A tailored series of engineered yeasts for the cell-dependent treatment of inflammatory bowel disease by rational butyrate supplementation

ABSTRACT

Intestinal microbiota dysbiosis and metabolic disruption are considered essential characteristics in inflammatory bowel disorders (IBD). Reasonable butyrate supplementation can help patients regulate intestinal flora structure and promote mucosal repair. Here, to restore microbiota homeostasis and butyrate levels in the patient’s intestines, we modified the genome of Saccharomyces cerevisiae to produce butyrate. We precisely regulated the relevant metabolic pathways to enable the yeast to produce sufficient butyrate in the intestine with uneven oxygen distribution. A series of engineered strains with different butyrate synthesis abilities was constructed to meet the needs of different patients, and the strongest can reach 1.8 g/L title of butyrate. Next, this series of strains was used to co-cultivate with gut microbiota collected from patients with mild-to-moderate ulcerative colitis. After receiving treatment with engineered strains, the gut microbiota and the butyrate content have been regulated to varying degrees depending on the synthetic ability of the strain. The abundance of probiotics such as Bifidobacterium and Lactobacillus increased, while the abundance of harmful bacteria like Candidatus Bacilloplasma decreased. Meanwhile, the series of butyrate-producing yeast significantly improved trinitrobenzene sulfonic acid (TNBS)-induced colitis in mice by restoring butyrate content. Among the series of engineered yeasts, the strain with the second-highest butyrate synthesis ability showed the most significant regulatory and the best therapeutic effect on the gut microbiota from IBD patients and the colitis mouse model. This study confirmed the existence of a therapeutic window for IBD treatment by supplementing butyrate, and it is necessary to restore butyrate levels according to the actual situation of patients to restore intestinal flora.

KEYWORDS:

• Inflammatory bowel disease
• butyrate production
• saccharomyces cerevisiae
• synthetic biology
• gut microbiota

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

Conceptualization: J.W., G.K., L.W., M.G., B.L., H.H. Experimental: J.W., G.K., L.W., M.G., S.M., S.Z., Z.F., Z.Z., X.C. Data analysis: J.W., G.K. L.W., S.M., S.Z., Y.F., B.L., H.H. Supervision: J.W., G.K., L.W., Z.F., Z.Z., B.L., H.H. Writing: J.W., G.K., L.W., M.G., B.L., H.H.

Abbreviations

IBD	=	Inflammatory bowel disease
SCFA	=	Short-chain fatty acid
GPD	=	Glycerol-3-phosphate dehydrogenase
DSS	=	Dextran sulfate sodium
UC	=	Ulcerative colitis
ACE	=	Abundance Coverage-based Estimator
DAI	=	Disease activity index
TNBS	=	Trinitro-benzene-sulfonic acid
BA	=	Butyric acid
TNF	=	Tumor necrosis factor
IL	=	Interleukin
ATP	=	Adenosine triphosphate
NADH	=	Nicotinamide adenine dinucleotide
HC	=	Healthy Control
CON	=	Control
eATP	=	Extracellular Adenosine triphosphate

Ethics approval and consent to participate

This experimental protocol was approved by the Institutional Animal Care and Use Committee at Tianjin University (Approval No. #TJUE-2023-183), and all animal experiments were conducted in accordance with the National Research Council Guide for Care and Use of Laboratory Animals.

In this study, we strictly complied with the ethical requirements for experimental animals and established clear humane endpoints. During the course of the experiments, some mice in the untreated and treated groups developed serious health problems, such as weight loss of more than 20%, blood in the stool, and locomotor disorders. To protect the welfare of the animals, we immediately terminated these experiments and euthanized them to alleviate their suffering. This practice demonstrated our respect for the lives of experimental animals while ensuring the scientific reliability of the experimental data.

All volunteers voluntarily donated their own stools and signed an informed consent form. Sample collection was approved by the Ethics Committee of Tianjin Medical University General Hospital.

Data availability statement

The 16S rRNA gene sequencing raw data generated in this study have been deposited in the NCBI under accession No. PRJNA998236. Other data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2316575

Additional information

Funding

The present study was supported by grants from the National Key Research and Development Project (Grant No. 2019YFA0905600), the Independent Innovation Foundation of Tianjin University (Grant No. 2023XQM-0014), the Science and Technology Program of Tianjin, China (Grant No. 22YFZCSN00090), and the China-CEEC Joint Education Project (Grant No. 2022196).