Category Archives: Metabolomics

March 4, 2015

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Human vaginal microbiome

Development of a microarray-based tool to characterize vaginal bacterial fluctuations: application to a novel antibiotic treatment for bacterial vaginosis – Federica Cruciani – Antimicrobial Agents and Chemotherapy

Human skin microbiome

Cutaneous Na+ Storage Strengthens the Antimicrobial Barrier Function of the Skin and Boosts Macrophage-Driven Host Defense – Jonathan Jantsch – Cell Metabolism

Review: Obesity, psoriasis, and microbiota: an unexplored dangerous connection? – Maria Grazia Roccia – Dermatologic Therapy

Animal and other models

The Gut Bacterium Bacteroides thetaiotaomicron Influences the Virulence Potential of the Enterohemorrhagic Escherichia coli O103:H25 – Hildegunn Iversen – PLOS ONE

Insights into the Staphylococcus aureus-Host Interface: Global Changes in Host and Pathogen Gene Expression in a Rabbit Skin Infection Model – Natalia Malachowa – PLOS ONE

Editorial: SIGNing a symbiotic treaty with gut microbiota – Geanncarlo Lugo-Villarino – The EMBO Journal

Animal microbiome

A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees – Dino P. McMahon – Journal of Animal Ecology

Plant microbiome

Review: Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture – Veronica Massena Reis and Kátia Regina dos Santos Teixeira – Journal of Basic Microbiology

Review: Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi – Miranda M. Hart – New Phytologist

Soil microbiome

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes – Jenni Hultman – Nature

Microbiome of the built environment

Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building – Tiffanie Ramos – PLOS ONE

Metabolomics

Programmed Evolution for Optimization of Orthogonal Metabolic Output in Bacteria – Todd T. Eckdahl – PLOS ONE

Microbes in the news

Salty Diet May Fight Invading Microbes – Cell Press – Laboratory Equipment

Characterizing permafrost microbes in a changing climate – Phys.org

Pollution, human health tracked with sewage microbes – Elizabeth Pennisi – Science Magazine News

New light shed on microbial battleground between soil, roots – Max Planck Institute – AG Professional

McDonald’s to Curb Purchases of Chicken Raised With Antibiotics in U.S. – David Kesmodel – Wall Street Journal

Widespread risk of infectious diseases to wild bees, new study reveals – Science Daily

Note: the plague bacterium itself was NOT found. NYC Rats Harbor Plague Fleas – Bob Grant – The Scientist

American Society for Microbiology receives grant to support ICAAC – EurekaAlert

Cause of tree-killing fungus uncovered: Extra genes – Science Daily

Hope from the Deeps for Coral Reefs – Veronique Greenwood – PBS Nova

Science, publishing, and career

Congrats Young Scientists, You Face The Worst Research Funding In 50 Years – Sam Stein – Huffington Post

Data visualization: Science on the map — Easy-to-use mapping tools give researchers the power to create beautiful visualizations of geographic data – Mark Zastrow – Nature

Satire: Evolutionist Loses It As Colleague Conflates Homology and Similarity Yet Again – The Allium

Bik’s Picks

Genetically speaking, mammals are more like their fathers – Science Daily

Where to Go When the Zombies Strike – Maggie Fox – NBC News

A Scientist Accidentally Developed Sunglasses That Could Correct Color Blindness — Li Zhou – Smithsonian Magazine

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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 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 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

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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

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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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February 17, 2015

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Too little time to cover everything from this 3-day weekend, but hopefully I can catch up tomorrow.

Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis – Baochen Shi – mBio

The hidden ‘mycobacteriome’ of the human healthy oral cavity and upper respiratory tract
Lilia Macovei – Journal of Oral Microbiology

Human vaginal microbiome

The Vaginal Microbiota over an 8- to 10-Year Period in a Cohort of HIV-Infected and HIV-Uninfected Women – Supriya D. Mehta – PLOS ONE

Human gut microbiome

Effects of polysaccharopeptide from Trametes versicolor and amoxicillin on the gut microbiome of healthy volunteers – Kumar Pallav – Gut Microbes

Animal models of microbiome research

Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation – Clara Moon – Nature

Voluntary and forced exercise differentially alter the gut microbiome in C57BL/6J mice – Jacob M. Allen – Journal of Applied Physiology

Commentary: Secret behind commensal resilience revealed – Christina Tobin Kåhrström – Nature Reviews Microbiology

Animal microbiome

Community structure of gut fungi during different developmental stages of the Chinese white pine beetle (Dendroctonus armandi) – Xia Hu – Scientific Reports

Persistent Shifts in Caribbean Coral Microbiota are Linked to the 2010 Warm Thermal Anomaly – Allison Tracy – Environmental Microbiology Reports

Review: Pathogenesis of canine atopic dermatitis: skin barrier and host–micro-organism interaction – Domenico Santoro – Veterinary Dermatology

Plant microbiome

Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities – Elisa Taschen – Environmental Microbiology

The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species – Sara Varela-Cervero – Environmental Microbiology

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

Soil microbiome

Plant diversity, soil biota and resistance to exotic invasion – Huixuan Liao – Diversity and Distributions

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLife

Water microbiome

Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China – Caiyun Yang – Scientific Reports

Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands) – Isabel Ferrera – PLOS ONE

Bioreactor microbiology

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters – Inka Vanwonterghem – Scientific Reports

Phages and viruses

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus – Yunzhou Wei – Nucleic Acids Research

Microbial Ecology

Patterns, causes and consequences of defensive microbiome dynamics across multiple scales – Andrew H. Smith – Molecular Ecology

Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients – Kari Anne Bråthen and Virve Tuulia Ravolainen – Journal of Ecology

Comment: The importance of soil archives for microbial ecology – Jan Dolfing & Youzhi Feng – Nature Reviews Microbiology

Editorial: Metabolites in differentiation – Andrea Du Toit – Nature Reviews Microbiology

Bioinformatics, metagenomics

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes – Thomas Brettin – Scientific Reports

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses – Marie Lisandra Zepeda Mendoza – Briefings in Bioinformatics

Correcting Illumina sequencing errors for human data – Heng Li – ArXiv

Not really microbial, but of possible interest: ModuleBlast: identifying activated sub-networks within and across species – Guy E. Zinman – Nucleic Acids Research

Metabolomics

A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples – Yuqing Huang – Scientific Reports

Pseudomonas aeruginosa manipulates redox and iron homeostasis of its microbiota partner Aspergillus fumigatus via phenazines – Benoit Briard – Scientific Reports

An overview of fecal preparation for global metabolic profiling – O. Deda – Journal of Pharmaceutical and Biomedical Analysis

Increased urinary indoxyl sulfate (indican): new insights into gut dysbiosis in Parkinson’s Disease – Cassani Erica – Parkinsonism & Related Disorders

Microbes in the news

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes – Jonathan Eisen – Phylogenomics / The Tree of Life Blog

A (not so!) Surprising Comparison of Male vs. Female Microbiomes – Alexandra Carmichael – uBiome

Microbes in the Gut Are Essential to Our Well-Being – David Grogan – Scientific American

Inflammatory Bowel Disease May Be from Mom’s Bacteria, not DNA – Christopher Wanjek – LiveScience

Mothers can pass traits to offspring through bacteria’s DNA, mouse study shows – Science Daily (about the Clara Moon paper in Nature; see above)

How Can Rivers And Streams Be Sources Of Antibiotic Resistant Bacteria? – James Maynard – TechTimes

Cooperative Control: With the help of a virus that infects its prey’s nervous system, a parasitoid wasp coerces a lady beetle to protect its young – Sandhya Sekar – The Scientist

Scientists turn the tables on drug-resistant bacteria by infecting them with bacteriophages – Phys.org

Science and career

Seven myths about scientists debunked – Jeffrey Craig, Marguerite Evans-Galea – the Conversation

Science and art

Microbial Masterpieces: Artist Anicka Yi explores the beauty of bacteria – Jenny Rood – The Scientist

2015 Year of the Phage – Life in our Phage World (Book, download)

Bik’s Picks

Demographic Clusters Identified within the Northern Gulf of Mexico Common Bottlenose Dolphin (Tursiops truncates) Unusual Mortality Event: January 2010 – June 2013 – Stephanie Venn-Watson – PLOS ONE

BP cherry-picks study to dodge blame for massive deaths of gulf dolphins – Michael Hiltzik – Los Angeles Times

Satire: Study Finds Jack Shit – The Onion

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February 12, 2015

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Happy Darwin Day! To celebrate, I’ll start of with an older paper:

What did Darwin say about microbes, and how did microbiology respond? – Maureen A. O’Malley – Trends in Microbiology

Two San Francisco Bay Area events of interest

Sat/Sun Feb 14/15: Family Science Days. Free event. Join the LSA, NASA, Science is Elementary (where I volunteer) and more at #FamSciDays!

Tue Feb 17, VLAB forum discussion: Gut-Feeling — Ventures into the Microbiome. Will bacteria enable personalized medicine?

General human microbiome

Review: Microbial Diversity: Relevance and Relationship Between Environmental Conservation And Human Health – Jeremias Pakulski Panizzon – Brazilian Archives of Biology and Technology

Human skin microbiome

Editorial: S. epidermidis Influence on Host Immunity: More Than Skin Deep – Richard L. Gallo – Cell Host & Microbe

Human gut microbiome

What role do bacteria play in persisting fistula formation in idiopathic and Crohn’s anal fistula? – P. J. Tozer – Colorectal Disease

Review: Spondyloarthritis and the Microbiome: New Insights From an Ancient Hypothesis – Julia Manasson, Jose U. Scher – Current Rheumatology Reports

Animal models of microbiome research

Editorial: TFH-IgA Responses Keep Microbiota in Check – Kanya Honda – Cell Host & Microbe

Effects of rearing temperature and dietary short-chain fructooligosaccharides supplementation on allochthonous gut microbiota, digestive enzymes activities and intestine health of turbot (Scophthalmus maximus L.) juveniles – I. Guerreiro – Aquaculture Nutrition

Animal microbiome

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Catacombs microbiome

When in Rome: Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies – Lucia Krakova – Environmental Microbiology

Soil and sediment microbiome

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems – Jun Gong – Environmental Microbiology

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group – Travis B. Meador – Environmental Microbiology

Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica – Sean T. S. Wei – Polar Biology

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments – Anniet M. Laverman – Environmental Science and Pollution Research

Temperature Sensitivity of Microbial Respiration of Fine Root Litter in a Temperate Broad-Leaved Forest – Naoki Makita, Ayumi Kawamura – PLOS ONE

Water microbiome

Review: Marine microbial community dynamics and their ecological interpretation – Jed A. Fuhrman – Nature Reviews Microbiology

Bioreactor microbiome

Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater – Hyun Min Jang – Water Research

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus – Xiao-Mei Su – Microbial Biotechnology

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology

Opinion/review: Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities – Shaman Narayanasamy – Microbial Biotechnology

Metabolomics and Proteomics

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities – Sandi Yen – Journal of Proteome Research

Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: a case-control study – Stephen J Fowler – Thorax

The Unipept metaproteomics analysis pipeline – Bart Mesuere – Proteomics

Review: A Biotechnological Approach to Microbial Based Perfumes and Flavours – Charu Gupta – Journal of Microbiology & Experimentation

Microbial Ecology

Ecological Perspectives on Synthetic Biology: Insights from Microbial Population Biology – Ana E. Escalante – Frontiers in Microbiology

Bioinformatics

A machine learning pipeline to improve De Bruijn graph metatranscriptomic assemblies – Hussein Mohsen – Bioinformatics

Techniques

Identification of response classes from heavy metal-tolerant soil microbial communities by highly resolved concentration-dependent screenings in a microfluidic system – Dana Kürsten – Methods in Ecology and Evolution

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria – Kelley A. Meinhardt – Environmental Microbiology Reports

Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples – Jan Mareš – Journal of Phycology

Other microbiology papers

Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack – Chamutal Gur – Immunity

Microbes in the news

Podcast on the NY Subway Microbiome paper (19 min): Listen To Our Conversation With The Microbe Map Man – Jody Avirgan – Five Thirty Eight

Another short Podcast: Subway DNA Survey Finds Microbes, Mozzarella and Mystery – Christopher Intagliata – Scientific American

What The Bacteria In Your Gut Have To Do With Your Physical And Mental Health – Carolyn Gregoire – The Huffington Post
Cecilia Westbrook Makes Yogurt With Her Own Vaginal Bacteria (NSFW) – David Moye – The Huffington Post

Bacteria, economics and our aging population – Julie Flaherty – MedicalXpress

Session Recap: Therapeutic Workshop “Trust Your Gut” with Martin Blaser et al. – BiotechNow

Is there a link between gut microbiota and Parkinson’s disease? – GutMicrobiotaWatch

Early microbiome development impacts later weight gain – Nathan Gray – NutraIngredients

Not all microbial strains are equally efficient – Kemin – All About Feed

The Nanotech View of the Microbiome (Kavli Roundtable) – Alan Brown – LiveScience

Bacteria protect intestinal tumor model from being killed by immune cells – Cell Press – Eureka Alert

A discussion of Casadevall and Pirofski’s Nature commentary: What’s The Damage? – Amesh Adalja – BifurcatedNeedle

New Non-Stick Coating Will Stop Bacteria Sticking to Medical Materials – Jamie Condliffe – GizModo

Science, publishing, and career

NIH proposal to create grant for aging scientists hits a nerve – Jocelyn Kaiser – Science

Social media: A network boost – How scientists can use Twitter to expand their social contacts and find jobs – Monya Baker – Nature

Elsevier Valentines – It all started with an innocent tweet. – Sylvain Deville – Storify

Bik’s Picks

U.S. Droughts Will Be the Worst in 1,000 Years – Mark Fischetti – Scientific American

Emaciated sea lion pup rescued from side of San Francisco highway – Reuters.com

Happy Darwin Day! Here are our favorite stories about evolution – Rachel Feltman – Washington Post

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February 10, 2015

Posted on by

Microbiome of pregnancy and birth

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan (Sam) Ma – Scientific Reports

Human respiratory microbiome

The nasal microbiota in health and disease: variation within and between subjects – Kristi Biswas – Frontiers in Microbiology

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis – Won Hee Jung – Mycoses

Human oral microbiome

Review: Salivary Diagnostics and the Oral Microbiome – Jennifer E. Kerr – Advances in Salivary Diagnostics

Review: Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses – Georgios Charalampakis – Virulence

Review: On the dynamics of root canal infections – what we understand and what we don’t – Matthias Zehnder – Virulence

Human gut microbiome

See also Rojo paper under Metabolomics

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences – Brett Wagner Mackenzie – Frontiers in Microbiology

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease – Weiwei Jiang – Scientific Reports

Intestinal Lesions Are Associated with Altered Intestinal Microbiome and Are More Frequent in Children and Young Adults with Cystic Fibrosis and Cirrhosis – Thomas Flass – PLOS ONE

The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing – LY Kwok – Beneficial Microbes

Review: Contribution of diet to the composition of the human gut microbiota – Daniela Graf – Microbial Ecology in Health and Disease

Animal microbiome

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing – Edward Alain B. Pajarillo – Asian-Australasian Journal of Animal Sciences

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Abstract: Bugs in bats 2: Analysis of microbial communities in faecal samples obtained from bats in the Netherlands – JCM Wolkers-Rooijackers – 11th Conference of the Dutch Society for Wildlife Health

Plant microbiome

Rapid quantification of rice root-associated bacteria by flow cytometry – G. Valdameri – Letters in Applied Microbiology

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria – Kiwamu Minamisawa – Frontiers in Microbiology

Characterization of Leaf Blade- and Leaf Sheath-Associated Bacterial Communities and Assessment of Their Responses to Environmental Changes in CO2, Temperature, and Nitrogen Levels under Field Conditions – Seishi Ikeda – Microbes and Environments

Soil, sediment, and rock microbiome

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice – J. J. Elser – Applied and Environmental Microbiology

Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils – Ning Wang – FEMS Microbiology Ecology

Analysis of Sclerotia-Associated Fungal Communities in Cool-Temperate Forest Soils in North Japan – Anzilni F. Amasya – Microbes and Environments

Water microbiome

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year – M. Korlević – Applied and Environmental Microbiology

Viruses and phages

Traces of ATCV-1 associated with laboratory component contamination – Kristín Rós Kjartansdóttir – PNAS USA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination – Robert H. Yolken – PNAS USA

Microbial Ecology

Temporal patterns of rarity provide a more complete view of microbial diversity – Ashley Shade, Jack A. Gilbert – Trends in Microbiology

Metagenomics

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

Metabolomics

Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases – David Rojo – Scientific Reports

Review: Animals in a bacterial world: opportunities for chemical ecology – Alexandra M. Cantley and Jon Clardy – Natural Product Reports

Bioinformatics

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies – Mohamed Mysara – Applied and Environmental Microbiology

Techniques

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – MicroBEnet

More microbes

Natural Green Coating Inhibits Adhesion of Clinically Important Bacteria – Danielle S. Trentin – Scientific Reports

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

Breastfeeding prepares a baby for solid food – Tim Sandle – Digital Journal

Gut microbiota reveal better ways of detecting (and preventing) colorectal cancer – Kristina Campbell – Microbiome Institute

Our Inner Viruses: Forty Million Years In the Making – Carl Zimmer – National Geographic

Our wine owes a debt to ancient viruses – Andrew Geering – Phys.org

Diet is the Chief Factor Behind Gut Microbiome Diversity, Study Shows – Patricia Inacio – IBD News Today

Citizen Oceanography Meets the Marine Microbiome – Rachelle Lauro – Mission Blue

Fecal Microbiota Transplants: An Insider’s Guide – Monica J. Smith

Science and Art

Researcher Determined to Play Piano Duet With Yellow Slime Mold – The Mary Sue

And the winners of the #spacemicrobes Microbial Playoffs are… – Arvind Suresh – Discover Magazine

A Beautiful Wallpaper Made With Smallpox Vaccine – Joseph Flaherty – Wired.com

Bik’s Picks
Stressed Young Bees Linked To Colony Collapse – Jim Algar – Tech Times

Meet Spot: New Breed of Robot Dog Climbs and Trots – Elizabeth Palermo – Live Science

Australia’s Shocking Rate Of Mammal Extinction Blamed On Cats And Red Foxes Brought Over By European Settlers – Rebekah Marcarelli – Headlines and Global News

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