Metagenomic and Bile Acid Metabolomic Analysis of Fecal Microbiota Transplantation for Recurrent Clostridiodes Difficile and/or Inflammatory Bowel Diseases

Abstract

Background. Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn’s disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions. Aim. To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI-IBD); 2.) rCDI with IBD (rCDI+IBD); 3.) UC patients without rCDI (UC-rCDI); 4.) CD patients without rCDI (CD-rCDI). Methods. We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials (Clinical Trials.gov ID NCT03268213, 479696, UC no rCDI ≥ 2x IND 1564 and NCT03267238, IND 16795). Fitted linear mixed models were used to examine the effects of four recipient groups, FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on microbial diversity and composition, bile acid metabolites and bile acid metabolizing enzyme gene abundance. Results. The pre-FMT stools collected from rCDI ± IBD recipients had reduced α-diversity compared to the healthy donor stools and was restored post-FMT. The α-diversity in the pre-FMT stools collected from UC-rCDI or CD-rCDI recipients did not differ significantly from donor stools. FMT normalized some recipient/donor ratios of genus level taxa abundance in the four groups. Fecal secondary BA levels, including some of the secondary BA epimers that exhibit in vitro immunomodulatory activities, were lower in rCDI±IBD and CD–rCDI but not UC-rCDI recipients compared to donors. FMT restored secondary BA levels. Metagenomic baiE gene and some of the eight bile salt hydrolase (BSH) phylotype abundances were significantly correlated with fecal BA levels. Conclusion. Restoration of multiple secondary BA levels, including BA epimers implicated in immunoregulation, are associated with restoration of fecal baiE gene counts, suggesting that the 7-α-dehydroxylation step is rate-limiting.

Offline Two-Dimensional Liquid Chromatography–Mass Spectrometry for Deep Annotation of the Fecal Metabolome Following Fecal Microbiota Transplantation

“…Our results confirmed previous trends that primary bile acids (i.e., glycocholic acid and taurocholic acid) decreased, and secondary bile acids (i.e., taurodeoxycholic acid, lithocholic acid, deoxycholic acid) increased following FMT (Figure 4A), reflecting recolonization of the gut with active microbiota. 29,54,61,62 N-acetylated amino acids (Figure 4B) have been reported to decrease with C. dif f colonization; 63 Nacetylarginine, N-acetyllysine, N-acetylvaline, N-acetylthreonine, and N-acetylglutamic acid were found to increase significantly following FMT. Prolylhydroxyproline, an amino acid that is beneficial for C. dif f growth, and released during toxin-mediated CDI from host collagen, 62−65 was also found to decrease substantially following FMT.…”

Digestive dynamics: Unveiling interplay between the gut microbiota and the liver in macronutrient metabolism and hepatic metabolic health

“…It involves transplantation of feces from a healthy donor to a receiver with dysbiosis (Gupta et al., 2016 ; Shasthry, 2020 ). This procedure is used to treat conditions such as inflammatory bowel diseases (Kedia et al., 2022 ; Tan et al., 2020 ), and has shown to correct dysbiosis, increase SCFA production (Su et al., 2022 ; Zhang, Jian, et al., 2023 ), restore normal BA composition, and alleviate liver injury in mice and humans (Bustamante et al., 2022 ; Hu et al., 2022 ; Liu, Fan, et al., 2021 ; Ramos et al., 2022 ; Weingarden et al., 2014 ; Xue et al., 2022 ).…”

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrentClostridioides difficileinfection

“…To date, multiple studies have reported structural changes to the microbiota in rCDI after FMT 14,[22][23][24][25][26] . Specifically, they have observed an increase in the number of commensal bacteria 4 from the Phyla of Firmicutes and Bacteroidetes, and a decrease in Proteobacteria 27 .…”

“…Specifically, they have observed an increase in the number of commensal bacteria 4 from the Phyla of Firmicutes and Bacteroidetes, and a decrease in Proteobacteria 27 . These changes are always accompanied with an increase in alpha diversity 14,[22][23][24][25][26] . While it is not known why an increase in alpha diversity allows for a successful FMT, a recent study found an increase in diversity were able to exclude both Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium from colonizing the gut through the mechanism of nutrient blocking, by consuming nutrients the pathogen needed 28 .…”

“…Gut bacteria drive changes to the bile acid pool through a variety of mechanisms, including deconjugation of bile acids by the removal of the conjugated amino acid via bile salt hydrolases (BSHs), and the generation of secondary bile acids by the removal of the 7α-hydroxyl group via the bile acid inducible (bai) operon. These enzymes are associated with successful FMTs in both human and mouse models 25,[40][41][42] . BSHs are known to deconjugate either glycine or taurine from host conjugated bile acids.…”