Category Archives: Bik’s Non-Microbiology Picks

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 18, 2015

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

Human oral microbiome

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

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

Human skin microbiome

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

Human respiratory microbiome

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

Human vaginal microbiome

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

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

Human gut microbiome

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

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

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

Animal and other models

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant microbiome

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

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

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

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

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

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

Soil microbiome

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

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

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

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

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

Water microbiome

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

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

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

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

Microbes of the Built Environment

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

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

Bioreactor microbiology

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

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

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

Phages, viruses, CRISPRs

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

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

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

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

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

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

Archaea

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

Microbial Ecology

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

Bioinformatics

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

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

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

Metagenomics

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

Metabolomics, proteomics

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

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

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

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

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

Other articles of interest

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

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

Microbes in the News

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

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

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

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

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

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

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

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

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

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

Science, publishing, and career

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

Motherhood: Biases in US academia – Nature

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

Bik’s Picks

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

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

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

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February 17, 2015

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

Microbiome of pregnancy and birth

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

Human oral microbiome

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

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

Human vaginal microbiome

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

Human gut microbiome

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

Plant microbiome

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

Bioreactor microbiology

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

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

Phages and viruses

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

Microbial Ecology

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

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

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

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

Bioinformatics, metagenomics

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

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

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

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

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

Metabolomics

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

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

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

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

Microbes in the news

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

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

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

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

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

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

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

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

Science and career

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

Science and art

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

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

Bik’s Picks

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

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

Satire: Study Finds Jack Shit – The Onion

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February 12, 2015

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

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

Two San Francisco Bay Area events of interest

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

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

General human microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

Animal models of microbiome research

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

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

Animal microbiome

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

Catacombs microbiome

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

Soil and sediment microbiome

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

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

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

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

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

Water microbiome

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

Bioreactor microbiome

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

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

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

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

Metabolomics and Proteomics

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

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

The Unipept metaproteomics analysis pipeline – Bart Mesuere – Proteomics

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

Microbial Ecology

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

Bioinformatics

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

Techniques

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

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

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

Other microbiology papers

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

Bik’s Picks

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

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

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

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February 11, 2015

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Human oral microbiome

Extensive Description and Comparison of Human Supra-Gingival Microbiome in Root Caries and Health – Lin Chen – PLOS ONE

Human gut microbiome

Characterization of the Gut Microbiota of Papua New Guineans Using Reverse Transcription Quantitative PCR – Andrew R. Greenhill – PLOS ONE

Animal models

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks – Andrey Morgun – Gut

Long-Lasting Effects of Early-Life Antibiotic Treatment and Routine Animal Handling on Gut Microbiota Composition and Immune System in Pigs – Dirkjan Schokker – PLOS ONE

Plant microbiome

A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey – Wayne Reeve – Standards in Genomics Sciences

More microbes

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens – Ramya Srinivasan – PLOS ONE

Mutualism Breakdown by Amplification of Wolbachia Genes – Ewa Chrostek – Luis Teixeira – PLOS Biology

Intranuclear bacteria: inside the cellular control center of eukaryotes – Frederik Schulz, Matthias Horn – Trends in Cell Biology

Microbes in the news

Satire: Fitbiotics: A secret supplements company, until now known only by high levels athletes, sells the fittest microbiome on Earth – The Megabiome

Must-read for anyone interested in the New York subway microbiome paper: There’s No Plague on the NYC Subway. No Platypuses Either – Ed Yong

Metagenomics best hit analysis: caveat emptor – Nick Loman – Github blog

Win a home microbiome analysis plus 50 giant microbes (if you subscribe to New Scientist) – New Scientist

Drs. Cardelli and Woolard Funded to Study Bacteria in the Intestine – LSU Health

From Solar Energy To Liquid Fuel: Scientists Use Bacteria The Way Plants Do – James Maynard – Tech Times

Science, publishing, and career

Science Communication in Less Than 140 Characters – Lauren Dobischok – Future Science Leaders

How Elementary School Teachers’ Biases Can Discourage Girls From Math and Science – Claire Cain Miller – New York Times

And the winner is: not science – Portrayals of science in the cinema are growing in sophistication — but not exactly at the speed of light – Colin Macilwain – Nature

Bik’s Picks

Chronic Fatigue Syndrome Gets a New Name – Karen Barrow – New York Times

Google Now Serving Fact-Checked Medical Search Results – Dan Van Winkle – The Mary Sue

Evolution of Darwin’s finches and their beaks revealed by genome sequencing – Sangeet Lamichhaney – Nature

Long read: The Food Babe: Enemy of Chemicals – James Hamblin – The Atlantic

Why Your Cat May Be More Human Than You Think – Karen Becker – Huffington Post

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February 10, 2015

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Microbiome of pregnancy and birth

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

Human respiratory microbiome

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

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

Human oral microbiome

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

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

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

Human gut microbiome

See also Rojo paper under Metabolomics

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

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

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

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

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

Animal microbiome

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

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

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

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

Plant microbiome

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

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

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

Soil, sediment, and rock microbiome

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

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

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

Water microbiome

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

Viruses and phages

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

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

Microbial Ecology

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

Metagenomics

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

Metabolomics

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

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

Bioinformatics

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

Techniques

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

More microbes

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

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

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

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

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

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

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

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

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

Science and Art

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

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

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

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

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

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

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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 6, 2015

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Pregnancy and birth microbiome

The composition of the gut microbiota throughout life, with an emphasis on early life – Juan Miguel Rodríguez – Microbial Ecology in Health and Disease

Review: Antenatal lower genital tract infection screening and treatment programs for preventing preterm delivery – Ussanee S Sangkomkamhang – Cochrane Library

Animal models of microbiome research

Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation – Edward Alain B. Pajarillo – Applied Microbiology and Biotechnology

Animal microbiome

Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae –
Timothy K. O’Connor – Frontiers in Microbiology

Plant microbiome

Agricultural probiotics enter spotlight – Jeffrey L Fox – Nature

Soil microbiome

Inorganic fungicides as routinely applied in organic and conventional agriculture can increase palatability but reduce microbial decomposition of leaf litter – Jochen P. Zubrod – Journal of Applied Ecology

Effect of diesel-oil addition on soil microbiological parameters in systems with and without plants – MC Petenello – Terra Latinoamericana

Does long-term use of mineral fertilizers affect the soil microbial biomass? – D Geisseler – Better Crops with Plant Food

News and views: Microbes: The chief ecological engineers in reinstating equilibrium in degraded ecosystems – Jay Shankar Singh – Agriculture, Ecosystems & Environment

Review: Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review – Marie Simonin, Agnès Richaume – Environmental Science and Pollution Research

Water microbiome

Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya – Tom O. Delmont – Frontiers in Microbiology

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait) – Pier Luigi Buttigieg – Frontiers in Microbiology

Aquifer environment selects for microbial species cohorts in sediment and groundwater – Laura A Hug – The ISME Journal

Fate of the Herbicide Alachlor Exposed to Different Microbial Consortia in Aquatic Systems – Armelle Paule – Water, Air, & Soil Pollution

Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi canyon 118 before the Deepwater Horizon disaster – Sarah Underwood – Deep Sea Research Part II: Topical Studies in Oceanography

Air microbiome

Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR – Min Wei – Journal of Environmental Sciences

Bioreactor and wastewater microbiology

Processing barley grain with lactic acid and tannic acid ameliorates rumen microbial fermentation and degradation of dietary fibre in vitro – Kathrin Deckardt – Journal of the Science of Food and Agriculture

Microbial community dynamics associated with veterinary antibiotics removal in constructed wetlands microcosms – Joana P. Fernandes – Bioresource Technology

Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing – Thorsten Köchling – Applied Microbiology and Biotechnology

Metabolomics and proteomics

Review: Nutriproteomics: Facts, concepts, and perspectives – Sascha Sauer and Toni Luge – Proteomics

Microbial Ecology

Dispersal among local communities does not reduce historical contingencies during metacommunity assembly – Zhichao Pu and Lin Jiang – Oikos

Functional dissimilarity across trophic levels as a driver of soil processes in a Mediterranean decomposer system exposed to two moisture levels – Mathieu Coulis – Oikos

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor – Alexandra Igorevna Klimenko – BMC Evolutionary Biology

Immunology

Recent infections are associated with decreased risk of rheumatoid arthritis: a population-based case-control study – Maria EC Sandberg – Annals of the Rheumatic Diseases

Viruses and phages

Assembly of viral genomes from metagenomes – Saskia L. Smits – Frontiers in Microbiology

Sorting of small infectious virus particles by flow virometry reveals distinct infectivity profiles – Raphaël Gaudin & Natasha S Barteneva – Nature Communications

Metagenomics and chromosomal organization

Novel assay to measure the plasmid mobilizing potential of mixed microbial communities – Uli Klümper – Frontiers in Microbiology

Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria – Ryan C. Lynch – Frontiers in Microbiology

Review: Evolution of small prokaryotic genomes – David J. Martínez-Cano – Frontiers in Microbiology

Bioinformatics

A Quick Guide for Building a Successful Bioinformatics Community – Aidan Budd – PLOS Computational Biology

Microbes in the news

Bacteria help breastfed babies digest solid food – Mark Derewicz – Futurity

From fourth-century soup to 21st-century procedure, fecal transplantation proves its worth against stubborn bacteria – VA Research Currents (HT: Inder Perkash)

Mapping the Microbes of the New York City Subway – Marcus Woo – Wired.com

Age-related hepatitis B infection and the gut microbiome – Heather Zeiger – Medical Xpress

Researchers Uncover Infant Gut Microbiome Alterations Linked to Type 1 Diabetes – GenomeWeb

Gut Bacteria Link Between Heart and Kidney Disease Strengthened – WH Wilson Tang – MedicalResearch.com

Nine ways your gut can protect your heart – Giovanni Campanile – Mens Fitness

New clinical study to focus on gut, autism connection (with James Versalovic) – Baylor College of Medicine

Science, publishing, and career

Frontiers for Young Minds – non-profit scientific journal for 8-15 year olds – Frontiers

A classroom experiment – Jeffrey Mervis – Science

Undergraduate research experiences: Impacts and opportunities – Marcia C. Linn – Science

Science by any means necessary (interview with Erich Jarvis) – Rachel Bernstein – Science

The Scientist’s Toolbox: Last Call – Name and describe a currently nonexistent invention that would make you a more effective scientist – Science

Breaking bad science – Joel Best – Science

Science and art

Cute pathology pictures – Seriously Science – Discover Magazine

Bik’s Picks

This college student is eating bugs for 30 days so you will too – Rachel Feltman – Washington Post

Where is Silicon Valley? – Jorge Guzman, Scott Stern – Science

Fire Department Saves Woman From Robot Vacuum Attack. It Begins. – Dan Van Winkle – The Mary Sue

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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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