⚠ About the network

The substances in "Bacteria-Substance-Disease Interaction/Association network" only cover therapeutic drugs. The network is presented for an intuitive visualization of the drugs that interact with microbiota bacteria, diseases that associated with microbiota bacteria changes, and disease-drug interactions. The interactive network is generated using Cytoscape.js.

How is the network built?

1. The first round of network build.
Bacteria-Drug edges: the bacteria-drug interactions recorded in MASI (irrespective of interaction direction).
Bacteria-Disease edges: the bacteria-disease associations recorded in MASI.
Disease-Drug edges: were extracted from Therapeutic Target Database (TTD) which provides approved disease indications of therapeutic drugs. So, disease-substance links presented here mean that drugs linked to a disease are used to treat this disease according to TTD database.

2. The second round of network build (network expansion).
Expend drug edges: drugs that associated with diseases included in the 1st round are added.
Expend disease edges: diseases that associated with drugs included in the 1st round are added.


Node shapes: drugs are presented with circles, diseases are presented with rectangles.
Node colors: drugs that interacted with the bacteria are colored with burgundy, diseases that associated with the microbiota bacteria changes are colored with dark green. Drugs and diseases that do not interact/associate with bacteria are in gray color.

⚠ About the relative abundance profile

The relative taxonomical abundance data (pre-processed using a unified analysis pipeline) was retrieved from curatedMetagenomicData resource [Edoardo Pasolli, et al. Nat Methods. 2017;14(11):1023-1024]. Data retrieved here was pre-processed as unified relative abundance: at each taxonomic level (e.g., species, genus, family), the sum of microbial abundance of individual microbiota sample was 1, and relative abundance of each microbe was log10 transformed [relative abundance ranges from -7 to 0].

Healthy samples and disease samples (only disease types with >= 20 samples were included) were grouped by age periods, patients’ country, or disease type to plot the relative abundance landscape using ggplot2 R package.