Metabolic Modelling Approaches for Describing and Engineering Microbial Communities

Abstract

Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to the awareness about their biotechnological influences in a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications (both in vivo and in silico) have been developed in the context of isolated microbes. In vivo microbial consortia development, i.e. to reproduce the community life conditions in the wet-lab, is extremely difficult and expensive requiring of computational approaches to advance knowledge about microbial communities, mainly with descriptive modelling, and further with engineering modelling. In this review we provide a detailed compilation of available examples of engineered microbial communities as a launch pad for an exhaustive and historical revision of those computational methods devoted so far toward the better understanding, and rational engineering of natural and synthetic microbial communities.

Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling

“…Metabolic modelling is a powerful modelling framework. It has been successfully used to study microbial physiology (Notebaart et al, 2008; Segrè et al, 2002; Shlomi et al, 2005; Varma & Palsson, 1994), to design strains for industrial and medical applications (Gu et al, 2019b; Lun et al, 2009; Mishra et al, 2018), and to explore questions in the field of evolution (Bajić et al, 2018; Barve & Wagner, 2013; William Harcombe et al, 2013; Ibarra et al, 2002; Notebaart et al, 2014; San Roman & Wagner, 2018, 2020; Sandberg et al, 2017) and ecology (Estrela, Sanchez‐Gorostiaga et al, 2020; Harcombe et al, 2014; Levy & Borenstein, 2013; Machado et al, 2021; McNally & Borenstein, 2018; Zelezniak et al, 2015), as reviewed previously (García‐Jiménez et al, 2021; Gu et al, 2019b; Mardinoglu & Nielsen, 2012). Though outside the scope of our work, the modelling framework used here can in principle also be used to study other ecological phenomena, such as successional dynamics (Bell & Pascual, 2020; Chase, 2003; Dini‐Andreote et al, 2014; Lockwood et al, 1997; Nemergut et al, 2007), and the role of historical contingency (or priority effects) in the assembly process (Chase, 2003; Fukami, 2015).…”

Defining the wheat microbiome: Towards microbiome-facilitated crop production

“…Ahemad and Khan [165] state that the exploitation of bacteria with multiple plant growth-promoting traits is beneficial, however, finding one bacterial strain with all desirable characteristics with the ability to colonize a variety of plant hosts and soil types is unlikely [166] , making the use of mixtures of microbes, also known as synthetic communities a good alternative. García-Jiménez et al [167] point out there are important considerations when designing SynComs such as how the communities will be structured to ensure stability and the desired output. It is therefore essential to understand the compatibility among the different members of a given synthetic community so that when co-inoculated they benefit the host, are not antagonistic toward one another, and are resilient when challenged with biotic and/or abiotic stresses.…”

Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents

“…In many cases this advises adoption of multi-strain and multi-species communities instead of focusing on single specimens. These assemblies can quickly adapt to specific conditions by changing their relative composition instead of regulating gene expression at individual levels [119–121]. Apart from combining biochemical capacities, the components of a microbial partnership can be physically connected by means of surface-exposed adhesins that follow certain association rules [122] and programmed to adapt what has been called synthetic morphologies [123,124].…”