Microbiome therapeutics - Advances and challenges

Abstract

The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota.

Keywords: Bacteriophage; Host-bacteria interactions; Microbial ecology; Microbiome; Synthetic biology.

Fig. 1. Approaches in Microbiota-Based Therapeutics

(A) Engineered microbes have been one strategy for microbiota-based therapies. Gene circuits are constructed using libraries of genetic parts to enable microbial production of therapeutic proteins. Introduction of these microorganisms into the endogenous microbiota allows for in situ detection of disease biomarkers and/or drug production. (B) Designer microbial consortia are informed by community profiling studies of clinical samples from healthy and diseased patients. Clinical isolates from these patients can then be assembled into a defined mixture of microorganisms that can reprogram the microbial ecology within an individual. (C) Bacteriophages, bacteriocins and small molecule antibiotics can be used to selectively eliminate deleterious microbes from the microbiota. Consequently, the loss of specific taxa elicits a global shift in the microbial community as new constituents occupy the niches of the eliminated microbes. The addition of engineered bacteria together with selective elimination of targeted strains may provide enhanced therapeutic efficacy.

Fig. 2. Examples of Additive Microbiota Therapies

(A) The vaginal commensal Lactobacillus jensenii was engineered to produce the antiviral protein cyanovirin-N. Colonization of the vagina by recombinant bacteria inhibits host-infection by chimeric simian/human immunodeficiency virus (SHIV) in a rhesus macaque model. (B) Lactococcus lactis was genetically modified to produce the anti-inflammatory cytokine interleukin-10 (IL-10). When administered to mice afflicted with colitis, L. lactis transiting through the gut can alleviate intestinal inflammation. (C) Probiotic Escherichia coli were engineered to synthesize N-acyl-phosphatidylethanolamines (NAPEs). Host-mediated conversion of NAPEs to N-acylethanolamides (NAEs) can prevent obesity in mice by inducing satiety and reducing food intake. (D) The endogenous urease (Ure⁺) activity of the mouse microbiota can exacerbate hyperammonemia caused by liver injury. Depletion of the native microbiota using antibiotics and polyethylene glycol and replacement with a urease-deficient (Ure⁻) microbial consortium can protect mice from hyperammonemia and its associated neurotoxicity.

Fig. 3. Challenges in Microbiota-Based Therapeutics

(A) While it is well known that immigrant microbes, antimicrobials, disease and diet can alter the composition of a microbial community, a set of predictive rules that explain the consequences of these perturbations has yet to be elucidated. (B) Choosing the correct microbial chassis for a microbiota-based therapeutic is challenging, as it is difficult to predict which microbe is best suited for any given application. Consequently, a therapeutic microbe may fail to survive in the target environment and/or engraft in the endogenous microbiota. (C) The development of biosensors capable of detecting biomarkers associated with disease is necessary for the realization of fully autonomous microbial therapeutics. For example, biomarkers produced as a result of intestinal inflammation (red diamonds) are detected by recombinant bacteria and allow expression of therapeutic proteins (blue hexagons). (D) Engineered microbes must be both evolutionary and phenotypically robust to prevent the loss or dysfunction of recombinant genetic material. (E) Safety and biocontainment of microbiota-based therapies is a significant challenge for clinical translation of basic research. Strategies may be needed to prevent transmission of therapeutic microbes from a patient to other individuals.