Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes

Abstract

Live bacterial therapeutics (LBT) could reverse disease by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally-raised (CR) hosts have been unsuccessful, because engineered microbial organisms (i.e., chassis) cannot colonize the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli isolated from stool cultures of CR mice were modified to express functional bacterial (bile salt hydrolase) and eukaryotic (Interleukin-10) genes. Reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect host physiology and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock-in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts, and enables LBT with curative intent.

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome

“…We plan to use recently developed tools to interrogate whether TRF-induced microbiome changes, such as the changes in conjugated and unconjugated bile acids, induce host metabolic change through functional manipulation of the gut microbiome in conventionally raised mice. A study in full conventional mice with engineered native bacteria that express bile salt hydrolase (BSH), an enzyme from the gut microbiome important for bile acid metabolism, shows that BSH affects glucose homeostasis ( Russell et al in press ). Thus, additional studies that allow for functional manipulation of the gut microbiome will allow us to determine contributions and causality of individual bacteria or bacterial functions on the mechanisms of action of TRF.…”

“…Although we have used the most state-of-the-art bioinformatic tools available to study the relationship between the gut microbiome and host transcription as part of our multi-omic analysis, these findings are still associative and require additional investigation. We plan to use functional manipulation of the gut microbiome through engineered native bacteria ( Russell et al in press ) to allow us to mechanistically investigate the relationship between specific bacterial functions and host physiological processes.…”

Distinct bile salt hydrolase substrate preferences dictate C. difficile pathogenesis

“…There is a growing appreciation for the roles that BSH substrate preferences play in the management of intestinal disease (6,8,44). This work stresses the distinction between the deconjugation of glycine and taurine-conjugated BAs, the latter of which has been shown to impact the establishment of colonization resistance against Klebsiella pneumoniae, the development of colorectal cancer and more recently metabolic disease (44)(45)(46). Our analysis of C. difficile-BA sensitivities motivated our investigation of glycine and taurine-preferring BSHs to inhibit C. difficile ex vivo and in vivo (Fig.…”

Turicibacterstrains differentially modify bile acids and host lipids

“…Though some host responses such as broadly decreased triglycerides were consistent across our BSH-recipient mice, the exact lipid and cholesterol responses differed, indicating that the type of deconjugations might have differing connections with host physiology. Further work will continue strengthening the exciting prospect of utilizing Turicibacter and/or its bile modifications to intentionally alter host lipid biology to improve host metabolic and lipid-associated health 66, 67 , as has been proposed with other bacteria 54, 68 . Beyond lipid biology, Turicibacter abundance has been correlated with diseases such as Parkinson’s disease 69 and depression 70 , and selective serotonin reuptake inhibitors (SSRIs) have been found to negatively affect Turicibacter growth and colonization 71 , potentially because they inhibit activity of its unique serotonin transporter 38 .…”