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Chang H, Liu Y, Wang Y, Li L, Mu Y, Zheng M, Liu J, Zhang J, Bai R, Li Y, Zuo X. Unveiling the Links Between Microbial Alteration and Host Gene Disarray in Crohn's Disease via TAHMC. Adv Biol (Weinh) 2024:e2400064. [PMID: 38837746 DOI: 10.1002/adbi.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/03/2024] [Indexed: 06/07/2024]
Abstract
A compelling correlation method linking microbial communities and host gene expression in tissues is currently absent. A novel pipeline is proposed, dubbed Transcriptome Analysis of Host-Microbiome Crosstalk (TAHMC), designed to concurrently restore both host gene expression and microbial quantification from bulk RNA-seq data. Employing this approach, it discerned associations between the tissue microbiome and host immunity in the context of Crohn's disease (CD). Further, machine learning is utilized to separately construct networks of associations among host mRNA, long non-coding RNA, and tissue microbes. Unique host genes and tissue microbes are extracted from these networks for potential utility in CD diagnosis. Experimental validation of the predicted host gene regulation by microbes from the association network is achieved through the co-culturing of Faecalibacterium prausnitzii with Caco-2 cells. Collectively, the TAHMC pipeline accurately recovers both host gene expression and microbial quantification from CD RNA-seq data, thereby illuminating potential causal links between shifts in microbial composition as well as diversity within CD mucosal tissues and aberrant host gene expression.
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Affiliation(s)
- Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yongshuai Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yijun Mu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Junfei Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jinghui Zhang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Runze Bai
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
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2
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Bermingham EN, Patterson KA, Shoveller AK, Fraser K, Butowski CF, Thomas DG. Nutritional needs and health outcomes of ageing cats and dogs: is it time for updated nutrient guidelines? Anim Front 2024; 14:5-16. [PMID: 38910950 PMCID: PMC11188961 DOI: 10.1093/af/vfae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024] Open
Affiliation(s)
| | - Keely A Patterson
- AgResearch, Palmerston North, New Zealand
- Massey University, Palmerston North, New Zealand
| | | | - Karl Fraser
- AgResearch, Palmerston North, New Zealand
- Riddet Institute, Palmerston North, New Zealand
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3
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Zhang Y, Anderson RC, You C, Purba A, Yan M, Maclean P, Liu Z, Ulluwishewa D. Lactiplantibacillus plantarum ST-III and Lacticaseibacillus rhamnosus KF7 Enhance the Intestinal Epithelial Barrier in a Dual-Environment In Vitro Co-Culture Model. Microorganisms 2024; 12:873. [PMID: 38792703 PMCID: PMC11124027 DOI: 10.3390/microorganisms12050873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Intestinal barrier hyperpermeability, which is characterised by impaired tight junction proteins, is associated with a variety of gastrointestinal and systemic diseases. Therefore, maintaining intestinal barrier integrity is considered one of the effective strategies to reduce the risk of such disorders. This study aims to investigate the potential benefits of two probiotic strains (Lactiplantibacillus plantarum ST-III and Lacticaseibacillus rhamnosus KF7) on intestinal barrier function by using a physiologically relevant in vitro model of the intestinal epithelium. Our results demonstrate that both strains increased transepithelial electrical resistance, a measure of intestinal barrier integrity. Immunolocalisation studies indicated that this improvement in barrier function was not due to changes in the co-localisation of the tight junction (TJ) proteins ZO-1 and occludin. However, we observed several modifications in TJ-related genes in response to the probiotics, including the upregulation of transmembrane and cytosolic TJ proteins, as well as TJ signalling proteins. Gene expression modulation was strain- and time-dependent, with a greater number of differentially expressed genes and higher fold-change being observed in the L. plantarum ST-III group and at the latter timepoint. Further studies to investigate how the observed gene expression changes can lead to enhanced barrier function will aid in the development of probiotic foods to help improve intestinal barrier function.
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Affiliation(s)
- Yilin Zhang
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China; (Y.Z.); (C.Y.); (M.Y.)
| | - Rachel C. Anderson
- AgResearch, Te Ohu Rangahau Kai, Palmerston North 4410, New Zealand; (R.C.A.); (A.P.)
| | - Chunping You
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China; (Y.Z.); (C.Y.); (M.Y.)
| | - Ajitpal Purba
- AgResearch, Te Ohu Rangahau Kai, Palmerston North 4410, New Zealand; (R.C.A.); (A.P.)
| | - Minghui Yan
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China; (Y.Z.); (C.Y.); (M.Y.)
| | - Paul Maclean
- AgResearch, Grasslands Research Centre, Palmerston North 4410, New Zealand;
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China; (Y.Z.); (C.Y.); (M.Y.)
| | - Dulantha Ulluwishewa
- AgResearch, Te Ohu Rangahau Kai, Palmerston North 4410, New Zealand; (R.C.A.); (A.P.)
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4
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Barnett AM, Mullaney JA, McNabb WC, Roy NC. Culture media and format alter cellular composition and barrier integrity of porcine colonoid-derived monolayers. Tissue Barriers 2024; 12:2222632. [PMID: 37340938 DOI: 10.1080/21688370.2023.2222632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/04/2023] [Indexed: 06/22/2023] Open
Abstract
Intestinal organoid technology has revolutionized our approach to in vitro cell culture due in part to their three-dimensional structures being more like the native tissue from which they were derived with respect to cellular composition and architecture. For this reason, organoids are becoming the new gold standard for undertaking intestinal epithelial cell research. Unfortunately, their otherwise advantageous three-dimensional geometry prevents easy access to the apical epithelium, which is a major limitation when studying interactions between dietary or microbial components and host tissues. To overcome this problem, we developed porcine colonoid-derived monolayers cultured on both permeable Transwell inserts and tissue culture treated polystyrene plates. We found that seeding density and culture format altered the expression of genes encoding markers of specific cell types (stem cells, colonocytes, goblets, and enteroendocrine cells), and barrier maturation (tight junctions). Additionally, we found that changes to the formulation of the culture medium altered the cellular composition of colonoids and of monolayers derived from them, resulting in cultures with an increasingly differentiated phenotype that was similar to that of their tissue of origin.
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Affiliation(s)
- Alicia M Barnett
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jane A Mullaney
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Liggins Institute, The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Liggins Institute, The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Liggins Institute, The High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Nutrition, The University of Otago, Dunedin, New Zealand
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5
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Liu T, Gu J, Fu C, Su L. Three-Dimensional Scaffolds for Intestinal Cell Culture: Fabrication, Utilization, and Prospects. TISSUE ENGINEERING. PART B, REVIEWS 2024; 30:158-175. [PMID: 37646409 DOI: 10.1089/ten.teb.2023.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The intestine is a visceral organ that integrates absorption, metabolism, and immunity, which is vulnerable to external stimulus. Researchers in the fields such as food science, immunology, and pharmacology have committed to developing appropriate in vitro intestinal cell models to study the intestinal absorption and metabolism mechanisms of various nutrients and drugs, or pathogenesis of intestinal diseases. In the past three decades, the intestinal cell models have undergone a significant transformation from conventional two-dimensional cultures to three-dimensional (3D) systems, and the achievements of 3D cell culture have been greatly contributed by the fabrication of different scaffolds. In this review, we first introduce the developing trend of existing intestinal models. Then, four types of scaffolds, including Transwell, hydrogel, tubular scaffolds, and intestine-on-a-chip, are discussed for their 3D structure, composition, advantages, and limitations in the establishment of intestinal cell models. Excitingly, some of the in vitro intestinal cell models based on these scaffolds could successfully mimic the 3D structure, microenvironment, mechanical peristalsis, fluid system, signaling gradients, or other important aspects of the original human intestine. Furthermore, we discuss the potential applications of the intestinal cell models in drug screening, disease modeling, and even regenerative repair of intestinal tissues. This review presents an overview of state-of-the-art scaffold-based cell models within the context of intestines, and highlights their major advances and applications contributing to a better knowledge of intestinal diseases. Impact statement The intestine tract is crucial in the absorption and metabolism of nutrients and drugs, as well as immune responses against external pathogens or antigens in a complex microenvironment. The appropriate experimental cell model in vitro is needed for in-depth studies of intestines, due to the limitation of animal models in dynamic control and real-time assessment of key intestinal physiological and pathological processes, as well as the "R" principles in laboratory animal experiments. Three-dimensional (3D) scaffold-based cell cultivation has become a developing tendency because of the superior cell proliferation and differentiation and more physiologically relevant environment supported by the customized 3D scaffolds. In this review, we summarize four types of up-to-date 3D cell culture scaffolds fabricated by various materials and techniques for a better recapitulation of some essential physiological and functional characteristics of original intestines compared to conventional cell models. These emerging 3D intestinal models have shown promising results in not only evaluating the pharmacokinetic characteristics, security, and effectiveness of drugs, but also studying the pathological mechanisms of intestinal diseases at cellular and molecular levels. Importantly, the weakness of the representative 3D models for intestines is also discussed.
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Affiliation(s)
- Tiange Liu
- Department of Food Science and Technology, National University of Singapore (Suzhou) Research Institute, Suzhou, China
| | - Jia Gu
- Department of Food Science and Technology, National University of Singapore (Suzhou) Research Institute, Suzhou, China
| | - Caili Fu
- Department of Food Science and Technology, National University of Singapore (Suzhou) Research Institute, Suzhou, China
| | - Lingshan Su
- Department of Food Science and Technology, National University of Singapore (Suzhou) Research Institute, Suzhou, China
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
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6
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Cameron O, Neves JF, Gentleman E. Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302165. [PMID: 38009508 PMCID: PMC10837392 DOI: 10.1002/advs.202302165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/12/2023] [Indexed: 11/29/2023]
Abstract
The intestine performs functions central to human health by breaking down food and absorbing nutrients while maintaining a selective barrier against the intestinal microbiome. Key to this barrier function are the combined efforts of lumen-lining specialized intestinal epithelial cells, and the supportive underlying immune cell-rich stromal tissue. The discovery that the intestinal epithelium can be reproduced in vitro as intestinal organoids introduced a new way to understand intestinal development, homeostasis, and disease. However, organoids reflect the intestinal epithelium in isolation whereas the underlying tissue also contains myriad cell types and impressive chemical and structural complexity. This review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. It also covers the cellular, biochemical and biophysical features of the intestinal microenvironment and how these can be replicated in vitro by combining strategies from organoid biology with materials science. Particularly accessible chemistries that mimic the native extracellular matrix are discussed, and bioengineering approaches that aim to overcome limitations in modelling the intestine are critically evaluated. Finally, the review considers how further advances may extend the applications of intestinal models and their suitability for clinical therapies.
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Affiliation(s)
- Oliver Cameron
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Joana F. Neves
- Centre for Host‐Microbiome InteractionsKing's College LondonLondonSE1 9RTUK
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
- Department of Biomedical SciencesUniversity of LausanneLausanne1005Switzerland
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7
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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8
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Kim R, Sung JH. Recent Advances in Gut- and Gut-Organ-Axis-on-a-Chip Models. Adv Healthc Mater 2024:e2302777. [PMID: 38243887 DOI: 10.1002/adhm.202302777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/21/2023] [Indexed: 01/22/2024]
Abstract
The human gut extracts nutrients from the diet while forming the largest barrier against the outer environment. In addition, the gut actively maintains homeostasis through intricate interactions with the gut microbes, the immune system, the enteric nervous system, and other organs. These interactions influence digestive health and, furthermore, play crucial roles in systemic health and disease. Given its primary role in absorbing and metabolizing orally administered drugs, there is significant interest in the development of preclinical in vitro model systems that can accurately emulate the intestine in vivo. A gut-on-a-chip system holds great potential as a testing and screening platform because of its ability to emulate the physiological aspects of in vivo tissues and expandability to incorporate and combine with other organs. This review aims to identify the key physiological features of the human gut that need to be incorporated to build more accurate preclinical models and highlights the recent progress in gut-on-a-chip systems and competing technologies toward building more physiologically relevant preclinical model systems. Furthermore, various efforts to construct multi-organ systems with the gut, called gut-organ-axis-on-a-chip models, are discussed. In vitro gut models with physiological relevance can provide valuable platforms for bridging the gap between preclinical and clinical studies.
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Affiliation(s)
- Raehyun Kim
- Department of Biological and Chemical Engineering, Hongik University, Sejong, 30016, Republic of Korea
| | - Jong Hwan Sung
- Department of Chemical Engineering, Hongik University, Seoul, 04066, Republic of Korea
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Bouges E, Segers C, Leys N, Lebeer S, Zhang J, Mastroleo F. Human Intestinal Organoids and Microphysiological Systems for Modeling Radiotoxicity and Assessing Radioprotective Agents. Cancers (Basel) 2023; 15:5859. [PMID: 38136404 PMCID: PMC10741417 DOI: 10.3390/cancers15245859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Radiotherapy is a commonly employed treatment for colorectal cancer, yet its radiotoxicity-related impact on healthy tissues raises significant health concerns. This highlights the need to use radioprotective agents to mitigate these side effects. This review presents the current landscape of human translational radiobiology, outlining the limitations of existing models and proposing engineering solutions. We delve into radiotherapy principles, encompassing mechanisms of radiation-induced cell death and its influence on normal and cancerous colorectal cells. Furthermore, we explore the engineering aspects of microphysiological systems to represent radiotherapy-induced gastrointestinal toxicity and how to include the gut microbiota to study its role in treatment failure and success. This review ultimately highlights the main challenges and future pathways in translational research for pelvic radiotherapy-induced toxicity. This is achieved by developing a humanized in vitro model that mimics radiotherapy treatment conditions. An in vitro model should provide in-depth analyses of host-gut microbiota interactions and a deeper understanding of the underlying biological mechanisms of radioprotective food supplements. Additionally, it would be of great value if these models could produce high-throughput data using patient-derived samples to address the lack of human representability to complete clinical trials and improve patients' quality of life.
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Affiliation(s)
- Eloïse Bouges
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium;
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Charlotte Segers
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
| | - Natalie Leys
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium;
| | - Jianbo Zhang
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, 1105 BK Amsterdam, The Netherlands
| | - Felice Mastroleo
- RadioPharma Research, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium; (E.B.); (C.S.); (N.L.)
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10
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Arcidiacono S, Spangler JR, Litteral V, Doherty LA, Stamps B, Walper S, Goodson M, Soares JW. In Vitro Fermentation Evaluation of Engineered Sense and Respond Probiotics in Polymicrobial Communities. ACS Biomater Sci Eng 2023; 9:5176-5185. [PMID: 37642529 DOI: 10.1021/acsbiomaterials.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Synthetic biology provides a means of engineering tailored functions into probiotic bacteria. Of particular interest is introducing microbial sense and response functions; however, techniques for testing in physiologically relevant environments, such as those for the intended use, are still lacking. Typically, engineered probiotics are developed and tested in monoculture or in simplified cocultures still within ideal environments. In vitro fermentation models using simplified microbial communities now allow us to simulate engineered organism behavior, specifically organism persistence and intended functionality, within more physiologically relevant, tailored microbial communities. Here, probiotic bacteria Escherichia coli Nissle and Lactobacillus plantarum engineered with sense and response functionalities were evaluated for the ability to persist and function without adverse impact on commensal bacteria within simplified polymicrobial communities with increasing metabolic competition that simulate gut microbe community dynamics. Probiotic abundance and plasmid stability, measured by viability qPCR, decreased for engineered E. coli Nissle relative to monocultures as metabolic competition increased; functional output was not affected. For engineered L. plantarum, abundance and plasmid stability were not adversely impacted; however, functional output was decreased universally as metabolic competition was introduced. For both organisms, adverse effects on select commensals were not evident. Testing engineered probiotics in more physiologically relevant in vitro test beds can provide critical knowledge for circuit design feedback and functional validation prior to the transition to more costly and time-consuming higher-fidelity testing in animal or human studies.
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Affiliation(s)
- Steven Arcidiacono
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Joseph R Spangler
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Vaughn Litteral
- UES Inc, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Laurel A Doherty
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Blake Stamps
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Scott Walper
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Michael Goodson
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Jason W Soares
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
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11
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Qi Y, Yu L, Tian F, Zhao J, Zhai Q. In vitro models to study human gut-microbiota interactions: Applications, advances, and limitations. Microbiol Res 2023; 270:127336. [PMID: 36871313 DOI: 10.1016/j.micres.2023.127336] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
In vitro models of the human gut help compensate for the limitations of animal models in studying the human gut-microbiota interaction and are indispensable in the clarification the mechanism of microbial action or in the high-throughput screening and functional evaluation of probiotics. The development of these models constitutes a rapidly developing field of research. From 2D1 to 3D2 and from simple to complex, several in vitro cell and tissue models have been developed and continuously improved. In this review, we categorized and summarized these models and described their development, applications, advances, and limitations by using specific examples. We also highlighted the best ways to select an appropriate in vitro model, and we also discussed which variables to consider when imitating microbial and human gut epithelial interactions.
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Affiliation(s)
- Yuli Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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12
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Gianetto-Hill CM, Vancuren SJ, Daisley B, Renwick S, Wilde J, Schroeter K, Daigneault MC, Allen-Vercoe E. The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function. Curr Protoc 2023; 3:e737. [PMID: 37093893 DOI: 10.1002/cpz1.737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The human colon is inhabited by a complex community of microbes. These microbes are integral to host health and physiology. Understanding how and when the microbiome causally influences host health will require microbiome models that can be tightly controlled and manipulated. While in vivo models are unrivalled in their ability to study host-microbial interplay, in vitro models are gaining in popularity as methods to study the ecology and function of the gut microbiota, and benefit from tight controllability and reproducibility, as well as reduced ethical constraints. In this set of protocols, we describe the Robogut, a single-stage bioreactor system designed to replicate the conditions of the distal human colon, to culture whole microbial communities derived from stool and/or colonic biopsy samples, with consideration of methods to create culture medium formulations and to build, run, and sample the bioreactor apparatus. Cleaning and maintenance of the bioreactor system are also described. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth medium preparation Support Protocol 1: Preparing medium supplements Basic Protocol 2: Preparing the bioreactor vessels Support Protocol 2: Making acid and base bottles Support Protocol 3: Preparing the effluent bottles Support Protocol 4: Making acid solution Support Protocol 5: Making base solution Basic Protocol 3: Preparing inoculum and inoculating bioreactors Alternate Protocol 1: Preparing inoculum less than 0.5% (w/v) of vessel volume Alternate Protocol 2: Preparing synthetic community aliquots and inoculation via the septum Alternate Protocol 3: Preparing inoculum from a tissue sample Basic Protocol 4: Sampling the bioreactor vessel Basic Protocol 5: Harvesting bioreactor vessel contents at end of experiment Support Protocol 6: Cleaning and sterilizing sampling needles Basic Protocol 6: Cleaning the bioreactor vessel Support Protocol 7: Cleaning bioreactor support bottles.
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Affiliation(s)
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Brendan Daisley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Michelle C Daigneault
- NuBiyota, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
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13
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Chapman JA, Stewart CJ. Methodological challenges in neonatal microbiome research. Gut Microbes 2023; 15:2183687. [PMID: 36843005 PMCID: PMC9980642 DOI: 10.1080/19490976.2023.2183687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/16/2023] [Indexed: 02/28/2023] Open
Abstract
Following microbial colonization at birth, the gut microbiome plays a vital role in the healthy development of human neonates and impacts both health and disease in later life. Understanding the development of the neonatal gut microbiome and how it interacts with the neonatal host are therefore important areas of study. However, research within this field must address a range of specific challenges that impact the design and implementation of research methods. If not considered ahead of time, these challenges have the potential to introduce biases into studies, negatively affecting the relevance, reproducibility, and impact of any findings. This review outlines the nature of these challenges and points to current and future solutions, as outlined in the literature, to assist researchers in the early stages of study design.
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Affiliation(s)
- Jonathan A Chapman
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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Elzinga J, Grouls M, Hooiveld GJEJ, van der Zande M, Smidt H, Bouwmeester H. Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions. Arch Toxicol 2023; 97:737-753. [PMID: 36680592 PMCID: PMC9862247 DOI: 10.1007/s00204-022-03430-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 01/22/2023]
Abstract
There is a need for standardized in vitro models emulating the functionalities of the human intestinal tract to study human intestinal health without the use of laboratory animals. The Caco-2 cell line is a well-accepted and highly characterized intestinal barrier model, which has been intensively used to study intestinal (drug) transport, host-microbe interactions and chemical or drug toxicity. This cell line has been cultured in different in vitro models, ranging from simple static to complex dynamic microfluidic models. We aimed to investigate the effect of these different in vitro experimental variables on gene expression. To this end, we systematically collected and extracted data from studies in which transcriptome analyses were performed on Caco-2 cells grown on permeable membranes. A collection of 13 studies comprising 100 samples revealed a weak association of experimental variables with overall as well as individual gene expression. This can be explained by the large heterogeneity in cell culture practice, or the lack of adequate reporting thereof, as suggested by our systematic analysis of experimental parameters not included in the main analysis. Given the rapidly increasing use of in vitro cell culture models, including more advanced (micro) fluidic models, our analysis reinforces the need for improved, standardized reporting protocols. Additionally, our systematic analysis serves as a template for future comparative studies on in vitro transcriptome and other experimental data.
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Affiliation(s)
- Janneke Elzinga
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Menno Grouls
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Meike van der Zande
- Wageningen Food Safety Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University and Research, Wageningen, The Netherlands
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15
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Biagini F, Daddi C, Calvigioni M, De Maria C, Zhang YS, Ghelardi E, Vozzi G. Designs and methodologies to recreate in vitro human gut microbiota models. Biodes Manuf 2022. [DOI: 10.1007/s42242-022-00210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractThe human gut microbiota is widely considered to be a metabolic organ hidden within our bodies, playing a crucial role in the host’s physiology. Several factors affect its composition, so a wide variety of microbes residing in the gut are present in the world population. Individual excessive imbalances in microbial composition are often associated with human disorders and pathologies, and new investigative strategies to gain insight into these pathologies and define pharmaceutical therapies for their treatment are needed. In vitro models of the human gut microbiota are commonly used to study microbial fermentation patterns, community composition, and host-microbe interactions. Bioreactors and microfluidic devices have been designed to culture microorganisms from the human gut microbiota in a dynamic environment in the presence or absence of eukaryotic cells to interact with. In this review, we will describe the overall elements required to create a functioning, reproducible, and accurate in vitro culture of the human gut microbiota. In addition, we will analyze some of the devices currently used to study fermentation processes and relationships between the human gut microbiota and host eukaryotic cells.
Graphic abstract
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16
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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17
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Young W, Maclean P, Dunstan K, Ryan L, Peters J, Armstrong K, Anderson R, Dewhurst H, van Gendt M, Dilger RN, Dekker J, Haggarty N, Roy N. Lacticaseibacillus rhamnosus HN001 alters the microbiota composition in the cecum but not the feces in a piglet model. Front Nutr 2022; 9:1002369. [PMID: 36386940 PMCID: PMC9650270 DOI: 10.3389/fnut.2022.1002369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/28/2022] [Indexed: 12/03/2022] Open
Abstract
The probiotic Lacticaseibacillus rhamnosus strain HN001 has been shown to have several beneficial health effects for both pediatric and maternal groups, including reduced risk of eczema in infants and gestational diabetes and postnatal depression in mothers. While L. rhamnosus HN001 appears to modify immune and gut barrier biomarkers, its mode of action remains to be fully elucidated. To gain insights into the role of HN001 on the infant microbiome, the impacts of L. rhamnosus HN001 supplementation was studied in 10-day old male piglets that were fed either infant formula, or infant formula with L. rhamnosus HN001 at a low (1.3 × 105 CFU/ml) or high dose (7.9 × 106 CFU/ml) daily for 24 days. The cecal and fecal microbial communities were assessed by shotgun metagenome sequencing and host gene expression in the cecum and colon tissue was assessed by RNA-seq. Piglet fecal samples showed only modest differences between controls and those receiving dietary L. rhamnosus HN001. However, striking differences between the three groups were observed for cecal samples. While total lactobacilli were significantly increased only in the high dose L. rhamnosus HN001 group, both high and low dose groups showed an up to twofold reduction across the Firmicutes phylum and up to fourfold increase in Prevotella compared to controls. Methanobrevibacter was also decreased in HN001 fed piglets. Microbial genes involved in carbohydrate and vitamin metabolism were among those that differed in relative abundance between those with and without L. rhamnosus HN001. Changes in the cecal microbiome were accompanied by increased expression of tight junction pathway genes and decreased autophagy pathway genes in the cecal tissue of piglets fed the higher dose of L. rhamnosus HN001. Our findings showed supplementation with L. rhamnosus HN001 caused substantial changes in the cecal microbiome with likely consequences for key microbial metabolic pathways. Host gene expression changes in the cecum support previous research showing L. rhamnosus HN001 beneficially impacts intestinal barrier function. We show that fecal samples may not adequately reflect microbiome composition higher in the gastrointestinal tract, with the implication that effects of probiotic consumption may be missed by examining only the fecal microbiome.
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Affiliation(s)
- Wayne Young
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- *Correspondence: Wayne Young,
| | - Paul Maclean
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Kelly Dunstan
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Leigh Ryan
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Jason Peters
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Kelly Armstrong
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Rachel Anderson
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Hilary Dewhurst
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | | | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - James Dekker
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Neill Haggarty
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Nicole Roy
- AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
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18
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Rudolph SE, Longo BN, Tse MW, Houchin MR, Shokoufandeh MM, Chen Y, Kaplan DL. Crypt-Villus Scaffold Architecture for Bioengineering Functional Human Intestinal Epithelium. ACS Biomater Sci Eng 2022; 8:4942-4955. [PMID: 36191009 PMCID: PMC10379436 DOI: 10.1021/acsbiomaterials.2c00851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crypt-villus architecture in the small intestine is crucial for the structural integrity of the intestinal epithelium and maintenance of gut homeostasis. We utilized three-dimensional (3D) printing and inverse molding techniques to form three-dimensional (3D) spongy scaffold systems that resemble the intestinal crypt-villus microarchitecture. The scaffolds consist of silk fibroin protein with curved lumens with rows of protruding villi with invaginating crypts to generate the architecture. Intestinal cell (Caco-2, HT29-MTX) attachment and growth, as well as long-term culture support were demonstrated with cell polarization and tissue barrier properties compared to two-dimensional (2D) Transwell culture controls. Further, physiologically relevant oxygen gradients were generated in the 3D system. The various advantages of this system may be ascribed to the more physiologically relevant 3D environment, offering a system for the exploration of disease pathogenesis, host-microbiome interactions, and therapeutic discovery.
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Affiliation(s)
- Sara E Rudolph
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Brooke N Longo
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Megan W Tse
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Megan R Houchin
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Mina M Shokoufandeh
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
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19
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The Therapeutic Role of Short-Chain Fatty Acids Mediated Very Low-Calorie Ketogenic Diet-Gut Microbiota Relationships in Paediatric Inflammatory Bowel Diseases. Nutrients 2022; 14:nu14194113. [PMID: 36235765 PMCID: PMC9572225 DOI: 10.3390/nu14194113] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
The very low-calorie ketogenic diet (VLCKD) has been recognized as a promising dietary regimen for the treatment of several diseases. Short-chain fatty acids (SCFAs) produced by anaerobic bacterial fermentation of indigestible dietary fibre in the gut have potential value for their underlying epigenetic role in the treatment of obesity and asthma-related inflammation through mediating the relationships between VLCKD and the infant gut microbiota. However, it is still unclear how VLCKD might influence gut microbiota composition in children, and how SCFAs could play a role in the treatment of inflammatory bowel disease (IBD). To overcome this knowledge gap, this review aims to investigate the role of SCFAs as key epigenetic metabolites that mediate VLCKD-gut microbiota relationships in children, and their therapeutic potential in IBD.
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20
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Nash T, Vervelde L. Advances, challenges and future applications of avian intestinal in vitro models. Avian Pathol 2022; 51:317-329. [PMID: 35638458 DOI: 10.1080/03079457.2022.2084363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
There is a rapidly growing interest in how the avian intestine is affected by dietary components and probiotic microorganisms, as well as its role in the spread of infectious diseases in both the developing and developed world. A paucity of physiologically relevant models has limited research in this essential field of poultry gut health and led to an over-reliance on the use of live birds for experiments. The intestine is characterized by a complex cellular composition with numerous functions, unique dynamic locations and interdependencies making this organ challenging to recreate in vitro. This review illustrates the in vitro tools that aim to recapitulate this intestinal environment; from the simplest cell lines, which mimic select features of the intestine but lack anatomical and physiological complexity, to the more recently developed complex 3D enteroids, which recreate more of the intestine's intricate microanatomy, heterogeneous cell populations and signalling gradients. We highlight the benefits and limitations of in vitro intestinal models and describe their current applications and future prospective utilizations in intestinal biology and pathology research. We also describe the scope to improve on the current systems to include, for example, microbiota and a dynamic mechanical environment, vital components which enable the intestine to develop and maintain homeostasis in vivo. As this review explains, no one model is perfect, but the key to choosing a model or combination of models is to carefully consider the purpose or scientific question.
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Affiliation(s)
- Tessa Nash
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Lonneke Vervelde
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, UK
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21
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Lee SY, Byun HJ, Choi H, Won JI, Han J, Park S, Kim D, Sung JH. Development of a Pumpless Microfluidic System to Study the Interaction between Gut Microbes and Intestinal Epithelial Cells. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-021-0268-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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Lian L, Zhou C, Tang G, Xie M, Wang Z, Luo Z, Japo J, Wang D, Zhou J, Wang M, Li W, Maharjan S, Ruelas M, Guo J, Wu X, Zhang YS. Uniaxial and Coaxial Vertical Embedded Extrusion Bioprinting. Adv Healthc Mater 2022; 11:e2102411. [PMID: 34860472 DOI: 10.1002/adhm.202102411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/22/2021] [Indexed: 12/12/2022]
Abstract
The 3D bioprinting technologies have attracted increasing attention due to their flexibility in producing architecturally relevant tissue constructs. Here, a vertical embedded extrusion bioprinting strategy using uniaxial or coaxial nozzles is presented, which allows formation of vertical structures of homogeneous or heterogeneous properties. By adjusting the bioprinting parameters, the characteristics of the bioprinted vertical patterns can be precisely controlled. Using this strategy, two proof-of-concept applications in tissue biofabrication are demonstrated. Specifically, intestinal villi and hair follicles, two liner-shaped tissues in the human body, are successfully generated with the vertical embedded bioprinting method, reconstructing some of their key structures as well as restoring partial functions in vitro. Caco-2 cells in the bioprinted intestinal villus constructs proliferated and aggregated properly, also showing functional biomarker expressions such as ZO-1 and villin. Moreover, preliminary hair follicle structures featuring keratinized human keratinocytes and spheroid-shaped human dermal papilla cells are formed after vertical bioprinting and culturing. In summary, this vertical embedded extrusion bioprinting technique harnessing a uniaxial or coaxial format will likely bring further improvements in the reconstruction of certain human tissues and organs, especially those with a linear structure, potentially leading to wide utilities in tissue engineering, tissue model engineering, and drug discovery.
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Affiliation(s)
- Liming Lian
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Cuiping Zhou
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
- Department of Emergency Nanfang Hospital Southern Medical University Guangzhou 510515 P. R. China
| | - Guosheng Tang
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
- NMPA & Guangdong Key Laboratory of Molecular Target & Clinical Pharmacology State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences The Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Maobin Xie
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Zixuan Wang
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Zeyu Luo
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Julia Japo
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Di Wang
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Jianhua Zhou
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Mian Wang
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Wanlu Li
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Sushila Maharjan
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Marina Ruelas
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Jie Guo
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
| | - Xunwei Wu
- Cutaneous Biology Research Center Massachusetts General Hospital Harvard Medical School Boston MA 02129 USA
| | - Yu Shrike Zhang
- Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA
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23
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Hentschel V, Seufferlein T, Armacki M. Intestinal organoids in coculture: redefining the boundaries of gut mucosa ex vivo modeling. Am J Physiol Gastrointest Liver Physiol 2021; 321:G693-G704. [PMID: 34643092 DOI: 10.1152/ajpgi.00043.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
All-time preservation of an intact mucosal barrier is crucial to ensuring intestinal homeostasis and, hence, the organism's overall health maintenance. This complex process relies on an equilibrated signaling system between the intestinal epithelium and numerous cell populations inhabiting the gut mucosa. Any perturbations of this delicate cross talk, particularly regarding the immune cell compartment and microbiota, may sustainably debilitate the intestinal barrier function. As a final joint event, a critical rise in epithelial permeability facilitates the exposure of submucosal immunity to microbial antigens, resulting in uncontrolled inflammation, collateral tissue destruction, and dysbiosis. Organoid-derived intestinal coculture models have established themselves as convenient tools to reenact such pathophysiological events, explore interactions between selected cell populations, and assess their roles with a central focus on intestinal barrier recovery and stabilization.
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Affiliation(s)
- Viktoria Hentschel
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Milena Armacki
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
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24
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Glowacki RWP, Engelhart MJ, Ahern PP. Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology. Front Microbiol 2021; 12:735562. [PMID: 34646255 PMCID: PMC8503645 DOI: 10.3389/fmicb.2021.735562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Morgan J. Engelhart
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Philip P. Ahern
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, United States
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25
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Organ-on-Chip Approaches for Intestinal 3D In Vitro Modeling. Cell Mol Gastroenterol Hepatol 2021; 13:351-367. [PMID: 34454168 PMCID: PMC8688162 DOI: 10.1016/j.jcmgh.2021.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022]
Abstract
The intestinal epithelium has one of the highest turnover rates in the human body, which is supported by intestinal stem cells. Culture models of intestinal physiology have been evolving to incorporate different tissue and microenvironmental elements. However, these models also display gaps that limit their similarity with native conditions. Microfluidics technology arose from the application of microfabrication techniques to fluid manipulation. Recently, microfluidic approaches have been coupled with cell culture, creating self-contained and modular in vitro models with easily controllable features named organs-on-chip. Intestine-on-chip models have enabled the recreation of the proliferative and differentiated compartments of the intestinal epithelium, the long-term maintenance of commensals, and the intraluminal perfusion of organoids. In addition, studies based on human primary intestinal cells have shown that these systems have a closer transcriptomic profile and functionality to the intestine in vivo, when compared with other in vitro models. The design flexibility inherent to microfluidic technology allows the simultaneous combination of components such as shear stress, peristalsis-like strain, 3-dimensional structure, oxygen gradient, and co-cultures with other important cell types involved in gut physiology. The versatility and complexity of the intestine-on-chip grants it the potential for applications in disease modeling, host-microbiota studies, stem cell biology, and, ultimately, the translation to the pharmaceutical industry and the clinic as a reliable high-throughput platform for drug testing and personalized medicine, respectively. This review focuses on the physiological importance of several components that have been incorporated into intestine-on-chip models and highlights interesting features developed in other types of in vitro models that might contribute to the refinement of these systems.
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26
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Sardelli L, Perottoni S, Tunesi M, Boeri L, Fusco F, Petrini P, Albani D, Giordano C. Technological tools and strategies for culturing human gut microbiota in engineered in vitro models. Biotechnol Bioeng 2021; 118:2886-2905. [PMID: 33990954 PMCID: PMC8361989 DOI: 10.1002/bit.27816] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/29/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022]
Abstract
The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.
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Affiliation(s)
- Lorenzo Sardelli
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Simone Perottoni
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Marta Tunesi
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Lucia Boeri
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Federica Fusco
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Paola Petrini
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Diego Albani
- Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Carmen Giordano
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
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27
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Zhang J, Hernandez-Gordillo V, Trapecar M, Wright C, Taketani M, Schneider K, Chen WLK, Stas E, Breault DT, Carrier RL, Voigt CA, Griffith LG. Coculture of primary human colon monolayer with human gut bacteria. Nat Protoc 2021; 16:3874-3900. [PMID: 34183870 PMCID: PMC9109719 DOI: 10.1038/s41596-021-00562-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
The presence of microbes in the colon impacts host physiology. Therefore, microbes are being evaluated as potential treatments for colorectal diseases. Humanized model systems that enable robust culture of primary human intestinal cells with bacteria facilitate evaluation of potential treatments. Here, we describe a protocol that can be used to coculture a primary human colon monolayer with aerotolerant bacteria. Primary human colon cells maintained as organoids are dispersed into single-cell suspensions and then seeded on collagen-coated Transwell inserts, where they attach and proliferate to form confluent monolayers within days of seeding. The confluent monolayers are differentiated for an additional 4 d and then cocultured with bacteria. As an example application, we describe how to coculture differentiated colon cells for 8 h with four strains of Bacteroides thetaiotaomicron, each engineered to detect different colonic microenvironments via genetically embedded logic circuits incorporating deoxycholic acid and anhydrotetracycline sensors. Characterization of this coculture system reveals that barrier function remains intact in the presence of engineered B. thetaiotaomicron. The bacteria stay close to the mucus layer and respond in a microenvironment-specific manner to the inducers (deoxycholic acid and anhydrotetracycline) of the genetic circuits. This protocol thus provides a useful mucosal barrier system to assess the effects of bacterial cells that respond to the colonic microenvironment, and may also be useful in other contexts to model human intestinal barrier properties and microbiota-host interactions.
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Affiliation(s)
- Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Martin Trapecar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mao Taketani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kirsten Schneider
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wen Li Kelly Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric Stas
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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28
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Wang C, Dang T, Baste J, Anil Joshi A, Bhushan A. A novel standalone microfluidic device for local control of oxygen tension for intestinal-bacteria interactions. FASEB J 2021; 35:e21291. [PMID: 33506497 DOI: 10.1096/fj.202001600rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
The intestinal environment is unique because it supports the intestinal epithelial cells under a normal oxygen environment and the microbiota under an anoxic environment. Due to importance of understanding the interactions between the epithelium and the microbiota, there is a strong need for developing representative and simple experimental models. Current approaches do not capture the partitioned oxygen environment, require external anaerobic chambers, or are complex. Another major limitation is that with the solutions that can mimic this oxygen environment, the oxygenation level of the epithelial cells is not known, raising the question whether the cells are hypoxic or not. We report standalone microfluidic devices that form a partitioned oxygen environment without the use of an external anaerobic chamber or oxygen scavengers to coculture intestinal epithelial and bacterial cells. By changing the thickness of the device cover, the oxygen tension in the chamber was modulated. We verified the oxygen levels using several tests: microscale oxygen sensitive sensors which were integrated within the devices, immunostaining of Caco-2 cells to determine hypoxia levels, and genetically encoded bacteria to visualize the growth. Collectively, these methods monitored oxygen concentrations in the devices more comprehensively than previous reports and allowed for control of oxygen tension to match the requirements of both intestinal cells and anaerobic bacteria. Our experimental model is supported by the mathematical model that considered diffusion of oxygen into the top chamber. This allowed us to experimentally determine the oxygen consumption rate of the intestinal epithelial cells under perfusion.
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Affiliation(s)
- Chengyao Wang
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Thao Dang
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Jasmine Baste
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Advait Anil Joshi
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
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29
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Wilkowska A, Szałach ŁP, Cubała WJ. Gut Microbiota in Depression: A Focus on Ketamine. Front Behav Neurosci 2021; 15:693362. [PMID: 34248517 PMCID: PMC8261217 DOI: 10.3389/fnbeh.2021.693362] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
According to the WHO, major depressive disorder is the leading cause of disability worldwide, and it is a major contributor to the overall global burden of disease. The pathophysiology of this common and chronic disease is still not completely understood. The gut microbiome is an increasingly recognized environmental factor that can have a role in depression, acting through the gut-microbiota-brain axis. The available treatment for depression is still insufficient since 30% of patients are treatment-resistant. There is an unquestionable need for novel strategies. Ketamine is an effective antidepressant in treatment-resistant patients. It is suggested that the antidepressant effect of ketamine may be partially mediated by the modification of gut microbiota. In this study, we presented a review of data on gut microbiota in depression with special attention to the effect of ketamine on the microbiome in animal models of depression. Earlier reports are preliminary and are still insufficient to draw firm conclusion, but further studies in this field might help to understand the role of the gut-brain axis in the treatment of depression and might be the ground for developing new effective treatment strategies.
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30
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Barnett AM, Mullaney JA, Hendriks C, Le Borgne L, McNabb WC, Roy NC. Porcine colonoids and enteroids keep the memory of their origin during regeneration. Am J Physiol Cell Physiol 2021; 320:C794-C805. [PMID: 33760661 DOI: 10.1152/ajpcell.00420.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development of alternative in vitro culture methods has increased in the last decade as three-dimensional organoids of various tissues, including those of the small and large intestines. Due to their multicellular composition, organoids offer advantages over traditionally used immortalized or primary cell lines. However, organoids must be accurate models of their tissues of origin. This study compared gene expression profiles with respect to markers of specific cell types (stem cells, enterocytes, goblet, and enteroendocrine cells) and barrier maturation (tight junctions) of colonoid and enteroid cultures with their tissues of origin and colonoids with enteroids. Colonoids derived from three healthy pigs formed multilobed structures with a monolayer of cells similar to the crypt structures in colonic tissue. Colonoid and enteroid gene expression signatures were more similar to those found for the tissues of their origin than to each other. However, relative to their derived tissues, organoids had increased gene expression levels of stem cell markers Sox9 and Lgr5 encoding sex-determining region Y-box 9 and leucine-rich repeat-containing G protein-coupled rector 5, respectively. In contrast, expression levels of Occl and Zo1 encoding occludin and zonula occludens 1, respectively, were decreased. Expression levels of the cell lineage markers Atoh1, Cga, and Muc2 encoding atonal homolog 1, chromogranin A, and mucin 2, respectively, were decreased in colonoids, whereas Sglt1 and Apn encoding sodium-glucose transporter 1 and aminopeptidase A, respectively, were decreased in enteroids. These results indicate colonoid and enteroid cultures were predominantly comprised of undifferentiated cell types with decreased barrier maturation relative to their tissues of origin.
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Affiliation(s)
- Alicia M Barnett
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jane A Mullaney
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Charlotte Hendriks
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Lisa Le Borgne
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Department of Nutrition, The University of Otago, Dunedin, New Zealand
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31
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Song WS, Shin SG, Jo SH, Lee JS, Jeon HJ, Kwon JE, Park JH, Cho S, Jeong JH, Kim BG, Kim YG. Development of an in vitro coculture device for the investigation of host-microbe interactions via integrative multiomics approaches. Biotechnol Bioeng 2021; 118:1612-1623. [PMID: 33421096 DOI: 10.1002/bit.27676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 01/05/2023]
Abstract
The commensal gut bacterium Akkermansia muciniphila is well known as a promising probiotic candidate that improves host health and prevents diseases. However, the biological interaction of A. muciniphila with human gut epithelial cells has rarely been explored for use in biotherapeutics. Here, we developed an in vitro device that simulates the gut epithelium to elucidate the biological effects of living A. muciniphila via multiomics analysis: the Mimetic Intestinal Host-Microbe Interaction Coculture System (MIMICS). We demonstrated that both human intestinal epithelial cells (Caco-2) and the anaerobic bacterium A. muciniphila can remain viable for 12 h after coculture in the MIMICS. The transcriptomic and proteomic changes (cell-cell junctions, immune responses, and mucin secretion) in gut epithelial cells treated with A. muciniphila closely correspond with those reported in previous in vivo studies. In addition, our proteomic and metabolomic results revealed that A. muciniphila activates glucose and lipid metabolism in gut epithelial cells, leading to an increase in ATP production. This study suggests that A. muciniphila improves metabolism for ATP production in gut epithelial cells and that the MIMICS may be an effective general tool for evaluating the effects of anaerobic bacteria on gut epithelial cells.
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Affiliation(s)
- Won-Suk Song
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Sung Gyu Shin
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Jae-Seung Lee
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Hyo-Jin Jeon
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Ji-Eun Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Ji-Hyeon Park
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Sungwoo Cho
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Jae Hyun Jeong
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Korea
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32
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Alsharairi NA. The Role of Short-Chain Fatty Acids in the Interplay between a Very Low-Calorie Ketogenic Diet and the Infant Gut Microbiota and Its Therapeutic Implications for Reducing Asthma. Int J Mol Sci 2020; 21:E9580. [PMID: 33339172 PMCID: PMC7765661 DOI: 10.3390/ijms21249580] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota is well known as playing a critical role in inflammation and asthma development. The very low-calorie ketogenic diet (VLCKD) is suggested to affect gut microbiota; however, the effects of VLCKD during pregnancy and lactation on the infant gut microbiota are unclear. The VLCKD appears to be more effective than caloric/energy restriction diets for the treatment of several diseases, such as obesity and diabetes. However, whether adherence to VLCKD affects the infant gut microbiota and the protective effects thereof on asthma remains uncertain. The exact mechanisms underlying this process, and in particular the potential role of short chain fatty acids (SCFAs), are still to be unravelled. Thus, the aim of this review is to identify the potential role of SCFAs that underlie the effects of VLCKD during pregnancy and lactation on the infant gut microbiota, and explore whether it incurs significant implications for reducing asthma.
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Affiliation(s)
- Naser A Alsharairi
- Heart, Mind & Body Research Group, Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
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33
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Biomimetic Gut Model Systems for Development of Targeted Microbial Solutions for Enhancing Warfighter Health and Performance. mSystems 2020; 5:5/5/e00487-20. [PMID: 33109750 PMCID: PMC7593588 DOI: 10.1128/msystems.00487-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human gut microbiome plays a vital role in both health and disease states and as a mediator of cognitive and physical performance. Despite major advances in our understanding of the role of gut microbes in host physiology, mechanisms underlying human-microbiome dynamics have yet to be fully elucidated. The human gut microbiome plays a vital role in both health and disease states and as a mediator of cognitive and physical performance. Despite major advances in our understanding of the role of gut microbes in host physiology, mechanisms underlying human-microbiome dynamics have yet to be fully elucidated. This knowledge gap represents a major hurdle to the development of targeted gut microbiome solutions influencing human health and performance outcomes. The microbiome as it relates to warfighter health and performance is of interest to the Department of Defense (DoD) with the development of interventions impacting gut microbiome resiliency among its top research priorities. While technological advancements are enabling the development of experimental model systems that facilitate mechanistic insights underpinning human health, disease, and performance, translatability to human outcomes is still questionable. This review discusses some of the drivers influencing the DoD’s interest in the warfighter gut microbiome and describes current in vitro gut model systems supporting direct microbial-host interactions.
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34
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Virumbrales-Muñoz M, Ayuso JM, Gong MM, Humayun M, Livingston MK, Lugo-Cintrón KM, McMinn P, Álvarez-García YR, Beebe DJ. Microfluidic lumen-based systems for advancing tubular organ modeling. Chem Soc Rev 2020; 49:6402-6442. [PMID: 32760967 PMCID: PMC7521761 DOI: 10.1039/d0cs00705f] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microfluidic lumen-based systems are microscale models that recapitulate the anatomy and physiology of tubular organs. These technologies can mimic human pathophysiology and predict drug response, having profound implications for drug discovery and development. Herein, we review progress in the development of microfluidic lumen-based models from the 2000s to the present. The core of the review discusses models for mimicking blood vessels, the respiratory tract, the gastrointestinal tract, renal tubules, and liver sinusoids, and their application to modeling organ-specific diseases. We also highlight emerging application areas, such as the lymphatic system, and close the review discussing potential future directions.
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Affiliation(s)
- María Virumbrales-Muñoz
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - José M Ayuso
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA and Morgridge Institute for Research, Madison, WI, USA
| | - Max M Gong
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA and Department of Biomedical Engineering, Trine University, Angola, IN, USA
| | - Mouhita Humayun
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Megan K Livingston
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Karina M Lugo-Cintrón
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Patrick McMinn
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Yasmín R Álvarez-García
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA. and University of Wisconsin Carbone Cancer Center, Madison, WI, USA and Department of Pathology & Laboratory Medicine, University of Wisconsin, Madison, WI, USA
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35
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Zhang J, Huang YJ, Yoon JY, Kemmitt J, Wright C, Schneider K, Sphabmixay P, Hernandez-Gordillo V, Holcomb SJ, Bhushan B, Rohatgi G, Benton K, Carpenter D, Kester JC, Eng G, Breault DT, Yilmaz O, Taketani M, Voigt CA, Carrier RL, Trumper DL, Griffith LG. Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium prausnitzii in continuous culture. MED 2020; 2:74-98.e9. [PMID: 33511375 DOI: 10.1016/j.medj.2020.07.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background The gut microbiome plays an important role in human health and disease. Gnotobiotic animal and in vitro cell-based models provide some informative insights into mechanistic crosstalk. However, there is no existing system for a long-term co-culture of a human colonic mucosal barrier with super oxygen-sensitive commensal microbes, hindering the study of human-microbe interactions in a controlled manner. Methods Here, we investigated the effects of an abundant super oxygen-sensitive commensal anaerobe, Faecalibacterium prausnitzii, on a primary human mucosal barrier using a Gut-MIcrobiome (GuMI) physiome platform that we designed and fabricated. Findings Long-term continuous co-culture of F. prausnitzii for two days with colon epithelia, enabled by continuous flow of completely anoxic apical media and aerobic basal media, resulted in a strictly anaerobic apical environment fostering growth of and butyrate production by F. prausnitzii, while maintaining a stable colon epithelial barrier. We identified elevated differentiation and hypoxia-responsive genes and pathways in the platform compared with conventional aerobic static culture of the colon epithelia, attributable to a combination of anaerobic environment and continuous medium replenishment. Furthermore, we demonstrated anti-inflammatory effects of F. prausnitzii through HDAC and the TLR-NFKB axis. Finally, we identified that butyrate largely contributes to the anti-inflammatory effects by downregulating TLR3 and TLR4. Conclusions Our results are consistent with some clinical observations regarding F. prausnitzii, thus motivating further studies employing this platform with more complex engineered colon tissues for understanding the interaction between the human colonic mucosal barrier and microbiota, pathogens, or engineered bacteria.
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Affiliation(s)
| | | | - Jun Young Yoon
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,School of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | | | | | | | | | | | | | - Brij Bhushan
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gar Rohatgi
- EPAM Continuum, 41 University Drive, Newtown, PA 18940, USA
| | - Kyle Benton
- EPAM Continuum, 41 University Drive, Newtown, PA 18940, USA
| | | | | | | | - David T Breault
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - David L Trumper
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Linda G Griffith
- Department of Biological Engineering.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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36
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Mohebali N, Ekat K, Kreikemeyer B, Breitrück A. Barrier Protection and Recovery Effects of Gut Commensal Bacteria on Differentiated Intestinal Epithelial Cells In Vitro. Nutrients 2020; 12:nu12082251. [PMID: 32731411 PMCID: PMC7468801 DOI: 10.3390/nu12082251] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Alterations in the gut microbiota composition play a crucial role in the pathogenesis of inflammatory bowel disease (IBD) as specific commensal bacterial species are underrepresented in the microbiota of IBD patients. In this study, we examined the therapeutic potential of three commensal bacterial species, Faecalibacterium prausnitzii (F. prausnitzii), Roseburia intestinalis (R. intestinalis) and Bacteroides faecis (B. faecis) in an in vitro model of intestinal inflammation, by using differentiated Caco-2 and HT29-MTX cells, stimulated with a pro-inflammatory cocktail consisting of interleukin-1β (IL-1β), tumor necrosis factor-α (TNFα), interferon-γ (IFNγ), and lipopolysaccharide (LPS). Results obtained in this work demonstrated that all three bacterial species are able to recover the impairment of the epithelial barrier function induced by the inflammatory stimulus, as determined by an amelioration of the transepithelial electrical resistance (TEER) and the paracellular permeability of the cell monolayer. Moreover, inflammatory stimulus increased claudin-2 expression and decreased occludin expression were improved in the cells treated with commensal bacteria. Furthermore, the commensals were able to counteract the increased release of interleukin-8 (IL-8) and monocyte chemoattractant protein-1 (MCP-1) induced by the inflammatory stimulus. These findings indicated that F. prausnitzii, R. intestinalis and B. faecis improve the epithelial barrier integrity and limit inflammatory responses.
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37
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Young W, Arojju SK, McNeill MR, Rettedal E, Gathercole J, Bell N, Payne P. Feeding Bugs to Bugs: Edible Insects Modify the Human Gut Microbiome in an in vitro Fermentation Model. Front Microbiol 2020; 11:1763. [PMID: 32793177 PMCID: PMC7390975 DOI: 10.3389/fmicb.2020.01763] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
We here report a study characterizing the potential for edible insects to act as a prebiotic by altering the bacterial composition of the human fecal microbiome, using batch cultures inoculated with fecal adult human donors. Black field cricket nymphs, grass grub larvae, and wax moth larvae were subjected to an in vitro digestion to simulate the oral, gastric, and small intestinal stages of digestion. The digested material was then dialyzed to remove small molecules such as amino acids and free sugars to simulate removal of nutrients through upper gastrointestinal tract digestion. The retentate, representing the digestion resistant constituents, was then fermented in fecal batch cultures for 4, 7, and 15 h to represent rapid and longer fermentation times. Batch cultures without any added substrates were also set up to act as controls. Additionally, phosphate-buffered saline was used as a no-protein control and milk powder as "standard" protein control. At the end of the incubation period, the bacterial pellets were collected for microbiome analysis by 16S rRNA gene amplicon sequencing. Analysis of fecal cultures showed striking differences in community composition. Each substrate led to significant differences across a wide range of taxa compared to each other and PBS controls. Among the differences observed, digested grass grub larvae increased proportions of Faecalibacterium and the Prevotella 2 group. Black field crickets increased the prevalence of the Escherichia-Shigella group, Dialister genus, and a group of unclassified Lachnospiraceae. Wax moth larvae promoted the expansion of the same group of unclassified Lachnospiraceae and the Escherichia/Shigella group. The increased Faecalibacterium observed in the cultures with grass grub larvae represents a noteworthy finding as this bacterium is widely thought to be beneficial in nature, with demonstrated anti-inflammatory properties and associations with gut health. We conclude that insects can differentially modulate the microbiome composition in batch cultures inoculated with adult fecal material after simulated in vitro digestion. Although the physiological impact in vivo remains to be determined, this study provides sound scientific evidence that investigating the potential for consuming insects for gut health is warranted.
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Affiliation(s)
- Wayne Young
- Food Nutrition & Health Team, AgResearch Grasslands, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition, National Science Challenges, Auckland, New Zealand
| | - Sai Krishna Arojju
- Forage Genetics Team, AgResearch Grasslands, Palmerston North, New Zealand
| | - Mark R. McNeill
- Biocontrol and Biosecurity Team, AgResearch Lincoln, Christchurch, New Zealand
| | - Elizabeth Rettedal
- Food Nutrition & Health Team, AgResearch Grasslands, Palmerston North, New Zealand
| | - Jessica Gathercole
- Proteins and Metabolites Team, AgResearch Lincoln, Christchurch, New Zealand
| | - Nigel Bell
- Soil Biology Team, AgResearch Ruakura, Hamilton, New Zealand
| | - Penny Payne
- People and Agriculture Team, AgResearch Ruakura, Hamilton, New Zealand
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Ceppa FA, Izzo L, Sardelli L, Raimondi I, Tunesi M, Albani D, Giordano C. Human Gut-Microbiota Interaction in Neurodegenerative Disorders and Current Engineered Tools for Its Modeling. Front Cell Infect Microbiol 2020; 10:297. [PMID: 32733812 PMCID: PMC7358350 DOI: 10.3389/fcimb.2020.00297] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
The steady increase in life-expectancy of world population, coupled to many genetic and environmental factors (for instance, pre- and post-natal exposures to environmental neurotoxins), predispose to the onset of neurodegenerative diseases, whose prevalence is expected to increase dramatically in the next years. Recent studies have proposed links between the gut microbiota and neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Human body is a complex structure where bacterial and human cells are almost equal in numbers, and most microbes are metabolically active in the gut, where they potentially influence other target organs, including the brain. The role of gut microbiota in the development and pathophysiology of the human brain is an area of growing interest for the scientific community. Several microbial-derived neurochemicals involved in the gut-microbiota-brain crosstalk seem implicated in the biological and physiological basis of neurodevelopment and neurodegeneration. Evidence supporting these connections has come from model systems, but there are still unsolved issues due to several limitations of available research tools. New technologies are recently born to help understanding the causative role of gut microbes in neurodegeneration. This review aims to make an overview of recent advances in the study of the microbiota-gut-brain axis in the field of neurodegenerative disorders by: (a) identifying specific microbial pathological signaling pathways; (b) characterizing new, advanced engineered tools to study the interactions between human cells and gut bacteria.
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Affiliation(s)
- Florencia Andrea Ceppa
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
| | - Luca Izzo
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
| | - Ilaria Raimondi
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
| | - Marta Tunesi
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Milan, Italy
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Kasper SH, Morell-Perez C, Wyche TP, Sana TR, Lieberman LA, Hett EC. Colorectal cancer-associated anaerobic bacteria proliferate in tumor spheroids and alter the microenvironment. Sci Rep 2020; 10:5321. [PMID: 32210258 PMCID: PMC7093526 DOI: 10.1038/s41598-020-62139-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Recent reports show that colorectal tumors contain microbiota that are distinct from those that reside in a 'normal' colon environment, and that these microbiota can contribute to cancer progression. Fusobacterium nucleatum is the most commonly observed species in the colorectal tumor microenvironment and reportedly influences disease progression through numerous mechanisms. However, a detailed understanding of the role of this organism in cancer progression is limited, in part due to challenges in maintaining F. nucleatum viability under standard aerobic cell culture conditions. Herein we describe the development of a 3-dimensional (3D) tumor spheroid model that can harbor and promote the growth of anaerobic bacteria. Bacteria-tumor cell interactions and metabolic crosstalk were extensively studied by measuring the kinetics of bacterial growth, cell morphology and lysis, cancer-related gene expression, and metabolomics. We observed that viable F. nucleatum assembles biofilm-like structures in the tumor spheroid microenvironment, whereas heat-killed F. nucleatum is internalized and sequestered in the cancer cells. Lastly, we use the model to co-culture 28 Fusobacterium clinical isolates and demonstrate that the model successfully supports co-culture with diverse fusobacterial species. This bacteria-spheroid co-culture model enables mechanistic investigation of the role of anaerobic bacteria in the tumor microenvironment.
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Affiliation(s)
- Stephen H Kasper
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA.
| | | | - Thomas P Wyche
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Theodore R Sana
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Linda A Lieberman
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Erik C Hett
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA.
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Kim R, Attayek PJ, Wang Y, Furtado KL, Tamayo R, Sims CE, Allbritton NL. An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. Biofabrication 2019; 12:015006. [PMID: 31519008 DOI: 10.1088/1758-5090/ab446e] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An oxygen gradient formed along the length of colonic crypts supports stem-cell proliferation at the normoxic crypt base while supporting obligate anaerobe growth in the anoxic colonic lumen. Primary human colonic epithelial cells derived from human gastrointestinal stem cells were cultured within a device possessing materials of tailored oxygen permeability to produce an oxygen-depleted luminal (0.8% ± 0.1% O2) and oxygen-rich basal (11.1% ± 0.5% O2) compartment. This oxygen difference created a stable oxygen gradient across the colonic epithelial cells which remained viable and properly polarized. Facultative and obligate anaerobes Lactobacillus rhamnosus, Bifidobacterium adolescentis, and Clostridium difficile grew readily within the luminal compartment. When formed along the length of an in vitro crypt, the oxygen gradient facilitated cell compartmentalization within the crypt by enhancing confinement of the proliferative cells to the crypt base. This platform provides a simple system to create a physiological oxygen gradient across an intestinal mimic while simultaneously supporting anaerobe co-culture.
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Affiliation(s)
- Raehyun Kim
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, NC, United States of America
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Liu Z, Subbaraj A, Fraser K, Jia H, Chen W, Day L, Roy NC, Young W. Human milk and infant formula differentially alters the microbiota composition and functional gene relative abundance in the small and large intestines in weanling rats. Eur J Nutr 2019; 59:2131-2143. [DOI: 10.1007/s00394-019-02062-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023]
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Mohajeri MH, Brummer RJM, Rastall RA, Weersma RK, Harmsen HJM, Faas M, Eggersdorfer M. The role of the microbiome for human health: from basic science to clinical applications. Eur J Nutr 2019; 57:1-14. [PMID: 29748817 PMCID: PMC5962619 DOI: 10.1007/s00394-018-1703-4] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 2017 annual symposium organized by the University Medical Center Groningen in The Netherlands focused on the role of the gut microbiome in human health and disease. Experts from academia and industry examined interactions of prebiotics, probiotics, or vitamins with the gut microbiome in health and disease, the development of the microbiome in early-life and the role of the microbiome on the gut–brain axis. The gut microbiota changes dramatically during pregnancy and intrinsic factors (such as stress), in addition to extrinsic factors (such as diet, and drugs) influence the composition and activity of the gut microbiome throughout life. Microbial metabolites, e.g. short-chain fatty acids affect gut–brain signaling and the immune response. The gut microbiota has a regulatory role on anxiety, mood, cognition and pain which is exerted via the gut–brain axis. Ingestion of prebiotics or probiotics has been used to treat a range of conditions including constipation, allergic reactions and infections in infancy, and IBS. Fecal microbiota transplantation (FMT) highly effective for treating recurrent Clostridium difficile infections. The gut microbiome affects virtually all aspects of human health, but the degree of scientific evidence, the models and technologies and the understanding of mechanisms of action vary considerably from one benefit area to the other. For a clinical practice to be broadly accepted, the mode of action, the therapeutic window, and potential side effects need to thoroughly be investigated. This calls for further coordinated state-of-the art research to better understand and document the human gut microbiome’s effects on human health.
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Affiliation(s)
- M Hasan Mohajeri
- DSM Nutritional Products Ltd, Kaiseraugst, Switzerland.
- University of Zurich, Irchel, Zurich, Switzerland.
| | | | - Robert A Rastall
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marijke Faas
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
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Lin C, Wan J, Lu Y, Zhang H, Chen X, Su Y, Zhu W. Active bacterial communities of pig fecal microbiota transplantation suspension prepared and preserved under different conditions. AMB Express 2019; 9:63. [PMID: 31076926 PMCID: PMC6510741 DOI: 10.1186/s13568-019-0787-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
Although fecal microbiota transplantation (FMT) has become a research hotspot, studies on comparison of the active fecal bacteria suspension under different preparation conditions are limited. This study investigated the abundances of active bacterial community in pig FMT suspension that produced under different oxygen concentrations or cryopreservation conditions. Fecal samples from a Landrace × Yorkshire sow were used to prepare fecal bacteria suspension under the anaerobic (AN group) and aerobic conditions (AE group), respectively. And then half of the anaerobic fecal bacteria suspension was cryopreservation in - 80 °C (AN-CR group) for 1 week. The microbial RNA in the fecal bacteria suspension was extracted before and after cryopreservation, and reverse transcribed into cDNA. MiSeq sequencing 16S rRNA gene of bacterial cDNA showed that the bacterial diversity in the AN group was significantly higher than that in the AE group. Comparing with the sows' fecal sample, the relative abundances of Lactobacillus johnsonii, Lactobacillus coleohominis and Parabacteroides merdae in AN, AE and AN-CR groups were reduced. The short-term cryopreservation had low impact on the structure of the active bacterial community in the fecal bacterial suspension. These results suggest that fecal bacteria suspension can be better prepared under strict anaerobic condition, and that fecal bacteria suspension can be cryopreserved in - 80 °C for a short time.
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Affiliation(s)
- Chunhui Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiajia Wan
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Lu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106 China
| | - He Zhang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xue Chen
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
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Almeida D, Machado D, Andrade JC, Mendo S, Gomes AM, Freitas AC. Evolving trends in next-generation probiotics: a 5W1H perspective. Crit Rev Food Sci Nutr 2019; 60:1783-1796. [PMID: 31062600 DOI: 10.1080/10408398.2019.1599812] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In recent years, scientific community has been gathering increasingly more insight on the dynamics that are at play in metabolic and inflammatory disorders. These rapidly growing conditions are reaching epidemic proportions, bringing clinicians and researcher's new challenges. The specific roles and modulating properties that beneficial/probiotic bacteria hold in the context of the gut ecosystem seem to be key to avert these inflammatory and diet-related disorders. Faecalibacterium prausnitzii, Akkermansia muciniphila and Eubacterium hallii have been identified as candidates for next generation probiotics (NGPs) with exciting potential for the prevention and treatment of such of dysbiosis-associated diseases. The challenges of these non-conventional native gut bacteria lie mainly on their extreme sensitivity to O2 traces. If these strains are to be used successfully in food, supplements or drugs they need to be stable and active in humans. In the present review, we present an overall perspective of the most updated scientific literature on the newly called NGPs through the 5W1H (What, Why, Who, Where, When, and How) method, an innovative and attractive problem-solving approach that provides the reader an effective understanding of the issue at hand.
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Affiliation(s)
- Diana Almeida
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal.,Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Daniela Machado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - José Carlos Andrade
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
| | - Sónia Mendo
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Ana Maria Gomes
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Ana Cristina Freitas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
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Zhang F, Zhang T, Zhu H, Borody TJ. Evolution of fecal microbiota transplantation in methodology and ethical issues. Curr Opin Pharmacol 2019; 49:11-16. [PMID: 31059962 DOI: 10.1016/j.coph.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
Abstract
Fecal microbiota transplantation (FMT), the core therapy for remodeling the gut microbiota with a long medical history, has gained great attention worldwide in recent years. Increasing studies have explored its indications, methodology, efficacy, safety, and ethics. Purified forms of FMT, using an automated method for the purification of fecal microbiota from stool, has become a reality. Colonic transendoscopic enteral tubing makes frequent FMT delivery into the whole colon feasible. This review focuses on the recent progress in laboratory preparation, updated clinical strategies, novel delivery methods, and ethical issues surrounding FMT in clinical studies.
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Affiliation(s)
- Faming Zhang
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China; Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 210011, China.
| | - Ting Zhang
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China; Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing 210011, China
| | - Heming Zhu
- Department of Acupuncture and Oriental Medicine, Maryland University of Integrative Health, Laurel, MD, United States
| | - Thomas J Borody
- Centre for Digestive Diseases, Five Dock, NSW 2046, Australia
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46
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The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut. Microbiol Mol Biol Rev 2019; 83:83/2/e00054-18. [PMID: 30867232 DOI: 10.1128/mmbr.00054-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticated in vitro cell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied to in vivo models that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accurate in vitro models of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut "core microbiota" are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.
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47
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Shin W, Wu A, Massidda MW, Foster C, Thomas N, Lee DW, Koh H, Ju Y, Kim J, Kim HJ. A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic Interface-on-a-Chip. Front Bioeng Biotechnol 2019; 7:13. [PMID: 30792981 PMCID: PMC6374617 DOI: 10.3389/fbioe.2019.00013] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging a modified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen microchannel is necessary and sufficient to create the steady-state vertical oxygen gradient in the AOI Chip. We confirmed that the created AOI does not compromise the viability, barrier function, mucin production, and the expression and localization of tight junction proteins in the 3D intestinal epithelial layer. Two obligate anaerobic commensal gut microbiome, Bifidobacterium adolescentis and Eubacterium hallii, that exert metabolic cross-feeding in vivo, were independently co-cultured with epithelial cells in the AOI Chip for up to a week without compromising any cell viability. Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells associated with intestinal metabolism, homeostasis, and immune regulation.
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Affiliation(s)
- Woojung Shin
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Alexander Wu
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Miles W Massidda
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Charles Foster
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Newin Thomas
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Dong-Woo Lee
- Department of Biotechnology, College of Life Science and Technology, Yonsei University, Seoul, South Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Youngwon Ju
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Joohoon Kim
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States.,Department of Medical Engineering, Yonsei University College of Medicine, Seoul, South Korea
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Metabolism of Caprine Milk Carbohydrates by Probiotic Bacteria and Caco-2:HT29⁻MTX Epithelial Co-Cultures and Their Impact on Intestinal Barrier Integrity. Nutrients 2018; 10:nu10070949. [PMID: 30041482 PMCID: PMC6073262 DOI: 10.3390/nu10070949] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022] Open
Abstract
The development and maturation of the neonatal intestine is generally influenced by diet and commensal bacteria, the composition of which, in turn, can be influenced by the diet. Colonisation of the neonatal intestine by probiotic Lactobacillus strains can strengthen, preserve, and improve barrier integrity, and adherence of probiotics to the intestinal epithelium can be influenced by the available carbon sources. The goal of the present study was to examine the role of probiotic lactobacilli strains alone or together with a carbohydrate fraction (CF) from caprine milk on barrier integrity of a co-culture model of the small intestinal epithelium. Barrier integrity (as measured by trans epithelial electrical resistance (TEER)), was enhanced by three bacteria/CF combinations (Lactobacillus rhamnosus HN001, L. plantarum 299v, and L. casei Shirota) to a greater extent than CF or bacteria alone. Levels of occludin mRNA were increased for all treatments compared to untreated co-cultures, and L. plantarum 299v in combination with CF had increased mRNA levels of MUC4, MUC2 and MUC5AC mucins and MUC4 protein abundance. These results indicate that three out of the four probiotic bacteria tested, in combination with CF, were able to elicit a greater increase in barrier integrity of a co-culture model of the small intestinal epithelium compared to that for either component alone. This study provides additional insight into the individual or combined roles of microbe–diet interactions in the small intestine and their beneficial contribution to the intestinal barrier.
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Arık YB, van der Helm MW, Odijk M, Segerink LI, Passier R, van den Berg A, van der Meer AD. Barriers-on-chips: Measurement of barrier function of tissues in organs-on-chips. BIOMICROFLUIDICS 2018; 12:042218. [PMID: 30018697 PMCID: PMC6019329 DOI: 10.1063/1.5023041] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/11/2018] [Indexed: 05/22/2023]
Abstract
Disruption of tissue barriers formed by cells is an integral part of the pathophysiology of many diseases. Therefore, a thorough understanding of tissue barrier function is essential when studying the causes and mechanisms of disease as well as when developing novel treatments. In vitro methods play an integral role in understanding tissue barrier function, and several techniques have been developed in order to evaluate barrier integrity of cultured cell layers, from microscopy imaging of cell-cell adhesion proteins to measuring ionic currents, to flux of water or transport of molecules across cellular barriers. Unfortunately, many of the current in vitro methods suffer from not fully recapitulating the microenvironment of tissues and organs. Recently, organ-on-chip devices have emerged to overcome this challenge. Organs-on-chips are microfluidic cell culture devices with continuously perfused microchannels inhabited by living cells. Freedom of changing the design of device architecture offers the opportunity of recapitulating the in vivo physiological environment while measuring barrier function. Assessment of barriers in organs-on-chips can be challenging as they may require dedicated setups and have smaller volumes that are more sensitive to environmental conditions. But they do provide the option of continuous, non-invasive sensing of barrier quality, which enables better investigation of important aspects of pathophysiology, biological processes, and development of therapies that target barrier tissues. Here, we discuss several techniques to assess barrier function of tissues in organs-on-chips, highlighting advantages and technical challenges.
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Affiliation(s)
| | - Marinke W van der Helm
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Mathieu Odijk
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Loes I Segerink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | | | - Albert van den Berg
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Andries D van der Meer
- Department of Applied Stem Cell Technologies, University of Twente, 7522 NB Enschede, The Netherlands
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Pham VT, Mohajeri MH. The application of in vitro human intestinal models on the screening and development of pre- and probiotics. Benef Microbes 2018; 9:725-742. [PMID: 29695182 DOI: 10.3920/bm2017.0164] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The importance of the gut microbiota community on host's health and disease has long been recognised and is well documented. The development of pro- and prebiotic interventions offers an opportunity for the modulation of the gut microbiota towards long lasting health. In vitro fermentation models were developed as a powerful tool to study the impact of pro- and prebiotics on the gut microbiota under tightly controlled conditions, which allow dynamic sampling over time in reactors mimicking different colon regions. These models have been further evolved to suit specific experimental purposes, e.g. including immobilised faecal microbiota, peristaltic movement, mucin microcosm and the ability to perform treatments in parallel. In this review we discuss the advantages, disadvantages and technical considerations of the most frequently used models. We further focus on recent advances in the application of these models in prebiotics and probiotics research and outline their predictability for clinical research.
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Affiliation(s)
- V T Pham
- 1 DSM Nutritional Products Ltd., R&D Human Nutrition and Health, P.O. Box 2676, 4002 Basel, Switzerland
| | - M H Mohajeri
- 1 DSM Nutritional Products Ltd., R&D Human Nutrition and Health, P.O. Box 2676, 4002 Basel, Switzerland.,2 University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland
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