Applications and research trends in organoid based infectious disease models

Abstract

Recently, three-dimensional (3D) cell culture technology has been developing rapidly, and disease-specific organoid models that can simulate human diseases are being developed. These models are being studied as a valuable tool that can be applied to pathogen biology research and drug screening analysis platforms to obtain fast, reliable, and reproducible results. Organoids are 3D cell aggregates formed from embryonic stem cells (ESCs), adult stem cells (ASCs), or induced pluripotent stem cells (iPSCs) through self-renewal and self-organization. They are also called mini-organs and have a structure and function similar to those of real organs, providing a more physiologically relevant model compared to traditional 2D cultures. In particular, due to the recent epidemics of infectious diseases such as coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many studies are using organoids for infectious disease research, enabling more accurate pathogen-host interaction modeling. In this review, we briefly introduce organoids and discuss research trends in developing organoid-based models of infectious diseases, focusing on organoids derived from the brain, liver, intestines, lung, kidney, skin, and blood vessels. These models hold significant potential for advancing our understanding of disease mechanisms and therapeutic development.

Introduction

Two-dimensional (2D) cultures and animal models have long been used to study human diseases. However, 2D cultures are unsuitable for modeling the immune system, its components, and specific functions. Although cells interact in 2D cultures by forming monolayers, these interactions are limited to a flat plane and cannot replicate the complex, multidimensional interactions are limited to a flat plane. They cannot replicate the complex, multidimensional interactions observed in natural microenvironments, which are better captured in three-dimensional (3D) systems. On the other hand, organoids are receiving a lot of attention in the biomedical field owing to their high biocompatibility and ability to mimic tissue structure and function¹. Organoids provide a 3D in vitro model and are emerging as an alternative to conventional 2D cell cultures, overcoming their limitations and potentially replacing time-consuming and expensive animal experiments. Additionally, they can help address the long-standing ethical issues associated with animal models. Recently, organoid-based high-throughput screening has been attracting attention because it can quickly generate and validate large amounts of data². As a result, organoid technology has been developing rapidly. In line with these advancements, recent studies have demonstrated diverse technical developments in organoid modeling. For instance, transplantation of brain organoids into rodents to recapitulate microglial function has suggested the potential application of these models in autism spectrum disorder (ASD) research³. Additionally, strategies such as long-term culturing⁴, morphogen screening⁵, and the integration of iPSC-derived microglia⁶ have significantly improved the biological reliability and applicability of organoid models. Organoids are used primarily to study infection mechanisms by mimicking normal tissues but are also being widely studied to mimic diseases such as cancer, dementia, and infections in vitro and to evaluate disease mechanisms or therapeutic effects⁷.

Infection is caused by a pathogen that multiplies within the host, leading to a disease or an immune response. Symptoms and diseases caused by infections with viruses, bacteria, and other microorganisms are called infectious diseases.

Infectious diseases have far-reaching effects on individual health and society as a whole. They cause disability and are the second leading cause of death worldwide, making them a major global health issue⁸. In particular, Human Immunodeficiency Virus (HIV)/acquired immune deficiency syndrome (AIDS), tuberculosis, and malaria have very high mortality rates. Accurate understanding of their mechanisms is essential to develop treatments for these infectious diseases⁹. To explore disease mechanisms or develop treatments, recent studies have utilized organoid models that mimic living organisms in vitro, serving as a step before conducting tests on humans. Existing infection models do not simulate the behavior of pathogens in the human body sufficiently well to the use of organoids allows to solve these problems.

Infectious disease models using intestinal, lung, brain, and liver organoids are being actively studied¹⁰. Brain organoids have been widely used to study neurological diseases. For example, intestinal organoids have been widely used to study interactions between intestinal pathogens and the host¹¹. Organoids can be applied to study of specific pathogens in various organs, which plays an important role in developing new drugs or treatments¹². Organoids are being actively used in infectious disease research due to the recent epidemics of infectious diseases such as coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Viruses such as SARS-CoV-2, as well as bacteria, parasites, and fungi, cause more than 10 million deaths worldwide each year, accounting for one-fifth of all deaths worldwide^13,14. In this review, we introduce specific examples of how organoids are used in infectious disease research and discuss research trends by classifying the cells used in organoid production by model.

Methods

Statement on the use of human participants and human participant cells

This study did not involve human participants or the use of human participant cells.

Results

Organoid definition

Organoids are small 3D organ-like structures formed from embryonic stem cells (ESCs), adult stem cells (ASCs), or induced pluripotent stem cells (iPSCs) or primary human tissues through self-renewal, differentiation, and self-organization. The suffix ‘oid’ confers the meaning ‘similar to an organ’. Organoids contain various types of cells and closely mimic the structure and function of human tissues and organs. Organoids made from human tumor cells have histological, genetic, molecular, and other characteristics similar to those found in the original tumor. They are used in drug research, toxicity assays, biomarker discovery, personalized medicine, disease modeling, and biobanks (Fig. 1).

Fig. 1.

Types of organoids based on cell origin. Types of organoids include ASCs, iPSCs, and ESCs. These are used in drug research, toxicity assays, biomarker discovery, personalized medicine, disease modeling, and biobank.

Organoids derived from ESCs, ASCs, and iPSCs cells, and primary human tissues are 3D structures formed through processes such as self-renewal and differentiation^15,16. The main application areas of organoids are disease models and regenerative therapy¹⁷. Simulating diseases such as cancer, dementia, and infection with cell-based organoid models can be used to study disease mechanisms instead of using humans or animals, and can also be used in the field of new drug development. Organoid disease models are being developed as an important test method that can reduce cost and time by verifying the performance of new drug candidates before clinical trials. Organoids mimic faithfully the human body, so they can be used to study various diseases that are difficult to study using existing animal disease models. When organoids are transplanted into damaged parts of an organ, they have a good ability to repair or replace damaged tissue. It is expected that this regenerative ability will be used to develop treatments for various incurable diseases.

Organoid-derived cell types and production methods

Organoids are manufactured by aggregating and recombining cells using 3D culture methods and contain specific cells that make up the modeled organ.

ESCs are extracted from embryos before differentiation. A blastocyst develops through the cell division of a fertilized egg, and an internal cell mass develops within the blastocyst. This mass gives rise to tissues such as blood, bone, and skin. ESCs can be isolated by separating internal mass cells and then differentiated into any type of cell or tissue by culturing them in vitro in a specific environment. Therefore, they are also called ‘pluripotent stem cells’¹⁸ (Supplementary Table S1).

ASCs go through an initial differentiation stage and differentiate only into cells with a defined function. They play a role in regenerating damaged tissue while maintaining the cellular characteristics of tissues or organs, e.g. when wounded skin heals and new skin grows. Representative ASCs are mesenchymal stem cells (MSCs)¹⁸. These cells are called"Adult Stem Cells"because they primarily function in tissue maintenance and regeneration in mature organisms. This terminology reflects their role in adult tissues, where they exhibit limited differentiation potential compared to ESCs but retain the ability to repair and regenerate specific tissues throughout life (Supplementary Table S1).

iPSCs are created by reprogramming mature somatic cells that have completed their growth and can no longer differentiate. These artificially created cells have the same function as ESCs. The advantage of iPSCs is that they can be obtained without using embryos, and since they are derived from mature cells, there is no problem with immune rejection¹⁸ (Supplementary Table S1).

Recently, primary human tissue cells derived directly from living tissues have also been attracting attention. These are cells derived directly from living tissues and maintain essential functional characteristics, and organoids produced based on these cells can maintain the structural and functional characteristics of the original tissues for a long time, and are widely used in various fields such as disease modeling, drug efficacy and toxicity evaluation, and regenerative medicine¹⁹.

For example, it has been shown that primary organoids can reproduce the tumorigenesis process in vitro through the introduction of oncogenes²⁰, There is also a case that showed that human adaptive immune response can be reproduced in vitro using organoids derived from human tonsil tissue²¹.

Organoids are produced mainly in a bottom-up manner from ESCs, ASCs, or iPSCs through self-renewal, differentiation, and self-organization (Supplementary Table S2). The bottom-up method has the advantage of being able to imitate the fine and complex organ structures very similar to those of the human body, but its disadvantage is the need to precisely control differentiation. This method sequentially creates the cells that make up the organ from a single stem cell.

The tissues and organs of our body are not simply a collection of cells, but rather a complex assembly of various substances surrounding the cells. This substance, called the extracellular matrix (ECM), plays an important role in addition to providing structural support.

The ECM not only serves as a support for cell attachment, but also transmits essential biochemical signals. It regulates important physiological processes such as cell proliferation, migration, differentiation, survival, and tissue structure maintenance²².

The composition of the ECM is slightly different for each organ, but it is composed of components such as fibrous proteins, proteoglycans, and glycosaminoglycans. These components are intertwined to form a complex three-dimensional network. This structure is both strong and flexible, allowing cells to function stably.

In addition to supporting cells, ECM also transmits signals to cells that determine the attachment location, migration path, growth rate, and differentiation direction of cells. In other words, ECM acts as a signal plate that guides cells to behave. ECM stores and releases signaling substances such as growth factors to regulate cell growth. Therefore, it is important to create an environment similar to ECM when growing cells in the laboratory²³.Organoids are generally cultured in hydrated polymer 3D hydrogel systems, and are formed through stem cell proliferation and self-organization within a 3D structure composed of ECM-derived proteins²⁴. These hydrogels can have various levels of elasticity, topographic permeability, and biodegradability, which greatly affect cell fate and function. ECM-based hydrogels are frequently utilized for organoid culture, with Matrigel in particular being widely used as the “golden standard” material to date²³.

Since recently, top-down methods are also being actively explored. A top-down method creates organ analogs by 3D printing of cells or tissues that have already differentiated into various functional cell types. This has the advantage of using differentiated cells or tissue-extracted cells, making it easier to ensure reproducibility and produce uniform organ replicas. The top-down organoid manufacturing uses a 3D bioprinter to connect various cells that make up the target organ and to create organoids with specific functions. The organ’s constituent cells are distributed in layers to create a shape similar to that of the target organ, co-cultured, and several cells together with the extracellular matrix are injected into a pre-designed scaffold or a bioprinted structure to mimic and function as the target organ. The advantage of this method is that it is highly reproducible because it is based on dividing, connecting, and culturing cells that have already differentiated into functional cells²⁵.

Advantages and disadvantages of 2D cell culture, 3D cell culture, and animal models

Cell culture research has mainly been conducted in a 2D cell culture environment. The problem with this environment is that the cells do not grow properly or their unique functions in the actual cell environment in the body are poorly reproduced. Due to these problems, 3D cell culture is receiving new attention. Its biggest advantage is that it can provide a 3D environment similar to that in the body, where the activity of cells is similar to that in vivo. This approach allows to apply biochemical and cell biological analysis techniques based on existing simple and efficient 2D cell culture to 3D cell culture and to overcome the limitations of 2D cell culture (Supplementary Table S3).

Types of infectious disease organoids

Infectious disease refers to “a disease that is caused by a specific pathogen or toxic substance of a pathogen and is spread from a person, animal, or other host infected with a pathogen or toxic substance to a susceptible host (human).”²⁶ Before testing treatments for infectious diseases on humans, organoid models are manufactured and studied in vitro. Infectious disease models that rely mainly on the intestine, lung, and liver organoids are being actively used. Due to the recent coronavirus pandemic, lung, blood vessel, and kidney organoid models are also being actively used (Fig. 2). Here we introduce organoid models of seven organs used in infectious disease research, classify them according to the cells used in each model, and introduce research trends that rely on these organoids.

Fig. 2.

Types of infectious disease organoids. Various types of infectious diseases occur in the brain, liver, lung, intestines, kidney, skin, and blood vessel. Organoids are being actively used to study these infectious diseases.

Brain

The brain is derived from the ectoderm, and brain organoids are being studied as an in vitro model for various diseases such as microcephaly. Because it is difficult to obtain brain cells for primary cell (PC) culture (PCC), most brain organoid models are developed, produced, and researched using iPSCs or ESCs. The brain is the most complex and irreplaceable organ in the human body and is virtually irreplaceable. In particular, no animal model capable of simulating the human cerebral cortex has been developed, so the development of a brain organoid model capable of simulating the cerebral cortex is urgently required. Zika virus (ZIKV), which infects the brain, is suspected of causing microcephaly in human fetuses²⁷. Because of the species specificity and cell type specificity of ZIKV, it is difficult to study it using mouse models or immortalized cell lines. The mechanism of ZIKV infection and microcephaly induction has been revealed using an in vitro brain organoid model capable of simulating fetal brain development^28–30 (Table 1).

Table 1.

Infectious disease organoid model by organ: brain, liver, intestine, lung, kidney, skin, blood vessels.

Organ	Cell source of organoid			Simulated infectious disease	Pathophysiological relevance	Key findings	Ref
	Stem/Primary	Species	Cell type
Brain	Embryonic Stem Cells (ESCs)	Human	Cell line (non-infected)	Zika Virus Infection(ZIKV Infection)	Cerebral cortex organoid’s ZIKV-induced neurodevelopmental disruption and epigenetic dysregulation	DNA methylation changes	31
						Growth inhibition	32
						Structural disorganization and apoptosis	33
	Induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Zika Virus Infection (ZIKV Infection)	Cerebral cortex organoid’s ZIKV-induced neurodevelopmental disruption and epigenetic dysregulation	Growth inhibition	28–30,32
						Loss of neural progenitor cells (NPCs) : Toll-like receptor 3 (TLR3) activation [26], general neurodevelopmental disruption [18], short transient receptor potential channel 4 (TRPC4)-dependent Ca2+influx [29]	28,33–35
						ZIKV-susceptible iPSC organoids difference than ZIKV-resistive ones : growth inhibition, loss of NPCs, cortical disorganization, and cell death	36
						DNA methylation changes	31
						Structural disorganization and apoptosis	33
						Reproduction of ZIKV-associated neuropathology	37
					Screening model for compounds suppressing ZIKV-induced neurotoxicity	High-throughput screening for compounds targeting ZIKV-induced NPC apoptosis	38
				Coronavirus Disease 2019 (COVID-19)	Neuronal infection and tauopathy induced by SARS-CoV-2	Neurons infection, Tau mislocalization to soma, and increased neuronal apoptosis upon SARS-CoV-2 exposure	39
				Herpes Simplex Virus-1 Infection (HSV-1 Infection)	HSV-1-induced Alzheimer’s-like neuropathology	Alzheimer’s-like pathology : amyloid beta (Aβ) accumulation, tau phosphorylation, impaired synaptogenesis	40,41
				Human Cytomegalovirus Infection (HCMV Infection)	Fetal neurodevelopmental impairment induced by HCMV	Reduced fetal neurodevelopmental gene expression, diminished organoid size, and inhibited neural rosette formation	42
				Human Immunodeficiency Virus-1 Infection (HIV-1 Infection)	HIV-induced neuroinflammation and network damage	Neural network disruption and increased proinflammatory cytokines	43
			Patient-derived (non-infected)	Herpes Simplex Virus-1 Infection (HSV-1 Infection)	HSV-1-induced Alzheimer’s-like neuropathology	Alzheimer’s-like pathology : amyloid beta (Aβ) accumulation, tau phosphorylation, impaired synaptogenesis	41
Liver	Induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Hepatitis B Virus Infection (HBV Infection)	Chronic HBV-induced hepatic dysfunction accompanied by viral persistence and inflammatory responses in iPSC-derived hepatocyte organoids	Covalently closed circular DNA (cccDNA) detection, Interferon-stimulated gene 15 (ISG15) and IL-6 upregulation associated with antiviral response	35
						IL-6 and interleukin-8 (IL-8) induction reflecting inflammatory shift from acute to chronic HBV infection	44
						Sustained cccDNA and HBsAg expression with preserved hepatocyte function in iPSC-derived micropatterned co-culture system (iMPCCs)	45
				Malaria	Models parasite invasion and liver-stage development with expression of malaria-specific antigens	Expression of plasmodium falciparum circumsporozoite protein (PfCSP) and liver stage antigen 1 (LSA1)	46
	Primary Cells (PCs)	Human	Cell line (non-infected, immortalized)	Pyogenic Liver Abscess	Simulates hepatic inflammation and immune activation under polymicrobial : E. coli, Staphylococcus aureus (S. aureus)	Increase in lactate dehydrogenase (LDH) release, TNF-α expression	47
				Amebic Liver Abscess	Reproduces acute hepatic cytotoxicity and inflammation induced by entamoeba histolytica (E. histolytica)	Hepatocyte detachment, IL-8 upregulation induced by E. histolytica infection	48
			Patient-derived (non-infected)	Hepatitis B Virus Infection (HBV Infection)	Exhibits early innate immune activation characteristic of acute HBV infection	Induction of innate immune genes including myxovirus resistance 1 (MX1) and 2’−5’-oligoadenylate synthetase 1 (OAS1) during acute phase	44
				Hepatitis C Virus Infection (HCV Infection)	Recapitulates infection dynamics using a hepatocyte-stromal co-culture derived from primary human liver tissue	Spatially localized expression of c-x-c motif chemokine ligand 10 (CXCL10), IL-8 in response to hepatotropic infection	49
					Demonstrates chronic HCV infection, including persistent intracellular RNA and limited antiviral response	Sustained HCV RNA replication for over 20 days with reduction in viral load following direct-acting antivirals (DAAs) treatment	50
				Coronavirus Disease 2019 (COVID-19)	Represents SARS-CoV-2-induced cholangiocytes damage and viral replication in bile duct organoids	Infection of angiotensin-converting enzyme 2 (ACE2+) cholangiocytes, bile duct structural damage	51
Large intestine	Embryonic Stem Cells (ESCs)	Human, Animal	Cell line (non-infected)	Coronavirus Disease 2019 (COVID-19)	Represents epithelial injury and antiviral immune response to SARS-CoV-2 in large intestinal organoids, modeling host -virus interactions	Upregulation of interferon-stimulated genes (ISGs), epithelial damage, impaired interferon, response during SARS-CoV-2 replication	52
	Adult Stem Cells (ASCs)	Human	Patient-derived (non-infected)	Clostridium Difficile Infection (C. difficile Infection)	Stimulates C. difficile toxin-induced barrier dysfunction and inflammation, explaining the mechanism of diarrhea	Reduction in mucin (MUC2) expression, alteration in mucin glycosylation, weakening of mucus barrier	53
				Escherichia Coli Infection (E. coli Infection)	Reflects barrier damage and epithelial dysfunction in enterohemorrhagic E. coli (EHEC)-associated colitis	Reduced mucus production, loss of intermicrovillar bridges, compromised epithelial barrier	54
Small intestine	Embryonic Stem Cells (ESCs)	Human	Cell line (non-infected)	Escherichia Coli Infection (E. coli Infection)	Demonstrates epithelial injury and innate immune activation induced by Shiga toxin-producing E. coli	Epithelial damage, increased permeability, IL-8 secretion in response to Shiga toxin-producing E. coli	55
	Adult Stem Cells (ASCs)	Human	Patient-derived (non-infected)	Cholera	Recapitulates cholera toxin-induced epithelial ion transport alteration and fluid secretion leading to secretory diarrhea	Cystic fibrosis transmembrane conductance regulator (CFTR)-mediated chloride secretion, epithelial swelling, secretory fluid accumulation	14
				Coronavirus Disease 2019 (COVID-19)	Models epithelial injury and antiviral response to SARS-CoV-2 in intestinal organoids	ACE2-mediated viral entry, productive infection in enterocytes, induction of interferon-stimulated ISGs	56
				Norovirus Infection	Reveals strain-specific replication and host susceptibility of norovirus in human enteroids	Higher infectivity and replication of genogroup II, genotype 4 (GII.4) than genogroup II, genotype 3 (GII.3) strains	57
	induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Salmonella Infection	Demonstrates Salmonella-induced epithelial invasion modeling early host–pathogen interaction and innate immune activation	Epithelial invasion, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation, increased TNF-α and IL-8, secretion of proinflammatory cytokines	58
	Primary Cells (PCs)	Human	Cell line (non-infected, immortalized)	Yersinia Pseudotuberculosis Infection (Y. pseudotuberculosis Infection)	Epithelial cell damage by Y. pseudotuberculosis, upregulation of inflammation-related genes under infection	Epithelial damage, Hypoxia-induced T3SS expression	59
			Patient-derived (non-infected)	Rotavirus Infection	Stimulates rotavirus strain-specific infectivity and epithelial response in small intestinal organoids	Strain-dependent epithelial damage, differential viral replication, enhanced antiviral gene expression by interferon-α (IFN-α) and ribavirin	60
						Preferential infection of enterocytes, minimal replication in goblet and Paneth cells, induction of type I/III interferons, upregulation of antiviral ISGs	61
				Cholera	Reveals blood group O-dependent exacerbation of cholera toxin-induced diarrheal response in small intestinal organoids	Blood group O-specific cyclic adenosine monophosphate (cAMP) elevation, enhanced CFTR-driven secretion, severe fluid loss	62
Lung	Embryonic Stem Cells (ESCs)	Human	Cell line (non-infected)	Coronavirus Disease 2019 (COVID-19)	SARS-CoV-2-induced epithelial damage and antiviral response in lung organoids modeling pulmonary pathology in COVID-19	Epithelial injury, upregulation of ISGs, suppression by Imatinib	52
				Respiratory Syncytial Virus Infection (RSV Infection), Parainfluenza Virus Infection (PIV Infection), Measles Virus Infection (MeV Infection)	Differential epithelial injury by respiratory viruses in ESC- and iPSC-derived lung organoids during lung development	Virus-specific syncytia formation and cilia loss by RSV, PIV3, MeV	63
				Respiratory Syncytial Virus Infection (RSV Infection)	In lung bud organoids, RSV-induced epithelial damage and mucus hypersecretion model early airway inflammation	Mucus accumulation, epithelial damage, higher expression of IL-6, IL-8, and granulocyte-macrophage colony-stimulating factor (GM-CSF)	64
	Adult Stem Cells (ASCs)	Human	Patient-derived (non-infected)	Influenza	Strain-dependent replication and interferon activation by influenza A viruses in airway epithelium	Higher replication of H7N9 and H1N1pdm, type I and III IFN upregulation	65
					Strain-specific replication and ciliated cell targeting in airway organoids reflecting transmissibility differences	Higher replication and ciliated cell targeting of H7N9 and H1N1pdm, lower replication of H7N2 and swine H1N1	66
	Induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Respiratory Syncytial Virus Infection (RSV Infection), Parainfluenza Virus Infection (PIV Infection), Measles Virus Infection (MeV Infection)	Differential epithelial injury by respiratory viruses in ESC- and iPSC-derived lung organoids during lung development	Epithelial injury, lower viral replication, lower IFN responses compared to ESC-derived organoids	63
				Respiratory Syncytial Virus Infection (RSV Infection)	In lung bud organoids, RSV-induced epithelial damage and mucus hypersecretion model early airway inflammation	Epithelial damage, lower expression of IL-6, IL-8, and GM-CSF compared to ESC-derived organoids	64
						IL-8 and IFN-γ secretion, collagen deposition, epithelial disruption, and antiviral efficacy of Nirsevimab and Palivizumab	67
				Coronavirus Disease 2019 (COVID-19)	Natural flavonoid-mediated suppression of SARS-CoV-2-induced epithelial infection and inflammatory response	Flavonoids K-4 and M-4 inhibit viral entry, spike protein expression, and pro-inflammatory cytokines: IL-6, interleukin-1 beta (IL-1β), tumor necrosis factor-alpha (TNF-α)	68
					Soluble ACE2 inhibits SARS-CoV-2 infection in human lung organoids, demonstrating antiviral efficacy	Reduced viral replication and infection by soluble ACE2	69
						Inhibition of viral replication and epithelial infection by soluble ACE2, Remdesivir, Camostat	70
	Primary Cells (PCs)	Human	Cell line (non-infected, immortalized)	Tuberculosis (TB)	Granulomatous inflammation features, including macrophage activation and cytokine release by mycobacterium tuberculosis (M. tb)	Increased bacterial load, macrophage activation, elevated tumor necrosis factor (TNF), IL-1β, IL-6 expression	71
				Hantavirus Pulmonary Syndrome (HPS)	Cytokine and elevated vascular endothelial growth factor A (VEGF-A) release by andes virus (ANDV) infection modeling pulmonary vascular leakage in HPS	Late viral replication peak, increased IL-6, TNF and VEGF-A secretion	72
			Cell line (non-infected, immortalized), Patient-derived (non-infected),	Pneumonia	Epithelial damage and cytokine release by S. aureus toxin modeling inflammatory lung injury in bacterial pneumonia	Disrupted epithelial structure, cytotoxicity, increased IL-6, IL-8, GM-CSF levels	73
			Patient-derived (non-infected)	Coronavirus Disease 2019 (COVID-19)	SARS-CoV-2-induced alveolar infection and surfactant loss modeling epithelial damage in COVID-19	Viral replication in alveolar cells, loss of alveolar type 2 cell (AT2) markers, reduced surfactant gene expression	74
Kidney	Induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Coronavirus Disease 2019 (COVID-19)	Epithelial injury by SARS-CoV-2 infection in kidney	SARS-CoV-2 replication, epithelial damage, suppression by soluble ACE2	69
	Primary Cells (PCs)	Human	Cell line (non-infected, immortalized)	Hemolytic Uremic Syndrome (HUS)	Epithelial injury and inflammatory response in kidney proximal tubule modeling hemolytic uremic syndrome by Shiga toxin-producing E. coli (Stx2)	Loss of tight junctions, increased apoptosis, LDH release, IL-6 and IL-8 secretion	75
Skin	Primary Cells (PCs)	Human	Cell line (non-infected, immortalized)	Herpes Simplex Virus-1 Infection (HSV-1 Infection)	Latent infection and UV-induced reactivation of HSV-1 in reconstructed 3D skin mimicking herpetic skin lesions	Latency in PC12 neurons, UVB-triggered viral reactivation, HaCaT cell lysis and plaque formation	76
				Invasive Tissue Infection	Streptococcus dysgalactiae subsp. equisimilis (SDSE)-induced epithelial cytotoxicity and inflammatory tissue damage modeling	Keratinocyte damage, high streptolysin O activity, pro-inflammatory cytokine induction, altered epithelial structure	77
Blood vessels	Induced Pluripotent Stem Cells (iPSCs)	Human	Cell line (non-infected)	Coronavirus Disease 2019 (COVID-19)	SARS-CoV-2 infection in vascular organoids modeling COVID-19-associated endotheliitis	SARS-CoV-2 replication, endothelial dysfunction, suppression by soluble ACE2	69

Stem/Primary: Stem cells (ESCs, ASCs, iPSCs), Primary cells (PCs).

Qian et al.²⁸ used human iPSCs to create human brain organoids, which resemble the forebrain structure during early fetal development and exposed the organoids to ZIKV. ZIKV primarily infected neural progenitor cells within the organoid and induced their apoptosis, suggesting that a shrinkage of the nerve cell layer causes fetal microcephaly (Supplementary Fig. S1).

Additionally, microcephaly was modeled using cerebral organoids produced from iPSCs derived from skin fibroblasts of patients with microcephaly³². The neuroepithelial tissue in patient-derived organoids was smaller than that in control organoids, which were generated from iPSCs reprogrammed from healthy donor fibroblasts under identical differentiation conditions. Moreover, nerve growth in the patient-derived organoids was excessive. This study found that damage to early progenitor cells leads to premature and excessive neural differentiation. The mechanism of microcephaly development was identified as failure of normal growth and differentiation of progenitor cell populations, leading to small brain size and formation of a small skull.

Brain organoids have also been used to model infections beyond ZIKV, such as SARS-CoV-2-induced neuronal damage and tauopathy, and HIV-related neuroinflammation via infected microglia^39,43. However, their lack of vasculature and immune cells limits the modeling of neuroimmune dynamics and blood–brain barrier (BBB) function^28,32,33. In particular, the absence of microglia impairs antiviral signaling pathways, including Toll-like receptor 3 (TLR3) activation and cytokine responses^33,43. Structural limitations are also evident, as prolonged culture without vasculature leads to necrotic cores due to inadequate oxygen and nutrient diffusion³². Nevertheless, brain organoids offer a useful platform for modeling virus-induced neural injury and screening for neuroprotective agents^36,38.

Liver

Approximately 2 million people around the world die every year from liver disease. The liver is actively studied as an organ due to its high unmet medical needs and commercial research potential. The liver develops through complex interactions between endodermal and mesodermal cells⁷⁸. Liver organoids are being used to study various diseases such as hepatitis B virus (HBV) infection, hepatitis C virus (HCV) infection, and amebic liver abscess. Research on SARS-CoV-2 infection mechanisms is also being conducted using a co-culture model with the virus. The liver is prone to toxic injury, so toxicity evaluation studies using liver organoids are also being actively conducted. Liver organoids have been developed using various protocols based on iPSCs, PCs, or cell lines (Table 1).

Malaria is caused by protozoan parasites such as Plasmodium berghei (P. berghei), Plasmodium yoelii (P. yoelii), Plasmodium falciparum (P. falciparum), and Plasmodium vivax (P. vivax) which invade hepatocytes in the liver during their life cycle. Malaria infection organoids were produced from iPSCs for antimalarial drug screening⁴⁶. The screening showed that Plasmodium-infected iHLCs were sensitive to atovaquone, and their sensitivity to primaquine was enhanced through chemical maturation. Amoebic liver abscess organoids were produced using cultures of liver sinusoidal endothelial cells and the cell lines Huh-7 (hepatoma cells) or Huh7-NTCP (hepatocytes)⁴⁷. Huh7-NTCP cells stably express sodium taurocholate cotransporting polypeptide (NTCP), a receptor for HBV. An infection model was created by simultaneously co-culturing hepatocytes in collagen with Entamoeba histolytica (E. histolytica), a protozoan parasite that causes amebiasis, and HBV, which causes a chronic infection (Supplementary Fig. S2). This co-culture model can ultimately be used to study chronic inflammation associated with cirrhosis and liver cancer^47,48.

Liver organoids have been used to model hepatotropic and parasitic infections, including HBV, HCV, Plasmodium, and Entamoeba histolytica^{35,44,46–48,50}. And they can recapitulate NTCP-mediated HBV entry and viral replication. In contrast, these infection processes are difficult to reproduce in animal models or 2D culture systems^35,44,50. Co-culture approaches have also facilitated studies of host–parasite interactions and hepatic injury^46–48. However, most models lack bile ducts, liver sinusoidal endothelial cells (LSECs), and Kupffer cells, limiting the simulation of bile transport, vascular responses, and immune-mediated damage^35,44,47. In addition, metabolic function and long-term viral persistence vary across models⁵⁰. Liver organoids have structural limitations, such as the lack of vascular and immune components. However, they are utilized to develop antiviral and antiparasitic therapeutic strategies, as they replicate the pathophysiology of chronic liver infections more effectively than animal models or 2D culture model.

Large and small intestines

The large and small intestines are the most exposed organs to bacterial and viruses. Co-culture models have been developed for various pathogens, such as Salmonella enteritidis, and Escherichia coli. The intestinal organoid model is being actively used in studies on organoid transplantation and organoid therapeutics, and also as a toxicity evaluation model to check gastrointestinal side effects (diarrhea, abdominal pain) of various drugs^79,80. Intestinal organoids can be cultured not only from iPSCs, ESCs, and ASCs, but also from human primary tissues obtained through minimally invasive procedures such as endoscopy. This enables the generation of patient-derived intestinal organoids, which enhances accessibility for personalized disease modeling and therapeutic screening⁶².

Patients infected with SARS-CoV-2 show intestinal symptoms such as abdominal pain and diarrhea^52,81. Due to its species specificity, SARS-CoV-2 is difficult to study using animal models such as mice and monkeys. However, because intestinal organoids express SARS-CoV-2 receptors similar to those in the human body, the mechanisms that cause the above intestinal symptoms can be analyzed (Table 1).

In large intestine organoids, it was confirmed that intestinal cells express angiotensin-converting enzyme 2 (ACE2), a SARS-CoV-2 receptor, capable of mediating SARS-CoV-2 infection⁵². Imatinib, mycophenolic acid, and quinacrine dihydrochloride inhibited SARS-CoV-2 infection in drug screening using this model (Supplementary Fig. S3).

Norovirus is a major pathogen that causes infectious acute enteritis. Norovirus organoids were produced by infecting intestinal epithelial organoids produced using ASCs derived from the human small intestine with norovirus⁵⁷. Norovirus replicated efficiently in these organoids, and its growth was further enhanced by bile. These findings suggest that intestinal epithelial organoids may be a useful in vitro model for analyzing the effects of antiviral drugs against norovirus.

Intestinal organoids have been used to model infections by major enteric pathogens, including norovirus^57,82, rotavirus^60,61,83, SARS-CoV-2⁵⁶, Clostridioides difficile (C. difficile)⁵³, and Shiga toxin-producing E. coli (STEC)^54,55. These models replicate core features of the intestinal epithelium, such as crypt–villus architecture, apical–basal polarity, and mucus secretion, and express relevant pathogen receptors^54,55,59. They support productive infection and facilitate studies of barrier disruption, cytokine responses, and host–pathogen interactions^56,57,61. However, the absence of immune cells and commensal microbiota limits their ability to model inflammation and microbe–epithelium cross^53,61. Toxin-induced responses can be partially recapitulated but fail to capture systemic effects such as neutrophil recruitment or enterotoxin-mediated inflammation^53,62. Though limited in physiological complexity, intestinal organoids serve as an in vitro system for exploring host–pathogen interactions and evaluating targeted therapies for gut infections^58,60.

Lung

The lung is a complex organ derived from the endoderm and mesoderm⁸⁴. The lung is used as a model to analyze the effectiveness of treatments for congenital diseases. In 2021, an organoid disease model study succeeded in uncovering the mechanism of SARS-CoV-2 infection by producing lung organoids infected with SARS-CoV-2. Lung organoid models are also used to study the pathogenesis of tuberculosis, pneumonia, and hantavirus pulmonary syndrome, and are widely used in the study of various pathogens. In addition to producing lung organoids from iPSCs or ESCs, research is also being actively conducted to produce them by culturing cells obtained from lung and airway biopsies of clinical patients (Table 1).

Lung tissue models for Mycobacterium tuberculosis infection were constructed by co-culturing human lung fibroblasts expressing type 1 collagen on a porous membrane with uninfected primary human monocytes and primary human macrophages infected with Mycobacterium tuberculosis⁷¹. Then, human bronchial epithelial cells were spread on the collagen–fibroblast matrix and further cultured. This multicellular tissue was exposed to air, and further culturing initiated extracellular matrix protein production, mucus secretion, and epithelial layer stratification. This lung infection organoid model demonstrated physiological responses resembling those of the human lung. It induced macrophage aggregation and monocyte migration at the infection site, reproducing key features of granuloma formation seen in tuberculosis. This organoid model of lung infection successfully mimicked the early stages of human tuberculosis granuloma.

In vitro models mimicking Staphylococcus aureus necrotizing pneumonia were produced by mixing lung fibroblasts with collagen and culturing them in the insert within the Transwell system Afterwards, bronchial epithelial cells were added and the culture was exposed to air. S. aureus strains isolated from patients with severe pneumonia (including necrotic pneumonia and pulmonary empyema), were used to infect lung organoids, while bacterial supernatant and purified α-toxin were applied to evaluate their effects on the organoids. Significant α-toxin-mediated lung epithelial damage causes PVL-mediated neutrophil cytotoxicity and the release of toxin-mediated cytokines and chemokines from the lung epithelium, leading to inflammation⁷³. Using a lung organoid model, it was confirmed that pneumonia isolates secrete high levels of α-toxin and PVL, causing inflammation. Toxin-mediated damage to infected lung organoids is inhibited by treatment with multi-specific intravenous immunoglobulin antibodies targeting α-toxin and PVL, which are present in supernatants of clinical isolates (Supplementary Fig. S4).

Andes virus (ANDV) causes hantavirus pulmonary syndrome. MRC-5 (a human lung fibroblast cell line) and 16HBE14 (a human bronchial epithelial layer cell line) were exposed to air to create a lung infection organoid model⁷². These organoids were infected with ANDV, and viral replication was detected about 1 week later. Viral replication was sustained for more than one week, as confirmed through quantitative analysis. This prolonged viral production was associated with increased levels of interferon lambda-1 (IFN-λ1), interferon lambda-2 (IFN-λ2), and interferon beta (IFNβ), along with elevated expression of the interferon-stimulated gene 56 (ISG56) mRNA. It was also cross-validated by examining whether the expression levels of pro-inflammatory cytokines interleukin 6 (IL-6) and interleukin 8 (IL-8) were increased in the Shiga toxin 2 (Stx2)-treated kidney organoid model. In this way, lung organoids enable long-term research on infectious diseases that is difficult to implement in monolayer cell culture models.

Lung organoids have been used to model infections by respiratory pathogens such as SARS-CoV-2^{63,64,66,69,74,85}, influenza virus^65,66, Mycobacterium tuberculosis⁷¹, Staphylococcus aureus⁷³, and hantavirus⁷². These models mimic key features of the airway epithelium under air–liquid interface conditions, including pseudostratification, mucus secretion, and cytokine release^65,71,73. They enable analysis of viral tropism, innate immune responses, and tissue damage in a human-relevant setting^63,66,74. However, most lung organoids lack vasculature and immune cells, limiting their ability to model systemic inflammation, immune infiltration, and vascular injury^71,72,74. Alveolar differentiation also remains incomplete in some models, restricting the study of distal lung infections^63,74. Despite these limitations, lung organoids serve as effective platforms for studying respiratory pathogens and evaluating targeted therapies⁶⁹.

Kidney, skin, and blood vessels

The kidney is a representative mesoderm-derived organ, and kidney organoids are actively studied for their efficacy as in vitro models of various kidney diseases. Although kidney organoids can be obtained through PCC, most models use ESCs or iPSCs due to the complex structure of the glomerulus. For example, kidney organoids have provided new information about hemolytic uremic syndrome (HUS), which was the first evaluation of kidney damage caused by Stx that is characterized by renal failure, hemolytic anemia, and thrombocytopenia (Table 1).

Stx and its variants are bacterial cytotoxins secreted by Shigella dysenteriae (S. dysenteriae) and Stx-producing E. coli during intestinal infections. In the absence of lipopolysaccharide (LPS), Stx2 is toxic in both 2D and 3D cell culture systems. In particular, kidney organoids made from human cell lines showed have higher levels of kidney injury marker 1 (Kim-1) than cells cultured in a 2D system⁷⁵. In a kidney organoid model treated with Stx2, secretion of inflammatory cytokines IL-6, IL-8, and tumor necrosis factor (TNF-α) was also found to increase.

Addition of human recombinant soluble ACE2 (hrsACE2) with SARS-CoV-2 inhibit the spread of SARS-CoV-2⁶⁹. The mechanism by which soluble ACE2 not only prevents lung damage but also blocks SARS-CoV-2 from entering target cells was confirmed in a kidney organoid model (Supplementary Fig. S5).

Kidney organoids have been used to model pathogen-induced renal injury, including SARS-CoV-2 infection⁶⁹ and Shiga toxin–mediated cytotoxicity⁷⁵. These models reproduce key features of proximal tubular damage and inflammatory cytokine responses. However, they lack vascular and immune components, limiting the study of systemic inflammation and vascular injury⁷⁵. Additionally, incomplete nephron patterning constrains the modeling of complex renal architecture. While fully replicating the complexity of the human kidney remains difficult, kidney organoids prove studying nephrotoxicity and evaluating renal-targeted therapies⁷⁵.

The skin is a multi-layered organ containing various components such as glands, hair follicles, temperature and pain nerves, and skin cells. Skin organoid models derived from iPSCs have limitations in mimicking aged skin. Nevertheless, skin organoids are widely used in infectious disease modeling and regenerative medicine (Table 1).

Bacterial and viral infection studies have been performed using human skin organoids⁷⁶. It is difficult to conduct studies on virus latency and virus reactivation in monolayer cell cultures because these cultures lack the complex 3D tissue architecture and cellular interactions found in natural tissues. A skin organoid with a multi-layer structure has been created to confirm the infiltration of herpes simplex virus type 1 (HSV-1). Skin organoids composed of stratified epithelium and fibroblast dermal layer were used to study the pathogenesis of Streptococcus dysgalactiae subsp. equisimilis (SDSE)⁷⁷. All SDSE strains can infect these organoids, and the bacteria look similar to those seen in tissue biopsies. An invasive SDSE strain spreads throughout the organoid epithelium, causing significant tissue damage through its destruction and separation from underlying tissue, which is similar to the infection symptoms and mechanisms in humans (Supplementary Fig. S6).

Skin organoids have been applied to model infections by HSV-1 and SDSE, recapitulating viral latency, bacterial invasion, and tissue injury^76,77. These models reproduce stratified epidermal–dermal structure, enabling analysis of pathogen behavior in a physiologically relevant context. However, they lack immune components and features of aged skin, limiting their ability to model inflammatory responses and age-dependent vulnerability^76,77. Even in the absence of immune elements and aging features, these skin organoids provide a valuable system for investigating localized infections and evaluating targeted treatments.

Blood vessels not only supply nutrients to organs, but also play an important role in the development, regeneration, and migration of brain nerve cells by providing a vascular microenvironment. Vascular organoids are used not only to simulate the path of infectious agents, but also to study the functions of specific proteins to prevent the spread of infectious diseases (Table 1).

Vascular organoids have recently been widely used to study SARS-CoV-2 infection. ACE2 is the main receptor for this infection. If a drug that inhibits the SARS-CoV-2–ACE2 interaction is developed, it is expected to be useful to treat COVID-19 patients A study using vascular organoids demonstrated that hrsACE2 binds to SARS-CoV-2 and reduces its entry into Vero cells by 1000–5000-fold, effectively blocking early infection⁶⁹ (Supplementary Fig. S7).

Vascular organoids have been used to model endothelial infection by SARS-CoV-2 via ACE2, enabling evaluation of antiviral strategies such as soluble ACE2 treatment⁶⁹. These models recapitulate key structural and functional features of human vasculature, including barrier properties and virus–receptor interactions. However, they lack immune cells and multicellular interactions with surrounding tissues, limiting their ability to simulate systemic inflammatory responses and inter-organ vascular effects. Although vascular organoid models have limitations, they provide a relevant platform for investigating vascular involvement in infectious diseases and evaluating targeted interventions.

Increasing importance of infectious diseases in the era of global environmental and societal change

In the twenty-first century, the emergence of various infectious diseases has significantly impacted human health and survival. In particular, the rapid spread of COVID-19 has posed serious challenges to society, the economy, and medical systems worldwide. Not only COVID-19, but also SARS-CoV in 2003, novel swine-origin influenza A (H1N1) virus in 2009, Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, ebolavirus in West Africa from 2013 to 2016, and ZIKV infection in 2015 all resulted in high morbidity and mortality^86,87. Infectious diseases can be caused not only by new viruses or bacteria but also by unicellular eukaryotic parasites and fungi, as well as by mutations or increased resistance of existing pathogens. Among infectious diseases, respiratory infections, diarrheal diseases, tuberculosis, AIDS, malaria, and Chagas disease can cause death⁸⁸. Emerging infectious diseases such as COVID-19 and infections caused by antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are a threat. They now spread easily due to global factors such as climate change, population movement, and international trade. Accordingly, it is urgent to prepare countermeasures such as vaccines and treatments^86,87.

Due to technological advancements that have led to the above global changes, the population continues to increase and climate is also changing. Infectious diseases easily spread across borders into many countries. Human health is closely connected to animals, which can serve as potential hosts of novel pathogens and the environment. As a result, it is tough to predict the emergence and decline of infectious diseases. Despite improvements in hygiene and access to health care worldwide, global changes are increasing the risk of infectious diseases⁸⁶.

The continued existence of infectious disease-causing pathogens increases the need to understand the basic mechanisms of disease development and to develop treatments. Research on the onset and mechanisms of infectious diseases is difficult due to the complex conditions of pathogen cultures. Many pathogens do not infect non-human laboratory animals or do not interact with cell lines cultured in two dimensions because of their specificity to the host. As a result, animal and 2D cell culture models do not guarantee reliable results in pathogen modeling or drug testing within an appropriate time^89,90. Long-term organoid platforms can solve these problems. Organoids have 3D structures and are composed of various cell types. They can reproduce physiological and pathological processes otherwise unique to human tissue⁹¹. Stem cells go through stages of self-renewal, differentiation, and self-organization under certain conditions. These stages are patterned and rearranged to have structures and functions similar to those of human organs^15,16. Therefore, organoid models are more complex than 2D monolayer cell cultures and have a tissue-like structure. To effectively utilize organoids in infectious disease research, various engineered strategies have been developed, including 3D-embedded culture, air–liquid interface (ALI) culture, and organ-on-a-chip (Table 2). The advantages and limitations of these strategies in organoid-based infectious disease models are summarized in Table 2.

Table 2.

Advantages and limitations of engineering strategies in organoid infectious disease models.

Organ	Engineered strategy	Advantages	Limitations	Ref
Brain	3D-embedded culture	Mimics layered brain structure, models neurotropic virus infection (e.g., ZIKV, SARS-CoV-2)	Lacks vasculature, risk of core necrosis	30,34,39
	Hanging drop culture	Enables neurosphere formation for early neuroinfection modeling	Limited tissue complexity, short-term culture	37
	Mini-bioreactor culture	Enhances maturation and region-specific development under ZIKV exposure	Requires specialized setup, batch variation	28,32,33,36,43
Liver	3D-embedded culture	Supports hepatocyte polarity, models viral and parasitic infections (e.g., HBV, HCV, E. histolytica)	Lacks perfusion and immune interaction	47,48
	Micropatterned co-culture	Maintains hepatocyte phenotype, supports HBV and HCV entry/replication	Requires micropatterning infrastructure	45,49
	Miniaturized bioreactor	Enables persistent HCV infection, long-term maintenance	Technically complex, expensive setup	50
Intestine	3D-embedded culture	Models Salmonella, E. coli, H. pylori, norovirus infections in crypt–villus structures	Closed lumen limits apical access	53,55,55,58
	ALI culture	Provides apical access for rotavirus, supports mucosal virus-host interactions	Short-lived, lacks immune elements	60,61
	Organ-on-a-chip	Enables flow, nutrient delivery, and dynamic host–pathogen interactions	Requires microfluidic setup, lower throughput	59,92
Lung	3D-embedded culture	Enabling antiviral screening of natural and synthetic compounds	Limited recapitulation of airway-specific structure and function due to absence of air–liquid interface	68,70
	ALI culture	Supports mucociliary differentiation, suitable for influenza and SARS-CoV-2 studies	Requires long-term differentiation, lacks immune cells	63,65–67
	Organ-on-a-chip	Simulates alveolar–capillary barrier for SARS-CoV-2 infection and drug testing	High complexity and cost	69
Kidney	3D-embedded culture	Models Shiga toxin-induced nephrotoxicity in human renal constructs	Lacks vascular perfusion and filtration function	75
Skin	3D-embedded culture	Models HSV-1 and SDSE infections, supports stratified epithelium and cytokine response	Lacks vasculature, immune cells, aging skin phenotype	76,77
Blood vessels	Organ-on-a-chip	Simulates endothelial–viral interactions, used for SARS-CoV-2 inhibition testing	Technically demanding, limited availability	69

Organoids are used as essential models in the research and development to treat new infectious diseases as they can provide fast and reliable information about pathogen biology and be used for drug screening⁹³ (Table 3).

Table 3.

Trends in organoid-based models for infectious diseases caused by virus, bacteria, and protozoa.

Type of infectious		Research content	Ref
Virus	Zika Virus (ZIKV)	Recapitulation of ZIKV-induced microcephaly, including neural progenitor loss and immune activation, using human brain organoids	28–34,36–38,94
	Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV)	Reproduction of HBV/HCV infection in iPSC- or patient-derived liver organoids for viral replication and immune responses	35,45,95
	Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)	Assessment of organ-specific infectivity, pathology, and drug responses using SARS-CoV-2-infected lung, intestinal, liver, and brain organoids	39,51,52,68–70,74,85
	Norovirus and Rotavirus	Modeling of viral replication and epithelial lesions using norovirus- or rotavirus-infected intestinal organoids	57,60,82,83
	Influenza Virus	Analysis of infection mechanisms and antiviral responses using influenza- or parainfluenza-infected airway and alveolar organoids	65,66,96,97
	Respiratory Syncytial Virus (RSV)	Modeling of mucus secretion abnormalities and epithelial inflammation using RSV-infected lung and airway organoids	64,67,95
	Herpes Simplex Virus (HSV) and Human Cytomegalovirus (HCV)	Recapitulation of neurodevelopmental impairment and signaling alterations using brain and neural organoids infected with HSV-1 and HCMV	40–42
	Human Immunodeficiency Virus (HIV)	Modeling of HIV-1-induced neuroinflammation and neuropathology using brain organoids containing HIV-infected microglia	43
Bacteria	Salmonella enterica	Modeling of bacterial invasion, proliferation, and epithelial responses using Salmonella-infected intestinal organoids	58
	Clostridium difficile (C. difficile)	Observation of NHE3 inhibition and mucus reduction in intestinal organoids infected with C. difficile	53
	Escherichia coli (E. coli)	Recapitulation of epithelial barrier disruption and cytotoxic responses using colon organoids infected with Shiga toxin-producing E. coli (STEC)	54,55,75
	Vibrio cholerae	Demonstration of blood group-dependent epithelial damage using intestinal organoids exposed to cholera toxin	62
	Mycobacterium tuberculosis (M. tuberculosis)	Modeling of granuloma-like structures and immune cell responses using lung tissue organoids infected with M. tuberculosis	71
	Staphylococcus aureus (S. aureus)	Recapitulation of toxin-mediated epithelial injury and inflammation using S. aureus-infected lung organoids	73
Protozoa	Plasmodium falciparum (P. falciparum)	Modeling of P. falciparum liver-stage infection and intrahepatic parasite development using iPSC-derived liver organoids	46
	Entamoeba histolytica (E. histolytica)	Modeling of hepatic invasion by E. histolytica using 3D human liver organoids, galectin-mediated adhesion and inflammatory responses	48

There are three main types of organoid models for infectious diseases, which are specifically designed to model infectious diseases caused by viruses, bacteria, and protozoa⁹⁸.

Discussion

Organoids mimic various organs and structures within the human body in vitro. They are very useful in the fields of new drug development. However, there are still technical and ethical limitations to the use of organoids. Their properties may vary depending on the manufacturing process and the diversity of the extracellular matrix used. These ingredients can affect gene expression and cell signaling pathways, leading to reproducibility problems. Organoids are artificially controlled differently from the in vivo environment, so they can be influenced by the artificial environment. For this reason, ensuring the reproducibility of organoid culture within and between laboratories is essential for the commercialization of organoid models. Organoids can be useful in a variety of fields, from clinical trials to personalized medicine, but there are also ethical considerations. Because ESCs are recognized as the beginning of human life, their use causes much ethical controversy. Because of this, much research for this purpose is being conducted on iPSCs⁹⁹. Organoids produced using somatic cell nuclear transfer are also proposed as an ESCs alternative because embryos created through in vitro fertilization can be viewed as donated organs.

Many recent studies have shown that organoids provide fast and reliable results in pathogen biology research and drug screening. In particular, they have been used as an important tool in SARS-CoV-2 research. They have also been used to identify the target tissues and entry mechanisms of pathogens and to validate therapeutic agents. However, improvements are still needed to more efficiently use and disseminate organoid technology in infectious disease research. Organoids have primarily been used as models to study viruses and test antiviral drugs. It has become possible to produce 3D cell culture models using bioprinting, making bacterial infection modeling feasible⁹². Companies developing treatments for infectious diseases will be able to provide new organoid models that can sort cell samples using techniques like fluorescence-activated cell Sorting (FACS) and combine them according to programmed functions, which can then be used to inoculate pathogens for research purposes. In conclusion, organoids will serve as an important tool in pathogen biology research and drug screening. Future research is expected to develop model systems containing more complex tissue structures to study diverse pathogens. These systems are expected to be good tools for new drug development and precision medicine research.

Author contributions

J.-O.R., Y.-J.S., E.L., S.-Y.L. and D.W.L. designed the research study. J.-O.R., Y.-J.S., S.-Y.L. and D.W.L. performed the research. S.-Y.L. and D.W.L. provided help and advice on research, data interpretation and discussion. J.-O.R., Y.-J.S., S.-Y.L. and D.W.L. analyzed the data. J.-O.R., Y.-J.S., E.L., S.-Y.L. and D.W.L. wrote the manuscript. All authors reviewed and approved the final manuscript.

Funding

Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education,RS-2024-00453887, the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT), RS-2023-00212410, This work was supported by Chungnam National University., ministry of food and drug safety, RS-2024-00332142, the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT), RS-2023-00222910.

Data availability

The datasets used and/or analysed during the current study available from the corresponding author on reasonable request. All data supporting the findings are available from the cited references.

Declarations

Competing interests

The authors declare no competing interests.

Supplementary Information

The online version contains supplementary material available at 10.1038/s41598-025-07816-7.