A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction

• Published in: PloS one Vol. 19; no. 7; p. e0300666
• Main Authors: Fofanova, Tatiana Y, Karandikar, Umesh C, Auchtung, Jennifer M, Wilson, Reid L, Valentin, Antonio J, Britton, Robert A, Grande-Allen, K Jane, Estes, Mary K, Hoffman, Kristi, Ramani, Sashirekha, Stewart, Christopher J, Petrosino, Joseph F
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.07.2024; Public Library of Science (PLoS)
• Subjects: Anaerobes; Anaerobic bacteria; Anaerobic conditions; Anaerobic microorganisms; Bacteria; Bacteria, Anaerobic - growth & development; Bacteria, Anaerobic - metabolism; Bacteroides thetaiotaomicron - metabolism; Biology and Life Sciences; Cell culture; Coculture Techniques - methods; Digestive system; Digestive tract; Epithelial cells; Epithelium; Gastrointestinal Microbiome; Gastrointestinal tract; Gene expression; Genes; Host Microbial Interactions; Humans; Hypoxia; Immunomodulation; In vivo methods and tests; Intestinal Mucosa - cytology; Intestinal Mucosa - metabolism; Intestinal Mucosa - microbiology; Intestine; Intestines - cytology; Intestines - microbiology; Medicine and Health Sciences; Microbiomes; Microbiota (Symbiotic organisms); Microorganisms; Morphology; Organoids; Organoids - metabolism; Organoids - microbiology; Oxygen; Oxygen - metabolism; Oxygen content; Oxygen requirement; Physical Sciences; Physiological aspects; Physiology; Research and Analysis Methods; Transcriptomics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0300666

Mechanistic investigation of host-microbe interactions in the human gut are hindered by difficulty of co-culturing microbes with intestinal epithelial cells. On one hand the gut bacteria are a mix of facultative, aerotolerant or obligate anaerobes, while the intestinal epithelium requires oxygen for growth and function. Thus, a coculture system that can recreate these contrasting oxygen requirements is critical step towards our understanding microbial-host interactions in the human gut. Here, we demonstrate Intestinal Organoid Physoxic Coculture (IOPC) system, a simple and cost-effective method for coculturing anaerobic intestinal bacteria with human intestinal organoids (HIOs). Using commensal anaerobes with varying degrees of oxygen tolerance, such as nano-aerobe Bacteroides thetaiotaomicron and strict anaerobe Blautia sp., we demonstrate that IOPC can successfully support 24-48 hours HIO-microbe coculture. The IOPC recapitulates the contrasting oxygen conditions across the intestinal epithelium seen in vivo. The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease.