Human oral microbiome
The cultivable microbiota of primary and secondary infected root canals, their susceptibility to antibiotics and association with the signs and symptoms of infection – M. E. Łysakowska – International Endodontic Journal
DGGE: Profiling of Oral and Nasal Microbiome in Children With Cleft Palate – Min Zhang – The Cleft Palate–Craniofacial Journal
Human gut microbiome
Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates – Doris Vandeputte – Gut
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett’s Esophagus Cohort – Alevtina Gall – PLOS ONE
Alterations in Intestinal Microbiota Correlate with Susceptibility to Type 1 Diabetes – Aimon K. Alkanani – Diabetes
Specific gut microbiota features and metabolic markers in postmenopausal women with obesity – LK Brahe – Nutrition & Diabetes
Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese – Takayoshi Hisada – Archives of Microbiology
Editorial: Gut bacteria feed a healthy brain – Denise Waldron – Nature Reviews Microbiology
Review: The gut microbiota of nonalcoholic fatty liver disease: current methods and their interpretation – Niels van Best – Hepatology International
Review: Can we change our microbiome to prevent colorectal cancer development? – Roberta M. Manzat-Saplacan – Acta Oncologica
Human genital microbiome
Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda – Cindy M. Liu – mBio
Models of microbiome
In pigs: Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype – Claire A Merrifield – ISME Journal
In goats: Postnatal bacterial succession and functional establishment of hindgut in supplemental feeding and grazing goats – J. Z. Jiao – Journal of Animal Science
In termites: Multiple analyses of microbial communities applied to the gut of the wood-feeding termite Reticulitermes flavipes fed on artificial diets – Cédric Tarayre – Symbiosis
Animal microbiome
Sponges: Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora – Zhao-Ming Gao – PeerJ
Sponges: Microbial diversity and putative diazotrophy in high and low microbial abundance Mediterranean sponges – Marta Ribes – Applied and Environmental Microbiology
Plant root and soil microbiome
Tree genotype mediates covariance among communities from microbes to lichens and arthropods – Louis J. Lamit – Journal of Ecology
Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of Copper – Murali Sharaff – Journal of Basic Microbiology
Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology
Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil – Linjing Deng – Applied Microbiology and Biotechnology
Soil Microbial Functions After Forest Fires Affected by the Compost Quality – René Guénon – Land Degradation & Development
Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning – Xian Liu – Microbial Ecology
Metagenome Sequencing Reveals Rhodococcus Dominance in Farpuk Cave, Mizoram, India, an Eastern Himalayan Biodiversity Hot Spot Region – Surajit De Mandal – Genome Announcements
The stability of textile azo dyes in soil and their impact on microbial phospholipid fatty acid profiles – Muhammad Imran – Ecotoxicology and Environmental Safety
Endophyte community composition is associated with dieback occurrence in an invasive tree – Tracey V. Steinrucken – Plant and Soil
Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems – Acacio Aparecido Navarrete – PLOS ONE
Resilience of soil microbial and nematode communities after biofumigant treatment with defatted seed meals – S. Mocali – Industrial Crops and Products
Effect of cassava mill effluent on biological activity of soil microbial community – Etinosa O. Igbinosa – Environmental Monitoring and Assessment
Editorial: An interkingdom partnership – Naomi Attar – Nature Reviews Microbiology
Review: Synergisms between microbial pathogens in plant disease complexes: a growing trend – Jay Ram Lamichhane – Frontiers in Plant Science
Review: Plant Virus Metagenomics: Advances in Virus Discovery – Marilyn J. Roossinck – Phytopathology
Water microbiome
Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens – Krista Peltoniemi – FEMS Microbiology Ecology
A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin? – Claudia Vannini – PLOS ONE
Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules – Marco Blöthe – Environmental Science & Technology
Editorial: Deep sequencing of the global oceans – Cláudio Nunes-Alves – Nature Reviews Microbiology
Extremophile microbiome
Microbial diversity of hypersaline environments: a metagenomic approach – Antonio Ventosa – Current Opinion in Microbiology
Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil – Julyan Arbel – Ecology and Evolution
Bioreactor microbiome
Evaluation of surfactants on waste activated sludge fermentation by pyrosequencing analysis – Aijuan Zhou – Bioresource Technology
Impact of the contemporary environment on denitrifying bacterial communities – Sarah K. Hathaway – Ecological Engineering
Food microbiology
Review: Wine microbiome, a dynamic world of microbial interactions – Youzhong Liu
Metagenomics and bioinformatics
Unusual biology across a group comprising more than 15% of domain Bacteria – Christopher T. Brown – Nature
Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1 – Morten Simonsen Dueholm – Genome Announcements
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs – Felipe A. Simão – Bioinformatics
Educating Future Nursing Scientists: Recommendations for Integrating Omics Content in PhD Programs – Yvette P. Conley – Nursing Outlook
Minireview: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes – Bikel Shirley – Computational and Structural Biotechnology Journal
Metabolomics and Proteomics
In dogs: Consumption of Cooked Navy Bean Powders Modulate the Canine Fecal and Urine Metabolome – M. Forster – Current Metabolomics
Needles in the Blue Sea: Sub-Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome – Mak A. Saito – Proteomics
New aminopeptidase from “microbial dark matter” archaeon – Karolina Michalska – The FASEB Journal
Review: Recent Advances in Metabolomics – E. Smith – Current Metabolomics
Microbial Ecology
Transplantability of a circadian clock to a noncircadian organism – Anna H. Chen – Science Advances
Review: Black Queen evolution: the role of leakiness in structuring microbial communities – J. Jeffrey Morris – Trends in Genetics
Techniques
Preferential Amplification of Pathogenic Sequences – Fang Ge – Scientific Reports
Phasing of single DNA molecules by massively parallel barcoding – Erik Borgström – Nature Communications
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of
SAR11 bacterioplankton – Amy Apprill – Aquatic Microbial Ecology
Microbes in the news
Newfound groups of bacteria are mixing up the tree of life – Robert Sanders – UC Berkeley
Report: Santa Cruz’s river bacteria comes from birds, not people – Samantha Clark – San Jose Mercury News
Shark Tank Product Improves Oral Health, Measuring Levels Of Bacteria That Cause Bad Breath – Samantha Olson – Medical Daily
Manatee County, not the animal: Bacteria Could Clean Manatee Water Supply – Associated Press
Bacteria Could Help Clean Groundwater Contaminated by Uranium Ore Processing, Rutgers Study Finds – Rutgers Today
BacteriaHysteria
How much bacteria is on money in your pocket? – Click2Houston
WHO: 200 disease-causing bacteria may be found in the kitchen – ABC/CBN news
Science, publishing, and career
Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas GD Masca – eLIFE
Dancers in the Dark: Scientific Careers According to a Gender-Blind Model of Promotion –
Ana M. González Ramos – Interdisciplinary Science Reviews
Incidence of Data Duplications in a Randomly Selected Pool of Life Science Publications – Morten P. Oksvold – Science and Engineering Ethics
Five things I learned when my research went viral – Heidi Appel – The Conversation
Bik’s Picks
Foie Gras: The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver – Lizhi Lu – Genome Biology
An estimate of the number of tropical tree species – JW Ferry Slik – PNAS
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Microbiome Digest - Bik's Picks 