Microbial model communities: To understand complexity, harness the power of simplicity

Abstract

Natural microbial communities are complex ecosystems with myriads of interactions. To deal with this complexity, we can apply lessons learned from the study of model organisms and try to find simpler systems that can shed light on the same questions. Here, microbial model communities are essential, as they can allow us to learn about the metabolic interactions, genetic mechanisms and ecological principles governing and structuring communities. A variety of microbial model communities of varying complexity have already been developed, representing different purposes, environments and phenomena. However, choosing a suitable model community for one's research question is no easy task. This review aims to be a guide in the selection process, which can help the researcher to select a sufficiently well-studied model community that also fulfills other relevant criteria. For example, a good model community should consist of species that are easy to grow, have been evaluated for community behaviors, provide simple readouts and - in some cases - be of relevance for natural ecosystems. Finally, there is a need to standardize growth conditions for microbial model communities and agree on definitions of community-specific phenomena and frameworks for community interactions. Such developments would be the key to harnessing the power of simplicity to start disentangling complex community interactions.

Keywords: Community-intrinsic properties; Interactions; Microbial communities; Model systems; Standardization.

Graphical abstract

Fig. 1

Stratification of microbial model communities by number of species in the model community and number of different types of measurable interaction behaviors as listed in the original publication of the model community (more measurable interactions may have been discovered since the original publication). For details on the communities, see Table 1.

Fig. 2

Representation of different genera across the microbial model communities identified in Table 1. Note that each genus can be represented by more than one species in a single model community, such as for Bacteroides and Pseudomonas, inflating the number for that genera. The purpose of the figure is to show a picture of the taxonomic distribution of current microbial model communities.

Fig. 3

Example of different types of interactions among (fictional) biofilm-forming microbes. In (A), all three species are able to form biofilm on their own, albeit in different quantities, while in (B) only A is capable of forming biofilm on its own, while B and C are boosting the biofilm formation ability of A, akin to the situation in the THOR and SXMP model communities. In both (A) and (B), three scenarios are depicted. First, a scenario where all three species compete for the same resources is presented (i.e. the maximal biofilm formation is capped at 3). Second, a scenario where each species uses their own set of resources and therefore show limited interactions with the other species (niche complementarity) is shown. The final scenario is one of community-intrinsic behaviors, where interactions and cooperation among the three species result in more efficient resource utilization and increased biofilm output.