Detecting host responses to microbial stimulation using primary epithelial organoids

ABSTRACT

The intestinal epithelium is constantly exposed to microbes residing in the lumen. Traditionally, the response to microbial interactions has been studied in cell lines derived from cancerous tissues, e.g. Caco-2. It is, however, unclear how the responses in these cancer cell lines reflect the responses of a normal epithelium and whether there might be microbial strain-specific effects. To address these questions, we derived organoids from the small intestine from a cohort of healthy individuals. Culturing intestinal epithelium on a flat laminin matrix induced their differentiation, facilitating analysis of microbial responses via the apical membrane normally exposed to the luminal content. Here, it was evident that the healthy epithelium across multiple individuals (n = 9) demonstrates robust acute both common and strain-specific responses to a range of probiotic bacterial strains (BB-12^Ⓡ, LGG^Ⓡ, DSM33361, and Bif195). Importantly, parallel experiments using the Caco-2 cell line provide no acute response. Collectively, we demonstrate that primary epithelial cells maintained as organoids represent a valuable resource for assessing interactions between the epithelium and luminal microbes across individuals, and that these models are likely to contribute to a better understanding of host microbe interactions.

KEYWORDS:

• Intestinal organoids
• probiotics
• microbiome
• intestinal epithelium
• bacterial–epithelial interactions

Author contribution

AB, AS, and KBJ conceived the project. JB, MJN, JS, CVM, AW, AB, AS, and KBJ designed experiments. IG, SS, and JH collected clinical samples. JB, MJN, JS, CVM, DR, JS, YC, AW, CB, PJS, MM, and SLH performed experiments. YC and AR analyzed RNAseq data sets. GM analyzed scSEQ data. KBJ wrote the manuscript with input from all authors. Funding Acquisition, AB, AS, and KBJ; Supervision, AB, AS, and KBJ.

Competing financial interests

JB, JS, YC, AW, CB, AB are or were at the time of the study employed by Chr. Hansen A/S, which produces and markets all four probiotic strains (LGG^Ⓡ, BB-12^Ⓡ, DSM33361, and Bif195). LGG^Ⓡ ISTILOS^TM, GALENEX^TM, and BB-12^Ⓡ are trademarks of Chr. Hansen A/S. The remaining authors report no conflict of interest.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2281012

Data availability statement

The expression data from CaCO2 cells stimulated with bacterial isolates are deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE231605. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231605

Additional information

Funding

Chr. Hansen A/S funded the clinical trial. Downstream experiments and analyses were funded by Innovation Fund Denmark (5158-00023B), European Union’s Horizon 2020 research and innovation programme (STEMHEALTH ERCCoG682665 to KBJ), the Novo Nordisk Foundation (NNF20OC0064376 to KBJ), and the Danish Medical Research Council (0134-00111B to KBJ). The Novo Nordisk Foundation Center for Stem Cell Medicine is supported by the Novo Nordisk Foundation (NNF21CC0073729). The Carlsberg Foundation supported the computer storage system used in the project (grant to AS and the Bioinformatics Centre). Element from some figures were adapted from Biorender^TM.