Category Archives: Techniques

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 20, 2015

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Human microbiome, general

Article collection (n=1?): Microbiota: Coevolution and the Modern Environment – Martin Katzman, Alan C. Logan – Journal of Physiological Anthropology

Review: Natural environments, ancestral diets, and microbial ecology: is there a modern “paleo-deficit disorder”? Part I – Alan C Logan – Journal of Physiological Anthropology

Human respiratory microbiome

Chronic Obstructive Pulmonary Disease Lung Microbiota Diversity May Be Mediated by Age or Inhaled Corticosteroid Use – Alexa A. Pragman – Journal of Clinical Microbiology

Reply to “Chronic Obstructive Pulmonary Disease Lung Microbiota Diversity May Be Mediated by Age or Inhaled Corticosteroid Use” – Marian Garcia-Nuñez – Journal of Clinical Microbiology

Fecal microbiota transplantation

ECCO congress abstract: FMT not effective in active UC patients – Haelio

MALDI-Tof MS

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation? – Sébastien Spinali – Journal of Clinical Microbiology

Immunology

Perspective: A common origin for immunity and digestion – Nichole A. Broderick – Frontiers in Immunology

Microbes in the news

Engineering the Human Microbiome Shows Promise for Treating Disease – Justin L. Sonnenburg – Scientific American

Book Review: “Philosophy of Microbiology”, by Maureen A. O’Malley – Adrian Woolfson – Science

UCLA Outbreak Highlights Challenge Of Curbing Infections – Jordan Rau – NPR

Title seems incorrect: Your Genes May Be Part Mom, Part Dad and Part Bacteria – Krystnell Storr – Science.Mic

Host influences bacterial metabolism – Phys.org

Bacteria-killing virus may help prevent root canal infections – DrBicuspid

Virus-cutting enzyme helps bacteria remember a threat – Phys.org

Science, publishing, and career

Putting the ‘Media’ in ‘Academia’ – Stewart Barker – MicrobeStew

College Faculties Have a Serious Diversity Problem – Marcus Woo – Wired.com

Satire: Grad Student Diagnosed With Early-Onset Thesis Fear – The Allium

Bik’s Picks

Nest Etiquette—Where Ants Go When Nature Calls – Tomer J. Czaczkes, Jürgen Heinze, Joachim Ruther – PLOS ONE

Why I’m Volunteering to Die on Mars – Sonia Van Meter – Time.com

How the sun can damage your skin even in the dark – Deborah Netburn – LA Times

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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 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 9, 2015

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Human oral microbiome

Pulp and plaque microbiotas of children with severe early childhood caries – Natalia I. Chalmers – Journal of Oral Microbiology

Analysis of oral microbial community and Th17-associated cytokines in saliva of patients with oral lichen planus – Kun Wang – Microbiology and Immunology

Human gut microbiome

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities – Jiachao Zhang – The ISME Journal

Distinct gut microbiota of healthy children from two different geographic regions of Thailand – Orawan La-ongkham – Archives of Microbiology

An Appropriate Cutoff Value for Determining the Colonization of Helicobacter pylori by the Pyrosequencing Method: Comparison with Conventional Methods – Jaeyeon Kim – Helicobacter

Review: Dysbiosis of the gut microbiota in disease – Simon Carding – Microbial Ecology in Health and Disease

Review: Manipulating the gut microbiota to maintain health and treat disease – Karen P. Scott – Microbial Ecology in Health and Disease

Fecal Transplants

Successful treatment of severe sepsis and diarrhea after vagotomy utilizing fecal microbiota transplantation: a case report – Qiurong Li – Critical Care

Animal models of microbiome research

Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs – Marcio C Costa – BMC Veterinary Research

Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract – Jyoti Shankar – Scientific Reports

Gut microbial markers are associated with diabetes onset, regulatory imbalance, and IFN-γ level in NOD Mice – Ł. Krych – Gut Microbes

Defective NOD2 peptidoglycan sensing promotes diet-induced inflammation, dysbiosis, and insulin resistance – Emmanuel Denou – EMBO Journal

Animal Microbiome

Internal Extracellular Bacteria of Diaphorina citri Kuwayama (Hemiptera: Psyllidae), the Asian Citrus Psyllid – Lakshmi D. Kolora – Current Microbiology

Soil Microbiome

Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem – Jun-Tao Wang- Journal of Soils and Sediments

Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics – Dini Nurdiani – Journal of Bioscience and Bioengineering

Microbial diversity of mangrove sediment in Shenzhen Bay and gene cloning, characterization of an isolated phytase-producing strain of SPC09 B. cereus – Shengpeng Zhang – Applied Microbiology and Biotechnology

Food Microbiology

Zooming into food-associated microbial consortia: A “cultural” evolution
Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Review: Emerging DNA-based technologies to characterize food ecosystems – Andrea Galimberti – Food Research International

Bioreactor microbiology

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities – Wuttichai Mhuantong – Biotechnology for Biofuels

Metabolomics

Defining the Microbial Effluxome in the content of the Host-Microbiome Interaction – Anastasios Ioannidis – Frontiers in Pharmacology

Reference-free comparison of microbial communities via de Bruijn graphs – Serghei Mangul and David Koslicki – preprint

A systematic evaluation of high-dimensional, ensemble-based regression for
exploring large model spaces in microbiome analyses – Jyoti Shankar – BMC Bioinformatics

Microbial Ecology

Opinion: Landscape community genomics: understanding eco-evolutionary processes in complex environments – Brian K. Hand – Trends in Ecology & Evolution

Techniques

Accurate, multi-kb reads resolve complex populations and detect rare
microorganisms – Itai Sharon – Genome Research

A simple separation method for downstream biochemical analysis of aquatic microbes – Cody E. Garrison, Alexander B. Bochdansky – Journal of Microbiological Methods

Microbes in the News

How to Make Breakfast With Your Vagina – Janet Jay – Motherboard

Breast IS best: Researchers say babies get microbes from mother’s milk that makes them ‘more ready’ to digest solid food – Mark Prigg – Daily Mail

Common antibiotics trigger significant changes in equine gut bacteria – study – Horsetalk

The Hungry Microbiome Part 4: The colon, colon cancer, and butyrate – Jesse Hawley – CSIRO

Google Maps for bacteria? How NYC subway swab could change public health (Podcast) – PBS Newshour

Investigation into possible spread of bacteria found in local primate center – Ashley Rodrigue – WWLTV

What friendly bacteria really CAN do for you… but probiotic makers are banned from telling us about – Sadie Nicholas – DailyMail UK

Bacteria Hysteria: ‘Bacteria and mold will accumulate’: Expert weighs in on bath towel use – Fox8.com

Gut Bacteria Differs in Gluten-free Celiac Patients with Persistent Symptoms – Jefferson Adams – Celiac.com

Bacterial DNA from the Black Death found in teeth – Yngve Vogt – MedicalXpress

UC Merced graduate student to continue oral bacteria research in Brazil – Ana B. Ibarra – Mercedsunstar

Meet the Poop-Sniffing Dogs That Are Saving Endangered Wildlife – Charyn Pfeuffer – Wired

Experimental drug containing tiny fragments of teenage acne bacteria trialled on MS patients – Lucie van den Berg – Herald Sun

Bacteria’s hidden traffic control – Phys.org

Science, publishing, career

How not to write a sequence assembly comparison paper – Keith Robison – Omics!Omics!

Research Misconduct Identified by the US Food and Drug Administration
Out of Sight, Out of Mind, Out of the Peer-Reviewed Literature – Charles Seiffe – JAMA Internal Medicine

Are Your Medications Safe? The FDA buries evidence of fraud in medical trials. My students and I dug it up. – Charles Seife – Slate

Bik’s Picks

The Champion Egg-Layers of the Bird World – Emma Bryce – Audubon

Enzyme rapidly reduces sulfites in wine – Tim Sandle – Digital Journal

NASA Mars Curiosity Rover Collects Soil Samples – Deborah Grace – Pierce Pioneer

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February 4, 2015

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Animal models of microbiome research

Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota – Han-Hsuan Chou – PNAS

Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-Yong Mao – Environmental Microbiology

Animal microbiome

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae) – Matteo Montagna – PLOS ONE

Plant microbiome

Editorial: Evolving insights to understanding mycorrhizas – Ian A. Dickie – New Phytologist

Soil and sediment microbiome

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Cyanobacteria drive community composition and functionality in rock–soil interface communities – Angel Valverde – Molecular Ecology

Water microbiome

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary – Erin M. Eggleston – Environmental Microbiology

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity – Matthieu Leray and Nancy Knowlton – PNAS USA

Bioinformatics

Phylogenomics with paralogs – Marc Hellmuth – PNAS USA

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets – Nikhil Chaudhary – PLOS ONE

DNA extraction and sequencing techniques

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform – Lucas Sinclair – PLOS ONE

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples – Androniki Psifidi – PLOS ONE

Metabolomics

Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD – Vicky De Preter – Gut

Probiotics

Review: The effects of consuming probiotic-fermented milk on the immune system: A review of scientific evidence – Lourdes Santiago-López – International Journal of Dairy Technology

Microbes in the News

Aquarium Microbiome Project – Shedd Aquarium

Video: Aquarium Microbiome Project – YouTube

A plea to stop ignoring microbial ecosystem effects of antimicrobial agents – Jonathan Eisen – MicroBEnet

Why you should embrace bacteria – Jody Berger – Deseret News

Infant Microbiota Influenced By Mother’s Birth Delivery, Gestation Period – Chris Weller – Medical Daily

Birth method, gestation duration may alter infants’ gut microbiota and influence later health – ASM

A warm (surprise!) welcome to the microbiome community – Alexandra Carmichael – uBiome

A Bacteria That Hasn’t Had To Evolve In More Than Two Billion Years – George Dvorsky – io9.com

Bik’s Picks

Cigarette Butt Decomposition and Associated Chemical Changes Assessed by 13C CPMAS NMR – Giuliano Bonanomi – PLOS ONE

What’s Up With That: Why Do Cats Love Boxes So Much? – Bryan Gardiner – Wired.com

Satire: Genome Study Finds Gene For Believing Genome Studies – The Allium

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February 3, 2015

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Pregnancy and birth

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio

Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE

Human oral microbiome

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports

Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology

Human respiratory microbiome

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE

Human gut microbiome

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Animal microbiome

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE

Plant microbiome

Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils

Soil microbiome

Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology

Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry

Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments

Water microbiome

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography

Microbiome of the built environment

Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment

Bioreactor microbiome

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports

Food microbiology

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology

Techniques

PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE

Bioinformatics, metagenomics

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE

In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research

SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics

A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Book: Biocode: The New Age of Genomics

Phages and viruses

Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE

Microbes in the news

The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio

The Human Microbiome and Media Confusion – Science in the News – Harvard

Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos

Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome

Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio

Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients

Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes

Science, publishing, and career

From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog

Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI

A Future Segregated by Science? – Charles M. Blow – New York Times

Bik’s Picks

Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily

Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs

Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press

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February 2, 2015

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The etiology of dental caries, viruses as commensals, genitalia-associated microbes in insects, and pizza metabolomics.

Human oral microbiome

Solving the etiology of dental caries – Aurea Simón-Soro, Alex Mira – Trends in Microbiology

Human gut microbiome

Expanding the Role of the Virome: Commensalism in the Gut – Ken Cadwell – Journal of Virology

Animal microbiome

Review: Genitalia-associated microbes in insects – Oliver Otti – Insect Science

Plant microbiome

Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale – Maarten van Geel – Molecular Ecology

Water microbiome

Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir – Peike Gao – Microbiology Open

Microbiome of the built environment

Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood – Joanne B Emerson – Environmental Science & Technology

Techniques

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLife

Microbial Ecology

Mycorrhizal ecology and evolution: the past, the present, and the future – Marcel G. A. van der Heijden – New Phytologist

Biotic interactions boost spatial models of species richness – Heidi K. Mod – Ecography

Metabolomics

Metabolomic applications in nutritional research: a perspective – Aoife O’Gorman and Lorraine Brennan – Journal of the Science of Food and Agriculture

Microbes in the news

Viral Virtuosos: New understanding of noncoding RNAs may solve a long-standing puzzle about how viruses orchestrate lifelong infections – Christopher S. Sullivan – The Scientist

The answer to fewer viruses in human DNA? We stopped biting each other – SBS

Bacteria used to yield pure water and produce hydrogen, the fuel of the future – Jayalakshmi K – IBTimes

Intestinal microbiome research – Rob Levey – New Hampshire Union Leader

The Energy of Life: Extremophiles should not be viewed through an anthropocentric lens – Jeffrey Marlow and Jan Amend – The Scientist

Bacteria May Help Battle Cancer, Study Suggests – Philly.com

Science and art

Gorgeous Photos Made From the Bacteria on Toilet Seats and iPhones – Liz Stinson – Wired.com

Lab Agar Drawings: Chromobacterium violaceum shaped into Biohazard Symbol – MicrobeWorld

Science, publishing, and career

Trust me, I’m a medical researcher – Jennifer Couzin-Frankel – Science

Balancing Privacy versus accuracy in research protocols – Science

Ten Simple Rules for Organizing an Unconference – Aidan Budd – PLOS Computational Biology

Bik’s Picks

‘DivSeek’ aims to mine the genetic treasure in seed bank vaults – Virginia Gewin – Science Magazine

Baby’s genes, not mom’s, may trigger some preterm births – ScienceDaily

Energy and Nutrient Intake From Pizza in the United States – Lisa M. Powell – Pediatrics

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