Translational Development of Microbiome‐Based Therapeutics: Kinetics of E. coli Nissle and Engineered Strains in Humans and Nonhuman Primates

Abstract

Understanding the pharmacology of microbiome‐based therapeutics is required to support the development of new medicines. Strains of E. coli Nissle (EcN) were genetically modified and administered to cynomolgus monkeys at doses of 1 × 109 and 1 × 1012 colony‐forming units (CFU)/day for 28 days. A clinical study to evaluate the exposure and clearance of EcN in healthy volunteers was also performed. Healthy subjects received oral doses of EcN, 2.5 to 25 × 109 CFU 3 times daily for 28 days or a single day. In cynomolgus monkeys, replicating strains yielded higher fecal concentrations than nonreplicating strains and persisted for longer following cessation of dosing. In the clinical study, all subjects cleared EcN following cessation of dosing with median clearance of 1 week. Quantitative methodology can be applied to microbiome‐based therapeutics, and similar kinetics and clearance were observed for EcN in cynomolgus monkeys and humans.

The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics

“…However, SCFAs used as purified substances, and not as a component of an inactivated microbial preparation, would not be considered postbiotics. ranging from inflammatory bowel disease to radiation induced mucositis and food allergy [151][152][153][154][155][156][157] . Some tanta lizing hints of clinical efficacy have been generated for GMOs 154,157 , but regulatory challenges, as well as the court of public opinion in some regions of the world, have hampered progress in this area.…”

Developing a new class of engineered live bacterial therapeutics to treat human diseases

“…Additionally, EcN may interact with the intestinal epithelium to stimulate antiinflammatory activities 24 , as well as to restore and maintain intestinal barrier function 25 . Notably, EcN does not exhibit longterm colonization in healthy humans after oral administration 17 . This is likely due to ecological stability of the human gut microbiota and exclusion of incoming new bacteria through a phenomenon termed colonization resistance 26 .…”

Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917

“…Additionally, because EcN can replicate in the host and continuously produce new curli fibers, we anticipate that steady-state levels of the displayed VHH multimers can be maintained for significant periods of time despite the harsh proteolytic environment and constant flow in the gut. Notably, the ability of EcN to maintain a steady-state density in the mammalian GI tract with regular dosing is supported by data in mice and humans [35, 40]. Progress has also been made using EcN in clinical trials as an engineerable chassis organism for therapeutic applications in the gut [73–76].…”

“…EcN has an excellent track record of safety through decades of use as a probiotic, and has also been shown to reduce the severity of ulcerative colitis symptoms [36], as well as interfere with the pathogenicity of several enteric pathogens [37], in part due to its ability to colonize the human gastrointestinal tract [38, 39]. Transient colonization of humans has also been shown using engineered EcN [40]. Notably, EcN and other laboratory E. coli strains can produce VHHs, as demonstrated by numerous studies [41, 42].…”