Sign up to save your podcasts
Or
Share Genome-based targeted sequencing as a reproducible microbial community profiling assay.
Share to email
Share to Facebook
Share to X
Share to email
Share to Facebook
Share to X
Or
Genome-based targeted sequencing as a reproducible microbial community profiling assay.
Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.08.07.241950v1?rss=1
Authors: Benjamino, J., Leopold, B., Phillips, D., Adams, M. D.
Abstract:
Current sequencing-based methods for profiling microbial communities rely on marker gene (e.g. 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. We present a new approach based on highly multiplexed oligonucleotide probes designed from reference genomes in a pooled primer-extension reaction during library construction to derive relative abundance data. This approach, termed MA GenTA: Microbial Abundances from Genome Tagged Analysis, enables quantitative, straightforward, cost-effective microbiome profiling that combines desirable features of both 16S rRNA and mWGS strategies. To test the utility of the MA-GenTA assay, probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, NMDS clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS and 16S rRNA datasets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes.
Copy rights belong to original authors. Visit the link for more info
View all episodes
By Multimodal LLCLink to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.08.07.241950v1?rss=1
Authors: Benjamino, J., Leopold, B., Phillips, D., Adams, M. D.
Abstract:
Current sequencing-based methods for profiling microbial communities rely on marker gene (e.g. 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. We present a new approach based on highly multiplexed oligonucleotide probes designed from reference genomes in a pooled primer-extension reaction during library construction to derive relative abundance data. This approach, termed MA GenTA: Microbial Abundances from Genome Tagged Analysis, enables quantitative, straightforward, cost-effective microbiome profiling that combines desirable features of both 16S rRNA and mWGS strategies. To test the utility of the MA-GenTA assay, probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, NMDS clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS and 16S rRNA datasets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes.
Copy rights belong to original authors. Visit the link for more info