Microbiome Digest, October 29, 2014

The genome of Mycoplasma Mnola, helminths in wild rats, fungi in strawberry roots, and the top 100 most cited papers of all time. Can you guess which one is #1?

Human genital microbiome

An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease – Jennifer M. Fettweis – PLOS ONE

“In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease.”

Human gut microbiome

Bacteriology and Changes in Antibiotic Susceptibility in Adults with Community-Acquired Perforated Appendicitis – Hong Gil Jeon – PLOS ONE

“We retrospectively reviewed records of adult patients diagnosed with perforated appendicitis at an 800-bed teaching hospital between January 2000 and December 2011. “

Animal microbiome

Changes in the intestinal bacterial community during the growth of white shrimp, Litopenaeus vannamei – Zhaobin Huang – Aquaculture Research

“In this study, we documented the changes in the intestinal bacterial community at four stages in Litopenaeus vannamei…, using 454 pyrosequencing techniques. “

Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics – Ryusei Tanaka – PLOS ONE

“In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups.”

Soil microbiome

Linking soil microbial communities to vascular plant abundance along a climate gradient – Luca Bragazza – New Phytologist

“Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance.”

* Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry – Srivathsa Nallanchakravarthula – PLOS ONE

“In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing.”

Metagenomics / Bioinformatics

Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes – Ying Yang – PLOS ONE

“A hybrid annotation pipeline proposed previously for taxonomic assignments was evaluated in this study for metagenomic sequences annotation of specific functional genes, such as antibiotic resistance genes, arsenic resistance genes and key genes in nitrogen metabolism. “

Metabolomics

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

“Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. “

Phages and viruses

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting – Gregory W. Goldberg – Nature

“Here we show that the Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phages. “

Science, publishing and career

The top 100 papers – Richard Van Noorden – Nature

“To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time.”

Bibliometrics: Is your most cited work your best? – John P. A. Ioannidis – Nature

“John P. A. Ioannidis and colleagues asked the most highly cited biomedical scientists to score their top-ten papers in six ways.”

Recommendations for the Role of Publishers in Access to Data – Jennifer Lin, Carly Strasser – PLOS Biology

“As appeals for public access of research data continue to proliferate, many scholarly publishers—alongside funders, institutions, and libraries—are expanding their role to address this need. “

How to Make More Published Research True – John P. A. Ioannidis – PLOS ONE

“Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted.”

Prominent Geomicrobiologist Dies – Tracy Vence – The Scientist

“Katrina Edwards, whose research focus was on discovering life beneath the ocean floor, has passed away at age 46.”

Bik’s Picks

The Art of Science: Popsicles Go Viral – The Finch and Pea

“Lick a virus? Probably not a good idea, unless it’s a Dangerous Popsicle, a sweet treat created by artist and designer Wei Li. “

Dozens of genes associated with autism in new research – Science Direct

“Two major genetic studies of autism, involving more than 50 laboratories worldwide, have newly implicated dozens of genes in the disorder. “

Antares Rocket Explosion Destroyed These Kids’ Science Projects – Rheana Murray – ABC News

“Students across the nation watched their science projects go up in flames as the rocket bound for the International Space Station exploded moments after takeoff.”

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