Category Archives: Built Environment Microbiology

February 27, 2015

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Human skin microbiome

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

Human gut microbiome

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

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

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

Animal and bioreactor models

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

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

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

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

Animal microbiome

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

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

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

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

Plant microbiome

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

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

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

Soil microbiome

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

Water microbiome

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

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

Microbiome of the built environment

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

Microbes in the news

The Case of the Curious Microbiome – Alexandra Carmichael – uBiomeBlog

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

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

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

Science, publishing, and career

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

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

Science and Art

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

Bik’s Picks

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

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

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

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

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February 25, 2015

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

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

Human oral microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

Animal models of microbiome research

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

Animal microbiome

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

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

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

Plant microbiome

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

Soil microbiome

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

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

Water microbiome

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

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

Microbiome of the built environment

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

Phages and viruses

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

Bioinformatics

Tools for Bacterial Comparative Genomics – Kat Holt – Holt Lab

Techniques

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

Metabolomics

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

Other papers of interest

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

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

Science, publishing and career

Scientists are cautious about public outreach – Chris Woolston – Nature

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

Science and art

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

Bik’s Picks

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

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

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

February 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 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 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 5, 2015

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Microbiome of pregnancy and birth

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes – Aleksandar D. Kostic – Cell Host & Microbe

Meeting abstracts in the Journal of Allergy and Clinical Immunology:
Influence of Infant Gut Microbiome on Development of Infant Regulatory T Cells – Kevin Bobbitt
The Infant Gut Microbiome Mediates the Association Between Breastfeeding and Allergic-like Response to Pets in Children – Alexandra R. Sitarik
Association of the Infant Gastrointestinal Microbiome with Nocturnal Symptoms in Children with Asthma – Albert M. Levin
Decrease in Diversity of Nasal Microbiota during Wheezing Episodes in Preschool Children – Gorka Alkorta-Aranburu

Maternal influences on fetal microbial colonization and immune development – Joann Romano-Keeler & Jörn-Hendrik Weitkamp – Pediatric Research

Human oral microbiome

Evaluation of human and microbial DNA content in subgingival plaque samples collected by paper points or curette – P.J. Pérez-Chaparro – Journal of Microbiological Methods

Human vaginal microbiome

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR – Takashi Kurakawa – Journal of Microbiological Methods

Human gut microbiome

Weight Gain After Fecal Microbiota Transplantation – Neha Alang and Colleen R. Kelly – Open Forum Infectious Diseases

The Gut Microbiota, Intestinal Permeability, Bacterial Translocation, and Nonalcoholic Fatty Liver Disease: What Comes First? – Erin Spengler, Rohit loomba – CMGH Cellular and Molecular Gastroenterology and Hepatology

$70 to read this one: Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy – Xiaobo Feng – The American Surgeon

Review: Gut Microbiota: Association with NAFLD and Metabolic Disturbances – E. Lau – BioMed Research International

Review: Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry – Eva M Selhub – Journal of Physiological Anthropology

Animal models of microbiome research

Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec – R. Khiaosa-ard – Journal of Dairy Science

Effect of feeding Jerusalem artichoke (Helianthus tuberosus) root as prebiotic on nutrient utilization, fecal characteristics and serum metabolite profile of captive Indian leopard (Panthera pardus fusca) fed a meat-on-bone diet – S.K. Pradhan – Zoo Biology

Comparative Analysis of Gastrointestinal Microbiota Between Normal and Caudal-Related Homeobox 2 (Cdx2) Transgenic Mice – Hirotsugu Sakamoto – Intestinal Research

Plant microbiome

Impact of mycorrhizal inoculation on the development of Intsia bijuga grown on soil under exotic species Casuarina equisetifolia plantation – Dina Ratahiriarisoa – Journal of Plant Sciences

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient – Susan G. Jarvis – New Phytologist

Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii – David H. Green – BioMed Research International

Review: The importance of the microbiome of the plant holobiont – Philippe Vandenkoornhuyse – New Phytologist

Soil microbiome

Soil microbial response to waste potassium silicate drilling fluid – Linjun Yao – Journal of Environmental Sciences

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218O – Elizabeth A. Rettedal and Volker S. Brözel – MicrobiologyOpen

Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils – Shamsa Akbar – Journal of Basic Microbiology

Microbiome of the built environment
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics – Ebrahim Afshinnekoo – Cell Systems

Food microbiology

Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos – Junichiro Marui – Bioscience of Microbiota, Food and Health

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

Bioinformatics

Programming: Pick up Python – A powerful programming language with huge community support – Jeffrey M. Perkel – Nature

Microbes in the news

Podcast: What lived in ancient human intestines? Interview with Jessica Metcalf – The Naked Scientists

Woman becomes obese after fecal transplant from overweight donor – Brooks Hays – UPI

Microbiome linked to type 1 diabetes: Shift in microbiome species diversity prior to disease onset – Science Daily

Gut microbes are good for mood – Xanthe Hunt – LongevityLive

Satire: Five Dead As Pro- and Anti-Microbiome Demonstrators Clash – The Allium

Video: The role of gut bacteria in brain disease – Robert Friedland – YouTube

Book: I, Superorganism – Jon Turney – IconBooks

Big Data and Bacteria: Mapping the New York Subway’s DNA – Robert Lee Hotz – Wall Street Journal

Drug-resistant bacteria lurk in subway stations, high school students discover – Science Daily

Among New York Subway’s Millions of Riders, a Study Finds Many Mystery Microbes – Elizabeth A. Harris – New York Times

Environmental factors may affect how infants’ gut bacteria mature – News Medical

Could Genetically Engineered Bacteria in Your Colon Replace Vitamins? – Sarah Zhang – GizModo

Why Measles Is the Most Contagious Virus – Mandy Oaklander – Time

Busting the 5-second rule: Robot, Petri dishes of bacteria part of science fair – Leigh Guidry – The Town Talk

Not about microbiology, but a very good read: High throughput sequencing for neuroscience – Sean Eddy – Cryptogenomicon

No Bik’s Picks today, sorry guys.

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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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January 27, 2015

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Human gut microbiome

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas – Chunguang Luan – Scientific Reports

Plant microbiome

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – Bin Ma – Journal of Applied Microbiology

Nostopeptolide plays a governing role during cellular differentiation of the symbiotic cyanobacterium Nostoc punctiforme – Anton Liaimer – PNAS USA

Air microbiome

Antibiotics, Bacteria, and Antibiotic Resistance Genes: Aerial Transport from Cattle Feed Yards via Particulate Matter – Andrew D. McEachran – Environmental Health Perspectives

Techniques

Review: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats – Jizhong Zhou – mBio

Bioinformatics

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline) – Murat Eren – Github

Why now is the time to learn R – David Smith – OpenSource

Other scientific papers of interest

Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses – Jennifer E. Cox – PNAS USA

Discussion: Mice are not men – H. Shaw Warren – PNAS USA
Reply to Warren et al. and Shay et al.: Commonalities across species do exist and are potentially important – Keizo Takao – PNAS USA

Microbes in the news

Dust From Factory Farms Carries Drugs, Poop Bacteria, and Antibiotic-Resistant Genes Far and Wide – Tom Philpott – Mother Jones

How does your gut garden grow? Feeding your intestinal bacteria in a positive way – Áilín Quinlan – Irish Independent

The expert’s view: Ted Dinan, Professor of Psychiatry at UCC, on microbiome and stool transplants – Irish Independent

Obama proposes sharp increase to fight drug-resistant bacteria – Amy R. Connolly – UPI

Antibiotics for travellers’ diarrhoea – super-bacteria as a souvenir – Päivi Lehtinen – University of Helsinki

Science, publishing, and career

Number of College Students Pursuing Science, Engineering Stagnates – Melissa Korn – Wall Street Journal

Baring it all: Some researchers believe that openness can promote constructive communication and enable science to move forward faster – Rachel Bernstein – Science Careers

Why women are ditching STEM careers-and how to change it – Vivian Giang – FastCompany

Science and art

“Blurred Bands”: 2015 Lab Grammys: 8 nominees for Lab Parody of the Year – Biotechniques.com

Science and Culture: Science on-screen and behind the scenes – Stephen Ornes – PNAS USA

Science And Art Need Each Other, And Here’s Why – Cheryl Eddy – io9.com

Winners of the British Heart Foundation’s annual Reflections of Research competition – Richard P Grant – The Guardian

Bik’s Picks

Science finds a new way to unboil an egg – Michelle Starr – CNET

Asteroid that flew past Earth has moon – Science Daily

The continental divide of 2014 temperature – Thomas Summer – Science News

Blizzard 2015: Science Experiments to Do With Snow – Alyssa Newcomb – ABC News

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January 26, 2015

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Human oral microbiome

* 16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries – Sri Nisha Jagathrakshakan – European Journal of Dentistry

Human urinary tract microbiome

The microbiome of the urinary tract—a role beyond infection – Samantha A. Whiteside – Nature Reviews Urology

Human gut microbiome

* Association between specific mucosa-associated microbiota in Crohn’s disease at the time of resection and subsequent disease recurrence: A pilot study – Peter De Cruz – Journal of Gastroenterology and Hepatology

Enhanced vaccination effect against influenza by prebiotics in elderly patients receiving enteral nutrition – Hiroyasu Akatsu – Geriatrics & Gerontology International

Review: The small bowel microbiota – Carthage Moran – Current Opinion in Gastroenterology

Animal microbiome

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay – Riazuddin Mohammed – Frontiers in Microbiology

Plant microbiome

Mycorrhizal networks and coexistence in species-rich orchid communities – Hans Jacquemyn – New Phytologist

A 3-year field investigation of impacts of Monsanto’s transgenic Bt-cotton NC 33B on rhizosphere microbial communities in northern China – Yan-Jun Zhang – Applied Soil Ecology

Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration of Douglas-fir – J. Marty Kranabetter – New Phytologist

Review: Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism – Ariane C. Kemen – New Phytologist

Soil and sediment microbiome

Soil microbial community composition does not predominantly determine the variance of heterotrophic soil respiration across four subtropical forests – Hui Wei – Scientific Reports

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses – Fabio Stagnari – Frontiers in Microbiology

Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c – Hazel A. Barton – Frontiers in Microbiology

Diversity of Soil Microbial Communities Formed by Different Light Penetrations in Forests (article in Korean) – Jun Ho Park – DBpia

Bacterial community composition of sediments from a milkfish Chanos chanos Forsskål farm – Sheila Mae S Santander-de Leon – Aquaculture Research

Bacterial diversity and fatty acid composition of hypersaline cyanobacterial mats from an inland desert wadi – Raeid M.M. Abed – Journal of Arid Environments

Study of the succession of microbial communities for sulfur cycle response to ecological factors change in sediment of sewage system – Yanchen Liu – Environmental Science and Pollution Research

Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link – Pablo Souza-Alonso – Journal of Environmental Science and Health, Part B: Pesticides, Food Contaminants, and Agricultural Wastes

Fire alters vegetation and soil microbial community in alpine meadow – Changting Wang – Land Degradation & Development

Long-term oil contamination increases deterministic assembly processes in soil microbes – Yuting Liang – Ecological Applications

Reduced vertical stratification of soil bacterial community structure and composition is associated with Bromus tectorum invasion of sagebrush steppe – Carolyn F. Weber – Journal of Arid Environments

Water microbiome

Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes – Mylène Hugon – Environmental Microbiology Reports

Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary – L. F. Messer – Aquatic Microbial Ecology

Assessing impact of acid mine drainage on benthic macroinvertebrates: can functional diversity metrics be used as indicators? – Fengzhi He – Journal of Freshwater Ecology

Microbial community of the deep-sea brine Lake Kryos seawater–brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA – Michail M. Yakimov – Environmental Microbiology

Microbiome of the built environment
Aeromonas biofilm on stainless steel: efficiency of commonly used disinfectants – Sara Craveiro – International Journal of Food Science & Technology

Fungi and the like

An improved high throughput sequencing method for studying oomycete communities – Rumakanta Sapkota, Mogens Nicolaisen – Journal of Microbiological Methods

Metagenomics and bioinformatics

VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data – Cedric C Laczny – Microbiome

GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics – Deepak Nag Ayyala, Shili Lin – Bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metagenomics shows low energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene dissemination from domestic wastewater – Beate Christgen – Environmental Science & Technology

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes – Mikihiko Kawai – Environmental Microbiology Reports

Techniques

Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities – Patrick K. H. Lee – Environmental Science & Technology

Infection and Immunity

Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection – Rodrigo J. Gonzalez – PLOS Pathogens

Hypotheses: Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space – Gerardo Suzán – Ecology and Evolution

Bacteria in the news

Immune System Promotes Digestive Health by Fostering Community of “Good” Gut Bacteria – University of Utah – LabManager

Breastmilk drug could fight resistant bacteria – The Local

Zombie bacteria in tuberculosis – Medical Express

Conversation Between “Good” Bacteria and Immune System Is Key to Digestive Health – Healthcare Utah

 

How Gut Bacteria Affect Brain Health – Sleep Review Magazine

Inflammatory Bowel Diseases Linked to Viruses – John Wilson – Utah People’s Post

Inflammatory bowel disease blamed on viruses – Regie Green – SMN Weekly

Oral Health Hack: Chewing Gum Removes Up To 100M Bacteria In 10 Minutes, Similar To Flossing – Lizette Borreli – Medical Daily

Understanding ‘Plant Microbiome’ Can Improve Farming And Plant Health – Elizabeth Bent – Science 2.0

Science Digested: A new mold species discovered on salami – Benjamin Wolfe – Microbial Foods

* Tricking Soil Bacteria to Grow in Lab: Discovering a Class of Antibiotics to Combat Drug-Resistant Bacteria – Kendra Witt – Daily Nexus

Bacteria Hysteria

How often do you change your pajamas? – Ali Berman – Mother Nature Network

Bik’s Picks

Wake no more – What if you could sleep 50 hours straight and still never feel truly awake? Welcome to the bizarre, distressing, and totally exhausting world of the hypersomniac – Virginia Hughes – Medium.com

Learning to Talk Like a Woman: For many transgender people, achieving a feminine voice can be difficult – Shivam Saini – The Atlantic

Is it OK to eat snow? Short answer: Yes, as long it’s fresh and white – Lydia Ramsey – Popular Science

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