Mutually helping microbes can evolve by hitchhiking

Microbial Interspecies Associations in Fracture-Related Infection

OBJECTIVES

Describe co-occurrence or clustering of microbial taxa in fracture-related infections to inform further exploration of infection-related interactions among them.

DESIGN

Retrospective review.

SETTING

Level 1 trauma center.

PATIENTS/PARTICIPANTS

Four hundred twenty-three patients requiring surgical intervention for deep surgical site infection between January 2006 and December 2015.

INTERVENTION

None.

MAIN OUTCOME MEASUREMENT

Connection between microbial taxa.

RESULTS

Methicillin-resistant Staphylococcus aureus, methicillin-sensitive Staphylococcus aureus, and coagulase-negative Staphylococcus represented the majority of monomicrobial observations (71%). Gram-negative rods, gram-positive rods, and anaerobes presented more frequently in polymicrobial infections. Enterobacter, vancomycin-sensitive Enterococcus, and Pseudomonas are present in polymicrobial infections with the highest frequencies and represent the top 3 most important nodes within the microorganism framework, with the highest network centrality scores.

CONCLUSIONS

The present study indicates that there are common microbial taxa (Enterobacter, Enterococcus, and Pseudomonas) that tend to co-occur with other microbes greater than 75% of the time. These commonly co-occurring microbes have demonstrated interactive relationships in other disease pathologies, suggesting that there may be similar important interactions in fracture-related infections. It is possible that these microbial communities play a role in the persistently high failure rate associated with management of infection after trauma. Future studies are needed to study the intermicrobial interactions that explain the frequency at which taxa co-occur. Understanding and potentially disrupting these intermicrobial relationships could inform improvements in the treatment of established infections and in the prevention of infection in high-risk patients.

LEVEL OF EVIDENCE

Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Nutrient Exchange of Carbon and Nitrogen Promotes the Formation of Stable Mutualisms Between Chlorella sorokiniana and Saccharomyces cerevisiae Under Engineered Synthetic Growth Conditions

Microbial biotechnological processes can be based on single species pure cultures or on multi-species assemblages. While these assemblages can be advantageous by offering more functionalities and more resilience to changing environmental conditions, they can be unpredictable and difficult to control under synthetically engineered growth conditions. To overcome the unpredictable nature of these microbial assemblages, the generation of stable mutualistic systems through synthetic ecology approaches may provide novel solutions for understanding microbial interactions in these environments. Here we establish a stable association between two evolutionarily unrelated, but biotechnologically complementary species isolated from winery wastewater; a strain of the yeast Saccharomyces cerevisiae and microalga, Chlorella sorokiniana. Yeast and microalgae were able to form obligate (interdependent) and non-obligate (facultative) mutualisms under engineered batch co-culture growth conditions. Obligate mutualism was maintained through the reciprocal exchange of carbon and nitrogen where the yeast ferments mannose to produce carbon dioxide for use by the microalga; and the microalga provides the yeast with nitrogen by metabolizing nitrite to ammonium. The effect of temperature and pH on the establishment of these mutualisms was evaluated and pH was found to be a key determinant for mutualism formation under obligatory conditions. Moreover, the combinations of the two species under non-obligatory growth conditions led to improvement in growth rate and biomass production when compared to single species cultures grown under the same conditions. Such engineered mutualisms are the first step in developing stable multi-species assemblages, while providing a system to generate novel insight into the evolution of mutualistic interactions between phylogenetically distant microorganisms.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Design, analysis and application of synthetic microbial consortia

The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.

Synthetic microbial consortia: from systematic analysis to construction and applications

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

The genotypic view of social interactions in microbial communities

Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage. We outline the logic and methods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage.