scholarly journals IDENTIFICATION AND CHARACTERIZATION OF NEUTRAL PROTEASE PRODUCING Paenibacillus Polymyxa SPECIES EMBS024 BY 16S rRNA GENE SEQUENCING

2012 ◽  
Vol 4 (5) ◽  
pp. 236-239 ◽  
Author(s):  
ANURAJ NS ◽  
◽  
SHEAZA AHMED ◽  
MUKESH YADAV ◽  
SNEHA SINGH ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
Paenibacillus Polymyxa ◽  
16S Rrna Gene Sequencing ◽  
Neutral Protease ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Identification And Characterization

Microbiota characterization of sheep milk and its association with somatic cell count using 16s rRNA gene sequencing

2019 ◽  
Vol 137 (1) ◽  
pp. 73-83 ◽  
Author(s):  
Cristina Esteban‐Blanco ◽  
Beatriz Gutiérrez‐Gil ◽  
Fernando Puente‐Sánchez ◽  
Héctor Marina ◽  
Javier Tamames ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cell Count ◽  
Somatic Cell Count ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sheep Milk ◽  
Rrna Gene Sequencing

scholarly journals Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome

mSphere ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Luisa W. Hugerth ◽  
Marcela Pereira ◽  
Yinghua Zha ◽  
Maike Seifert ◽  
Vilde Kaldhusdal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Best Practices ◽  
16S Rrna Gene ◽  
In Silico ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Rrna Gene Sequencing

ABSTRACT The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing. IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.

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