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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Microbiome Digest - Bik's Picks 