IDDF2023-ABS-0089 Shifts of gut microbiota in fecal microbiota transplantation for ulcerative colitis detected by a novel absolute abundance quantitative method

Background

High-throughput sequencing has been widely used in characterizing microbial communities and revealing microbial-host interactions. However, the abundance produced by this technique is semi-quantitative, leading researchers to focus on the relative abundance of microbes and ignore the total microbial load. Moreover, changes in relative abundance do not accurately reflect the actual shifts in microbial load, which may hinder further microbiological research.

Methods

In this study, a bacterial absolute abundance quantitative method based on high-throughput 16S rRNA gene V4 sequencing was developed and used to reveal the changes in the gut microbiota of patients with ulcerative colitis (UC) who underwent fecal microbiota transplantation (FMT) (IDDF2023-ABS-0089 Figure 1 (a) Design and workflow of spike-in bacterium DNA). Samples were collected and analyzed before FMT (W0) and at 1 (W1), 4(W4) and 12 (W12) weeks after FMT.

Results

The spike-in bacterium Bacillus baekryungensis 700Cs for absolute abundance analysis was well distinguishable from the gut bacteria and did not affect the bacterial composition of fecal samples. The overall bacterial communities changed significantly (P<0.01) after FMT (IDDF2023-ABS-0089 Figure 1 (b) The absolute abundance of Donor, FMT (W0) and at 1 (W1), 4(W4) and 12 (W12) weeks after FMT), characterized by enrichment of 14 genera (eg Prevotella_9, Megamonas) and depletion of 29 genera (eg Veillonella, Escherichia-Shigella). Furthermore, gut bacterial communities of patients who achieved clinical remission (Rm) were shifted toward donors at W1, much earlier than these are not achieving clinical remission (NRm). The load of Ruminococcaceae_UCG-002, Ruminococcaceae_UCG-003 and Ruminococcaceae_UCG-005 were significantly (P<0.05) increased in Rm. The abundances of Eubacterium_coprostanoligenes_group, Coprococcus_3 and Holdemanella were significantly (P<0.05) increased for two consecutive timepoints post-FMT in Rm group, and that Christensenellaceae_R-7_group in the W1 was significantly (P<0.05) greater than that of W0 (IDDF2023-ABS-0089 Figure 1 (c) The significantly different taxa between W0 and W4 in patients with UC achieving clinical remission after FMT). Meanwhile, the abundances of un_f_Enterobacteriaceae, Haemophilus and Actinomyces were significantly decreased for 2 or 3 consecutive timepoints post-FMT in the Rm group.

Conclusions

Adopting this method, we identified significant shifts in gut bacteria of patients with UC after FMT, especially in the clinical remission group, including the increase of Ruminococcaceae_UCG-002, Coprococcus_3, Christensenellaceae_R-7 and decrease of Veillonella and Haemophilus. Their results show that FMT is a feasible therapeutic option in the treatment of UC and identified microbes that may contribute to the therapeutic efficacy.