March 28, 2016

Oral microbiome and smoking, a bacterial genome from a germ-free mouse isolate, semi-arid soils, jellyfish, OTU picking methods, and the best hypervariable regions in the 16S rRNA gene.

Human oral microbiome

Cigarette smoking and the oral microbiome in a large study of American adults – Jing Wu – The ISME Journal

Human gut microbiome

Persisting changes of intestinal microbiota after bowel lavage and colonoscopy – Drago, Lorenzo – European Journal of Gastroenterology & Hepatology

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations – Rashmi Sinha – PLOS ONE

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India – Saurabh Kedia – Journal of Gastroenterology

Review: Gut Microbiota and Lifestyle Interventions in NAFLD – David Houghton – MDPI International Journal of Molecular Sciences

Review: Microbiota-gut-brain signalling in Parkinson’s disease: Implications for non-motor symptoms – Valeria D. Felice – Parkinsonism & Related Disorders

PhD Thesis: Development and analysis of molecular methods for functional metagenomics of the human gut microbiome – Kathy Lam – University of Waterloo

Animal models

Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease – Irina A. Kirpich – The American Journal of Pathology

Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse – T. A. Auchtung – Genome Announcements

Animal microbiome

Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes – Daniel F. R. Cleary – FEMS Microbial Ecology

Review: Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases – Mikolaj M. Raszek – Frontiers in Genetics

Plant, root, and soil microbiome

Soil characteristics driving arbuscular mycorrhizal fungi communities in semiarid Mediterranean soils – Maria del Mar Alguacil – Applied and Environmental Microbiology

454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems – Elham A. Kazeeroni – Frontiers in Plant Science

Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis – Zhiyuan Yao – Journal of Soils and Sediments

Soil communities are affected by CO2 belowground emissions at a natural vent in Spain – I. Fernández-Montiel – Soil Biology and Biochemistry

No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium) – Florine Degrune – Agriculture, Ecosystems & Environment

Bacteria play a more important role than nutrients in the accumulation of tetracycline resistance in manure-treated soil – Shuang Peng – Biology and Fertility of Soils

Review: Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism – Sofie Thijs – Frontiers in Microbiology

Water microbiome

Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids – Jean-Paul Baquiran – Frontiers in Microbiology

Streams: Regional and global elevational patterns of microbial species richness and evenness – Jianjun Wang – Ecography

Extremophile microbiome

Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes – Daniel R. Colman – Frontiers in Microbiology

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments – Alexander Crits-Christoph – Frontiers in Microbiology

Bioinformatics and metagenomics

Application of database-independent approach to assess the quality of OTU picking methods – Patrick D Schloss – BioRxiv

MG-Digger: an automated pipeline to search for giant virus-related sequences in metagenomes – Jonathan Verneau – Frontiers in Microbiology

MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices – Dinghua Li – Methods

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis – Bo Yang – BMC Bioinformatics

Absent words and the (dis)similarity analysis of DNA sequences: an experimental study – Mohammad Saifur Rahman – BMC Research Notes

Book chapter: Bidirectional Variable-Order de Bruijn Graphs – Djamal Belazzougui – LATIN 2016: Theoretical Informatics


Review: Translating RNA sequencing into clinical diagnostics: opportunities and challenges – Sara A. Byron – Nature Reviews Genetics


Modification of a high- throughput automatic microbial cell enumeration system for ship board analyses – Christin M. Bennke – Applied and Environmental Microbiology

More microbiology

Rare-earth elementsRare-earth separation using bacteria – William Bonificio – Environmental Science & Technology Letters

Expression of HIV-1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus – Angela Marcobal – AIDS Research and Human Retroviruses

Review: Studying Bacterial Multispecies Biofilms: Where to Start? – Henriette L. Røder – Trends in Microbiology

Microbes in the news

Osel scientists engineer vaginal lactobacillus to express neutralizing HIV-1 antibody fragments – EurekAlert

‘Good’ bacteria could save amphibians hit by fungal diseases – Adam Wernick – PRI

Forget Chocolate Rabbits: Microbiologists Celebrate Easter With Bacteria Bunny – ABC News

Psychobiotics Will Use Bacteria to Alter Your Brain Through Your Gut – Ben Guarino – Inverse

Low FODMAP diet may significantly improve IBS symptoms – Healio

Scientists to drill into dinosaur-killing blast – Eric Hand – Science

Rage Disorder Linked with Parasite Found in Cat Feces. Toxoplasmosis may alter brain chemistry is people exhibiting bouts of explosive anger – Christopher Wanjek – Scientific American

Bacteria Hysteria

Would you dare to bacteria-test your entire life? Katherine Keogh did … and the result will shock all house-proud readers – Katherine Keogh – Daily Mail



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