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Gut microbe centric pages

Similar to disease centric pages, there are two types of gut microbe centric webpages , i.e., the information is organized around the microbe(s), including:

  • the gut microbes page that lists all gut microbes identified in the qualified samples collected in GMrepo,
  • the single taxon page that lists its associated diseases and distributions across diseases. If a taxon is a disease marker, the relevant information will also be included.

These pages will be described in detail below.

fontawesome-solid-book-open: All gut microbes

This page lists all gut microbes at species and genus levels included in
GMrepo. It consists of three sections.

1. Overview

This part provides simple statistics on the gut microbes collected in our database, for example:

Microbe stats

2. Lists of all gut microbes

This part contains two data tables that list all gut microbes at species and genus levels respectively, and their associated phenotypes (i.e., diseases and health).

Species table

Users can click any of the taxa to view all relevant information of the taxon in our database in more detail.

Tip

  • Because there are so many identified species (genera), this table lists a subset of which that are found in two or more samples with median relative abundances >= 0.01%.
  • Users can use the widgets above the data table to search and filter the contents of the table. For example, users can enter a search term Bacteroides to find all species that contain Bacteroides in their names.

3. Statistics on taxon prevalence in phenotypes and samples

This part contains two histograms.

The first shows the distribution of the taxa in the phenotypes, while the second shows distribution of all the taxa in the samples.

Taxon prevalence

For example, the first bar in the left panel means that about 47.5% of all species are found in four or fewer (0–4) phenotypes.

fontawesome-solid-book-open: Detailed information on a specific taxon

This webpage contains almost all information on a taxon in our database, including:

  • its association with diseases,
  • its prevalence and abundances across diseases,
  • whether it is a marker, in how many diseases it serves as a marker, and its trends (i.e., enrichment and depletion) in diseases and healthy controls.

Here we use Fusobacterium nucleatum as an example to show the contents of this page.

1. Overview

This part summarizes very briefly the number of runs in which Fusobacterium nucleatum can be found, and the number of phenotypes (diseases and health) it is associated with.

It also includes links to external databases, including:

2. Stats on associated phenotypes

This part contains a table and a barplot.

The table lists the associated diseases and the prevalence of Fusobacterium nucleatum in the corresponding disease-associated samples.

Associated phenotypes

Users can click a disease name, e.g., Crohn Disease, to view more information on gut microbes associated with the disease in our database.

The barplot shows basically the same statistics:

Phenotype barplot

Tip

  • By default, phenotypes with more than 50 valid runs will be included in this barplot.
  • Users may increase/decrease this threshold using widgets above.
  • Here prevalence is defined as percentage of runs in which the current taxon is present (with relative abundance >= 0.01%) out of valid runs.

3. Relative abundances of the taxon in different diseases and healthy samples

The relative abundances of the taxon across diseases and health are shown in:

  • a density plot, and
  • a boxplot.

See this example.

4. Marker taxon

Please consult the marker identification documentation for more details on how markers are identified.

Note

The markers are identified on a per-project basis, and between:

  • either a disease and health (e.g., colorectal cancer (CRC) vs. healthy controls),
  • or different stages of the same disease (e.g., CRC and adenoma)

In
GMrepo,
marker information in this microbe-centric page is presented using a table and a barplot.

As shown below is the barplot view of Fusobacterium nucleatum as a marker taxon:

FN marker

Note

  • From this plot we can see that F. nucleatum has been identified as a marker in many diseases.
  • It shows consistent enrichment in diseases as compared with healthy controls.
  • It also shows consistent trend in multiple projects related to the same disease (e.g., Colorectal Neoplasms (CRC)).