Kelsey Miller’s research while affiliated with Kaleido Biosciences and other places

Background Increasing evidence indicates that an altered gut microbiome participates in the development of cardiometabolic syndrome and associated risk factors, such as insulin resistance, dyslipidemia, and obesity, and that targeting the gut microbiome is a promising strategy to lower the risk for cardiometabolic diseases. Part of this reduction is mediated by specific metabolites generated by the gut microbiome. Propionate, a short-chain fatty acid (SCFA) produced from dietary glycans by certain gut microbes is known to exert multiple beneficial metabolic effects. Here, we identify KB39, a novel gut microbiome-targeting synthetic glycan selected for its strong propionate-producing capacity, and demonstrate its effects in vivo to reduce cardiometabolic disease using western diet-fed LDL receptor knock-out mice. Methods Ex vivo fermentation screening of a large library of synthetic glycan ensembles was performed using gut microbiome communities from healthy subjects and overweight patients with type 2 diabetes. A synthetic glycan identified for its high propionate-producing capacity (KB39) was then tested in vivo for effects on systemic, blood and cecal metabolic parameters in Ldlr -/- mice fed a western diet. Results Ex vivo screening of ~600 synthetic glycans using human gut microbiota from healthy subjects and patients with type 2 diabetes identified a novel glycan (KB39) with high propionate-producing capacity that increased propionate contribution to total SCFA and propionate-producing bacterial taxa compared to negative control. In western diet-fed Ldlr -/- mice, KB39 treatment resulted in an enrichment in propiogenic bacteria and propionate biosynthetic genes in vivo and an increase in absolute and relative amounts of propionate in the cecum. This also resulted in significant decreases in serum total cholesterol, LDL-cholesterol, and insulin levels, as well as reduced hepatic triglycerides and cholesterol content compared to non-treated animals. Importantly, KB39 treatment significantly reduced atherosclerosis, liver steatosis and inflammation, upregulated hepatic expression of genes involved in fatty acid oxidation and downregulated transcriptional markers of inflammation, fibrosis and insulin resistance with only a mild lowering of body weight gain. Conclusions Our data show that KB39, a novel synthetic glycan supporting a high propionate-producing microbiome, can reduce cardiometabolic risk factors and disease in mice and suggest this approach could be of benefit for the prevention or treatment of cardiometabolic diseases in humans. CLINICAL PERSPECTIVE What is new? A novel synthetic glycan, KB39, was selected from a library of compounds for its high propionate-producing capacity and beneficial effects on the human gut microbiome composition KB39 modulates the gut microbiome for high propionate production and significantly reduces cardiometabolic risk factors and disease in a murine model of cardiometabolic diseases What are the clinical implications? KB39, delivered orally, could be of benefit for the prevention or treatment of cardiometabolic diseases in humans The efficacy of KB39 in mice compared to the clinical drug fenofibrate justifies further study in humans

The pathogenesis of ulcerative colitis (UC) involves genetic susceptibility, immune-mediated tissue injury and environmental factors including disturbances of the gut microbiota. Nearly all current approved therapies modify host immunity, rather than directly targeting the microbiota. Fecal microbiota transplantation provides encouraging evidence for the therapeutic potential of gut microbiome modulation. Bacteria in the GI tract are ecologically differentiated by their ability to use specific glycans as growth substrates, making glycans a promising and safe alternative to target the microbiome. To explore this, we used an ex vivo fecal microbiota culture system to identify a synthetic glycan (KB295) with desirable microbiological activity and conducted a proof of principle study of safety and tolerability of KB295 in patients with UC. Fecal microbial communities from healthy subjects were incubated anaerobically with and without (negative control) KB295. KB295 increased short chain fatty acid (SCFA) production across ten fecal samples to a median concentration of 47.0 mM compared to 15.2 mM with the negative control in culture supernatants, including increases in acetate, propionate, and butyrate in all cases. Metagenomic sequencing of the ex vivo fecal pellets revealed that KB295 depleted pathobionts in the family Enterobacteriaceae to a median relative abundance of 10.8% compared to 38.2% with the negative control. Pathobiont depletion was associated with enrichments of diverse genera in the phyla Bacteroidetes and Firmicutes. Twelve patients with mild to moderate UC were enrolled in an open-label single-arm study with an 8-week intake of KB295. KB295 was well tolerated with generally mild adverse events, and only one AE resulted in discontinuation. The most frequently occurring adverse events were changes in bowel habit, flatulence, and headache. Fecal calprotectin and lactoferrin decreased by median values of 69.0% (n=11) and 86.0% (n=6), respectively, from screening to the end of the KB295 intake. Consistent with the ex vivo preclinical findings, of the subjects for whom we have data to date, the relative abundance of the fecal pathobiont family Enterobacteriaceae decreased from five participants, and the commensal genus Parabacteroides was enriched in four of five participants. These results establish a proof of principle for the glycobiological modulation of gut microbiome composition and function and provide insight into the potential utility of this strategy in patients with ulcerative colitis. The safety, tolerability, and encouraging evidence for reduced inflammation with KB295 call for a Phase 2 study, which is planned.

Introduction and objectives Hepatic encephalopathy (HE) is a complication of cirrhosis linked to the microbiome. We aimed to characterize the fecal microbiome of patients with prior and future overt HE, and explore the relationship between fecal species, short-chain fatty acids (SCFAs) and ammonia on HE pathogenesis. Materials and methods Consecutive inpatients and outpatients with cirrhosis were recruited. A single stool sample was collected and underwent shallow shotgun sequencing, and SCFA and ammonia quantification. Patients were followed until the end of the study period. Prior and new overt HE was diagnosed by the treating hepatologist. Results Forty-nine patients with cirrhosis, mean MELD-Na 20 (SD = 9) and 33 (67%) with a history of OHE provided a stool sample. Over a median 85 days of follow up (interquartile range 34 to 181 days), 16 developed an OHE episode. Eight fecal bacterial species were associated with a history of OHE, and no species predicted future OHE. Bacterial species positively associated with SCFA content were inversely related to cirrhosis disease severity. Patients with a history of OHE had lower concentrations of 6 fecal SCFAs. Fecal ammonia concentrations were similar between those with and without a history of OHE (273 μmol/g ± 214 vs. 327 ± 234, P = 0.43). Conclusions We found 8 fecal species and 6 SCFAs linked to OHE. Many of the species inversely linked to OHE also have an association with SCFA production. Further work is needed to detail this relationship and to develop targeted interventions to treat HE.

Background Infections with Carbapenem-resistant Enterobacteriaceae (CRE) and vancomycin-resistant Enterococci (VRE) can result in a 50% mortality rate in compromised hosts. A major risk factor for clinical infection is intestinal colonization with CRE or VRE. There are currently no FDA-approved compounds to decolonize these organisms from the gastrointestinal tract (gut). Commensal microbes offer protection from pathogen infection; however, in immunocompromised hosts or with antibiotic treatment, the protective properties of the microbial community are compromised, leaving the gut susceptible to pathogen colonization. Higher concentrations of pathogens within the gut correlate with an increased risk of infection with MDROs. Our hypothesis is that reducing colonization of the gut with MDROs would reduce the likelihood of a clinical infection. Methods Kaleido built a platform that emulates the gut environment and allows for high throughput screening of Kaleido’s Microbiome Metabolic Therapies (MMT™) in human gut microbiomes ex vivo. Over 500 compounds were screened for their ability to reduce the levels of CRE and VRE in fecal microbial communities from both healthy subjects and critically ill patients receiving broad-spectrum antibiotics. Results Kaleido’s lead MMTs selectively favor the growth of the commensal microbiota at the expense of pathogens, resulting in a decrease of CRE and VRE from 80% of the initial community to 5% in a single batch culture, as measured by 16S rRNA gene and shotgun metagenomic sequencing. Lead MMTs do not support growth of CRE and VRE strains in culture, nor of other pathogens frequently encountered in critically ill and immunocompromised patients, such as Clostridium difficile and common fungal pathogens. Conclusion These results suggest that intervention with MMTs may reduce CRE and VRE colonization and support further evaluation in patients colonized with CRE or VRE pathogens. Disclosures All authors: No reported disclosures.