The microbiota search functionality is designed to enable users to identify the conditions associated with the occurrence of a particular microbe or taxonomic group.
This search functionality suits users that are interested in understanding particular component of the microbiota. The search interface provides the ability to select the microbiota of interest and define a cutoff level above which samples will be considered positive for the search. The search functionality also allows the taxonomic list to be limited to only those groups confirmed or annotated as cultured from the human gastrointestinal tract.
Search results includes Analysis Overview, Prevalence Distribution and Co-occurring Species.
- Analysis Overview of sample characteristics where the taxonomic group is detected including age, gender, disease state and ethnicity distribution.
- Prevalence Distribution displays the relative abundance of the searched group across all samples in which it was detected
- Co-occurring Species allows one to identify the co-occurring taxonomic groups that associate more frequently than would be expected by chance with the searched species or group.
An example of this search functionality is illustrated in the text tutorial included below.
The microbiota search is designed to enable users to search for conditions in which a particular species or phylogenetic group is found. To perform this search select the phylogenetic level and species or group of interest.
The minimum cutoff will determine what level of detection is required for the group to be considered present in each sample considered
The search results initially compare the occurrence of the phylogenetic group with the full background dataset. Enrichment is also calculated to facilitate identification of potentially biologically relevant relationships. The options are found under "Detection Conditions"
The "Prevalence Distribution" option displays all the samples in which the group of interest was detected. This graph provides quantification by sample. Hovering the mouse over the individual samples will provide further metadata associated with the samples
The "Co-occurring Species Coverage" option allows identification of shared community structure between samples containing the group of interest. This display is similar to the display described in the comparison search tutorial.
More information can be found on other search functionality on the help page