General microbiome papers
Review: The Microbiome: A Contributor to Health and Disease – Bailus Walker Jr. – Journal of the Health Care for the Poor and Underserved
Human oral microbiome
Transduction-mediated horizontal gene transfer in the oral microbiome – Roy H. Stevens – Frontiers in Cellular and Infection Microbiology
Human respiratory microbiome
Review: The lung mycobiome: an emerging field of the human respiratory microbiome – Linh D. N. Nguyen – Frontiers in Microbiology
Human gut microbiome
Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages – Se-Hoon Park – BMC Microbiology
Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality – Yanfei Chen – Journal of Gastroenterology and Hepatology
Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj – Abiola Olumuyiwa Olaitan – International Journal of Antimicrobial Agents
Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine
Human vaginal microbiome
Correlates of the molecular vaginal microbiota composition of African women – Raju Gautam – BMC Infectious Diseases
Animal microbiome
In chickens: Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences – Dragana Stanley – BMC Microbiology
Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh – Andrea M. Larsen – Microbial Ecology
Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences – Sandra Pucciarelli – Microbial Ecology
Plant microbiome
Phenotypic and genetic characterization of rhizobia isolated from Hedysarum flexuosum in Northwest region of Morocco – Fatima Ezzakkioui – Journal of Basic Microbiology
Biotic and abiotic predictors of fungal colonization in grasses of the Colorado Rockies – Luciana B. Ranelli – Diversity and Distributions
Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Martina Köberl – Frontiers in Microbiology
Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. – Armin Erlacher – Frontiers in Microbiology
Soil and sediment microbiome
Agricultural intensification and the functional capacity of soil microbes on smallholder African farms – Stephen A. Wood – Journal of Applied Ecology
Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology
Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees – Michaela Urbanová – Soil Biology and Biochemistry
Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia – Robert Duran – Environmental Science and Pollution Research
Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation – Maria E. Hernandez – PeerJ
Water microbiome
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs – Peter Menzel – Microbial Ecology
Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients – Jiwen Liu – Frontiers in Microbiology
Microbiome of the built environment
Thesis: Longitudinal and spatial characterization of microbial communities in offices – John Chase – Northern Arizona University
Bacterial transfer to beverages during drinking games: ‘beer pong’ – Paul L. Dawson – Int. J. Food Safety, Nutrition and Public Health
Food microbiology
High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia – Wenjun Liu – BMC Microbiology
Microbiological Changes and Biodiversity of Cultivable Indigenous Bacteria in Sanbao Larger Yellow Croaker (Pseudosciaena crocea), a Chinese Salted and Fermented Seafood – He Zhang – Journal of Food Sciences
Bioreactor microbiology
A methodological framework for linking bioreactor function to microbial communities and environmental conditions – Francis L de los Reyes III – Current Opinion in Biotechnology
Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing – Haihan Zhang – BMC Microbiology
Phages and viruses
No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales – Uri Gophna – ISME Journal
Inactivation of an Enveloped Surrogate Virus in Human Sewage – Lisa M. Casanova – Environ. Sci. Technol. Lett.
Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing – Friederike S. Rossmann – PLOS Pathogens
Archaea
Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing – Vanessa D. Nkamga – Current Microbiology
Bioinformatics and metagenomics
The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: Case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia – E. González-Tortuero – Molecular Ecology Resources
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics – Sandeep K Kushwaha – BMC Bioinformatics
Spaced seeds improve metagenomic classification – Karel Bˇrinda – ArXiv
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K – Naama M. Kopelman – Molecular Ecology Resources
PhD thesis: Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome – Sharon I. Greenblum – University of Washington
Masters thesis: MR-CUDASW – GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data – Amir Muhammadzadeh
Testing ecological theories with sequence similarity networks: marine ciliates
exhibit similar geographic dispersal patterns as multicellular organisms – Dominik Forster – BMC Biology
A Brief Review of Software Tools for Pangenomics – Jingfa Xiao – Genomics, Proteomics & Bioinformatics
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes – Xavier Didelot – PLOS Computational Biology
Ten years of pan-genome analyses – George Vernikos – Current Opinion in Microbiology
Metabolomics and proteomics
Towards further defining the proteome of mouse saliva – Anne A Blanchard – Proteome Science
Protein Complexes in Bacteria – J. Harry Caufield – PLOS Computational Biology
Review: Metabolomics and Diabetes: Analytical and Computational Approaches – Kelli M. Sas – Diabetes
Techniques
Inosine at Different Primer Positions to Study Structure and Diversity of Prokaryotic Populations – Eitan Ben-Dov and Ariel Kushmaro – Current Issues Molecular Biology
Negligible effect of X-ray μ-CT scanning on archaea and bacteria in an agricultural soil – Hannes Schmidt – Soil Biology and Biochemistry
Microbes in the news
Diet, Location And Your Kid’s Gut Bacteria – Stefania Hartley – Asian Scientist Magazine
Killing off one Bacterium Can Lead to Obesity – Noel Angeles – SMN Weekly
The Human Microbiome Through an Oral Healthcare Lens – Natasha Singh – Oral Health Group
Yes Virginia, there is a paper on microbial transfer during beer pong – Jonathan Eisen
First detailed evidence of bacteria at the lower size limit of life – Science Codex
How Small Can Life Get? These Ultra-Small Bacteria May Be At The Limit – Science 2.0
Title Fail: Deadly bacteria outbreak linked to UCLA microscopes – Standard Examiner
The bioMASON Startup Grows Bricks from Bacteria – Annie Pilon – Small Biz Trends
Deadly bacteria release sparks concern at Louisiana lab – Alison Young – USA Today
Science, publishing and career
Riding Out Rejection: How to navigate the choppy waters of scientific publication – Kate Yandell – The Scientist
Medical Journals and Free Speech – Joel Bakan – Pediatrics
How to Write a Presubmission Inquiry – Thomas Lengauer, Ruth Nussinov – PLOS Computational Biology
Chill GPS: Keeping track of frozen biological samples – Jeffrey M. Perkel – The Scientist
Science and Art
Move over #TheDress and #LlamaDrama, this weekend’s Twitter storm was all about #SciArt – Twitter
Bik’s Picks
Scientists have created the perfect music for cats – Fiona MacDonald – Science Alert
Gulf of Mexico Turns Deadly for Dolphins – Rachel Nuwer – New York Times
‘Skeletorus’ and ‘Sparklemuffin’ the Newest Spiders – Agata Blaszczak Boxe – Live Science
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