Skip to main content

IMAP: Integrated Microbiome Analysis Pipelines: End-to-End Practical User Guides Using Integrated Approaches

3 Overview of Mothur classification methods

There are four methods that can be used to profile microbial communities present in a sample. Here we briefly decribe each method:

3.1 Classify OTUs

  • OTUs (Operational Taxonomic Units (OTUs)) are clusters of similar sequences and are commonly accepted as analytical units in microbial profiling when using 16S rRNA gene markers.

3.2 Classify Phylotypes

  • A phylotype in microbiome research is a DNA sequence or group of sequences sharing more than an arbitrarily chosen level of similarity of a 16S rRNA gene marker.

3.3 Classify ASVs

  • ASVs Amplicon Sequence Variants (ASVs)in microbiome research is any inferred single DNA sequences recovered from a bioinformatics analysis of 16S rRNA marker genes.
  • ASV is typically really a cluster of sequences that are one or two bases apart from each other.

3.4 Classify Phylogenies

  • Microbial phylogenies are from gene sequence homologies. Models of mutation determine the most-likely evolutionary histories.