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García Mendez D, Sanabria J, Wist J, Holmes E. Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6213-6225. [PMID: 37070710 PMCID: PMC10143624 DOI: 10.1021/acs.jafc.2c08146] [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: 11/20/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 05/03/2023]
Abstract
Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.
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Affiliation(s)
- David
Felipe García Mendez
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
| | - Janeth Sanabria
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
- Environmental
Microbiology and Biotechnology Laboratory, Engineering School of Environmental
& Natural Resources, Engineering Faculty, Universidad del Valle—Sede Meléndez, Cali, Colombia 76001
| | - Julien Wist
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
- Chemistry
Department, Universidad del Valle, 76001, Cali, Colombia
| | - Elaine Holmes
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
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A Study and Modeling of Bifidobacterium and Bacillus Coculture Continuous Fermentation under Distal Intestine Simulated Conditions. Microorganisms 2022; 10:microorganisms10050929. [PMID: 35630373 PMCID: PMC9147766 DOI: 10.3390/microorganisms10050929] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/10/2022] Open
Abstract
The diversity and the stability of the microbial community are associated with microecological interactions between its members. Antagonism is one type of interaction, which particularly determines the benefits that probiotics bring to host health by suppressing opportunistic pathogens and microbial contaminants in food. Mathematical models allow for quantitatively predicting intrapopulation relationships. The aim of this study was to create predictive models for bacterial contamination outcomes depending on the probiotic antagonism and prebiotic concentration. This should allow an improvement in the screening of synbiotic composition for preventing gut microbial infections. The functional model (fermentation) was based on a three-stage continuous system, and the distal colon section (N2, pH 6.8, flow rate 0.04 h–1) was simulated. The strains Bifidobacterium adolescentis ATCC 15703 and Bacillus cereus ATCC 9634 were chosen as the model probiotic and pathogen. Oligofructose Orafti P95 (OF) was used as the prebiotic at concentrations of 2, 5, 7, 10, 12, and 15 g/L of the medium. In the first stage, the system was inoculated with Bifidobacterium, and a dynamic equilibrium (Bifidobacterium count, lactic, and acetic acids) was achieved. Then, the system was contaminated with a 3-day Bacillus suspension (spores). The microbial count, as well as the concentration of acids and residual carbohydrates, was measured. A Bacillus monoculture was studied as a control. The stationary count of Bacillus in monoculture was markedly higher. An increase (up to 8 h) in the lag phase was observed for higher prebiotic concentrations. The specific growth rate in the exponential phase varied at different OF concentrations. Thus, the OF concentration influenced two key events of bacterial infection, which together determine when the maximal pathogen count will be reached. The mathematical models were developed, and their accuracies were acceptable for Bifidobacterium (relative errors ranging from 1.00% to 2.58%) and Bacillus (relative errors ranging from 0.74% to 2.78%) count prediction.
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Fournier E, Roussel C, Dominicis A, Ley D, Peyron MA, Collado V, Mercier-Bonin M, Lacroix C, Alric M, Van de Wiele T, Chassard C, Etienne-Mesmin L, Blanquet-Diot S. In vitro models of gut digestion across childhood: current developments, challenges and future trends. Biotechnol Adv 2021; 54:107796. [PMID: 34252564 DOI: 10.1016/j.biotechadv.2021.107796] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/08/2023]
Abstract
The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.
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Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Charlène Roussel
- Laval University, INAF Institute of Nutrition and Functional Foods, G1V 0A6 Quebec, Canada
| | - Alessandra Dominicis
- European Reference Laboratory for E. coli, Istituto Superiore di Sanità, Rome, Italy
| | - Delphine Ley
- Université Lille 2, Faculté de Médecine, Inserm U995 Nutritional Modulation of Infection and Inflammation, 59045 Lille, France
| | - Marie-Agnès Peyron
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Valérie Collado
- Université Clermont Auvergne, EA 4847, CROC, Centre de Recherche en Odontologie Clinique, 63000 Clermont-Ferrand, France
| | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zürich, Switzerland
| | - Monique Alric
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Tom Van de Wiele
- Ghent University, Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000 Ghent, Belgium
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France.
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O'Donnell MM, Rea MC, Shanahan F, Ross RP. The Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colon. Front Microbiol 2018; 9:1844. [PMID: 30147684 PMCID: PMC6096000 DOI: 10.3389/fmicb.2018.01844] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
Ex vivo colon fermentation systems are highly versatile as models for analyzing gastrointestinal tract microbiota composition and functionality. Ex vivo colon models range in size and functionality from bench-top micro fermenters to large units housed in individualized cabinets. The length of set-up time (including stabilization periods) for each fermentation system can range from hours to weeks to months. The aim of this study was to investigate a single-use cassette mini-fermentation system as a reproducible batch model of the colon. The online data log from the cassettes (triplicate wells across four different cassettes, n = 12) was sensitive enough to identify real-time changes in pH, temperature, dissolved oxygen or liquid addition (sodium hydroxide) during the runs which could be addressed if an alarm set-point was triggered. The alpha diversity indices also showed little variation between cassettes with the samples clustering around the mean. The weighted beta diversity PCoA analysis illustrated that 95% of the variance between the samples was accounted for by the time-point and not the fermentation run/cassette used. The variation in taxonomic diversity between cassettes was limited to less than 20 out of 115 genera. This study provides evidence that micro-bioreactors provide some very attractive advantages as batch models for the human colon. We show for the first time the use of the micro-Matrix a 24-well sophisticated parallel controlled cassette-based bioreactors as a batch colon model. We demonstrated a high level of reproducibility across fermentation cassettes when used in conjunction with a standardized fecal microbiota. The machine can operate 24 individual fermentations simultaneously and are relatively cost effective. Based on next generation sequencing analysis, the micro-bioreactors offer a high degree of reproducibility together with high-throughput capacity. This makes it a potential system for large screening projects that can then be scaled up to large fermenters or human/animal in vivo experiments.
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Affiliation(s)
- Michelle M O'Donnell
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Mary C Rea
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - R P Ross
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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Vamanu E, Pelinescu D. Effects of mushroom consumption on the microbiota of different target groups – Impact of polyphenolic composition and mitigation on the microbiome fingerprint. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.07.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Vamanu E, Pelinescu D, Sarbu I. Comparative Fingerprinting of the Human Microbiota in Diabetes and Cardiovascular Disease. J Med Food 2016; 19:1188-1195. [PMID: 27898282 DOI: 10.1089/jmf.2016.0085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diabetes and cardiovascular diseases are major causes of morbidity and mortality worldwide, and are associated with changes in the human gut microbiota. To better understand the relationships between diet, disease, and the colonic microbiome, we used the in vitro GIS1 system and repetitive element palindromic polymerase chain reaction (rep-PCR) to determine the microbial fingerprints in individuals with these diseases and compared them with the fingerprints in healthy controls. Clear differences were apparent in the three groups. The diabetes group showed significantly increased aerobic bacteria, increased coliforms, and reduced bifidobacteria; the balance between beneficial and pathogenic bacteria was disturbed; significant numbers of clostridia were present; and the proportions of various major bacterial groups were unstable through the length of the colon. The microbiota of the cardiovascular group had high numbers of beneficial strains and more closely resembled the control microbiota. Different patterns of lactic acid bacteria were observed in the three groups, and there was a direct link between the presence of lactate and the colonic pH. Ammonium, a microbial metabolite associated with colonic cancer, was associated with consistently high levels of Gram-positive bacteria in the diabetic patients. In the cardiovascular patients and controls, each colonic segment showed a distinct microbial fingerprint, whereas in the diabetics, the same rep-PCR profile occurred in all three segments. The diversity of beneficial bacteria was reduced in patients with a nutritional or cardiovascular disease. Both diabetes and cardiovascular disease are associated with changes in the colonic microbial fingerprint. This study of microbial microbiota fingerprint modification has direct applicability in medical practice.
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Affiliation(s)
- Emanuel Vamanu
- 1 Faculty of Biotechnology, University of Agronomic Science and Veterinary Medicine , Bucharest, Romania
| | - Diana Pelinescu
- 2 Department of Genetics, Faculty of Biology, University of Bucharest , Bucharest, Romania
| | - Ionela Sarbu
- 2 Department of Genetics, Faculty of Biology, University of Bucharest , Bucharest, Romania
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Probiotic Strains Influence on Infant Microbiota in the In Vitro Colonic Fermentation Model GIS1. Indian J Microbiol 2015; 55:423-9. [PMID: 26543268 DOI: 10.1007/s12088-015-0542-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022] Open
Abstract
The main goal of our study was to evaluate the effect of the individual administration of five lyophilized lactic acid bacteria strains (Lactobacillus fermentum 428ST, Lactobacillus rhamnosus E4.2, Lactobacillus plantarum FCA3, Lactobacillus sp. 34.1, Weissella paramesenteroides FT1a) against the in vitro simulated microbiota of the human colon using the GIS1 system. The influence on the metabolic activity was also assessed by quantitative determination of proteins and polysaccharides at each segment of human colon. The obtained results indicated that the lactic acid bacteria L. rhamnosus E4.2 and W. paramesenteroides FTa1 had better efficiency in synthesising exopolysaccharides and also a better probiotic potential and therefore could be recommended for use in probiotics products or food industry.
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Vamanu E. Effect of gastric and small intestinal digestion on lactic acid bacteria activity in a GIS1 simulator. Saudi J Biol Sci 2015; 24:1453-1457. [PMID: 30294212 PMCID: PMC6169548 DOI: 10.1016/j.sjbs.2015.06.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/23/2015] [Accepted: 06/28/2015] [Indexed: 11/17/2022] Open
Abstract
The selection of probiotic strains resistant to gastrointestinal transit is an important stage when developing supplements that contain viable biomass. A total of six strains belonging to different genotypes were tested and compared with both a positive and negative control (Lactobacillus plantarum 5s). Significant differences were found between strains as a result of gastrointestinal transit using the in vitro GIS1 static simulator. The Lactobacillus rhamnosus 428ST strain showed maximum viability as a result of in vitro transit, featuring a survival capacity value, Cs, of over 50 ± 0.01%. The remaining genotypes that were tested showed significant reductions in the enzymes and bile salts at the time of action. The value of the survivability capacity was directly correlated with the synthesis of exopolysaccharides and lactic acid. The test results of the GIS1 system have been compared with those of other studies on gastrointestinal transit resistance that used dynamic models.
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Affiliation(s)
- Emanuel Vamanu
- University of Agronomic Science and Veterinary Medicine, Faculty of Biotechnology, 59 Marasti blvd, 1 district, 011464 Bucharest, Romania
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Vamanu E, Sarbu I, Nedelcu I, Pelinescu D. Study of PROEXO product influence on infant microbiota in an in vitro colonic fermentation system. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0947-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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10
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An in vitro evaluation of antioxidant and colonic microbial profile levels following mushroom consumption. BIOMED RESEARCH INTERNATIONAL 2013; 2013:289821. [PMID: 24027755 PMCID: PMC3762205 DOI: 10.1155/2013/289821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/15/2013] [Accepted: 07/18/2013] [Indexed: 01/27/2023]
Abstract
The biological activity of mushroom consumption is achieved by the antioxidant effect of constituent biomolecules released during digestion. In the following study, the consumption of mushroom fungi was determined to increase the number of Lactobacillus and Bifidobacterium strains within the colon. The main phenolic antioxidant compounds identified were both gentisic and homogentisic acids. Moreover, the flavonoid catechin as well as a significant amount of δ- and γ-tocopherols was determined. The amount of Lactobacillus and Bifidobacterium strains from different sections of the human colon was significantly correlated with levels of antioxidative biomolecules. The experimental data clearly demonstrate a significant impact of mushroom consumption on the fermentative function of microorganisms in the human colon, resulting in the homeostasis of normal physiological colonic functions.
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