI Annual Meeting Research Links Infants’ Microbiome to Development of Immune System, Allergic Diseases and Asthma – Our Midland

Examining the Hygiene Hypothesis and the Role of the Microbiome in Allergic Disease – Rodrigo Barros – HCP Live

The Role of the Skin Microbiome in Health and Disease – Rodrigo Barros – HCP Live

Facebook banned “Human Microbiome” artist picture for being ‘overly sexual’ – Hannah Parry – Mail Online

Campus bacteria: The whats and wheres of Columbia’s most infamous bacteria (e.g. the Sweatococcus @ Dodge Gym Equipment) – Sophia Hotung – Columbia Spectator

Bacteria connect to each other and exchange nutrients – Phys.org

Researchers explore influence of host organisms on bacterial metabolism – News Medical

Blood tests indicate scientist may not have been sickened at Tulane primate center – Kim Chatelain – Nola

We’re all hosts on a viral planet: E. coli O157 edition – Doug Powell – BarfBlog

Bik’s Picks

Surprise! 1,000-Year-Old Mummy Found in Buddha Statue – NBC News

Crews free humpback whale tangled in fishing line off Hawaii – Fox News

Satire: Collective Cleanliness: A Meta-Discursive Study of Academic Tearoom Culture – Lotta Washinup and Duya Dishez – Journal of Applied Elbow Grease

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February 19, 2015

Posted on by

A new edition of Frontiers in Microbiology, and pretty much the whole Table of Contents was of interest! Here we go:

Human gut microbiome

Perspective: Aging and the human gut microbiota—from correlation to causality – Sitaraman Saraswati and Ramakrishnan Sitaraman – Frontiers in Microbiology

Review: Intestinal mucosal tolerance and impact of gut microbiota to mucosal tolerance – Dimitry A. Chistiakov – Frontiers in Microbiology

Animal models of microbiome research

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice – Aaron C. Ericsson – PLOS ONE

Germ-free mice, but still of interest: Microbiota-Independent Ameliorative Effects of Antibiotics on Spontaneous Th2-Associated Pathology of the Small Intestine – Daehee Han – PLOS ONE

Maternal Antibiotic-Induced Early Changes in Microbial Colonization Selectively Modulate Colonic Permeability and Inducible Heat Shock Proteins, and Digesta Concentrations of Alkaline Phosphatase and TLR-Stimulants in Swine Offspring – Marie-Edith Arnal – PLOS ONE

Workshop: Mouse Microbiota: genotype-phenotype control and technological challenges (March 2015, in Portugal) – Infrafrontier

Animal microbiome

The Dynamic Distribution of Porcine Microbiota across Different Ages and Gastrointestinal Tract Segments – Wenjing Zhao – PLOS ONE

Characterization of shed medicinal leech mucus reveals a diverse microbiota -Brittany M. Ott – Frontiers in Microbiology

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis
Ren-Mao Tian – Frontiers in Microbiology

Review: Microbes in the coral holobiont: partners through evolution, development, and ecological interactions – Janelle R. Thompson – Frontiers in Cellular and Infection Microbiology

Plant microbiome

Hypothesis: Mutualism–parasitism paradigm synthesized from results of root-endophyte models – Keerthi G. Mandyam and Ari Jumpponen – Frontiers in Microbiology

Soil microbiome

Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem – Trinity L. Hamilton – Frontiers in Microbiology

Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1 – Liqiang Yang – PLOS ONE

Water microbiome

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey – D’Arcy R. Meyer-Dombard – Frontiers in Microbiology

Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community – Verena S. Brauer – Frontiers in Microbiology

Editorial: Metal economy in host-microbe interactions – Frédéric J. Veyrier and Mathieu F. Cellier – Frontiers in Cellular and Infection Microbiology

Editorial: Antibiotic resistance genes in food and gut (non-pathogenic) bacteria. Bad genes in good bugs – Henk Aarts and Abelardo Margolles – Frontiers in Microbiology

Metagenomics

Phylogenetic Profiling: How Much Input Data Is Enough? – Nives Škunca, Christophe Dessimoz – PLOS ONE

Deconstruction of Archaeal Genome Depict Strategic Consensus in Core Pathways Coding Sequence Assembly – Ayon Pal – PLOS ONE

Perspective: Reconstructing each cell’s genome within complex microbial communities—dream or reality? – Scott Clingenpeel – Frontiers in Microbiology

Perspective: Finding and identifying the viral needle in the metagenomic haystack: trends and challenges – Hayssam Soueidan – Frontiers in Microbiology

Perspective: Metagenomics of plant and fungal viruses reveals an abundance of persistent lifestyles – Marilyn J. Roossinck – Frontiers in Microbiology

Metabolomics

Statistical methods for handling unwanted variation in metabolomics data – Alysha M. De Livera – Analytical Chemistry

Review: Fungal secondary metabolite dynamics in fungus–grazer interactions: novel insights and unanswered questions – Marko Rohlfs – Frontiers in Microbiology

Other articles of interest

Improving the Robustness of Complex Networks with Preserving Community Structure – Yang Yang – PLOS ONE

Techniques

A Simple Method for Encapsulating Single Cells in Alginate Microspheres Allows for Direct PCR and Whole Genome Amplification – Saharnaz Bigdeli – PLOS ONE

Microbes in the news

Innovations in the microbiome – Nature/Scientific American collaboration on the human microbiome. Some articles:
Microbiome Research May Soon Pay Off Big – Rob Knight – Scientific American
Genes and Microbes Influence One Another, Scientists Find – Ruth Ley – Scientific American

Pull Up A Stool And Let’s Talk About Your Microbiome – Bill Sullivan – The Scope

L.A. hospital warns 179 patients possibly exposed to “superbug” from endoscopies – Steve Gorman – Reuters

Stalking a wily foe: U-M scientists figure out how C. difficile bacteria wreak havoc in the gut – Kara Gavin – University of Michigan

Studying microbes in health and disease – Katherine Unger Baillie – Penn Current

And they still do! Microbes may have covered Earth 3.2 billion years ago – Charles Q Choi – Mother Nature Network

Toothpaste-mouth rinse combo washes out harmful bacteria – Janice Neumann – Reuters

Aetokthonos hydrillicola – the “eagle killer”: Bald eagles are starting to flourish again — but hold the confetti – The Washington Post

Virus found in sewage shows promise in treating dental procedure infections – Catherine Paddock – Medical News Today

Science, publishing, and career

What pushes scientists to lie? The disturbing but familiar story of Haruko Obokata – John Rasko and Carl Power – The Guardian

Science and art

Wind-Created Sand Sculptures on Lake Michigan Beach – Josh Nowicki – WILX.com

Bik’s picks

New York City Could See 6-Foot Sea Rise, Tripling of Heat Waves by 2100 – Colin Sullivan – Scientific American

Starving Sea Lion Pups in California: Warmer Ocean Could Be to Blame – NBC News

Changing insights: Love to eat eggs? U.S. panel now says they’re not a health risk – Yasmeen Abutaleb – Reuters

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February 18, 2015

Posted on by

There has been an incredible amount of microbiome papers that came out in the past three days. If this is an increasing trend (and I have every reason to believe it is) I will be needing some help in the future getting this daily digest out. Any volunteers in the fields of plant, soil, or water microbiome research to help me out?

Human oral microbiome

Metagenomic Sequencing Indicates That the Oropharyngeal Phageome of Individuals With Schizophrenia Differs From That of Controls – Robert H. Yolken – Schizophrenia Bulletin

Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease (Periodontitis, EB) – Akiko Endo – ISME Journal

Human skin microbiome

Review: Are Demodex Mites Principal, Conspirator, Accomplice, Witness or Bystander in the Cause of Rosacea? – WenChieh Chen, Gerd Plewig – American Journal of Clinical Dermatology $

Human respiratory microbiome

High Individuality of Respiratory Bacterial Communities in a Large Cohort of Adult Cystic Fibrosis Patients under Continuous Antibiotic Treatment – Rolf Kramer – PLOS ONE

Human vaginal microbiome

Rapid and profound shifts in the vaginal microbiota following antibiotic treatment for bacterial vaginosis – Bryan T. Mayer – The Journal of Infectious Diseases

The Impact of Hormonal Contraception and Pregnancy on Sexually Transmitted Infections and on Cervicovaginal Microbiota in African Sex Workers – Hanneke Borgdorff – Sexually Transmitted Diseases

Human gut microbiome

Potential use of probiotic and commensal bacteria as non-antibiotic strategy against vancomycin-resistant enterococci – Laureen Couzet – FEMS Microbiology Letters

Review: Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome? – Dana Berg – Expert Review of Gastroenterology & Hepatology

Review: Biotic interactions and temporal dynamics of the human gastrointestinal microbiota – Pål Trosvik – ISME Journal

Animal and other models

Development and pyrosequencing analysis of an in-vitro oral biofilm model – James O Kistler – BMC Microbiology

Respiratory Microbiota Dynamics following Streptococcus pneumoniae Acquisition in Young and Elderly Mice – Cassandra L. Krone – Infection and Immunity

Animal microbiome

Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen – Krishna M. Singh – Journal of Applied Genetics

Experimental replacement of an obligate insect symbiont – Nancy A. Morana,1 and Yueli Yun – PNAS USA
Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan – Muhammad Zubair Shabbir – Poultry Science

The Microbiome of Field-Caught and Laboratory-Adapted Australian Tephritid Fruit Fly Species with Different Host Plant Use and Specialisation – J. L. Morrow – Microbial Ecology

New insights into the fungal community from the raw genomic sequence data of fig wasp
Ceratosolen solmsi – Li-Hua Niu – BMC Microbiology
Metagenomic characterisation of viral communities in corals: Mining biological signal from methodological noise – Elisha M. Wood-Charlson – Environmentl Microbiology Reports

Phylogenetic diversity of sulfate-reducing Desulfovibrio associated with three South China Sea Sponges – Dan Zhang – Letters in Applied Microbiology

Diversity of Actinobacteria Associated with the Marine Ascidian Eudistoma toealensis – Georg Steinert – Marine Biotechnology

Species specificity of symbiosis and secondary metabolism in ascidians – Ma Diarey B Tianero – ISME Journal

Plant microbiome

Editorial: Focus on The Good, the Bad and the Unknown: Genomics-Enabled Discovery of Plant-Associated Microbial Processes and Diversity – Gwyn Beattie – Molecular Plant-Microbe Interactions

Seasonal Community Succession of the Phyllosphere Microbiome – Julia K. Copeland – Molecular Plant-Microbe Interactions

The Linkages between Plant Species Composition and Soil Microbial Communities: What about Symbiotic Microorganisms within Man-Made Tree Plantations? – Godar Sene – Biodiversity Management & Forestry

High-Throughput Sequencing in Studies of Lichen Population Biology – Silke Werth – Recent Advances in Lichenology $

Short-term impacts of energy wood harvesting on ectomycorrhizal fungal communities of Norway spruce saplings – Karoliina Huusko – ISME Journal

Editorial: Root surface as a frontier for plant microbiome research – Marcel G. A. van der Heijden and Klaus Schlaeppi – PNAS USA

Soil microbiome

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-13C-acetate probing coupled with pyrosequencing – Long-Jun Ding –

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette – Felix Beulig – ISME Journal

Effect of Monospecific and Mixed Sea-Buckthorn (Hippophae rhamnoides) Plantations on the Structure and Activity of Soil Microbial Communities – Xuan Yu – PLOS ONE

Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia – Jörg Schnecker – Soil Biology and Biochemistry

Perspective: Protection of Antarctic microbial communities – ‘out of sight, out of mind’ – Kevin A. Hughes – Frontiers in Microbiology

Water microbiome

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics – Carolina Megumi Mizuno – mBio

A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens
Enrique Zozaya-Valdes – Frontiers in Microbiology

Metagenomics Reveals Planktonic Bacterial Community Shifts across a Natural CO2 Gradient in the Mediterranean Sea – Ashvini Chauhan – Genome Announcements
Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples – Violetta La Cono – Environmental Microbiology Reports

Review: Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes – Alexandra Z. Worden – Science

Microbes of the Built Environment

Pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in Seri Kembangan, Malaysia, and their correlation with grades of food premises – Noor-Azira Abdul-Mutalib – International Journal of Food Microbiology $

Review: The dual role of microbes in corrosion – Nardy Kip and Johannes A van Veen – ISME Journal

Bioreactor microbiology

Metagenomic Analysis of the Sludge Microbial Community in a Lab-Scale Denitrifying Phosphorus Removal Reactor – Xiao-Mei Lv – Applied Biochemistry and Biotechnology $

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions – Yvonne Stolze – Biotechnology for Biofuels

Comparative metagenomics demonstrating different degradative capacity of activated biomass treating hydrocarbon contaminated wastewater – Trilok Chandra Yadav – Bioresource Technology

Phages, viruses, CRISPRs

Editorial: How bacteria get spacers from invaders – Ido Yosef & Udi Qimron – Nature
refers to the following 2 papers:

Cas9 specifies functional viral targets during CRISPR–Cas adaptation – Robert Heler – Nature

Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity – James K. Nuñez – Nature

Review: Big things in small packages: the genetics of filamentous phage and effects on fitness of their host – Anne Mai-Prochnow – FEMS Microbiology Reviews

Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations – Pauline D. Scanlan – Molecular Biology and Evolution

Virus characterization and discovery in formalin-fixed paraffin-embedded tissues – Rogier Bodewes – Journal of Virological Methods

Archaea

Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from hypersaline, meromictic Transylvanian lakes – Andreea Baricz – Extremophiles $

Microbial Ecology

DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens – Thierry Comtet – Biological Invasions

Bioinformatics

Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis, and beyond – Sungmin Lee – ArXiv

Indexing arbitrary-length k-mers in sequencing reads – Tomasz Kowalski – ArXiv

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning – Afiahayati, Kengo Sato and Yasubumi Sakakibara – DNA Research

Metagenomics

Perspective: The Newest “Omics”—Metagenomics and Metabolomics—Enter the Battle against the Neglected Tropical Diseases – Geoffrey A. Preidis, Peter J. Hotez – PLOS Neglected Tropical Diseases

Metabolomics, proteomics

Review: Exopolysaccharides Produced by Lactic Acid Bacteria and Bifidobacteria as Fermentable Substrates by the Intestinal Microbiota – Nuria Salazar – Critical Reviews in Food Science and Nutrition

A Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections – Christian Lassek – Molecular and Cellular Proteomics

Microbes Promote Amino Acid Harvest to Rescue Undernutrition in Drosophila – Ryuichi Yamada – Cell Reports

PhD Dissertation: The human microbiome and interactions with disease states, medical interventions, and the metabolome – Luke Kenneth Ursell – University of Colorado at Boulder

Review: Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: a review – Aleksandra Duda-Chodak – European Journal of Nutrition

Other articles of interest

Editorial: Balancing copy number in ribosomal DNA – John H. Malone – PNAS USA

Review: Epithelial Cell Contributions to Intestinal Immunity – Lora V. Hooper – Advances in Immunology $

Microbes in the News

Among Trillions of Microbes in the Gut, a Few Are Special – Moises Velasquez-Manoff – Scientific American

New Emphasis on Microbiome in Upper Airways Could Advance URTI Treatment in Cystic Fibrosis – Ana Pamplona – Cystic Fibrosis News Today

Mental Health May Depend on Creatures in the Gut: The microbiome may yield a new class of psychobiotics for the treatment of anxiety, depression and other mood disorders – Charles Schmidt – Scientific American

Gut Feelings: Diet, Depression and Bacteria – Paul Spector – Huffington Post

Inflammatory Bowel Disease Transmitted by Maternal Bacteria – Christopher Wanjek – Scientific American

Mapping the gut microbiome to better understand its role in obesity – Medical Xpress

Ghent University Hospital Researchers Find That Young Mice Microbiome Influences Later Onset of Autoimmune Disease – Daniela Semedo – Scleroderma News

Scientists Say that Bacteria Live in Placenta – Noel Angeles – SMN Weekly

Distemper virus affects wild carnivores of all stripes – Merry R. Buckley – Cornell University

Oil Eating Microbes Have Worldwide Underground Connections – David Biello – Scientific American (Podcast 2 min)

Science, publishing, and career

Announcement: Nature journals offer double-blind review: Starting in March, Nature and the monthly Nature research journals will offer an alternative to conventional peer review – Nature
Workplace safety: Risky encounters – Chris Woolston – Nature

Motherhood: Biases in US academia – Nature

Same Behavior, Different Consequences: Reactions to Men’s and Women’s Altruistic Citizenship Behavior – Heilman, Madeline E.; Chen, Julie J. – Journal of Applied Psychology

Bik’s Picks

Moth tails divert bat attack: Evolution of acoustic deflection – Jesse R. Barber – PNAS USA

Sea Snail Teeth Tops Spider Silk as Strongest Material on Earth – Becky Oskin – LiveScience / NBC News

Caffeine and Nicotine May Protect Bees Against Intestinal Parasites – Entomology Today

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