Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling

Abstract

We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia.

Figure 1. Bacterial biodiversity as deduced from 16S amplicon high-throughput sequencing of ten replicated culture lines subcultured in parallel nine times (t₁ to t₉).

(A) pool of pine-tree resin samples was used to inoculate ten independent minimum broth media supplemented with resin as the main carbon source. Sub-culturing was carried out after 4 (t₁-t₂, t₂-t₃), 3 (t₃-t₄, t₇-t₈), or 2 days (t₄-t₅, t₅-t₆, t₆-t₇, t₈-t₉) and the complete assay lasted 24 days. Each bar represents an independent experiment at a given time. The taxonomic assignation of each OTU is available in Table 1.

Figure 2. Correlations and interactions among OTUs.

Representation of the 3D positions of identified OTUs in our samples, where the distance corresponds to the amount of linear statistical correlation. Smaller distances mean stronger positive correlation and larger distances show stronger negative correlation. Sizes of the spheres are proportional to the relative abundances in logarithmic scale, while colors indicate putative bacterial consortia (OTU groups positively correlated). Blue bonds show the strength of significant positive interactions linking two OTUs, where the width of the bonds linearly scales with the relative strength of the interaction. Bonds linking OTUs 4–7 and 3–10 are hidden in this 3D perspective. The plotting code is available as Supplementary Data. The main consortia are colored as follows: yellow (Pseudomonas alcaligenes, Acinetobacter sp., Moraxellaceae OTU, Comamonadaceae OTU); blue (two species of the genus Comamonas, Zooglea sp., Neisseriaceae OTU, Burkholderiales OTU); and red (three species of the Stenotrophomonas genus, Pseudoxanthomonas mexicana, Luteimonas sp.). OTUs are numbered according to Table 1.