BMB Reports 2023; 56(1): 15-23
Intestinal organoids as advanced modeling platforms to study the role of host-microbiome interaction in homeostasis and disease
Ji-Su Ahn1,2,3,#, Min-Jung Kang1,#, Yoojin Seo1,* & Hyung-Sik Kim1,2,3,*
1Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan 50612, 2Department of Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, 3Education and Research Team for Life Science on Dentistry, Pusan National University, Yangsan 50612, Korea
Correspondence to: Yoojin Seo, Tel: +82-51-510-8235; Fax: +82-51-510-8210; E-mail:; Hyung-Sik Kim, Tel: +82-51-510-8231; Fax: +82-51-510-8210; E-mail:
#These authors contributed equally to this work.
Received: October 20, 2022; Revised: November 14, 2022; Accepted: November 14, 2022; Published online: November 14, 2022.
© Korean Society for Biochemistry and Molecular Biology. All rights reserved.

cc This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
After birth, animals are colonized by a diverse community of microorganisms. The digestive tract is known to contain the largest number of microbiome in the body. With emergence of the gut-brain axis, the importance of gut microbiome and its metabolites in host health has been extensively studied in recent years. The establishment of organoid culture systems has contributed to studying intestinal pathophysiology by replacing current limited models. Owing to their architectural and functional complexity similar to a real organ, co-culture of intestinal organoids with gut microbiome can provide mechanistic insights into the detrimental role of pathobiont and the homeostatic function of commensal symbiont. Here organoid-based bacterial co-culture techniques for modeling host-microbe interactions are reviewed. This review also summarizes representative studies that explore impact of enteric microorganisms on intestinal organoids to provide a better understanding of host-microbe interaction in the context of homeostasis and disease.
Keywords: Intestinal organoid, Microbiome, Pathobiont, Probiotics, Symbiont

Growing evidence supports that microorganisms and their byproducts can affect an individual’s phenotype and vice versa (1). With advances in high-throughput sequencing technology in the last decade, great efforts have been devoted to understanding host-microbiome interactions. Numerous works have demonstrated that the microbiome not only shapes the host immune system, but also correlates with tissue homeostasis and pathophysiology of diseases (2). Of note, the gut is the most heavily colonized organ. It contains over 70% of total symbionts. Significant dysbiosis has been found in gut luminal and fecal microbiota according to disease cohort studies, suggesting a causal relationship between the gut and its microbiota in host health (3-5). For a mechanistic study, a germ-free mouse model has been widely used to assess impact of the microbiome on disease progression. However, significant differences in microbial tropism, cellular composition, and microenvironment cues such as metabolic pathways between human and mouse often hinder interpretation of results (6). In this aspect, organoid technology has brought great advances in modeling of host-microbiome interaction in vitro. Organoids are self-organizing 3D structures with multiple differentiated cells derived from tissue-specific stem cells (7). With support of niche factors and extracellular matrix (ECM), LGR5-expressing crypt columnar cells can generate intestinal organoids (IOs), the first established epithelial organoids that could recapitulate the crypt-villus axis and lumen structures (8). Besides structural similarity, they can mimic several physiological properties of the gut such as selective absorption, barrier function, and mucus production. In addition, optimized culture conditions ensure robust generation and establishment of personalized- or genetically manipulated IOs (9, 10), overcoming limitations of conventional in vitro models. In this mini-review, we will briefly introduce current methodology for microbe-IO co-culture. We then summarize representative findings describing the impact of symbiont and pathobiont as well as probiotic candidates in host health using co-culture systems to provide insights into the importance of cross-talk between host and microorganisms.


To investigate interactions between IOs and microbes, it is essential to mimic the naïve gut environment harboring microbes. In the gastrointestinal tract, microbes exist within the lumen and directly interact with the intestinal epithelium through the apical side. In contrast, typical IOs have basal-out structures. Therefore, co-culture methods that allow physiologically relevant interaction are required for modeling microbial infections.


Microinjection of bacteria directly into the lumen of IOs can facilitate bacterial contact with the apical side of the epithelium (11, 12). Since the closed lumen has low oxygen tension, microinjection can improve the infection efficiency of anaerobic bacteria (13). Given that manual injection is a highly labor-intensive, time-consuming procedure (14, 15), a high-throughput organoid microinjection platform has been developed (16). However, since it is not a perfect anaerobic co-culture system, maintenance of a long-term culture of IOs with anaerobic bacteria is limited.

Suspension culture with IOs

Microbes can be simply treated to organoid growth media or embedded with ECM during IO culture. It is the most common method to study host-microbe interaction so far. Organoids can be cultured with live- and heat-killed (HK) bacteria or with conditioned media containing their byproducts, including bacterial toxins and metabolites (17-19). However, this method restricts the access of bacteria to the apical side of IOs. To overcome this limitation, IOs can be mechanically shredded to expose the luminal side and then re-seeded into ECM following co-culture with live bacteria (20, 21).

Organoid-derived monolayers (ODMs)

ODMs are established by seeding dissociated 3D-grown IOs on a Transwell plate to expose the apical surface upward with media (22, 23). ODMs can recapitulate cell compositions of gastrointestinal epithelium such as enterocytes, goblet cells, Paneth cells, and other cell populations (24). This monolayer culture provides practical advantages of easy microbial access to the luminal side and convenient sample collection compared to ECM-embedded classical IOs. However, 2D-grown epithelial stem cells usually undergo differentiation. They cannot be sub-cultured or maintained for a long time. Thus, many cells are needed each time. In addition, it is hard to obtain morphological information with ODM method (25). ODM culture technique can be further modified by exposing the upper side of the layer to air to generate an oxygen gradient. With the air-liquid interface (ALI) culture method, in which the basolateral side and the apical side contact with media and surrounding air, respectively, ODMs can differentiate into more mature epithelial cells such as mucus-secreting goblet cells than 3D organoids (26, 27). In addition, IHACS (intestinal hemi-anaerobic co-culture system), composed of a hypoxic apical chamber sealed with a rubber plug and a basal chamber in normal oxygen concentration can facilitate the survival of both epithelial cells and microbes (28, 29).

Organoids with reversed polarity

The apical-out IO model is an alternative to microinjection which has limitations of laborious processes and requirement of special equipment. Reversion of epithelial polarity is performed by removing ECM and maintaining suspended IOs in the low-attachment plate, where spontaneous polarity changes from basal-out to apical-out occur (30). Apical-out IOs allow direct interactions between the epithelium and microbes. Functional assays for nutrient uptake and epithelial barrier integrity can also be performed since epithelial cells within apical-out IOs can differentiate into a more mature state than conventional IOs (30).


Co-culture with pathobionts

Pathobiont has a significant impact on host health. Enteric infections by bacterial pathogens are responsible for various diarrheal diseases, particularly in developing countries. Dysbiosis in the gut microbiome can lead to several enteric and systemic disorders (31). Moreover, the rapid increase of antibiotic-resistant pathogens has become a critical threat in recent years (32). Thus, numerous efforts have been made to evaluate and understand the detrimental impact of pathobionts on the gut using IOs (Table 1).

Shigella flexceri: Shigella flexneri infection is a leading cause of acute diarrhea, fever, and stomach pain in humans, particularly young children (33). ODM culture is the most frequently used in vitro model to study the role of S. flexneri in intestinal epithelial injury. After administration, S. flexneri exhibits high bacterial adherence rates in ODMs and induces maturation of M cells with upregulation of pro-inflammatory signals (24, 34, 35). Infection by S. flexneri can also trigger IL-8 secretion and mucin glycoprotein MUC2 expression (24, 35). S. flexneri can invade ODMs via the basolateral side, while disruption of the tight junctions in the epithelial barrier allows S. flexneri to invade ODMs via the apical surface (36). In addition, the killing potency of bacteriophages targeting S. flexneri has been tested in an ODM-based co-culture model to find alternatives to current antibiotics (34). Interestingly, bacterial adherence and invasion capacity in ODMs are significantly inhibited by the presence of bacteriophage.

Salmonella enterica: Salmonella enterica is a major pathogen for food-borne diarrheal diseases such as typhoid fever known to be caused by S. enterica serovar Typhimurium (37). Zhang et al. have investigated S. Typhimurium pathogenesis in the intestine using a microinjection method (38). In their study, disruption of epithelial tight junction and increment of inflammatory cytokine by NF-κB activation were observed in IOs upon administration of S. Typhimurium. Moreover, infection by Salmonella led to reduced Lgr5 expression, suggesting suppression of stem cell population. In an apical-out organoid model, S. Typhimurium invaded the apical epithelial surface more efficiently than invading the basolateral surface, which induced actin ruffles (30). Of note, key components for bacterial invasion have been revealed with a co-culture system. For instance, colonization of S. Typhimurium after microinjection into the lumen of IOs is dependent on an important virulence factor, type III secretion system 1 (TTSS-1), and its flagellar motility (39). The invasion capacity of S. Typhimurium is also mediated by invA (40) and Pathogenicity Island (SPI)-derived Type 3 secretion systems (T3SS) (41). Interestingly, a deficiency of phospholipid transporter YrbE in S. enterica serovar Typhi can lead to upregulation of flagellin, which enhances pro-inflammatory IL-8 expression in ODM (42).

Escherichia coli: Most Escherichia coli strains are commensal bacteria in the large intestine. However, several pathogenic strains are important causes of diarrheal illness and food poisoning (43). For example, enterohemorrhagic E. coli (EHEC) serotype O157:H7 is responsible for fatal foodborne diarrheal diseases (44, 45). After co-culturing with human ODMs, EHEC can readily colonize differentiated human ODMs. It especially targets MUC2 and microvillar resident protein PCDH24 at the early stage of infection (46). EHEC can also secrete extracellular serine protease EspP that exhibits enterotoxin activity by stimulating an electrogenic ion transporter, leading to reduced PCDH24 and brush border damage, while the enterotoxin-producing activity of EHEC in human IOs is independent of EspP activity (47).

Meanwhile, enterotoxigenic E. coli (ETEC) infection is associated with high mortalities in developing countries (48). ETEC can secrete heat-stable enterotoxin (ST) and heat-labile enterotoxin (LT) into the intestinal epithelium, which can induce cGMP and cAMP stimulation (49). Indeed, ST-induced cGMP synthesis followed by apical efflux of cGMP into the basolateral space has been observed in the human ODM model. However, disruption of phosphodiesterase PDE5 can reverse this phenomenon, revealing that cyclic nucleotide export and degradation can be initiated by enterotoxins (50). Given their importance in domestic animal farms, IOs have been established from porcine small intestine to generate ODM to investigate ETEC pathogenesis in pig gut (51). ETEC exhibits F4 fimbriae-mediated adhesion to porcine ODM as observed in vivo, indicating the utility of porcine IOs and co-culture systems to study enteric pathobionts in industrial animals.

Recent studies have shown that genotoxic colibactin-secreting E. coli strains are more abundantly detected in colorectal cancer (CRC) tissues than in healthy ones (52) and that pks genome is responsible for colibactin production (53). Indeed, long-term exposure (over five months) of human IOs to pks+ E. coli performed by luminal microinjection can lead to accumulation of genetic mutations in epithelial cells (54). Interestingly, organoids upon short-term exposure to pks+ E. coli also exhibit DNA damage, enhanced proliferation, and Wnt-independent abnormal growth (21). These studies demonstrate a hypothesis regarding the pks+ E. coli can mediate the tumorigenic process in CRC development.

Clostridium difficile: Clostridium difficile accounts for a significant proportion of antibiotic-induced diarrhea and colitis (55). Microinjection of C. difficile into IOs can lead to a reduction of Na+/H+ exchanger 3 (NHE3) with organoid swelling, which can recapitulate the in vivo situation of C. difficile-induced chronic diarrhea (56). Main virulence factors of C. difficile including C. difficile toxin A (TcdA), C. difficile toxin B (TcdB), and C. difficile transferase (CDT) can collapse the adherens junction through disruption E-Cadherin and actin-cytoskeleton (18, 57). Similarly, human ODMs express a high level of TcdA receptor (58). TcdA can disrupt the barrier function of human IOs upon C. difficile microinjection into the lumen for up to 12 h (11). TcdB can further inhibit epithelial regeneration by impairing stem cell functions in IOs established from C. difficile-infected mice (57). In this context, several studies have targeted C. difficile toxins to neutralize the harmful impact of C. difficile and found that administration of human serum albumin (HSA) and antibiotic bacitracin could prevent the toxic effect of TcdA and TcdB in IOs (59, 60). Co-culture of C. difficile and IOs has also provided insights into the physiological response of epithelial cells to resist microbial infection as reported by Liu et al. (19). In their work, the protective role of Paneth cells during C. difficile infection was investigated in murine and human IOs. It was shown that constitutive activation of signal transducer and activator of transcription 5 (STAT5) signaling could potentiate anti-bacterial and niche-supporting functions of Paneth cells in response to inflammatory cytokines and bacterial toxin, thus reducing C. difficile cytotoxicity.

Vibrio cholerae: Vibrio cholerae is an important cause of epidemic diarrhea, which is mediated by cholera toxin (CT) (61). Several studies have reported that treatment of IOs with CT can activate cAMP pathway, which induces acute swelling of IOs due to fluid accumulation in the lumen (62, 63). In this aspect, organoid swelling assay has been used for testing CT inhibitors (63). Interestingly, IOs derived from O-blood group show more elevated cAMP response upon CT administration than IOs derived from A-blood groups (64).

Listeria monocytogenes: Listeria monocytogenes is an opportunistic food-borne pathogen that causes listeriosis in immunocompromised individuals (65). In vitro infection of L. monocytogenes in IOs can stimulate organoid growth and induce differentiation into Paneth cells by regulating the expression of transcriptional factors Math1 and Sox9 (20). Another study has shown that L. monocytogenes can lead to Paneth cell induction in IOs by inhibiting Notch signaling and activating the toll-like receptor (TLR) 2/4 pathway with upregulation of opsonin protein CCN1 (66, 67). When the infection efficiency of L. monocytogenes was assessed in IOs exhibiting different polarity, basal-out IOs were more susceptible to L. monocytogenes invasion than apical-out ones because L. monocytogenes could bind to basolateral receptors after targeting cell extrusion regions (30). Interestingly, luminal microinjection of L. monocytogenes into IOs also demonstrated that crosslinking between bacterial internalin A (InlA) and E-cadherin on goblet cells could mediate the invasive process of Listeria, allowing its entry from lumen to the basal side despite the presence of epithelial barriers (68). Meanwhile, quantitative proteomic analysis has revealed that L. monocytogenes could differentially regulate the transcriptional activity and metabolism of IOs depending on their strains and serotypes (69).

Other pathogenic bacteria: A positive correlation between the abundance of Campylobacter species in CRC tissues and CRC development has been confirmed (70). Specifically, Campylobacter jejuni can induce DNA damage and intestinal inflammation by producing genotoxin (71). In line with previous studies, treatment with bacterial lysate from C. jejuni can lead to accumulation of DNA damage with increased γH2AX induction in human IOs, while ablation of cytolethal distending toxin (CDT) can abrogate pro-inflammatory- and genotoxic impact of C. jejuni (72).

Since the gut is part of the digestive tract, oral pathogenic bacteria can be detrimental to the intestine. For instance, Fusobacterium nucleatum in the gastrointestinal tract is positively associated with the development of gut inflammation and CRC (73). Interestingly, treatment with outer membrane vesicles (OMV) produced by F. nucleatum subsp. polymorphum can promote proinflammatory responses by stimulating tumor necrosis factor (TNF) secretion and NF-κB activation in human ODMs (74). Lipopolysaccharides (LPS) derived from Porphyromonas gingivalis, another major oral bacterium responsible for periodontitis, can regulate differentiated epithelial cell marker expression in murine IOs (75).

Co-culture with commensal bacteria and probiotics

Recent evidence has shown that probiotics can provide beneficial effects on the host by improving the balance of gut microbiota composition and promoting intestinal mucosal barrier function, indicating their therapeutic potential to treat a variety of intestinal disorders as shown below (Table 2) (76, 77).

Lactobacillus: Most Lactobacillus species including L. reuteri, L. rhamnosus, and L. acidophilus are regarded as important probiotics in the intestine. They have been reported to be able to improve proliferation, regeneration, and maturation of IOs (78).

L. reuteri can enhance the recovery of Lgr5+ cells and epithelial barrier after TNF-induced intestinal damage by activating the Wnt/β-catenin pathway in IOs (79). When L. reuteri D8 was co-cultured with murine IOs in the presence of lamina propria lymphocytes (LPLs), L. reuteri D8 could stimulate the proliferation of stem cells and Paneth cell induction by up-regulating the secretion of IL-22 mediated by STAT3 signaling activation (80). The role of L. reuteri in modulating host immunomodulation has also been investigated in an IOs-dendritic cell (DC) co-culture system (81). It was verified that both L. reuteri and its bacterial surface components could promote IL-10 production and DC maturation (81).

Administration of L. rhamnosus GG (LGG) to an IO culture system can provide some protection against rotavirus infection by up-regulating antiviral secretory factors such as interferon-α (IFN-α) and CXC motif chemokine ligand 1 (CXCL1) via activation of TLR3 pathway in epithelial cells (82). Han et al. have also investigated the therapeutic potential of LGG in irritable bowel syndrome (IBS) using IO-based co-culture systems with a focus on barrier function (83). Interestingly, they found that LGG significantly upregulated junctional marker expression and prevented the increase in organoid permeability in response to treatment with IFN-γ or fecal supernatants obtained from IBS patients, indicating a beneficial role of LGG in the maintenance of gut barrier integrity.

The protective effect of Lactobacillus species on intestinal epithelial damage has been also exhibited by L. acidophilus. To evaluate whether L. acidophilus could suppress the detrimental impact of pathobionts on IOs, L. acidophilus and S. typhimurium were treated simultaneously to dissociated IOs. Cellular properties of IOs were then assessed (84). In that work, S. Typhimurium significantly reduced the organoid-forming efficiency, which could be reversed by co-treatment with L. acidophilus. L. acidophilus could also enhance the differentiation into secretory lineage cells and, which in turn increased the production of mucus and antibacterial peptides to strengthen the mucosal barrier by regulating S. typhimurium-mediated hyperactivation of TLR2- and Wnt/β-catenin signaling pathways. Of note, Sittipo et al. have revealed dynamic changes in the prevalence of Lactobacillus species in murine stool samples after irradiation exposure using 16S rRNA-based oligotyping analysis (85) and reported the contribution of L. acidophilus to functional recovery of radiation-induced epithelial injury both in vitro and in vivo. Treatment of irradiated IOs with HK L. acidophilus can significantly enhance the organoid formation capacity with goblet cell enrichment, suggesting that administration of L. acidophilus and its derivatives might be beneficial to restoring intestinal homeostasis and barrier function impeded by pathogenic bacterial infection or irradiation.

Bifidobacterium: Bifidobacterium is another commensal probiotic bacterium that participates in the homeostasis of the gut microorganism community (86). Bifidobacterium, the dominant species in the large intestine, requires an anaerobic environment (78). In this context, IHACS, which mimics physiological gut anaerobic conditions in vitro, is useful for culturing IOs with Bifidobacterium (29). With this oxygen-controlled co-culture system, B. adolescentis could be successfully propagated with ODM. Importantly, only live B. adolescentis, not heat-killed bacteria or bacterial culture supernatant, could increase the expression of stem cell and goblet cell markers of ODM upon co-culture, demonstrating the importance of viability of bacteria in studying host-microbe interactions.

Escherichia coli: Benefits of commensal bacteria E. coli Nissle against dysbiosis have been confirmed in IOs (87). E. coli Nissle can protect human IOs from pathogenic E. coli-mediated disruption of the epithelial barrier, increased oxidative stress, and apoptosis. In addition, microinjection of a non-pathogenic E. coli strain ECOR2 into human IOs can lead to transient changes in the oxygen concentration without causing any harmful impact on epithelial cells (88). After colonization, E. coli strain ECOR2 can increase the production of antimicrobial peptides and improve tissue maturation of IOs.


Organoid technology holds great potential to overcome limitations of conventional models such as 2D cell lines and experimental animals for modeling human anatomy and physiology. However, several challenging issues have to be solved to achieve advanced modeling of host-microorganism interactions with IOs. First, the absence of other cellular components except for epithelial cells is the main limitation of present IOs. Compared to pluripotent stem cell-derived organoids, which exhibit diverse cellular complexity, most adult stem cell-derived organoids like IOs consist of restricted lineage-derived cells that impede modeling of naïve microenvironment (89). Considering that microorganisms usually elicit an immune response and a repair process, which are predominantly mediated by regional immune cells and stromal cells respectively, the addition of these cells to an IO-microbe co-culture system would be necessary to recapitulate in vivo circumstances. Optimization of culture conditions is another important challenging issue. Although IOs are generally maintained under neutral, normoxic conditions, a dynamic range of oxygen concentration and pH found in the gut can significantly influence bacterial colonization patterns (90). Since oxygen availability strictly regulates bacterial behavior including growth, metabolism, and stress resistance, providing adequate oxygen gradient to both mammalian cells and microorganisms using advanced techniques such as microfluidic systems would be required to recapitulate in vivo situations. These improvements can also help us evaluate IO responses to a polymicrobial infection, which will provide clues about the role of dysbiosis in enteric disorder progression and greatly contribute to the understanding of disease mechanisms and establishing an effective therapeutic strategy.


This study was supported by the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT (2018-R1A5A2023879, 2019-R1A2C2085876) and the Ministry of Education (2021-R1I1A1A01055654). Korean Fund for Regenerative Medicine (KFRM) grant funded by the Ministry of Science and ICT and the Ministry of Health & Welfare (22A0205L1) also supported this project.


The authors have no conflicting interests.


Studies reporting host-pathogenic bacteria interactions using organoids

Bacteria Source of organoid Culture system Key findings References
Shigella flexneri Human small intestine, colon ODM ↑IL-8 secretion (24)
Human (unspecified) ODM ↑IL-8 secretion (34)
↑Muc2 expression
Human small intestine ODM Basolateral infection, (35)
↑Pro-inflammatory signals
Human small intestine, colon ODM Testing the therapeutic effect of bacteriophage (36)
Salmonella enterica Human small intestine 3D-microinjection ↓Organoid growth (38)
↑NF-kB signaling
↑Pro-inflammatory cytokine,
↓LGR5 expression
Human/mouse small intestine 3D-microinjection Recapitulation of early infection cycle, TTSS-1 is required for colonization (39)
Human iPSC 3D-microinjection ↑Proinflammatory cytokines, InvA-dependent invasion (40)
Human ESC 3D-microinjection T3SS-1-dependent invasion, (41)
↑Inflammatory chemokine
Human small intestine, colon Apical-out Cytoskeletal rearrangement (30)
Human small intestine ODM YrbE-dependent inflammatory response (42)
EHEC Human colon ODM ↓Colonic mucus (45)
Brush border damage
Human colon ODM Change in active ion transport (47)
ETEC Human small intestine ODM PDE5-mediated restriction of intracellular cGMP accumulation (50)
Pig small intestine ODM F4-mediated adhesion (51)
pks+ E. coli Human colon ODM Long-term exposure caused mutational signature (54)
Human/mouse colon ODM/Shredded 3D ↑Proliferation Wnt-independent growth (21)
Clostridium difficile Human iPSC, ESC 3D-microinjection ↓Epithelial barrier function (11)
Human iPSC 3D-microinjection ↓NHE3 expression (56)
Human/mouse colon 3D derived from infected mice/3D-toxin treatment ↓Adherens junction, (57)
↓Epithelial regeneration
Human small intestine ODM Adherence mechanism in human ODM model (58)
Human iPSC 3D-toxin treatment ↓Transmembrane adhesion protein (18)
Human iPSC 3D-toxin treatment Protective effect of HSA (59)
Human (unspecified) 3D-toxin treatment Protective effect of antibiotic Bacitracin (60)
Human/mouse iPSC 3D-microinjection Protective effect of Paneth cells on C. difficile-infected IO (19)
Vibrio cholerae Mouse small intestine 3D-toxin treatment ↑cAMP pathway (62)
Human small intestine 3D-toxin treatment Testing CT inhibitor with swelling assay (63)
Human small intestine 3D-toxin treatment O-blood group exhibited different responses to CT (64)
Listeria monocytogenes Mouse small intestine Shredded 3D ↑Organoid growth (20)
↓Lgr5+ ISCs
↑Paneth cells
Mouse small intestine Shredded 3D ↑TNFa (66)
↑Paneth cell, goblet cell
↓Notch signaling
Mouse small intestine Shredded 3D ↑TLR 2/4 signaling (67)
Human small intestine, colon Apical-out Binding with basolateral receptor (30)
Mouse small intestine 3D-microinjection InlA-Ecad-dependent translocation through goblet cells (68)
Mouse (unspecified) Shredded 3D TMT-based quantitative proteomic analysis in different strains (69)
Campylobacter jejuni Mouse small intestine 3D-bacterial lysate DNA damage (72)
Fusobacterium nucleatum Human (unspecified) ODM-OMV treatment ↑TNF, NF-κB, MAPK signaling (74)
Porphyromonas gingivalis Mouse small intestine 3D Regulation of cell composition (75)

Studies reporting host-probiotic bacteria interactions using organoids

Bacteria Source of organoid Culture system Key findings References
Lactobacillus reuteri D8 Mouse small intestine 3D ↑Intestinal epithelial regeneration (79)
Mouse small intestine 3D ↑Proliferation of intestinal epithelial stem cells (80)
Lactobacillus reuteri Mouse small intestine 3D ↑Dendritic cell maturation and IL-10 production (81)
Lactobacillus rhamnosus GG Mouse small intestine 3D ↑Expression of TLR3 (82)
Mouse small intestine, colon 3D-microinjection ↑Epithelial barrier function (83)
Lactobacillus acidophilus Mouse small intestine 3D ↑Protects the intestinal mucosa against pathogen (84)
Mouse small intestine 3D -HK bacteria ↑Intestinal epithelial function and differentiation (85)
Bifidobacterium adolescentis Human colon ODM ↑Differentiation of goblet cell and stem cell (29)
Escherichia coli Nissle Human small intestine 3D-microinjection ↑Epithelial barrier function (87)
Nonpathogenic E. coli Human small intestine 3D-microinjection ↑Epithelial proliferation & secretion of anti-microbial peptide (88)

  1. Ley RE, Peterson DA and Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837-848
    Pubmed CrossRef
  2. Lynch JB and Hsiao EY (2019) Microbiomes as sources of emergent host phenotypes. Science 365, 1405-1408
    Pubmed CrossRef
  3. Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y and Andoh A (2018) Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol 11, 1-10
    Pubmed CrossRef
  4. Baumler AJ and Sperandio V (2016) Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535, 85-93
    Pubmed KoreaMed CrossRef
  5. Park EM, Chelvanambi M, Bhutiani N, Kroemer G, Zitvogel L and Wargo JA (2022) Targeting the gut and tumor microbiota in cancer. Nat Med 28, 690-703
    Pubmed CrossRef
  6. Nguyen TLA, Vieira-Silva S, Liston A and Raes J (2015) How informative is the mouse for human gut microbiota research?. Dis Model Mech 8, 1-16
    Pubmed KoreaMed CrossRef
  7. Kim J, Koo BK and Knoblich JA (2020) Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol 21, 571-584
    Pubmed KoreaMed CrossRef
  8. Sato T, Vries RG, Snippert HJ et al (2009) Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262-265
    Pubmed CrossRef
  9. Menche C and Farin HF (2021) Strategies for genetic manipulation of adult stem cell-derived organoids. Exp Mol Med 53, 1483-1494
    Pubmed KoreaMed CrossRef
  10. Min S, Kim S and Cho SW (2020) Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp Mol Med 52, 227-237
    Pubmed KoreaMed CrossRef
  11. Leslie JL, Huang S, Opp JS et al (2015) Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function. Infect Immun 83, 138-145
    Pubmed KoreaMed CrossRef
  12. Zhang Y and Yu LC (2008) Microinjection as a tool of mechanical delivery. Curr Opin Biotechnol 19, 506-510
    Pubmed CrossRef
  13. Poletti M, Arnauts K, Ferrante M and Korcsmaros T (2021) Organoid-based models to study the role of host-microbiota Interactions in IBD. J Crohns Colitis 15, 1222-1235
    Pubmed KoreaMed CrossRef
  14. Ginga NJ, Slyman R, Kim GA et al (2022) Perfusion system for modification of luminal contents of human intestinal organoids and realtime imaging analysis of microbial populations. Micromachines 13 Basel, 131
    Pubmed KoreaMed CrossRef
  15. Puschhof J, Pleguezuelos-Manzano C, Martinez-Silgado A et al (2021) Intestinal organoid cocultures with microbes. Nat Protoc 16, 4633-4649
    Pubmed CrossRef
  16. Williamson IA, Arnold JW, Samsa LA et al (2018) A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology. Cell Mol Gastroenterol Hepatol 6, 301-319
    Pubmed KoreaMed CrossRef
  17. Chen Y, Cao K, Liu H et al (2021) Heat killed Salmonella typhimurium protects intestine against radiation injury through wnt signaling pathway. J Oncol 2021, 5550956
    Pubmed KoreaMed CrossRef
  18. Fischer S, Uckert AK, Landenberger M et al (2020) Human peptide alpha-defensin-1 interferes with Clostridioides difficile toxins TcdA, TcdB, and CDT. FASEB J 34, 6244-6261
    Pubmed CrossRef
  19. Liu R, Moriggl R, Zhang D et al (2019) Constitutive STAT5 activation regulates Paneth and Paneth-like cells to control Clostridium difficile colitis. Life Sci Alliance 2, e201900296
    Pubmed KoreaMed CrossRef
  20. Huang J, Zhou C, Zhou G, Li H and Ye K (2021) Effect of Listeria monocytogenes on intestinal stem cells in the co-culture model of small intestinal organoids. Microb Pathog 153, 104776
    Pubmed CrossRef
  21. Iftekhar A, Berger H, Bouznad N et al (2021) Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells. Nat Commun 12, 1003
    Pubmed KoreaMed CrossRef
  22. Sato T, Stange DE, Ferrante M et al (2011) Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology 141, 1762-1772
    Pubmed CrossRef
  23. Thorne CA, Chen IW, Sanman LE, Cobb MH, Wu LF and Altschuler SJ (2018) Enteroid monolayers reveal an autonomous WNT and BMP circuit controlling intestinal epithelial growth and organization. Dev Cell 44, 624-633
    Pubmed KoreaMed CrossRef
  24. Nickerson KP, Llanos-Chea A, Ingano L et al (2021) A versatile human intestinal organoid-derived epithelial monolayer model for the study of enteric pathogens. Microbiol Spectr 9, e0000321
    Pubmed KoreaMed CrossRef
  25. Zhang J, Hernandez-Gordillo V, Trapecar M et al (2021) Coculture of primary human colon monolayer with human gut bacteria. Nat Protoc 16, 3874-3900
    Pubmed KoreaMed CrossRef
  26. Nossol C, Diesing AK, Walk N et al (2011) Air-liquid interface cultures enhance the oxygen supply and trigger the structural and functional differentiation of intestinal porcine epithelial cells (IPEC). Histochem Cell Biol 136, 103-115
    Pubmed KoreaMed CrossRef
  27. Sachs N, Papaspyropoulos A, Zomer-van Ommen DD et al (2019) Long-term expanding human airway organoids for disease modeling. EMBO J 38, e100300
    Pubmed KoreaMed CrossRef
  28. Kim R, Attayek PJ, Wang Y et al (2019) An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. Biofabrication 12, 015006
    Pubmed KoreaMed CrossRef
  29. Sasaki N, Miyamoto K, Maslowski KM, Ohno H, Kanai T and Sato T (2020) Development of a scalable coculture system for gut anaerobes and human colon epithelium. Gastroenterology 159, 388-390
    Pubmed CrossRef
  30. Co JY, Margalef-Catala M, Li X et al (2019) Controlling epithelial polarity: a human enteroid model for host-pathogen interactions. Cell Rep 26, 2509-2520
    Pubmed KoreaMed CrossRef
  31. Troeger C, Blacker BF, Khalil IA et al (2018) Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect Dis 18, 1211-1228
    Pubmed KoreaMed CrossRef
  32. Hazen TH, Michalski J, Nagaraj S, Okeke IN and Rasko DA (2017) Characterization of a large antibiotic resistance plasmid found in enteropathogenic escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and shigella strains. Antimicrob Agents Chemother 61, e00995-17
    Pubmed KoreaMed CrossRef
  33. Livio S, Strockbine NA, Panchalingam S et al (2014) Shigella isolates from the global enteric multicenter study inform vaccine development. Clin Infect Dis 59, 933-941
    Pubmed KoreaMed CrossRef
  34. Llanos-Chea A, Citorik RJ, Nickerson KP et al (2019) Bacteriophage therapy testing against shigella flexneri in a novel human intestinal organoid-derived infection model. J Pediatr Gastroenterol Nutr 68, 509-516
    Pubmed KoreaMed CrossRef
  35. Ranganathan S, Doucet M, Grassel CL, Delaine-Elias B, Zachos NC and Barry EM (2019) Evaluating shigella flexneri pathogenesis in the human enteroid model. Infect Immun 87, e00740-18
    Pubmed KoreaMed CrossRef
  36. Koestler BJ, Ward CM, Fisher CR, Rajan A, Maresso AW and Payne SM (2019) Human intestinal enteroids as a model system of shigella pathogenesis. Infect Immun 87, e00733-18
    Pubmed KoreaMed CrossRef
  37. Jajere SM (2019) A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance. Vet World 12, 504-521
    Pubmed KoreaMed CrossRef
  38. Zhang YG, Wu S, Xia Y and Sun J (2014) Salmonella-infected crypt-derived intestinal organoid culture system for host-bacterial interactions. Physiol Rep 2, e12147
    Pubmed KoreaMed CrossRef
  39. Geiser P, Di Martino ML, Samperio Ventayol P et al (2021) Salmonella enterica serovar typhimurium exploits cycling through epithelial cells to colonize human and murine enteroids. mBio 12, e02684-20
    Pubmed KoreaMed CrossRef
  40. Forbester JL, Goulding D, Vallier L et al (2015) Interaction of Salmonella enterica serovar typhimurium with intestinal organoids derived from human induced pluripotent stem cells. Infect Immun 83, 2926-2934
    Pubmed KoreaMed CrossRef
  41. Lawrence AE, Abuaita BH, Berger RP et al (2021) Salmonella enterica serovar typhimurium SPI-1 and SPI-2 shape the global transcriptional landscape in a human intestinal organoid model system. mBio 12, e00399-21
    Pubmed KoreaMed CrossRef
  42. Verma S, Prescott RA, Ingano L et al (2020) The YrbE phospholipid transporter of Salmonella enterica serovar Typhi regulates the expression of flagellin and influences motility, adhesion and induction of epithelial inflammatory responses. Gut Microbes 11, 526-538
    Pubmed KoreaMed CrossRef
  43. Blount ZD (2015) The unexhausted potential of E. coli. Elife 4, e05826
    Pubmed KoreaMed CrossRef
  44. Kaper JB, Nataro JP and Mobley HL (2004) Pathogenic Escherichia coli. Nat Rev Microbiol 2, 123-140
    Pubmed CrossRef
  45. Takeda Y (1997) Enterohaemorrhagic Escherichia coli. World Health Stat Q 50, 74-80
    Pubmed CrossRef
  46. In J, Foulke-Abel J, Zachos NC et al (2016) Enterohemorrhagic Escherichia coli reduce mucus and intermicrovillar bridges in human stem cell-derived colonoids. Cell Mol Gastroenterol Hepatol 2, 48-62
    Pubmed KoreaMed CrossRef
  47. Tse CM, In JG, Yin J et al (2018) Enterohemorrhagic E. coli (EHEC)-secreted serine protease EspP stimulates electrogenic ion transport in human colonoid monolayers. Toxins (Basel) 10, 351
    Pubmed KoreaMed CrossRef
  48. Kotloff KL, Nataro JP, Blackwelder WC et al (2013) Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet 382, 209-222
    Pubmed CrossRef
  49. Evans DJ Jr and Evans DG (1973) Three characteristics associated with enterotoxigenic Escherichia coli isolated from man. Infect Immun 8, 322-328
    Pubmed KoreaMed CrossRef
  50. Foulke-Abel J, Yu H, Sunuwar L et al (2020) Phosphodiesterase 5 (PDE5) restricts intracellular cGMP accumulation during enterotoxigenic Escherichia coli infection. Gut Microbes 12, 1752125
    Pubmed KoreaMed CrossRef
  51. Vermeire B, Gonzalez LM, Jansens RJJ, Cox E and Devriendt B (2021) Porcine small intestinal organoids as a model to explore ETEC-host interactions in the gut. Vet Res 52, 94
    Pubmed KoreaMed CrossRef
  52. Dejea CM, Fathi P, Craig JM et al (2018) Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592-597
    Pubmed KoreaMed CrossRef
  53. Escobar-Paramo P, Le Menac'h A, Le Gall T et al (2006) Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates. Environ Microbiol 8, 1975-1984
    Pubmed CrossRef
  54. Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A et al (2020) Mutational signature in colorectal cancer caused by genotoxic pks(+) E. coli. Nature 580, 269-273
    Pubmed KoreaMed CrossRef
  55. Chandrasekaran R and Lacy DB (2017) The role of toxins in Clostridium difficile infection. FEMS Microbiol Rev 41, 723-750
    Pubmed KoreaMed CrossRef
  56. Engevik MA, Engevik KA, Yacyshyn MB et al (2015) Human Clostridium difficile infection: inhibition of NHE3 and microbiota profile. Am J Physiol Gastrointest Liver Physiol 308, G497-G509
    Pubmed KoreaMed CrossRef
  57. Mileto SJ, Jarde T, Childress KO et al (2020) Clostridioides difficile infection damages colonic stem cells via TcdB, impairing epithelial repair and recovery from disease. Proc Natl Acad Sci U S A 117, 8064-8073
    Pubmed KoreaMed CrossRef
  58. Engevik MA, Danhof HA, Chang-Graham AL et al (2020) Human intestinal enteroids as a model of Clostridioides difficile-induced enteritis. Am J Physiol Gastrointest Liver Physiol 318, G870-G888
    Pubmed KoreaMed CrossRef
  59. di Masi A, Leboffe L, Polticelli F et al (2018) Human serum albumin is an essential component of the host defense mechanism against clostridium difficile intoxication. J Infect Dis 218, 1424-1435
    Pubmed CrossRef
  60. Zhu Z, Schnell L, Muller B, Muller M, Papatheodorou P and Barth H (2019) The antibiotic bacitracin protects human intestinal epithelial cells and stem cell-derived intestinal organoids from clostridium difficile toxin TcdB. Stem Cells Int 2019, 4149762
    Pubmed KoreaMed CrossRef
  61. Sigman M and Luchette FA (2012) Cholera: something old, something new. Surg Infect (Larchmt) 13, 216-222
    Pubmed CrossRef
  62. Foulke-Abel J, In J, Yin J et al (2016) Human enteroids as a model of upper small intestinal ion transport physiology and pathophysiology. Gastroenterology 150, 638-649
    Pubmed KoreaMed CrossRef
  63. Zomer-van Ommen DD, Pukin AV, Fu O et al (2016) Functional characterization of cholera toxin inhibitors using human intestinal organoids. J Med Chem 59, 6968-6972
    Pubmed CrossRef
  64. Kuhlmann FM, Santhanam S, Kumar P, Luo Q, Ciorba MA and Fleckenstein JM (2016) Blood group O-dependent cellular responses to cholera toxin: parallel clinical and epidemiological links to severe cholera. Am J Trop Med Hyg 95, 440-443
    Pubmed KoreaMed CrossRef
  65. Radoshevich L and Cossart P (2018) Listeria monocytogenes: towards a complete picture of its physiology and pathogenesis. Nat Rev Microbiol 16, 32-46
    Pubmed CrossRef
  66. Zhou C, Zhang Y, Bassey A, Huang J, Zou Y and Ye K (2022) Expansion of intestinal secretory cell population induced by listeria monocytogenes infection: accompanied with the inhibition of NOTCH pathway. Front Cell Infect Microbiol 12, 793335
    Pubmed KoreaMed CrossRef
  67. Zhou C, Zou Y, Zhang Y, Teng S and Ye K (2022) Involvement of CCN1 protein and TLR2/4 signaling pathways in intestinal epithelial cells response to listeria monocytogenes. Int J Mol Sci 23, 2739
    Pubmed KoreaMed CrossRef
  68. Kim M, Fevre C, Lavina M, Disson O and Lecuit M (2021) Live imaging reveals listeria hijacking of E-cadherin recycling as it crosses the intestinal barrier. Curr Biol 31, 1037-1047
    Pubmed CrossRef
  69. Zhou C, Zou Y, Huang J et al (2022) TMT-based quantitative proteomic analysis of intestinal organoids infected by listeria monocytogenes strains with different virulence. Int J Mol Sci 23, 6231
    Pubmed KoreaMed CrossRef
  70. Wu N, Yang X, Zhang R et al (2013) Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb Ecol 66, 462-470
    Pubmed CrossRef
  71. Phongsisay V (2016) The immunobiology of Campylobacter jejuni: innate immunity and autoimmune diseases. Immunobiology 221, 535-543
    Pubmed CrossRef
  72. He Z, Gharaibeh RZ, Newsome RC et al (2019) Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut 68, 289-300
    Pubmed KoreaMed CrossRef
  73. Shang FM and Liu HL (2018) Fusobacterium nucleatum and colorectal cancer: a review. World J Gastrointest Oncol 10, 71-81
    Pubmed KoreaMed CrossRef
  74. Engevik MA, Danhof HA, Ruan W et al (2021) Fusobacterium nucleatum secretes outer membrane vesicles and promotes intestinal inflammation. mBio 12, e02706-20
    Pubmed KoreaMed CrossRef
  75. Seo Y, Oh SJ, Ahn JS, Shin YY, Yang JW and Kim HS (2019) Implication of Porphyromonas gingivalis in colitis and homeostasis of intestinal epithelium. Lab Anim Res 35, 26
    Pubmed KoreaMed CrossRef
  76. Khan R, Petersen FC and Shekhar S (2019) Commensal bacteria: an emerging player in defense against respiratory pathogens. Front Immunol 10, 1203
    Pubmed KoreaMed CrossRef
  77. Lordan C, Thapa D, Ross RP and Cotter PD (2020) Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes 11, 1-20
    Pubmed KoreaMed CrossRef
  78. Park NY and Koh A (2022) From the dish to the real world: modeling interactions between the gut and microorganisms in gut organoids by tailoring the gut milieu. Int J Stem Cells 15, 70-84
    Pubmed KoreaMed CrossRef
  79. Wu H, Xie S, Miao J et al (2020) Lactobacillus reuteri maintains intestinal epithelial regeneration and repairs damaged intestinal mucosa. Gut Microbes 11, 997-1014
    Pubmed KoreaMed CrossRef
  80. Hou QH, Ye LL, Liu HF et al (2018) Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22. Cell Death Differ 25, 1657-1670
    Pubmed KoreaMed CrossRef
  81. Engevik MA, Ruan W, Esparza M et al (2021) Immunomodulation of dendritic cells by Lactobacillus reuteri surface components and metabolites. Physiol Rep 9, e14719
    Pubmed KoreaMed CrossRef
  82. Aoki-Yoshida A, Saito S, Fukiya S et al (2016) Lactobacillus rhamnosus GG increases Toll-like receptor 3 gene expression in murine small intestine ex vivo and in vivo. Benef Microbes 7, 421-429
    Pubmed CrossRef
  83. Han X, Lee A, Huang S, Gao J, Spence JR and Owyang C (2019) Lactobacillus rhamnosus GG prevents epithelial barrier dysfunction induced by interferon-gamma and fecal supernatants from irritable bowel syndrome patients in human intestinal enteroids and colonoids. Gut Microbes 10, 59-76
    Pubmed KoreaMed CrossRef
  84. Lu X, Xie S, Ye L, Zhu L and Yu Q (2020) Lactobacillus protects against S. typhimurium-induced intestinal inflammation by determining the fate of epithelial proliferation and differentiation. Mol Nutr Food Res 64, e1900655
    Pubmed CrossRef
  85. Sittipo P, Pham HQ, Park CE et al (2020) Irradiation-induced intestinal damage is recovered by the indigenous gut bacteria lactobacillus acidophilus. Front Cell Infect Microbiol 10, 415
    Pubmed KoreaMed CrossRef
  86. Pino A, Benkaddour B, Inturri R et al (2022) Characterization of Bifidobacterium asteroides Isolates. Microorganisms 10, 655
    Pubmed KoreaMed CrossRef
  87. Pradhan S and Weiss AA (2020) Probiotic properties of escherichia coli nissle in human intestinal organoids. mBio 11, e01470-20
    Pubmed KoreaMed CrossRef
  88. Hill DR, Huang S, Nagy MS et al (2017) Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. Elife 6, e29132
    Pubmed KoreaMed CrossRef
  89. Kim J, Koo BK and Knoblich JA (2020) Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol 21, 571-584
    Pubmed KoreaMed CrossRef
  90. Lee JY, Tsolis RM and Baumler AJ (2022) The microbiome and gut homeostasis. Science 377, eabp9960
    Pubmed CrossRef

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Funding Information
  • National Research Foundation of Korea
      2018-R1A5A2023879, 2019-R1A2C2085876, 2021-R1I1A1A01055654
  • Ministry of Science and ICT, South Korea
      2018-R1A5A2023879, 2019-R1A2C2085876, 22A0205L1
  • Ministry of Education
  • Korean Fund for Regenerative Medicine
  • Ministry of Health and Welfare


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