As you said in your question "16S rRNA sequencing uses PCR to amplify a specific region of DNA", that is the main difference. 16S rRNA amplicon sequencing will sequence only the 16s gene in the provided DNA sample. Whereas, metagenomic will sequence all or most of the genes within a provided DNA sample. So, with 16s sequencing, one can get only the taxonomic information (from which bacteria does the 16s sequence came) while from metagenomics, both taxonomy and functional potential of the sample can be determined.
Note: There are some algorithms like PICRUSt which can PREDICT functional genes from 16s sequencing. But this can be used only for prediction and not conformation of a particular functional gene.
Hi Temoor, Although the metagenome is all of the genes present, 16S genes that are present represent a part of the overall metagenome and can be considered by some to also be metagenomics. In general if taxonomic identification of bacteria is what you are looking for 16S can provide the information with greatly reduced less cost for library perparation, sequencing and computational effort. I use both, routinely depending on the what it is I am looking for. 16S data often is sufficient and is an order of magnitude less expensive than shotgun metagenomics when depth and library prep are taken into account. It has limitations, it gives no direct information regarding pathway abundance etc (although it can be infered). Also no primer set for 16S amplification is truly universal, so some may be missed. A good discussion can be found at https://blog.microbiomeinsights.com/16s-rrna-sequencing-vs-shotgun-metagenomic-sequencing
Agree with Frank, and Shailesh.16S rRNA gene sequencing method sequences 16s rRNA gene of bacteria but whole metagenomic sequencing sequences whole genome. So we can get the compositional (not only bacteria but other microbes too) and functional data of microbes. PICRUST can predict functional data from 16sRNA sequencing data. 16S rRNA is less expensive than WGS.
Hi Frank R Burns Thilini Jayasinghe Shailesh Nair, Thanks so much for checking out the question and leaving a comment!
Dear Temoor,
All the above information are valid and have shed light on the differences. They are two different things entirely.
Find time to visit this blog to learn more about the confusiion in usage of the two terms.
https://phylogenomics.blogspot.com/2012/08/referring-to-16s-surveys-as.html?m=1
The 16S rRNA gene sequencing is used as a tool to identify bacteria at the species level and assist with differentiation between closely related bacterial species, however metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments.
In other words, metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat.
16S rRNA sequencing uses PCR to amplify a specific region of DNA", that is the main difference. 16S rRNA amplicon sequencing will sequence only the 16s gene in the provided DNA sample. Whereas, metagenomic will sequence all or most of the genes within a provided DNA sample. So, with 16s sequencing, one can get only the taxonomic information (from which bacteria does the 16s sequence came) while from metagenomics, both taxonomy and functional potential of the sample can be determined.
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