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Vorländer D, Schultz G, Hoffmann K, Rasch D, Dohnt K. PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions. Biotechnol Bioeng 2024; 121:1118-1143. [PMID: 38151924 DOI: 10.1002/bit.28636] [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: 07/07/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023]
Abstract
A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.
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Affiliation(s)
- David Vorländer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Gábor Schultz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristin Hoffmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Detlev Rasch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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2
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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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3
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Comolli J, Walsh DI, Bobrow J, Lennartz CL, Guido NJ, Thorsen T. An in vitro platform for study of the human gut microbiome under an oxygen gradient. Biomed Microdevices 2023; 25:14. [PMID: 37014472 PMCID: PMC10073063 DOI: 10.1007/s10544-023-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2023] [Indexed: 04/05/2023]
Abstract
The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. We have developed an in vitro 40-plex platform that provides an oxygen gradient to support simultaneous maintenance of microaerobic and anaerobic microbes from the gut microbiome that can aid in rapid characterization of microbial interactions and direct comparison of individual microbiome samples. In this report, we demonstrate that the platform more closely maintained the microbial diversity and composition of human donor fecal microbiome samples than strict anaerobic conditions. The oxygen gradient established in the platform allowed the stratification and subsequent sampling of diverse microbial subpopulations that colonize microaerobic and anaerobic micro-environments. With the ability to run forty samples in parallel, the platform has the potential to be used as a rapid screening tool to understand how the gut microbiome responds to environmental perturbations such as toxic compound exposure, dietary changes, or pharmaceutical treatments.
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Affiliation(s)
- James Comolli
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - David I Walsh
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Johanna Bobrow
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Chelsea L Lennartz
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Nicholas J Guido
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA
| | - Todd Thorsen
- Biological & Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA, USA.
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4
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Kim HJ, Mo SJ, Kim J, Nam B, Park SD, Sim JJ, Sim J, Lee JL. Organic vegetable juice supplement alleviates hyperlipidemia in diet-induced obese mice and modulates microbial community in continuous colon simulation system. Food Sci Nutr 2023; 11:1531-1543. [PMID: 36911823 PMCID: PMC10002948 DOI: 10.1002/fsn3.3193] [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: 08/04/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
In this study, we investigated the effects of organic vegetable juice (OVJ) supplementation on modulating the microbial community, and how its consumption ameliorated blood-lipid profiles in diet-induced obese mice. Here, we studied the alleviating effect of hyperlipidemia via animal experiments using diet-induced obese mice and analyzed the effect of OVJ on the microbial community in continuous colon simulation system. OVJ consumption did not have a significant effect on weight loss but helped reduce the weight of the epididymis fat tissue and adipocytes. Additionally, blood-lipid profiles, such as triglyceride, high-density lipoprotein, and glucose, were improved in the OVJ-fed group. Expression levels of genes related to lipid synthesis, including SREBP-1, PPARγ, C/EBPα, and FAS, were significantly decreased. In addition, OVJ treatment significantly reduced inflammatory cytokines and oxidative stress. OVJ supplement influenced intestinal bacterial composition from phylum to genus level, including decreased Proteobacteria in the ascending colon in the phylum. At the family level, Akkermansia, which are associated with obesity, were significantly augmented in the transverse colon and descending colon compared to the control juice group. In addition, treatment with OVJ affected predicted lipid-metabolism-function genes related to lipid synthesis. These results suggest that OVJ supplementation may modulate gut microbial community and reduce the potential symptom of hyperlipidemia in diet-obese mice.
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Affiliation(s)
| | | | - Jisoo Kim
- R&BD Center, hy Co., Ltd. Yongin-si Korea
| | - Bora Nam
- R&BD Center, hy Co., Ltd. Yongin-si Korea
| | | | | | - Jaehun Sim
- R&BD Center, hy Co., Ltd. Yongin-si Korea
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5
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McCoubrey LE, Favaron A, Awad A, Orlu M, Gaisford S, Basit AW. Colonic drug delivery: Formulating the next generation of colon-targeted therapeutics. J Control Release 2023; 353:1107-1126. [PMID: 36528195 DOI: 10.1016/j.jconrel.2022.12.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/26/2022]
Abstract
Colonic drug delivery can facilitate access to unique therapeutic targets and has the potential to enhance drug bioavailability whilst reducing off-target effects. Delivering drugs to the colon requires considered formulation development, as both oral and rectal dosage forms can encounter challenges if the colon's distinct physiological environment is not appreciated. As the therapeutic opportunities surrounding colonic drug delivery multiply, the success of novel pharmaceuticals lies in their design. This review provides a modern insight into the key parameters determining the effective design and development of colon-targeted medicines. Influential physiological features governing the release, dissolution, stability, and absorption of drugs in the colon are first discussed, followed by an overview of the most reliable colon-targeted formulation strategies. Finally, the most appropriate in vitro, in vivo, and in silico preclinical investigations are presented, with the goal of inspiring strategic development of new colon-targeted therapeutics.
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Affiliation(s)
- Laura E McCoubrey
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alessia Favaron
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Atheer Awad
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Mine Orlu
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Simon Gaisford
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Abdul W Basit
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK.
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6
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Zhang X, Fang Y, Yang G, Hou X, Hai Y, Xia M, He F, Zhao Y, Liu S. Isolation and characterization of a novel human intestinal Enterococcus faecium FUA027 capable of producing urolithin A from ellagic acid. Front Nutr 2022; 9:1039697. [PMID: 36438752 PMCID: PMC9682137 DOI: 10.3389/fnut.2022.1039697] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 10/29/2023] Open
Abstract
Urolithin A (UA) has received considerable research attention because of its health benefits. However, only a few strains have been reported to produce UA from ellagic acid (EA), and the molecular mechanisms underlying the gut microbiota-mediated transformation of ellagic acid into urolithin A is limited. In the present study, a single strain FUA027 capable of converting ellagic acid into UA in vitro was isolated from the fecal samples. The strain was identified as Enterococcus faecium through the morphological, physiological, biochemical and genetic tests. UA was produced at the beginning of the stationary phase and its levels peaked at 50 h, with the highest concentration being 10.80 μM. The strain Enterococcus faecium FUA027 is the first isolated strain of Enterococcus sp. producing urolithin A from ellagic acid, which may be developed as probiotics and used to explore molecular mechanisms underlying the biotransformation of ellagic acid into UA.
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Affiliation(s)
- Xiaomeng Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Yaowei Fang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Guang Yang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Xiaoyue Hou
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Yang Hai
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, China
| | - Mengjie Xia
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Fuxiang He
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Yaling Zhao
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Shu Liu
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
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7
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Wagner A. Competition for nutrients increases invasion resistance during assembly of microbial communities. Mol Ecol 2022; 31:4188-4203. [PMID: 35713370 PMCID: PMC9542400 DOI: 10.1111/mec.16565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022]
Abstract
The assembly of microbial communities through sequential invasions of microbial species is challenging to study experimentally. Here, I used genome‐scale metabolic models of multiple species to model community assembly. Each such model represents all known biochemical reactions that a species uses to build biomass from nutrients in the environment. Species interactions in such models emerge from first biochemical principles, either through competition for environmental nutrients, or through cross‐feeding on metabolic by‐products excreted by resident species. I used these models to study 250 community assembly sequences. In each such sequence, a community changes through successive species invasions. During the 250 assembly sequences, communities become more species‐rich and invasion‐resistant. Resistance against both constructive and destructive invasions – those that entail species extinction – is associated with high community productivity, high biomass, and low concentrations of unused carbon. Competition for nutrients outweighs the influence of cross‐feeding on the growth rate of individual species. In a community assembly network of all communities that arise during the 250 assembly sequences, some communities occur more often than expected by chance. These include invasion resistant “attractor” communities with high biomass that arise late in community assembly and persist preferentially because of their invasion resistance. Genome‐scale metabolic models can reveal generic properties of microbial communities that are independent of the resident species and the environment.
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Affiliation(s)
- Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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8
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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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9
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Renwick S, Ganobis CM, Elder RA, Gianetto-Hill C, Higgins G, Robinson AV, Vancuren SJ, Wilde J, Allen-Vercoe E. Culturing Human Gut Microbiomes in the Laboratory. Annu Rev Microbiol 2021; 75:49-69. [PMID: 34038159 DOI: 10.1146/annurev-micro-031021-084116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Caroline M Ganobis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Riley A Elder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Connor Gianetto-Hill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Gregory Higgins
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Avery V Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
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10
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Auger C, Vinaik R, Appanna VD, Jeschke MG. Beyond mitochondria: Alternative energy-producing pathways from all strata of life. Metabolism 2021; 118:154733. [PMID: 33631145 PMCID: PMC8052308 DOI: 10.1016/j.metabol.2021.154733] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022]
Abstract
It is well-established that mitochondria are the powerhouses of the cell, producing adenosine triphosphate (ATP), the universal energy currency. However, the most significant strengths of the electron transport chain (ETC), its intricacy and efficiency, are also its greatest downfalls. A reliance on metal complexes (FeS clusters, hemes), lipid moities such as cardiolipin, and cofactors including alpha-lipoic acid and quinones render oxidative phosphorylation vulnerable to environmental toxins, intracellular reactive oxygen species (ROS) and fluctuations in diet. To that effect, it is of interest to note that temporal disruptions in ETC activity in most organisms are rarely fatal, and often a redundant number of failsafes are in place to permit continued ATP production when needed. Here, we highlight the metabolic reconfigurations discovered in organisms ranging from parasitic Entamoeba to bacteria such as pseudomonads and then complex eukaryotic systems that allow these species to adapt to and occasionally thrive in harsh environments. The overarching aim of this review is to demonstrate the plasticity of metabolic networks and recognize that in times of duress, life finds a way.
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Affiliation(s)
- Christopher Auger
- Ross Tilley Burn Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
| | - Roohi Vinaik
- University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - Marc G Jeschke
- Ross Tilley Burn Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada; University of Toronto, Toronto, Ontario M5S 1A1, Canada.
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11
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Firrman J, Liu L, Tanes C, Friedman ES, Bittinger K, Daniel S, van den Abbeele P, Evans B. Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13056-13067. [PMID: 31690071 DOI: 10.1021/acs.jafc.9b05202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatographies coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC and the TC and DC regions in terms of short-chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understand the structure-function relationship of the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wyndmoor, Pennsylvania 19038, United States
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | | | - Bradley Evans
- Proteomics & Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, United States
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12
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Poeker SA, Lacroix C, de Wouters T, Spalinger MR, Scharl M, Geirnaert A. Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota. Front Microbiol 2019; 10:1166. [PMID: 31191488 PMCID: PMC6548829 DOI: 10.3389/fmicb.2019.01166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.
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Affiliation(s)
- Sophie A Poeker
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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13
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Guzman-Rodriguez M, McDonald JAK, Hyde R, Allen-Vercoe E, Claud EC, Sheth PM, Petrof EO. Using bioreactors to study the effects of drugs on the human microbiota. Methods 2018; 149:31-41. [PMID: 30102990 DOI: 10.1016/j.ymeth.2018.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
The study of complex microbial communities has become a major research focus as mounting evidence suggests the pivotal role microbial communities play in host health and disease. Microbial communities of the gastrointestinal tract, known as the gut microbiota, have been implicated in aiding the host with vitamin biosynthesis, regulation of host energy metabolism, immune system development, and resistance to pathogen invasion. Conversely, disruptions of the gut microbiota have been linked to host morbidity, including the development of inflammatory diseases, metabolic disorders, increased cardiovascular risk, and increased risk of infectious diseases. However, studying the gut microbiota in humans and animals is challenging, as many microorganisms are fastidious with unique nutritional or environmental requirements that are often not met using conventional culture techniques. Bioreactors provide a unique solution to overcome some of the limitations of conventional culture techniques. Bioreactors have been used to propagate and establish complex microbial communities in vitro by recapitulating the physiological conditions found in the GI tract. These systems further our understanding of microbial physiology and facilitate our understanding of the impact of medications and xenobiotics on microbial communities. Here, we review the versatility and breadth of bioreactor systems that are currently available and how they are being used to study faecal and defined microbial communities. Bioreactors provide a unique opportunity to study complex microbial interactions and perturbations in vitro in a controlled environment without confounding biotic and abiotic variables.
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Affiliation(s)
- Mabel Guzman-Rodriguez
- Gastrointestinal Disease Research Unit, Kingston Health Sciences Center, Kingston, ON, Canada
| | - Julie A K McDonald
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Richard Hyde
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Erika C Claud
- Departments of Pediatrics and Medicine, The University of Chicago, Chicago, IL, United States
| | - Prameet M Sheth
- Gastrointestinal Disease Research Unit, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Division of Microbiology and Infectious Diseases, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
| | - Elaine O Petrof
- Gastrointestinal Disease Research Unit, Kingston Health Sciences Center, Kingston, ON, Canada; Division of Microbiology and Infectious Diseases, Kingston Health Sciences Center, Kingston, ON, Canada; Department of Medicine, Kingston Health Sciences Center, Kingston, ON, Canada
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14
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Liu L, Firrman J, Tanes C, Bittinger K, Thomas-Gahring A, Wu GD, Van den Abbeele P, Tomasula PM. Establishing a mucosal gut microbial community in vitro using an artificial simulator. PLoS One 2018; 13:e0197692. [PMID: 30016326 PMCID: PMC6050037 DOI: 10.1371/journal.pone.0197692] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10–20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.
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Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Audrey Thomas-Gahring
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Gary D. Wu
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
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Cha KH, Lee EH, Yoon HS, Lee JH, Kim JY, Kang K, Park JS, Jin JB, Ko G, Pan CH. Effects of fermented milk treatment on microbial population and metabolomic outcomes in a three-stage semi-continuous culture system. Food Chem 2018; 263:216-224. [PMID: 29784310 DOI: 10.1016/j.foodchem.2018.04.095] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/18/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022]
Abstract
We investigated the impact of a fermented milk product on gut microbiota and their metabolism in 3 different conditions of the colon with a systemic viewpoint. An in vitro semi-continuous anaerobic cultivation was used to assess the colon compartment-specific influence of fermented milk, followed by a multiomics approach combining 16S rDNA amplicon sequencing and nuclear magnetic resonance (NMR) spectroscopy. The microbiome profiling and metabolomic features were significantly different across three colon compartments and after fermented milk treatment. Integrative correlation analysis indicated that the alteration of butyrate-producing microbiota (Veillonella, Roseburia, Lachnospira, and Coprococcus) and some primary metabolites (butyrate, ethanol, lactate, and isobutyrate) in the treatment group had a strong association with the fermented milk microorganisms. Our findings suggested that fermented milk treatment significantly affected microbial population in an in vitro cultivation system as well as the colonic metabolome in different ways in each of colon compartment.
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Affiliation(s)
- Kwang Hyun Cha
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea; Department of Environmental Health Sciences, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea.
| | - Eun Ha Lee
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea.
| | - Hyo Shin Yoon
- Department of Environmental Health Sciences, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jae Ho Lee
- R&BD Center, Korea Yakult Co. Ltd., Yongin 17086, Republic of Korea.
| | - Joo Yun Kim
- R&BD Center, Korea Yakult Co. Ltd., Yongin 17086, Republic of Korea.
| | - Kyungsu Kang
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea.
| | - Jin-Soo Park
- Natural Constituents Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea.
| | - Jong Beom Jin
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea.
| | - GwangPyo Ko
- Department of Environmental Health Sciences, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul 08826, Republic of Korea; KoBioLabs, Inc., 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Cheol-Ho Pan
- Systems Biotechnology Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea.
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16
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In vitro rumen fermentation of soluble and non-soluble polymeric carbohydrates in relation to ruminal acidosis. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1307-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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17
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Zeng H, Huang C, Lin S, Zheng M, Chen C, Zheng B, Zhang Y. Lotus Seed Resistant Starch Regulates Gut Microbiota and Increases Short-Chain Fatty Acids Production and Mineral Absorption in Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9217-9225. [PMID: 28954513 DOI: 10.1021/acs.jafc.7b02860] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lotus seed resistant starch, known as resistant starch type 3 (LRS3), was orally administered to mice to investigate its effects on the gut microbiota, short-chain fatty acids (SCFAs) production, and mineral absorption. The results showed that mice fed LRS3 displayed a lower level of gut bacterial diversity than other groups. The numbers of starch-utilizing and butyrate-producing bacteria, such as Lactobacillus and Bifidobacterium and Lachnospiraceae, Ruminococcaceae, and Clostridium, respectively, in mice increased after the administration of medium and high doses of LRS3, while those of Rikenellaceae and Porphyromonadaceae decreased. Furthermore, SCFAs and lactic acid in mice feces were affected by LRS3, and lactate was fermented to butyrate by gut microbiota. LRS3 enhanced the intestinal absorption of calcium, magnesium, and iron, and this was dependent on the type and concentration of SCFAs, especially butyrate. Thus, LRS3 promoted the production of SCFAs and mineral absorption by regulating gut microbiota in mice.
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Affiliation(s)
- Hongliang Zeng
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
- Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University , Fuzhou 350002, China
| | - Cancan Huang
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
| | - Shan Lin
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
| | - Mingjing Zheng
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
| | - Chuanjie Chen
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
| | - Baodong Zheng
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
- Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University , Fuzhou 350002, China
| | - Yi Zhang
- College of Food Science, Fujian Agriculture and Forestry University , Fuzhou, Fujian P. R. China 350002
- Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University , Fuzhou 350002, China
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18
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Defois C, Ratel J, Denis S, Batut B, Beugnot R, Peyretaillade E, Engel E, Peyret P. Environmental Pollutant Benzo[ a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota. Front Microbiol 2017; 8:1562. [PMID: 28861070 PMCID: PMC5559432 DOI: 10.3389/fmicb.2017.01562] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/02/2017] [Indexed: 01/23/2023] Open
Abstract
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.
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Affiliation(s)
- Clémence Defois
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Jérémy Ratel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Sylvain Denis
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Bérénice Batut
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Réjane Beugnot
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Eric Peyretaillade
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Erwan Engel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Pierre Peyret
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
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Gaci N, Chaudhary PP, Tottey W, Alric M, Brugère JF. Functional amplification and preservation of human gut microbiota. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1308070. [PMID: 28572754 PMCID: PMC5443092 DOI: 10.1080/16512235.2017.1308070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Abstract
Background: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. Objective: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. Design: Taking advantage of in vitro gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations. Preservation efficiencies were determined after 3 and 6 months and compared with the fresh initial microbiota diversity and metabolic activity, using the chemostat-based Environmental Control System for Intestinal Microbiota (ECSIM) in vitro model of the gut environment. Microbial populations were tested for fermentation gas, short-chain fatty acids, and composition of amplified and resuscitated microbiota, encompassing methanogenic archaea. Results: Amplification of the microbial repertoire from a fresh fecal sample was achieved with high fidelity. Dimethylsulfoxide, alone or mixed with other CPAs, showed the best efficiency for functional preservation, and the duration of preservation had little effect. Conclusions: The amplification and resuscitation of fecal microbiota can be performed using specialized in vitro gut models. Correct amplification of the initial microbes should ease the sharing of clinical samples and improve the safety of fecal microbiota transplantation. Abbreviations: CDI, Clostridium difficile infection; CPA, cryoprotective agent; D, DMSO, dimethylsulfoxide; FMT, fecal microbiota transplantation; G, glycerol; IBD, inflammatory bowel disease; P, PEG-4000, polyethylene glycol 4000 g.mol−1; SCFA, short-chain fatty acid; SNR, signal-to-noise ratio
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Affiliation(s)
- Nadia Gaci
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | | | - William Tottey
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Monique Alric
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
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20
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Tottey W, Feria-Gervasio D, Gaci N, Laillet B, Pujos E, Martin JF, Sebedio JL, Sion B, Jarrige JF, Alric M, Brugère JF. Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence. J Neurogastroenterol Motil 2017; 23:124-134. [PMID: 27530163 PMCID: PMC5216643 DOI: 10.5056/jnm16042] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/13/2016] [Accepted: 06/14/2016] [Indexed: 12/19/2022] Open
Abstract
Background/Aims Human gut microbiota harbors numerous metabolic properties essential for the host’s health. Increased intestinal transit time affects a part of the population and is notably observed with human aging, which also corresponds to modifications of the gut microbiota. Thus we tested the metabolic and compositional changes of a human gut microbiota induced by an increased transit time simulated in vitro. Methods The in vitro system, Environmental Control System for Intestinal Microbiota, was used to simulate the environmental conditions of 3 different anatomical parts of the human colon in a continuous process. The retention times of the chemostat conditions were established to correspond to a typical transit time of 48 hours next increased to 96 hours. The bacterial communities, short chain fatty acids and metabolite fingerprints were determined. Results Increase of transit time resulted in a decrease of biomass and of diversity in the more distal compartments. Short chain fatty acid analyses and metabolite fingerprinting revealed increased activity corresponding to carbohydrate fermentation in the proximal compartments while protein fermentations were increased in the lower parts. Conclusions This study provides the evidence that the increase of transit time, independently of other factors, affects the composition and metabolism of the gut microbiota. The transit time is one of the factors that explain some of the modifications seen in the gut microbiota of the elderly, as well as patients with slow transit time.
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Affiliation(s)
- William Tottey
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - David Feria-Gervasio
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - Nadia Gaci
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - Brigitte Laillet
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, Saint-Genès Champanelle, France
| | - Estelle Pujos
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, Saint-Genès Champanelle, France
| | - Jean-François Martin
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, Saint-Genès Champanelle, France
| | - Jean-Louis Sebedio
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, Saint-Genès Champanelle, France
| | - Benoit Sion
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - Jean-François Jarrige
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - Monique Alric
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
| | - Jean-François Brugère
- EA 4678 CIDAM, Clermont Université, Université d'Auvergne, CRNH Auvergne, Clermont-Ferrand, France
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21
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O'Donnell MM, Rea MC, O'Sullivan Ó, Flynn C, Jones B, McQuaid A, Shanahan F, Ross RP. Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias. J Microbiol Methods 2016; 129:109-116. [PMID: 27498348 DOI: 10.1016/j.mimet.2016.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/22/2016] [Accepted: 08/02/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND In-vitro gut fermentation systems provide suitable models for studying gut microbiota composition and functionality. However, such methods depend on the availability of donors and the assumption of reproducibility between microbial communities before experimental treatments commence. The aim of this study was to develop a frozen standardised inoculum (FSI) which minimizes inter-individual variation and to determine its stability over time using culture-dependent and culture-independent techniques. RESULTS A method for the preparation difference of a FSI is described which involves pooling the faecal samples, centrifugation and pelleting of the cell biomass and finally homogenising the cell pellets with phosphate buffer and glycerol. Using this approach, no significant difference in total anaerobe cell viability was observed between the fresh standardised inoculum (before freezing) and the 12days post freezing FSI. Moreover, Quantitative PCR revealed no significant alterations in the estimated bacterial numbers in the FSI preparations for any of the phyla. MiSeq sequencing revealed minute differences in the relative abundance at phylum, family and genus levels between the FSI preparations. Differences in the microbiota denoted as significant were limited between preparations in the majority of cases to changes in percentage relative abundance of ±0.5%. The independently prepared FSIs revealed a high degree of reproducibility in terms of microbial composition between the three preparations. CONCLUSIONS This study provides a method to produce a standardised human faecal inoculum suitable for freezing. Based on culture-dependent and independent analysis, the method ensures a degree of reproducibility between preparations by lessening the effect of inter-individual variation among the donors, thereby making the system more suitable for the accurate interpretation of the effects of experimental treatments.
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Affiliation(s)
- Michelle M O'Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Mary C Rea
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Órla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland
| | - Cal Flynn
- Kerry Ingredients, Tralee Road, Listowel, Co. Kerry, Ireland
| | - Beth Jones
- Kerry Ingredients & Flavours, Americas Regional Headquarters, 3330 Millington Road, Beloit, WI 53511, United States
| | - Albert McQuaid
- Kerry Ingredients, Tralee Road, Listowel, Co. Kerry, Ireland
| | | | - R Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Institute, University College Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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22
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Takagi R, Sasaki K, Sasaki D, Fukuda I, Tanaka K, Yoshida KI, Kondo A, Osawa R. A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics. PLoS One 2016; 11:e0160533. [PMID: 27483470 PMCID: PMC4970706 DOI: 10.1371/journal.pone.0160533] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 02/06/2023] Open
Abstract
We devised a single-batch fermentation system to simulate human colonic microbiota from fecal samples, enabling the complex mixture of microorganisms to achieve densities of up to 1011 cells/mL in 24 h. 16S rRNA gene sequence analysis of bacteria grown in the system revealed that representatives of the major phyla, including Bacteroidetes, Firmicutes, and Actinobacteria, as well as overall species diversity, were consistent with those of the original feces. On the earlier stages of fermentation (up to 9 h), trace mixtures of acetate, lactate, and succinate were detectable; on the later stages (after 24 h), larger amounts of acetate accumulated along with some of propionate and butyrate. These patterns were similar to those observed in the original feces. Thus, this system could serve as a simple model to simulate the diversity as well as the metabolism of human colonic microbiota. Supplementation of the system with several prebiotic oligosaccharides (including fructo-, galacto-, isomalto-, and xylo-oligosaccharides; lactulose; and lactosucrose) resulted in an increased population in genus Bifidobacterium, concomitant with significant increases in acetate production. The results suggested that this fermentation system may be useful for in vitro, pre-clinical evaluation of the effects of prebiotics prior to testing in humans.
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Affiliation(s)
- Risa Takagi
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
| | - Kengo Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- * E-mail:
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
| | - Itsuko Fukuda
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- Research Center for Food Safety and Security, Graduate School of Agricultural Science, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
| | - Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
| | - Ken-ichi Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- Organization of Advanced Science and Technology, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- Organization of Advanced Science and Technology, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Ro Osawa
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- Organization of Advanced Science and Technology, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
- Research Center for Food Safety and Security, Graduate School of Agricultural Science, Kobe University, 1–1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657–8501, Japan
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Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
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Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
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Krishnan S, Alden N, Lee K. Pathways and functions of gut microbiota metabolism impacting host physiology. Curr Opin Biotechnol 2015; 36:137-45. [PMID: 26340103 DOI: 10.1016/j.copbio.2015.08.015] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 01/13/2023]
Abstract
The bacterial populations in the human intestine impact host physiological functions through their metabolic activity. In addition to performing essential catabolic and biotransformation functions, the gut microbiota produces bioactive small molecules that mediate interactions with the host and contribute to the neurohumoral axes connecting the intestine with other parts of the body. This review discusses recent progress in characterizing the metabolic products of the gut microbiota and their biological functions, focusing on studies that investigate the responsible bacterial pathways and cognate host receptors. Several key areas are highlighted for future development: context-based analysis targeting pathways; integration of analytical approaches; metabolic modeling; and synthetic systems for in vivo manipulation of microbiota functions. Prospectively, these developments could further our mechanistic understanding of host-microbiota interactions.
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Affiliation(s)
- Smitha Krishnan
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, United States
| | - Nicholas Alden
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, United States
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, United States.
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Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions. Appl Microbiol Biotechnol 2015; 99:5801-15. [DOI: 10.1007/s00253-015-6739-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/23/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
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26
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Barroso E, Cueva C, Peláez C, Martínez-Cuesta MC, Requena T. Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2014.12.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Tralau T, Sowada J, Luch A. Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology? Expert Opin Drug Metab Toxicol 2014; 11:411-25. [PMID: 25476418 DOI: 10.1517/17425255.2015.990437] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Our microbiome harbours a metabolic capacity far beyond our own. Moreover, its gene pool is highly adaptable and subject to selective pressure, including host exposure to xenobiotics. Yet, the resulting adaptations do not necessarily follow host well-being and can therefore contribute to disease or unfavourable metabolite production. AREAS COVERED This review provides an overview of our host-microbiome relationship in light of bacterial (xenobiotic) metabolism, community dynamics, entero-endocrine crosstalk, dysbiosis and potential therapeutic targets. In addition, it will highlight the need for a systematic analysis of the microbiome's potential for substance toxification. EXPERT OPINION The influence of our microbiota reaches from primary metabolites to secondary effects such as substrate competition or the activation of eukaryotic Phase I and Phase II enzymes. Further on it plays a hitherto underestimated role in drug metabolism, toxicity and pathogenesis. These effects are partly caused by entero-endocrine crosstalk and interference with eukaryotic regulatory networks. On first sight, the resulting concept of a metabolically competent microbiome adds enormous complexity to human physiology. Yet, the potential specificity of microbial targets harbours therapeutic promise for diseases such as diabetes, cancer and psychiatric disorders. A better physiological and biochemical understanding of the microbiome is thus of high priority for academia and biomedical research.
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Affiliation(s)
- Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Department of Chemicals and Product Safety , Max-Dohrn Strasse 8-10, 10589 Berlin , Germany
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Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF. Archaea and the human gut: New beginning of an old story. World J Gastroenterol 2014; 20:16062-16078. [PMID: 25473158 PMCID: PMC4239492 DOI: 10.3748/wjg.v20.i43.16062] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/14/2014] [Accepted: 07/22/2014] [Indexed: 02/06/2023] Open
Abstract
Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.
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