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Caffrey EB, Sonnenburg JL, Devkota S. Our extended microbiome: The human-relevant metabolites and biology of fermented foods. Cell Metab 2024; 36:684-701. [PMID: 38569469 DOI: 10.1016/j.cmet.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.
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Affiliation(s)
- Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA.
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel Diseases Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Salsinha AS, Pimentel LL, Fontes AL, Gomes AM, Rodríguez-Alcalá LM. Microbial Production of Conjugated Linoleic Acid and Conjugated Linolenic Acid Relies on a Multienzymatic System. Microbiol Mol Biol Rev 2018; 82:e00019-18. [PMID: 30158254 PMCID: PMC6298612 DOI: 10.1128/mmbr.00019-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conjugated linoleic acids (CLAs) and conjugated linolenic acids (CLNAs) have gained significant attention due to their anticarcinogenic and lipid/energy metabolism-modulatory effects. However, their concentration in foodstuffs is insufficient for any therapeutic application to be implemented. From a biotechnological standpoint, microbial production of these conjugated fatty acids (CFAs) has been explored as an alternative, and strains of the genera Propionibacterium, Lactobacillus, and Bifidobacterium have shown promising producing capacities. Current screening research works are generally based on direct analytical determination of production capacity (e.g., trial and error), representing an important bottleneck in these studies. This review aims to summarize the available information regarding identified genes and proteins involved in CLA/CLNA production by these groups of bacteria and, consequently, the possible enzymatic reactions behind such metabolic processes. Linoleate isomerase (LAI) was the first enzyme to be described to be involved in the microbiological transformation of linoleic acids (LAs) and linolenic acids (LNAs) into CFA isomers. Thus, the availability of lai gene sequences has allowed the development of genetic screening tools. Nevertheless, several studies have reported that LAIs have significant homology with myosin-cross-reactive antigen (MCRA) proteins, which are involved in the synthesis of hydroxy fatty acids, as shown by hydratase activity. Furthermore, it has been suggested that CLA and/or CLNA production results from a stress response performed by the activation of more than one gene in a multiple-step reaction. Studies on CFA biochemical pathways are essential to understand and characterize the metabolic mechanism behind this process, unraveling all the gene products that may be involved. As some of these bacteria have shown modulation of lipid metabolism in vivo, further research to be focused on this topic may help us to understand the role of the gut microbiota in human health.
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Affiliation(s)
- Ana S Salsinha
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Lígia L Pimentel
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
- Centro de Investigação em Tecnologias e Sistemas de Informação em Saúde, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Unidade de Investigação de Química Orgânica, Produtos Naturais e Agroalimentares, Universidade de Aveiro, Aveiro, Portugal
| | - Ana L Fontes
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
- Unidade de Investigação de Química Orgânica, Produtos Naturais e Agroalimentares, Universidade de Aveiro, Aveiro, Portugal
| | - Ana M Gomes
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Luis M Rodríguez-Alcalá
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago de Chile, Chile
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Yang B, Gao H, Stanton C, Ross RP, Zhang H, Chen YQ, Chen H, Chen W. Bacterial conjugated linoleic acid production and their applications. Prog Lipid Res 2017; 68:26-36. [PMID: 28889933 DOI: 10.1016/j.plipres.2017.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/29/2017] [Accepted: 09/06/2017] [Indexed: 11/19/2022]
Abstract
Conjugated linoleic acid (CLA) has been shown to exert various potential physiological properties including anti-carcinogenic, anti-obesity, anti-cardiovascular and anti-diabetic activities, and consequently has been considered as a promising food supplement. Bacterial biosynthesis of CLA is an attractive approach for commercial production due to its high isomer-selectivity and convenient purification process. Many bacterial species have been reported to convert free linoleic acid (LA) to CLA, hitherto only the precise CLA-producing mechanisms in Propionibacterium acnes and Lactobacillus plantarum have been illustrated completely, prompting the development of recombinant technology used in CLA production. The purpose of the article is to review the bacterial CLA producers as well as the recent progress on describing the mechanism of microbial CLA-production. Furthermore, the advances and potential in the heterologous expression of CLA genetic determinants will be presented.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - He Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland; College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China.
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Enjalbert F, Combes S, Zened A, Meynadier A. Rumen microbiota and dietary fat: a mutual shaping. J Appl Microbiol 2017; 123:782-797. [DOI: 10.1111/jam.13501] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 01/01/2023]
Affiliation(s)
- F. Enjalbert
- GenPhySE; Université de Toulouse, INRA, INPT, ENVT; Castanet Tolosan France
| | - S. Combes
- GenPhySE; Université de Toulouse, INRA, INPT, ENVT; Castanet Tolosan France
| | - A. Zened
- GenPhySE; Université de Toulouse, INRA, INPT, ENVT; Castanet Tolosan France
| | - A. Meynadier
- GenPhySE; Université de Toulouse, INRA, INPT, ENVT; Castanet Tolosan France
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Hackmann TJ, Firkins JL. Electron transport phosphorylation in rumen butyrivibrios: unprecedented ATP yield for glucose fermentation to butyrate. Front Microbiol 2015; 6:622. [PMID: 26157432 PMCID: PMC4478896 DOI: 10.3389/fmicb.2015.00622] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/08/2015] [Indexed: 12/19/2022] Open
Abstract
From a genomic analysis of rumen butyrivibrios (Butyrivibrio and Pseudobutyrivibrio sp.), we have re-evaluated the contribution of electron transport phosphorylation (ETP) to ATP formation in this group. This group is unique in that most (76%) genomes were predicted to possess genes for both Ech and Rnf transmembrane ion pumps. These pumps act in concert with the NifJ and Bcd-Etf to form a electrochemical potential (ΔμH+ and ΔμNa+), which drives ATP synthesis by ETP. Of the 62 total butyrivibrio genomes currently available from the Hungate 1000 project, all 62 were predicted to possess NifJ, which reduces oxidized ferredoxin (Fdox) during pyruvate conversion to acetyl-CoA. All 62 possessed all subunits of Bcd-Etf, which reduces Fdox and oxidizes reduced NAD during crotonyl-CoA reduction. Additionally, 61 genomes possessed all subunits of the Rnf, which generates ΔμH+ or ΔμNa+ from oxidation of reduced Fd (Fdred) and reduction of oxidized NAD. Further, 47 genomes possessed all six subunits of the Ech, which generates ΔμH+ from oxidation of Fdred. For glucose fermentation to butyrate and H2, the electrochemical potential established should drive synthesis of ∼1.5 ATP by the F0F1-ATP synthase (possessed by all 62 genomes). The total yield is ∼4.5 ATP/glucose after accounting for three ATP formed by classic substrate-level phosphorylation, and it is one the highest yields for any glucose fermentation. The yield was the same when unsaturated fatty acid bonds, not H+, served as the electron acceptor (as during biohydrogenation). Possession of both Ech and Rnf had been previously documented in only a few sulfate-reducers, was rare in other rumen prokaryotic genomes in our analysis, and may confer an energetic advantage to rumen butyrivibrios. This unique energy conservation system might enhance the butyrivibrios’ ability to overcome growth inhibition by unsaturated fatty acids, as postulated herein.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
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Fukuda S, Nakanishi Y, Chikayama E, Ohno H, Hino T, Kikuchi J. Evaluation and characterization of bacterial metabolic dynamics with a novel profiling technique, real-time metabolotyping. PLoS One 2009; 4:e4893. [PMID: 19287504 PMCID: PMC2654759 DOI: 10.1371/journal.pone.0004893] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 02/16/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Environmental processes in ecosystems are dynamically altered by several metabolic responses in microorganisms, including intracellular sensing and pumping, battle for survival, and supply of or competition for nutrients. Notably, intestinal bacteria maintain homeostatic balance in mammals via multiple dynamic biochemical reactions to produce several metabolites from undigested food, and those metabolites exert various effects on mammalian cells in a time-dependent manner. We have established a method for the analysis of bacterial metabolic dynamics in real time and used it in combination with statistical NMR procedures. METHODOLOGY/PRINCIPAL FINDINGS We developed a novel method called real-time metabolotyping (RT-MT), which performs sequential (1)H-NMR profiling and two-dimensional (2D) (1)H, (13)C-HSQC (heteronuclear single quantum coherence) profiling during bacterial growth in an NMR tube. The profiles were evaluated with such statistical methods as Z-score analysis, principal components analysis, and time series of statistical TOtal Correlation SpectroScopY (TOCSY). In addition, using 2D (1)H, (13)C-HSQC with the stable isotope labeling technique, we observed the metabolic kinetics of specific biochemical reactions based on time-dependent 2D kinetic profiles. Using these methods, we clarified the pathway for linolenic acid hydrogenation by a gastrointestinal bacterium, Butyrivibrio fibrisolvens. We identified trans11, cis13 conjugated linoleic acid as the intermediate of linolenic acid hydrogenation by B. fibrisolvens, based on the results of (13)C-labeling RT-MT experiments. In addition, we showed that the biohydrogenation of polyunsaturated fatty acids serves as a defense mechanism against their toxic effects. CONCLUSIONS RT-MT is useful for the characterization of beneficial bacterium that shows potential for use as probiotic by producing bioactive compounds.
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Affiliation(s)
- Shinji Fukuda
- RIKEN Research Center for Allergy and Immunology, Suehiro-cho, Yokohama, Japan
- International Graduate School of Arts and Sciences, Yokohama City University, Suehiro-cho, Yokohama, Japan
| | - Yumiko Nakanishi
- International Graduate School of Arts and Sciences, Yokohama City University, Suehiro-cho, Yokohama, Japan
- RIKEN Plant Science Center, Suehiro-cho, Yokohama, Japan
| | | | - Hiroshi Ohno
- RIKEN Research Center for Allergy and Immunology, Suehiro-cho, Yokohama, Japan
- International Graduate School of Arts and Sciences, Yokohama City University, Suehiro-cho, Yokohama, Japan
| | - Tsuneo Hino
- Department of Life Science, Meiji University, Tama-ku, Kawasaki, Japan
- * E-mail: (TH); (JK)
| | - Jun Kikuchi
- International Graduate School of Arts and Sciences, Yokohama City University, Suehiro-cho, Yokohama, Japan
- RIKEN Plant Science Center, Suehiro-cho, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Japan
- * E-mail: (TH); (JK)
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Vlaeminck B, Mengistu G, Fievez V, de Jonge L, Dijkstra J. Effect of In Vitro Docosahexaenoic Acid Supplementation to Marine Algae-Adapted and Unadapted Rumen Inoculum on the Biohydrogenation of Unsaturated Fatty Acids in Freeze-Dried Grass. J Dairy Sci 2008; 91:1122-32. [DOI: 10.3168/jds.2007-0537] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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