Bacterial Wars-a tool for the prediction of bacterial predominance based on network analysis measures

Abstract

Bacterial Wars (BW) is a network-based tool that applies a two-step pipeline to display information on the competition of bacterial species found in the same microbiome. It utilizes antimicrobial peptide (AMP) sequence similarities to obtain a relationship between species. The working hypothesis (putative AMP defense) is that friendly species share sequence similarity among the putative AMPs of their proteomes and are therefore immune to their AMPs. This may not happen in competing bacterial species with dissimilar putative AMPs. Similarities in the putative AMPs of bacterial proteomes may be thus used to predict predominance. The tool provides insights as to which bacterial species are more likely to 'die' in a competing environmental niche.

Figure 1.

BW web interface—taxa upload example. Step 1 shows the loaded list of taxa as a table of pairwise species relationships with respect to common AMPs (from BW database). The BW network generated from the table is also shown. Clicking on a node (species) highlights all neighboring species edges (shown as red edges). The node size and color reflect the Die scores (larger nodes - most likely to ‘die’, small nodes—less likely to ‘die’, green color—negative Die score, red color - positive Die score). Step 2 shows the bar chart output of the predicted Die scores. Species with the highest and lowest Die scores are labelled and shown with arrows in the bar chart.

Figure 2.

BW output for taxa in the gut microflora simulating infection by S. enteritidis. (A) Network of species with S. enteriditis showing large node with a negative Die score. (B) BW Die score bar chart for taxa in the gut microflora simulating infection by S. enteritidis.

Figure 3.

BW output for taxa simulating the lung microbiota of CF patients. (A) Network of species. (B) BW Die score bar chart for taxa simulating the lung microbiota of CF patients.