rpS3 marker gene analysis

Knowledge graph centered on rpS3 marker gene analysis with 68 nodes and 133 connections. Top connected: leaf water content, Crested Butte, carbon cycling, biogeochemical reactions, nitrogen retention.

Method synopsis

Taxonomic classification of microbial communities using ribosomal protein S3 (rpS3) marker genes identified through Hidden Markov Models and phylogenetic analysis.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock (2019), Ecology and Evolution. Implementations in other papers (listed below) may differ.

1. Taxonomic classification using rpS3 markers
   Microbial community structure was assessed according to the abundance of the ribosomal protein S3 (rpS3) marker gene by modifying the method described by Anantharaman et al. (2016). Archaeal, eukaryotic, and bacterial rpS3 protein sequences were identified using Hidden Markov Models (HMM) (Finn et al., 2015). Ten rpS3 reference sequences which compose TIGRFam's TIGR01009 model were added to the protein sequences that were identified by HMMs and aligned with MAFFT.
   Quantities: Ten rpS3 reference sequences from TIGR01009 model, 3,536 rpS3 amino acid sequences identified and clustered into 1,660 clusters at 99% identityDuration: Not specifiedConditions: 99% identity threshold for clustering
   Equipment: Hidden Markov Models (HMM), MAFFT alignment software

Typical Equipment

• Hidden Markov Models (HMM)
• MAFFT alignment software

Output Measurements

• taxonomic abundance
• phylogenetic relationships

Papers Using This Protocol (1)

Species Studied With This Protocol

Places Where Used