Pilot 29 – Venkatesh

P30 CFRTC – Pilot 29

Microbiome-targeted Diets for Rectifying GI Dysfunction in People with Cystic Fibrosis

PI: Sid Venkatesh, PhD
Assistant Professor, Institute for Systems Biology
Affiliate Assistant Professor, Microbiology

Abstract: People with CF (PwCF) are afflicted with persistent gastrointestinal (GI) symptoms including abdominal pain, bowel obstruction, impaired gut transit times, and gut inflammation. The advent of CF modulator therapy has significantly improved quality of life in PwCF, but evidence to date suggests that the modulators have limited effects on GI dysfunction. Malnutrition (i.e., undernutrition and obesity) also remains a significant concern in PwCF and is associated with impaired pulmonary function. Thus, there is an urgent demand to develop nutritional interventions that combat GI dysfunction and malnutrition in PwCF.

A number of studies have reported disruptions in gut microbial community assembly and function in children with CF compared to healthy controls. Analyses of serially collected fecal samples from CF infants have revealed that they exhibit high relative abundances of pathobionts and low relative abundances of beneficial bacterial strains compared to healthy children (termed “microbiota immaturity”) that is significantly associated with growth faltering, altered predicted capability to produce short-chain fatty acids (SCFAs), and lower circulating levels of insulin-like growth factors (IGFs). Many growth-associated bacterial strains with beneficial effects are less abundant or absent in the gut microbiota of PwCF.

Our past work in developing microbiota-directed foods that demonstrate treatment efficacy in malnourished children has raised the possibility that this approach may be generalizable to PwCF. Our central hypothesis is that microbiota immaturity is a contributing cause, rather than an effect, of GI dysfunction and inflammation in PwCF and that therapeutic strategies that target the CF microbiota will improve health outcomes. The objective of this work is to identify diets that rectify GI dysfunction in PwCF by restoring a healthy configuration of the microbiota. We propose to develop a preclinical model using FMTs from PwCF and healthy controls to gnotobiotic mice and to administer a panel of whole diets- a high-saturated fat, high-sugar “Western” Diet (WD), a High-Fiber Diet (HFiD), a Mediterranean Diet (MedD) and Fermented Foods (FFs).

Leveraging the ability to colonize gnotobiotic mice with fecal microbiota from either PwCF (PwCF-FMT) or healthy, age-matched donors (Healthy-FMT), Aim 1 will characterize microbiota immaturity and GI dysfunction and inflammation in a mouse model. By measuring (A) absolute abundances of community members in the fecal microbiota using 16S amplicon sequencing, (B) fecal levels of SCFAs using targeted mass spectrometry, (C) fecal levels of calprotectin and colonic inflammatory cytokines using ELISAs, and (D) gut transit times with carmine dye assays, we will analyze if PwCF-FMTs are able to produce microbial communities and donor phenotypes in gnotobiotic mice. Results from these experiments are expected to advance our understanding of causal mechanisms by which the CF microbiota might contribute to GI dysfunction and inflammation.

Employing groups of gnotobiotic mice harboring fecal microbiota of PwCF donors and administering them a panel of whole diets, Aim 2 will identify nutritional interventions that rectify gut microbiota immaturity in PwCF-FMT mice. At the end of each diet administration and prior to switching to the next diet, we will analyze treatment efficacy by measuring (A) absolute abundances of beneficial strains in the fecal microbiota using 16S amplicon sequencing, (B) fecal levels of SCFAs and calprotectin using targeted mass spectrometry and ELISAs and (C) fecal levels of total IgA. Results from these experiments are expected to inspire the development of microbiota-targeted nutritional interventions for PwCF.