Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention

(2025) 13:212 Ba et al. Microbiome https://doi.org/10.1186/s40168-025-02204-9 Microbiome Open Access RESEARCH Improving fecal transplantation precision for enhanced maturation of intestinal function in germ‑free mice through microencapsulation and probiotic intervention Furong Ba1†, Wei Wang2†, Yilun Huang3†, Shuobo Zhang1, Bo Qiu1, Siyuan Xie1, Lvwan Xu1, Wang Gao4, Xiaoqin Zhang5, Zhenyu Wen5, Qifan Wang5, Hainv Gao6, Guoping Sheng6, Björn Berglund7, Ping Li8*, Lanjuan Li1,4,9* and Mingfei Yao1,4,9* Background Fecal microbiota transplantation (FMT) has emerged as a widely used treatment for various diseases. While previous efforts have focused on selecting “super donors”, the precise modulation of donor microbiota to enhance FMT efficacy remains a critical challenge. This study aimed to develop strategies to modify donor microbiota to promote gastrointestinal development and maturation in germ-free mice. Probiotic Pediococcus pentosaceus Li05 (Li05) was used as gut microbiota modulator to establish a healthier donor fecal microbiota, and a microencapsulation method was applied to ensure high bacterial viability during gastrointestinal tract transition. Results Probiotic intervention initially altered the stability of the gut microbiota but eventually fostered a more complex bacterial interaction network and established a new equilibrium within 14 days. Transplantation of encapsulated Li05-modulated fecal microbiota significantly promoted epithelial development, improved barrier function, and altered the colonic transcriptome profile. These effects were found to be more dependent on the abundance of some bacterial genera instead of their co-occurrence network, and the key functional bacterial genera associated with these benefits were believed to be Parabacteroides, Parasutterella, Lachnoclostridium, Muribaculum and Desulfovibrio. Notably, both encapsulation and probiotic modulation played critical roles in enhancing the functional efficacy of these key bacterial genera, and the community composed of key functional bacteria demonstrated an antagonistic relationship with other bacterial communities. Moreover, encapsulated Li05-modulated fecal microbiota induced dramatical changes in host lipid metabolism, especially the bile acids and their derives. Sporobiota gained the function of promoting epithelium development gene expression only after Li05-modulation since high abundance of Lachnoclostridium was introduced. Conclusion These findings underscore the importance of encapsulation and donor microbiota modulation in FMT and provide valuable strategies for improving transplantation precision and outcomes. † Furong Ba, Wei Wang and Yilun Huang contributed equally to this work. *Correspondence: Ping Li Lanjuan Li Mingfei Yao Full list of author information is available at the end of the article © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. Ba et al. Microbiome (2025) 13:212 Page 2 of 23 Keywords Fecal microbiota transplantation, Pediococcus pentosaceus Li05, Microencapsulation, Gut microbiota, Intestinal function, Bile acids, Sporobiota Graphical Abstract Introduction The gut microbiota plays a critical role in various physiological and pathological processes in the host body by generating metabolites and interacting with gut tissue cells [1]. Disorder in the gut microbiota, either in composition or microbial abundance, is a crucial causative factor of intra- or extra- gastrointestinal diseases [1]. One of most direct and efficacious ways to modulate the gut microbiota is through fecal microbiota transplantation (FMT) [2], as have been successfully demonstrated though its application for Clostridioides difficile infection (CDI), which provided new insights into therapeutic value of gut microbiota modulation [3]. As an emerging therapy, the selection and process of donors’ stool are crucial determinants of FMT efficacy [4]. Although guidelines [5, 6] for usage of FMT currently exist, and many cases of therapeutic usage have been documented [7], FMT remains controversial. Concerns about pathogen transmission and the difficulty to fully define the composition of fecal transplants currently limit further application of FMT. As a result, considerable effort has recently been directed at establishing methodologies for determination of microbial signatures of FMT donors [4]. The rationale for application of FMT for treatment of intestinal diseases, such as CDI and inflammatory bowel disease (IBD), has its basis in its ability to enhance gut barrier function [8–10]. Given the link between the microbiota and the gut barrier [11], screening for functional key bacteria with therapeutic value in FMT donor stool is worthwhile. Various methods of FMT [12–15], including artificial synthetic bacterial community for regulating gut microbiota have been studied [16]. For instance, Yang et al. found that whole intestinal microbiota transplantation more effectively replicates donor communities and alleviates colitis in mice compared to transplantation of fecal microbiota [15]. Probiotics, as one alternative to FMT in modeling gut microbiota [2], play a positive role in maintaining intestinal health. However, current existing donor inclusion and exclusion criteria lack consensus on probiotic supplementation restrictions [5, 6, 17–21]. Given that FMT efficacy depends critically on donor microbiota composition, probiotic intervention may modify the microbial composition of donor feces and affect FMT. However, the potential of probiotic-modulated microbiome in the context of FMT has not been thoroughly explored. The primary methods for administering FMT include enema, endoscopic infusion, nasoenteric tube delivery, and oral administration. Traditional FMT routes demonstrate significant therapeutic efficacy, but their invasive nature and procedural complexity hinder widespread clinical adoption. In contrast, oral administration is Ba et al. Microbiome (2025) 13:212 widely regarded as the most pro (...truncated)