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Yang J, Cassaday J, Wyche TP, Squadroni B, Newhard W, Trinh H, Cabral D, Hett E, Sana TR, Lee K, Kasper S. A perfusion host-microbe bioreactor (HMB) system that captures dynamic interactions of secreted metabolites between epithelial cells cocultured with a human gut anaerobe. Biotechnol Bioeng 2024; 121:2691-2705. [PMID: 38715197 DOI: 10.1002/bit.28730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/18/2024] [Accepted: 04/18/2024] [Indexed: 08/15/2024]
Abstract
The human microbiota impacts a variety of diseases and responses to therapeutics. Due to a lack of robust in vitro models, detailed mechanistic explanations of host-microbiota interactions cannot often be recapitulated. We describe the design and development of a novel, versatile and modular in vitro system that enables indirect coculture of human epithelial cells with anaerobic bacteria for the characterization of host-microbe secreted metabolite interactions. This system was designed to compartmentalize anaerobes and human cells in separate chambers conducive to each organism's requisite cell growth conditions. Using perfusion, fluidic mixing, and automated sample collection, the cells continuously received fresh media, while in contact with their corresponding compartments conditioned supernatant. Supernatants from each chamber were collected in a cell-free time-resolved fashion. The system sustained low oxygen conditions in the anaerobic chamber, while also supporting the growth of a representative anaerobe (Bacteroides thetaiotaomicron) and a human colonic epithelial cell line (Caco-2) in the aerobic chamber. Caco-2 global gene expression changes in response to coculture with B. thetaiotaomicron was characterized using RNA sequencing. Extensive, targeted metabolomics analysis of over 150 central carbon metabolites was performed on the serially collected supernatants. We observed broad metabolite changes in host-microbe coculture, compared to respective mono-culture controls. These effects were dependent both on sampling time and the compartment probed (apical vs. basolateral). Coculturing resulted in the depletion of several important metabolites, including guanine, uridine 5'-monophosphate, asparagine, and thiamine. Additionally, while Caco-2 cells cultured alone predominantly affected the basolateral metabolite milieu, increased abundance of 2,3-dihydroxyisovalerate and thymine on the basolateral side, occurred when the cells were cocultured with B. thetaiotaomicron. Thus, our system can capture the dynamic, competitive and cooperative processes between host cells and gut microbes.
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Affiliation(s)
- Jingyun Yang
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | | | | | | | | | - Huong Trinh
- Merck & Co., Inc., West Point, Pennsylvania, USA
| | | | - Erik Hett
- Merck & Co., Inc., Cambridge, Massachusetts, USA
| | | | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
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2
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Firrman J, Friedman ES, Hecht A, Strange WC, Narrowe AB, Mahalak K, Wu GD, Liu L. Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro. mBio 2024; 15:e0094324. [PMID: 38727244 PMCID: PMC11237543 DOI: 10.1128/mbio.00943-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota in vitro using human small intestinal ileostomy effluent as the inocula, we show here that the infusion of physiologically relevant levels of oxygen, normally found in the proximal small intestine, reduced deconjugation of primary bile acids, in part, through the expansion of bacterial taxa known to have a low abundance of BSHs. Further recapitulating the small intestinal bile acid composition of the small intestine, limited conversion of primary into secondary bile acids was observed. Remarkably, these effects were preserved among four separate communities, each inoculated with a different small intestinal microbiota, despite a high degree of taxonomic variability under both anoxic and aerobic conditions. In total, these results provide evidence for a previously unrecognized role that the oxygenated environment of the small intestine plays in the maintenance of normal digestive physiology. IMPORTANCE Conjugated primary bile acids are produced by the liver and exist at high concentrations in the proximal small intestine, where they are critical for proper digestion. Deconjugation of these bile acids with subsequent transformation via dehydroxylation into secondary bile acids is regulated by the colonic gut microbiota and reduces their digestive function. Using an in vitro platform modeling the small intestinal microbiota, we analyzed the ability of this community to transform primary bile acids and studied the effect of physiological levels of oxygen normally found in the proximal small intestine (5%) on this metabolic process. We found that oxygenation of the small intestinal microbiota inhibited the deconjugation of primary bile acids in vitro. These findings suggest that luminal oxygen levels normally found in the small intestine may maintain the optimal role of bile acids in the digestive process by regulating bile acid conversion by the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron Hecht
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - William C. Strange
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
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Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M. Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities. Microb Biotechnol 2024; 17:e14509. [PMID: 38878269 PMCID: PMC11179620 DOI: 10.1111/1751-7915.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/18/2024] Open
Abstract
The availability of microbial biobanks for the storage of individual gut microbiota members or their derived and artificially assembled consortia has become fundamental for in vitro investigation of the molecular mechanisms behind microbe-microbe and/or microbe-host interactions. However, to preserve bacterial viability, adequate storage and processing technologies are required. In this study, the effects on cell viability of seven different combinations of cryoprotective agents were evaluated by flow cytometry for 53 bacterial species representing key members of the human gut microbiota after one and 3 months of cryopreservation at -80°C. The obtained results highlighted that no universal cryoprotectant was identified capable of guaranteeing effective recovery of intact cells after cryopreservation for all tested bacteria. However, the presence of inulin or skimmed milk provided high levels of viability protection during cryoexposure. These results were further corroborated by cryopreserving 10 artificial gut microbiota produced through in vitro continuous fermentation system technology. Indeed, in this case, the inclusion of inulin or skimmed milk resulted in a high recovery of viable cells, while also allowing consistent and reliable preservation of the artificial gut microbiota biodiversity. Overall, these results suggest that, although the efficacy of various cryoprotective agents is species-specific, some cryoprotectants based on glycerol and the addition of inulin or skimmed milk are preferable to retain viability and biodiversity for both single bacterial species and artificial gut microbiota.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Kim R, Sung JH. Microfluidic gut-axis-on-a-chip models for pharmacokinetic-based disease models. BIOMICROFLUIDICS 2024; 18:031507. [PMID: 38947281 PMCID: PMC11210976 DOI: 10.1063/5.0206271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/05/2024] [Indexed: 07/02/2024]
Abstract
The low success rate of new drugs transitioning from animal testing to human clinical trials necessitates the development of more accurate and representative in vitro models. Recent advances in multi-organ-on-a-chip technology offer promising avenues for studying complex organ-organ interactions. Gut-liver-on-a-chip systems hold particular promise for mimicking the intricate interplay between the gut and liver, which play crucial roles in nutrient absorption, drug metabolism, detoxification, and immune response. Here, we discuss the key components of the gut-liver axis, including the gut epithelium, liver cells, gut microbiota, and their roles in the organ functions. We then explore the potential of gut-liver-on-a-chip models to replicate the intricate interactions between the two organs for pharmacokinetic studies and their expansion to more complicated multi-organ models. Finally, we provide perspectives and future directions for developing more physiologically relevant gut-liver-axis models for more efficient drug development, studying liver diseases, and personalizing treatment strategies.
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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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Chen X, Moreno LL, Tang X, Gasaly N, Schols HA, de Vos P. A novel "microbiota-host interaction model" to study the real-time effects of fermentation of non-digestible carbohydrate (NDCs) on gut barrier function. Curr Res Food Sci 2024; 8:100736. [PMID: 38681527 PMCID: PMC11052908 DOI: 10.1016/j.crfs.2024.100736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
In this study, an in vitro co-culture model using an electric cell-substrate impedance sensing system (ECIS) for testing the impact of real-time fermentation of non-digestible carbohydrates (NDCs) by the intestinal microbiota on gut barrier function was established. We applied Lactobacillus plantarum WCFS1 as a model intestinal bacterium and alginate-pectin as immobilization polymers as well as a source of NDCs to determine the impact of pectin fermentation on the barrier function of T84 gut epithelial cells. In the first design, L. plantarum WCFS1 was encapsulated in an alginate capsule followed by embedding in an agar layer to mimic a firm mucus layer that might be present in the colon. In this experimental design, the presence of the agar layer interfered with the transepithelial electrical resistance (TEER) measurement of T84 cells. Subsequently, we removed the agar layer and used encapsulated bacteria in an alginate gel and found that the TEER measurement was adequate. The encapsulation of the L. plantarum WCFS1 does avoid direct contact with cells. Also, the encapsulation system allows higher amounts of packing densities of L. plantarum WCFS1 in a limited space which can limit the oxygen concentration within the capsule and therefore create anaerobic conditions. To test this design, T84 cells were co-incubated with L. plantarum alginate-capsules supplemented with graded loads of fermentable pectin (0, 4, and 8 mg/ml per capsule) to investigate the effect of pectin fermentation on gut barrier function. We observed that as the pectin content in the L. plantarum capsules increased, pectin showed a gradually stronger protective effect on the TEER of the gut epithelium. This could partly be explained by enhanced SCFA production as both lactate and acetate were enhanced in L. plantarum containing alginate capsules with 8 mg/ml pectin. Overall, this newly designed in vitro co-culture model allows for studying the impact of bacteria-derived fermentation products but also for studying the direct effects of NDCs on gut barrier function in a relatively high-throughput way.
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Affiliation(s)
- Xiaochen Chen
- Immunoendocrinology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Luis Llanos Moreno
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Tang
- Immunoendocrinology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Naschla Gasaly
- Immunoendocrinology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Henk A. Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Paul de Vos
- Immunoendocrinology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Sardelli L, Campanile M, Boeri L, Donnaloja F, Fanizza F, Perottoni S, Petrini P, Albani D, Giordano C. A novel on-a-chip system with a 3D-bioinspired gut mucus suitable to investigate bacterial endotoxins dynamics. Mater Today Bio 2024; 24:100898. [PMID: 38204482 PMCID: PMC10776420 DOI: 10.1016/j.mtbio.2023.100898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024] Open
Abstract
The possible pathogenic impact of pro-inflammatory molecules produced by the gut microbiota is one of the hypotheses considered at the basis of the biomolecular dialogue governing the microbiota-gut-brain axis. Among these molecules, lipopolysaccharides (LPS) produced by Gram-negative gut microbiota strains may have a potential key role due to their toxic effects in both the gut and the brain. In this work, we engineered a new dynamic fluidic system, the MINERVA device (MI-device), with the potential to advance the current knowledge of the biological mechanisms regulating the microbiota-gut molecular crosstalk. The MI-device supported the growth of bacteria that are part of the intestinal microbiota under dynamic conditions within a 3D moving mucus model, with features comparable to the physiological conditions (storage modulus of 80 ± 19 Pa, network mesh size of 41 ± 3 nm), without affecting their viability (∼ 109 bacteria/mL). The integration of a fluidically optimized and user-friendly design with a bioinspired microenvironment enabled the sterile extraction and quantification of the LPS produced within the mucus by bacteria (from 423 ± 34 ng/mL to 1785 ± 91 ng/mL). Compatibility with commercially available Transwell-like inserts allows the user to precisely control the transport phenomena that occur between the two chambers by selecting the pore density of the insert membrane without changing the design of the system. The MI-device is able to provide the flow of sterile medium enriched with LPS directly produced by bacteria, opening up the possibility of studying the effects of bacteria-derived molecules on cells in depth, as well as the assessment and characterization of their effects in a physiological or pathological scenario.
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Affiliation(s)
- L. Sardelli
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - M. Campanile
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - L. Boeri
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - F. Donnaloja
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - F. Fanizza
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - S. Perottoni
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - P. Petrini
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
| | - D. Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - C. Giordano
- Department of Chemistry, Materials and Chemical Engineering ‘Giulio Natta,’ Politecnico di Milano, Milan, Italy
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Cai J, Auster A, Cho S, Lai Z. Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage. J Adv Res 2023; 52:171-201. [PMID: 37419381 PMCID: PMC10555929 DOI: 10.1016/j.jare.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND The gut microbiome is a diverse system within the gastrointestinal tract composed of trillions of microorganisms (gut microbiota), along with their genomes. Accumulated evidence has revealed the significance of the gut microbiome in human health and disease. Due to its ability to alter drug/xenobiotic pharmacokinetics and therapeutic outcomes, this once-forgotten "metabolic organ" is receiving increasing attention. In parallel with the growing microbiome-driven studies, traditional analytical techniques and technologies have also evolved, allowing researchers to gain a deeper understanding of the functional and mechanistic effects of gut microbiome. AIM OF REVIEW From a drug development perspective, microbial drug metabolism is becoming increasingly critical as new modalities (e.g., degradation peptides) with potential microbial metabolism implications emerge. The pharmaceutical industry thus has a pressing need to stay up-to-date with, and continue pursuing, research efforts investigating clinical impact of the gut microbiome on drug actions whilst integrating advances in analytical technology and gut microbiome models. Our review aims to practically address this need by comprehensively introducing the latest innovations in microbial drug metabolism research- including strengths and limitations, to aid in mechanistically dissecting the impact of the gut microbiome on drug metabolism and therapeutic impact, and to develop informed strategies to address microbiome-related drug liability and minimize clinical risk. KEY SCIENTIFIC CONCEPTS OF REVIEW We present comprehensive mechanisms and co-contributing factors by which the gut microbiome influences drug therapeutic outcomes. We highlight in vitro, in vivo, and in silico models for elucidating the mechanistic role and clinical impact of the gut microbiome on drugs in combination with high-throughput, functionally oriented, and physiologically relevant techniques. Integrating pharmaceutical knowledge and insight, we provide practical suggestions to pharmaceutical scientists for when, why, how, and what is next in microbial studies for improved drug efficacy and safety, and ultimately, support precision medicine formulation for personalized and efficacious therapies.
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Affiliation(s)
- Jingwei Cai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA.
| | - Alexis Auster
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Sungjoon Cho
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
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Čeprnja M, Hadžić E, Oros D, Melvan E, Starcevic A, Zucko J. Current Viewpoint on Female Urogenital Microbiome-The Cause or the Consequence? Microorganisms 2023; 11:1207. [PMID: 37317181 DOI: 10.3390/microorganisms11051207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
An increasing amount of evidence implies that native microbiota is a constituent part of a healthy urinary tract (UT), making it an ecosystem on its own. What is still not clear is whether the origin of the urinary microbial community is the indirect consequence of the more abundant gut microbiota or a more distinct separation exists between these two systems. Another area of uncertainty is the existence of a link between the shifts in UT microbial composition and both the onset and persistence of cystitis symptoms. Cystitis is one of the most common reasons for antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of the majority of cystitis cases is a single pathogen overgrowth or a systemic disorder affecting the entire urinary microbiota. There is an increasing trend in studies monitoring changes and dynamics of UT microbiota, but this field of research is still in its infancy. Using NGS and bioinformatics, it is possible to obtain microbiota taxonomic profiles directly from urine samples, which can provide a window into microbial diversity (or the lack of) underlying each patient's cystitis symptoms. However, while microbiota refers to the living collection of microorganisms, an interchangeably used term microbiome referring to the genetic material of the microbiota is more often used in conjunction with sequencing data. It is this vast amount of sequences, which are truly "Big Data", that allow us to create models that describe interactions between different species contributing to an UT ecosystem, when coupled with machine-learning techniques. Although in a simplified predator-prey form these multi-species interaction models have the potential to further validate or disprove current beliefs; whether it is the presence or the absence of particular key players in a UT microbial ecosystem, the exact cause or consequence of the otherwise unknown etiology in the majority of cystitis cases. These insights might prove to be vital in our ongoing struggle against pathogen resistance and offer us new and promising clinical markers.
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Affiliation(s)
- Marina Čeprnja
- Biochemical Laboratory, Special Hospital Agram, Polyclinic Zagreb, 10000 Zagreb, Croatia
| | - Edin Hadžić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Damir Oros
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Ena Melvan
- Department of Biological Science, Faculty of Science, Macquarie University, Sydney, NSW 2109, Australia
| | - Antonio Starcevic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
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Hall V, Bendtsen KMS. Getting closer to modeling the gut-brain axis using induced pluripotent stem cells. Front Cell Dev Biol 2023; 11:1146062. [PMID: 37065853 PMCID: PMC10102862 DOI: 10.3389/fcell.2023.1146062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
The gut microbiome (GM), the gut barrier, and the blood-brain barrier (BBB) are key elements of the gut-brain axis (GBA). The advances in organ-on-a-chip and induced pluripotent stem cell (iPSCs) technology might enable more physiological gut-brain-axis-on-a-chip models. The ability to mimic complex physiological functions of the GBA is needed in basic mechanistic research as well as disease research of psychiatric, neurodevelopmental, functional, and neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease. These brain disorders have been associated with GM dysbiosis, which may affect the brain via the GBA. Although animal models have paved the way for the breakthroughs and progression in the understanding of the GBA, the fundamental questions of exactly when, how, and why still remain unanswered. The research of the complex GBA have relied on equally complex animal models, but today’s ethical knowledge and responsibilities demand interdisciplinary development of non-animal models to study such systems. In this review we briefly describe the gut barrier and BBB, provide an overview of current cell models, and discuss the use of iPSCs in these GBA elements. We highlight the perspectives of producing GBA chips using iPSCs and the challenges that remain in the field.
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Dijk W, Villa C, Benedé S, Vassilopoulou E, Mafra I, Garrido-Arandia M, Martínez Blanco M, Bouchaud G, Hoppenbrouwers T, Bavaro SL, Giblin L, Knipping K, Castro AM, Delgado S, Costa J, Bastiaan-Net S. Critical features of an in vitro intestinal absorption model to study the first key aspects underlying food allergen sensitization. Compr Rev Food Sci Food Saf 2023; 22:971-1005. [PMID: 36546415 DOI: 10.1111/1541-4337.13097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
New types of protein sources will enter our diet in a near future, reinforcing the need for a straightforward in vitro (cell-based) screening model to test and predict the safety of these novel proteins, in particular their potential risk for de novo allergic sensitization. The Adverse Outcome Pathway (AOP) for allergen sensitization describes the current knowledge of key events underlying the complex cellular interactions that proceed allergic food sensitization. Currently, there is no consensus on the in vitro model to study the intestinal translocation of proteins as well as the epithelial activation, which comprise the first molecular initiation events (ME1-3) and the first key event of the AOP, respectively. As members of INFOGEST, we have highlighted several critical features that should be considered for any proposed in vitro model to study epithelial protein transport in the context of allergic sensitization. In addition, we defined which intestinal cell types are indispensable in a consensus model of the first steps of the AOP, and which cell types are optional or desired when there is the possibility to create a more complex cell model. A model of these first key aspects of the AOP can be used to study the gut epithelial translocation behavior of known hypo- and hyperallergens, juxtaposed to the transport behavior of novel proteins as a first screen for risk management of dietary proteins. Indeed, this disquisition forms a basis for the development of a future consensus model of the allergic sensitization cascade, comprising also the other key events (KE2-5).
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Affiliation(s)
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Sara Benedé
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
| | - Emilia Vassilopoulou
- Nutritional Sciences and Dietetics, International Hellenic University, Thessaloniki, Greece
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Mónica Martínez Blanco
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
- Division of Immunology, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Tamara Hoppenbrouwers
- Food Quality & Design, Wageningen University & Research, Wageningen, The Netherlands
- Wageningen Food and Biobased Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Simona Lucia Bavaro
- Institute of Sciences of Food Production, National Research Council (Ispa-Cnr), Campus Universitario Ecotekne, Lecce, Italy
| | - Linda Giblin
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | | | - Ana Maria Castro
- Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Susana Delgado
- Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Shanna Bastiaan-Net
- Wageningen Food and Biobased Research, Wageningen University & Research, Wageningen, The Netherlands
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11
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Xu R, Li Q, Wang H, Su Y, Zhu W. Reduction of Redox Potential Exerts a Key Role in Modulating Gut Microbial Taxa and Function by Dietary Supplementation of Pectin in a Pig Model. Microbiol Spectr 2023; 11:e0328322. [PMID: 36475916 PMCID: PMC9927287 DOI: 10.1128/spectrum.03283-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Pectin exists in a vast range of plants and has a long history of acting as a functional food additive with potential prebiotic effects on intestinal health. However, knowledge of how pectin regulates gut microbial communities is still insufficient and limited. Here, metatranscriptome sequencing revealed that a pectin-enriched diet (PEC) decreased the abundances of fungal keystone taxa (e.g., amino acid-producing Kazachstania spp.) and their genes involved in oxidative phosphorylation, while it increased the abundance of sulfate-reducing Desulfovibrio spp., and methane-producing Methanobrevibacter spp. in colon microbiomes. Furthermore, we first confirmed that PEC decreased fecal redox potential in a fistula pig model, which could be supported by the enrichment of antioxidants (e.g., inosine) in feces. Fecal metagenome analysis disclosed that certain microbial taxa promoted inosine biosynthesis from pectin degradation, including Prevotella, which plays an essential role in pectin biodegradation. Overall, these results demonstrate that pectin decreases the redox potential in pig hindgut to modulate microbial composition and functions, and specific microorganisms generate reducing agents in the course of pectin degradation to decrease redox potential of microbial ecosystem. IMPORTANCE Collective studies indicate that pectin degradation promotes extensive microorganisms that can be involved in pectin degradation directly or indirectly, or benefit from the altered physiological conditions caused by pectin ingestions. Our study focuses on effects of pectin on gut microbial taxa and functions, as well as its interactions with altered environmental features. Our results demonstrate pectin-induced proreducing shifts on colon microbial taxa and functions, and first confirm that pectin decreases hindgut redox potential, which is an important environmental feature that can modulate microbial communities. These results infer that there is bidirectional regulation between microbiota and redox potential during pectin degradation. In general, this investigation proposes new insights into the pectin-modulating gut microbial ecosystem and also provides new perspectives for targeting modulation of gut microbiota.
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Affiliation(s)
- Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 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, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 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, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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12
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Xian C, Zhang J, Zhao S, Li XG. Gut-on-a-chip for disease models. J Tissue Eng 2023; 14:20417314221149882. [PMID: 36699635 PMCID: PMC9869227 DOI: 10.1177/20417314221149882] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
The intestinal tract is a vital organ responsible for digestion and absorption in the human body and plays an essential role in pathogen invasion. Compared with other traditional models, gut-on-a-chip has many unique advantages, and thereby, it can be considered as a novel model for studying intestinal functions and diseases. Based on the chip design, we can replicate the in vivo microenvironment of the intestine and study the effects of individual variables on the experiment. In recent years, it has been used to study several diseases. To better mimic the intestinal microenvironment, the structure and function of gut-on-a-chip are constantly optimised and improved. Owing to the complexity of the disease mechanism, gut-on-a-chip can be used in conjunction with other organ chips. In this review, we summarise the human intestinal structure and function as well as the development and improvement of gut-on-a-chip. Finally, we present and discuss gut-on-a-chip applications in inflammatory bowel disease (IBD), viral infections and phenylketonuria. Further improvement of the simulation and high throughput of gut-on-a-chip and realisation of personalised treatments are the problems that should be solved for gut-on-a-chip as a disease model.
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Affiliation(s)
| | | | | | - Xiang-Guang Li
- Xiang-Guang Li, Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, No. 100 Waihuan Xi Road (GDUT), Panyu District, Guangzhou 510006, China.
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13
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Kang SG, Choi YY, Mo SJ, Kim TH, Ha JH, Hong DK, Lee H, Park SD, Shim JJ, Lee JL, Chung BG. Effect of gut microbiome-derived metabolites and extracellular vesicles on hepatocyte functions in a gut-liver axis chip. NANO CONVERGENCE 2023; 10:5. [PMID: 36645561 PMCID: PMC9842828 DOI: 10.1186/s40580-022-00350-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Metabolism, is a complex process involving the gut and the liver tissue, is difficult to be reproduced in vitro with conventional single cell culture systems. To tackle this challenge, we developed a gut-liver-axis chip consisting of the gut epithelial cell chamber and three-dimensional (3D) uniform-sized liver spheroid chamber. Two cell culture chamber compartments were separated with a porous membrane to prevent microorganisms from passing through the chamber. When the hepG2 spheroids cultured with microbiota-derived metabolites, we observed the changes in the physiological function of hepG2 spheroids, showing that the albumin and urea secretion activity of liver spheroids was significantly enhanced. Additionally, the functional validation of hepG2 spheroids treated with microbiota-derived exosome was evaluated that the treatment of the microbiota-derived exosome significantly enhanced albumin and urea in hepG2 spheroids in a gut-liver axis chip. Therefore, this gut-liver axis chip could be a potentially powerful co-culture platform to study the interaction of microbiota and host cells.
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Affiliation(s)
- Seong Goo Kang
- Department of Biomedical Engineering, Sogang University, Seoul, 04107, Korea
| | - Yoon Young Choi
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, Korea
| | | | - Tae Hyeon Kim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, Korea
| | - Jang Ho Ha
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, Korea
| | | | - Hayera Lee
- R&BD Center, hy Co., Ltd., Yongin-Si, Korea
| | | | | | | | - Bong Geun Chung
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, Korea.
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, Korea.
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14
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Sanabria J, Egan S, Masuda R, Lee AJ, Gibson GR, Nicholson JK, Wist J, Holmes E. Overview of the Nomenclature and Network of Contributors to the Development of Bioreactors for Human Gut Simulation Using Bibliometric Tools: A Fragmented Landscape. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11458-11467. [PMID: 36095091 PMCID: PMC9501909 DOI: 10.1021/acs.jafc.2c03597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The evolution of complex in vitro models of the human gastrointestinal system to interrogate the biochemical functionality of the gut microbiome has augmented our understanding of its role in human physiology and pathology. With 5718 authors from 52 countries, gut bioreactor research reflects the growing awareness of our need to understand the contribution of the gut microbiome to human health. Although a large body of knowledge has been generated from in vitro models, it is scattered and defined by application-specific terminologies. To better grasp the capacity of bioreactors and further our knowledge of the human gastrointestinal system, we have conducted a cross-field bibliometric search and mapped the evolution of human gastrointestinal in vitro research. We present reference material with the aim of identifying key authors and bioreactor types to enable researchers to make decisions regarding the choice of method for simulating the human gut in the context of microbiome functionality.
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Affiliation(s)
- Janeth Sanabria
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle-Sede Meléndez, Cali 76001, Colombia
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
| | - Siobhon Egan
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
| | - Reika Masuda
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
| | - Alex J Lee
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AH, United Kingdom
| | - Jeremy K Nicholson
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
- Institute of Global Health Innovation, Faculty of Medicine, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Julien Wist
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
- Chemistry Department, Universidad del Valle, Cali 76001, Colombia
| | - Elaine Holmes
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, Western Australia WA6150, Australia
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
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15
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Sardelli L, Vangosa FB, Merli M, Ziccarelli A, Visentin S, Visai L, Petrini P. Bioinspired in vitro intestinal mucus model for 3D-dynamic culture of bacteria. BIOMATERIALS ADVANCES 2022; 139:213022. [PMID: 35891596 DOI: 10.1016/j.bioadv.2022.213022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/27/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
The intestinal mucus is a biological barrier that supports the intestinal microbiota growth and filters molecules. To perform these functions, mucus possesses optimized microstructure and viscoelastic properties and it is steadily replenished thus flowing along the gut. The available in vitro intestinal mucus models are useful tools in investigating the microbiota-human cells interaction, and are used as matrices for bacterial culture or as static component of microfluidic devices like gut-on-chips. The aim of this work is to engineer an in vitro mucus models (I-Bac3Gel) addressing in a single system physiological viscoelastic properties (i.e., 2-200 Pa), 3D structure and suitability for dynamic bacterial culture. Homogeneously crosslinked alginate hydrogels are optimized in composition to obtain target viscoelastic and microstructural properties. Then, rheological tests are exploited to assess a priori the hydrogels capability to withstand the flow dynamic condition. We experimentally assess the suitability of I-Bac3Gels in the evolving field of microfluidics by applying a dynamic flow to a bacterial-loaded mucus model and by monitoring E. coli growth and survival. The engineered models represent a step forward in the modelling of the mucus, since they can answer to different urgent needs such as a 3D structure, bioinspired properties and compatibility with dynamic system.
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Affiliation(s)
- Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy.
| | - Francesco Briatico Vangosa
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Marta Merli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Anna Ziccarelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Sonja Visentin
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
| | - Livia Visai
- Molecular Medicine Department (DMM), Center for Health Technologies (CHT), UdR INSTM, University of Pavia, Pavia, Italy; Department of Occupational Medicine, Toxicology and Environmental Risks, Istituti Clinici Scientifici (ICS) Maugeri, IRCCS, Pavia, Italy
| | - Paola Petrini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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16
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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17
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Boeri L, Donnaloja F, Campanile M, Sardelli L, Tunesi M, Fusco F, Giordano C, Albani D. Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy. Neurobiol Dis 2022; 164:105614. [PMID: 35017031 DOI: 10.1016/j.nbd.2022.105614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.
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Affiliation(s)
- Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marta Tunesi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Federica Fusco
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy.
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18
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Zuppi M, Hendrickson HL, O’Sullivan JM, Vatanen T. Phages in the Gut Ecosystem. Front Cell Infect Microbiol 2022; 11:822562. [PMID: 35059329 PMCID: PMC8764184 DOI: 10.3389/fcimb.2021.822562] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 12/23/2022] Open
Abstract
Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.
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Affiliation(s)
- Michele Zuppi
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Heather L. Hendrickson
- The School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Justin M. O’Sullivan
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Tommi Vatanen
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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19
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Russo E. The gut microbiota as a biomarker in epilepsy. Neurobiol Dis 2021; 163:105598. [PMID: 34942335 DOI: 10.1016/j.nbd.2021.105598] [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: 11/22/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are defined as objectively measurable variables of a biologic process, either physiologic or pathologic, that provide reliable information on the status of that specific process in a specific moment. Validated biomarkers in epilepsy research represent an urgent unmet need being essential to improve research quality; as an example, biomarkers in epileptogenesis identifying these subjects at risk to develop epilepsy after an initial insult definitively would lead to an improvement in clinical studies to find antiepileptogenic drugs. The gut microbiota (GM) has recently encountered the interest of neuroscience which confirmed its clear involvement in several neurological disorders. GM's role in epilepsy has only recently been studied, however, interesting results are already available. Besides the interest in GM as a suitable therapeutic target and a few preclinical and clinical studies indicating the potential antiseizure effects of GM manipulation, microbiota composition has been found altered in patients with epilepsy as well as some animal models. Only few studies have tried to analyse GM composition as a suitable biomarker and, despite very promising, several drawbacks limit our understanding. On the other hand, GM composition may be useful in discriminating drug-resistant from drug-responsive patients at any stage or patients at risk of developing epilepsy after an insult. The main limitation in the area is the lack of large studies in homogeneous patients and standardization is a must for a proper understanding. Finally, considering the number of variables coming both from epilepsy and GM, big data analysis as in the case of genetics should be considered.
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Affiliation(s)
- Emilio Russo
- Department of Science of Health, School of Medicine, University Magna Graecia of Catanzaro, Via T. Campanella, 115, 88100 Catanzaro, Italy.
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20
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Hernalsteens S, Huang S, Cong HH, Chen XD. The final fate of food: On the establishment of in vitro colon models. Food Res Int 2021; 150:110743. [PMID: 34865762 DOI: 10.1016/j.foodres.2021.110743] [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] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.
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Affiliation(s)
- Saartje Hernalsteens
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
| | | | - Hai Hua Cong
- College of Food Science and Engineering - Dalian Ocean University, China
| | - Xiao Dong Chen
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
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21
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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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