IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

Abstract

The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

Pyrosequencing reveals specific associations of bacterial clades Roseobacter and Flavobacterium with the harmful dinoflagellate Cochlodinium polykrikoides growing in culture

“…The method of combining a clone library with Sanger sequencing has often provided insufficient coverage to fully describe and compare microbial communities (Curtis et al, 2006). In contrast, NGS allows the collection of thousands of sequences from many samples simultaneously (Andersson et al, 2008;Danovaro et al, 2016;Hamady, Walker, Harris, Gold, & Knight, 2008) and can provide much deeper insights into the diversity of microbial communities (Herlemann et al, 2011;Lagkouvardos et al, 2016;Nair, Puthusseri, Vincent, & Bhat, 2017;Sogin et al, 2006).…”

Performing Skin Microbiome Research: A Method to the Madness

“…Analysis pipelines, e.g. QIIME (Caporaso et al , 2010) mothur (Schloss et al , 2009), and IMNGS (Lagkouvardos et al , 2016), have tutorials and best practices with parameters that should be evaluated for appropriate use with a particular dataset. There are many approaches to analyzing 16S rRNA gene sequencing data and the following overview briefly highlights most commonly used methods.…”

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

“…Enterobacteriaceae are well known gut colonisers, and all the ESKAPE pathogens can be isolated from environmental sources [58], however systematic comparisons of isolation rates across environmental and animal sources are lacking. We used the IMNGS website [59] to query the growing body of publicly available 16S taxonomic profiling data for the presence of Gram negative opportunists across a wide range of sample types (Fig 3A). These data confirm the three Enterobacteriaceae species are frequent commensals of humans and animals, with E. coli the most commonly detected; however K. pneumoniae and E. cloaceae showed equivalent or even greater prevalence amongst plant and environmental samples (7--14%), whereas E. coli was significantly less common in these niches (3--4%, p=0.01).…”