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Feng C, Wu Y, Cai Z, Song Z, Shim YY, Reaney MJT, Wang Y, Zhang N. A comparative study on flaxseed lignan biotransformation through resting cell catalysis and microbial fermentation by β-glucosidase production Lactiplantibacillus plantarum. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5869-5881. [PMID: 38407005 DOI: 10.1002/jsfa.13412] [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: 11/08/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Flax lignan has attracted much attention because of its potential bioactivities. However, the bioavailability of secoisolariciresinol diglucoside (SDG), the main lignan in flaxseed, depends on the bioconversion by the colon bacteria. Lactic acid bacteria (LAB) with β-glucosidase activity has found wide application in preparing bioactive aglycone. RESULTS LAB strains with good β-glucosidase activity were isolated from fermented tofu. Their bioconversion of flax lignan extract was investigated by resting cell catalysis and microbial fermentation, and the metabolism of SDG by Lactiplantibacillus plantarum C5 following fermentation was characterized by widely targeted metabolomics. Five L. plantarum strains producing β-glucosidase with broad substrate specificity were isolated and identified, and they all can transform SDG into secoisolariciresinol (SECO). L. plantarum C5 resting cell reached a maximum SDG conversion of 49.19 ± 3.75%, and SECO generation of 21.49 ± 1.32% (0.215 ± 0.013 mm) at an SDG substrate concentration of 1 mM and 0.477 ± 0.003 mm SECO was produced at 4 mm within 24 h. Although sixteen flax lignan metabolites were identified following the fermentation of SDG extract by L. plantarum C5, among them, four were produced following the fermentation: SECO, demethyl-SECO, demethyl-dehydroxy-SECO and isolariciresinol. Moreover, seven lignans increased significantly. CONCLUSION Fermentation significantly increased the profile and level of flax lignan metabolites, and the resting cell catalysis benefits from higher bioconversion efficiency and more straightforward product separation. Resting cell catalysis and microbial fermentation of flax lignan extract by the isolated β-glucosidase production L. plantarum could be potentially applied in preparing flax lignan ingredients and fermented flaxseed. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chengcheng Feng
- Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
| | - You Wu
- Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
| | - Zizhe Cai
- Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
| | - Ziliang Song
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Youn Young Shim
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Martin J T Reaney
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Yong Wang
- Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
| | - Ning Zhang
- Department of Food Science and Engineering, Jinan University, Guangzhou, China
- Guangdong Joint International Research Centre of Oilseed Biorefinery, Nutrition and Safety, Department of Food Science and Engineering, Jinan University, Guangzhou, China
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Mo Y, Li Y, Liang S, Wang W, Zhang H, Zhao J, Xu M, Zhang X, Cao H, Xie S, Lv Y, Wu Y, Zhang Z, Yang W. Urinary enterolignans and enterolignan-predicting microbial species are favourably associated with liver fat and other obesity markers. Food Funct 2024. [PMID: 38874113 DOI: 10.1039/d3fo05632e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Aims: Plant-derived lignans may protect against obesity, while their bioactivity needs gut microbial conversion to enterolignans. We used repeated measures to identify enterolignan-predicting microbial species and investigate whether enterolignans and enterolignan-predicting microbial species are associated with obesity. Methods: Urinary enterolignans, fecal microbiota, body weight, height, and circumferences of the waist (WC) and hips (HC) were repeatedly measured at the baseline and after 1 year in 305 community-dwelling adults in Huoshan, China. Body composition and liver fat [indicated by the controlled attenuation parameter (CAP)] were measured after 1 year. Multivariate-adjusted linear models and linear mixed-effects models were used to analyze single and repeated measurements, respectively. Results: Enterolactone and enterodiol levels were both inversely associated with the waist-to-hip ratio, body fat mass (BFM), visceral fat level (VFL), and liver fat accumulation (all P < 0.05). Enterolactone levels were also associated with lower WC (β = -0.0035 and P = 0.013) and HC (β = -0.0028 and P = 0.044). We identified multiple bacterial genera whose relative abundance was positively associated with the levels of enterolactone (26 genera) and enterodiol (22 genera, all P false discovery rate < 0.05), and constructed the enterolactone-predicting microbial score and enterodiol-predicting microbial score to reflect the overall enterolignan-producing potential of the host gut microbiota. Both these scores were associated with lower body weight and CAP (all P < 0.05). The enterolactone-predicting microbial score was also inversely associated with the BFM (β = -0.1128 and P = 0.027) and VFL (β = -0.1265 and P = 0.044). Conclusion: Our findings support that modulating the host gut microbiome could be a potential strategy to prevent obesity by enhancing the production of enterolignans.
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Affiliation(s)
- Yufeng Mo
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics/Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Anhui Medical University, Hefei, Anhui, China
| | - Yamin Li
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Shaoxian Liang
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Wuqi Wang
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Honghua Zhang
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Jiajia Zhao
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Mengting Xu
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Xiaoyu Zhang
- Department of Physical Examination Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hongjuan Cao
- Department of Chronic Non-communicable Diseases Prevention and Control, Lu'an Municipal Center for Disease Control and Prevention, Lu'an, Anhui, China
| | - Shaoyu Xie
- Department of Chronic Non-communicable Diseases Prevention and Control, Lu'an Municipal Center for Disease Control and Prevention, Lu'an, Anhui, China
| | - Yaning Lv
- Technology Center of Hefei Customs, and Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, Anhui, China
| | - Yaqin Wu
- Technology Center of Hefei Customs, and Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, Anhui, China
| | - Zhuang Zhang
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Wanshui Yang
- Department of Nutrition, Center for Big Data and Population Health of IHM, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics/Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Anhui Medical University, Hefei, Anhui, China
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3
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Ookoshi K, Sawane K, Fukumitsu S, Aida K. Availability of dietary secoisolariciresinol diglucoside on borderline blood cholesterol level in men: a randomized, parallel, controlled, double-blinded clinical trial. J Clin Biochem Nutr 2024; 74:261-266. [PMID: 38799144 PMCID: PMC11111469 DOI: 10.3164/jcbn.23-122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/23/2024] [Indexed: 05/29/2024] Open
Abstract
Borderline low-density lipoprotein cholesterol levels (120-139 mg/dl) increase the risk of cardiovascular disease. Therefore, the use of functional dietary nutrients is expected to control blood low-density lipoprotein cholesterol levels. This study aimed to evaluate the effect of dietary secoisolariciresinol diglucoside on blood cholesterol in healthy adults with borderline low-density lipoprotein cholesterol levels. A randomized, parallel, controlled, double-blinded clinical trial was performed for participants with borderline low-density lipoprotein cholesterol levels, for 12 weeks with secoisolariciresinol diglucoside (60 mg/day) or placebo. Lipid profile [low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol/high-density lipoprotein cholesterol ratio, total cholesterol, and triglycerides] and liver disease risk markers were measured at weeks 0, 4, 8, and 12. Analyzing 36 participants in each group revealed a significant interaction between treatment and time, indicating reduced low-density lipoprotein cholesterol (p = 0.049) and total cholesterol (p = 0.020) levels in secoisolariciresinol diglucoside-receiving men but not women. However, no significant differences were observed in other markers regardless of gender. The results suggest that a daily intake of 60 mg of secoisolariciresinol diglucoside lowers low-density lipoprotein cholesterol and total cholesterol levels in men with borderline low-density lipoprotein cholesterol, proposing secoisolariciresinol diglucoside potential as a functional dietary nutrient for cardiovascular disease prevention. This study was registered in the UMIN-CTR database (UMIN000046202).
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Affiliation(s)
- Kouta Ookoshi
- Innovation Center, Central Research Laboratory, NIPPN Corporation, 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Kento Sawane
- Innovation Center, Central Research Laboratory, NIPPN Corporation, 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Satoshi Fukumitsu
- Innovation Center, Central Research Laboratory, NIPPN Corporation, 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Kazuhiko Aida
- Innovation Center, Central Research Laboratory, NIPPN Corporation, 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
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Chiang BH, Vega G, Dunwoody SC, Patnode ML. Bacterial interactions on nutrient-rich surfaces in the gut lumen. Infect Immun 2024:e0048023. [PMID: 38506518 DOI: 10.1128/iai.00480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.
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Affiliation(s)
- Bo Huey Chiang
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Giovanni Vega
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Sarah C Dunwoody
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Michael L Patnode
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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5
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Hu J, Mesnage R, Tuohy K, Heiss C, Rodriguez-Mateos A. (Poly)phenol-related gut metabotypes and human health: an update. Food Funct 2024; 15:2814-2835. [PMID: 38414364 DOI: 10.1039/d3fo04338j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Dietary (poly)phenols have received great interest due to their potential role in the prevention and management of non-communicable diseases. In recent years, a high inter-individual variability in the biological response to (poly)phenols has been demonstrated, which could be related to the high variability in (poly)phenol gut microbial metabolism existing within individuals. An interplay between (poly)phenols and the gut microbiota exists, with (poly)phenols being metabolised by the gut microbiota and their metabolites modulating gut microbiota diversity and composition. A number of (poly)phenol metabolising phenotypes or metabotypes have been proposed, however, potential metabotypes for most (poly)phenols have not been investigated, and the relationship between metabotypes and human health remains ambiguous. This review presents updated knowledge on the reciprocal interaction between (poly)phenols and the gut microbiome, associated gut metabotypes, and subsequent impact on human health.
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Affiliation(s)
- Jiaying Hu
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
| | - Robin Mesnage
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
- Buchinger Wilhelmi Clinic, Überlingen, Germany
| | - Kieran Tuohy
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds, UK
| | - Christian Heiss
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
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6
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Viehof A, Haange SB, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T. The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice. MICROBIOME RESEARCH REPORTS 2024; 3:14. [PMID: 38841406 PMCID: PMC11149096 DOI: 10.20517/mrr.2023.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 06/07/2024]
Abstract
The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis, but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.
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Affiliation(s)
- Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Theresa Streidl
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technical University of Munich, Freising 85354, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
- Institute of Biochemistry, University of Leipzig, Leipzig 04109, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
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7
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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8
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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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Ono E, Murata J. Exploring the Evolvability of Plant Specialized Metabolism: Uniqueness Out Of Uniformity and Uniqueness Behind Uniformity. PLANT & CELL PHYSIOLOGY 2023; 64:1449-1465. [PMID: 37307423 PMCID: PMC10734894 DOI: 10.1093/pcp/pcad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/28/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
The huge structural diversity exhibited by plant specialized metabolites has primarily been considered to result from the catalytic specificity of their biosynthetic enzymes. Accordingly, enzyme gene multiplication and functional differentiation through spontaneous mutations have been established as the molecular mechanisms that drive metabolic evolution. Nevertheless, how plants have assembled and maintained such metabolic enzyme genes and the typical clusters that are observed in plant genomes, as well as why identical specialized metabolites often exist in phylogenetically remote lineages, is currently only poorly explained by a concept known as convergent evolution. Here, we compile recent knowledge on the co-presence of metabolic modules that are common in the plant kingdom but have evolved under specific historical and contextual constraints defined by the physicochemical properties of each plant specialized metabolite and the genetic presets of the biosynthetic genes. Furthermore, we discuss a common manner to generate uncommon metabolites (uniqueness out of uniformity) and an uncommon manner to generate common metabolites (uniqueness behind uniformity). This review describes the emerging aspects of the evolvability of plant specialized metabolism that underlie the vast structural diversity of plant specialized metabolites in nature.
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Affiliation(s)
- Eiichiro Ono
- Suntory Global Innovation Center Ltd. (SIC), 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
| | - Jun Murata
- Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
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10
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Deng ZL, Pieper DH, Stallmach A, Steube A, Vital M, Reck M, Wagner-Döbler I. Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics. MICROBIOME 2023; 11:269. [PMID: 38037086 PMCID: PMC10691019 DOI: 10.1186/s40168-023-01713-9] [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: 12/28/2022] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the backbone of treatment of pouchitis; however, antibiotic-resistant pouchitis develops in 5-10% of those patients. It has been shown that fecal microbiota transplantation (FMT) is an effective treatment for UC, but results for FMT antibiotic-resistant pouchitis are inconsistent. METHODS To uncover which metabolic activities were transferred to the recipients during FMT and helped the remission, we performed a longitudinal case study of the gut metatranscriptomes from three patients and their donors. The patients were treated by two to three FMTs, and stool samples were analyzed for up to 140 days. RESULTS Reduced expression in pouchitis patients compared to healthy donors was observed for genes involved in biosynthesis of amino acids, cofactors, and B vitamins. An independent metatranscriptome dataset of UC patients showed a similar result. Other functions including biosynthesis of butyrate, metabolism of bile acids, and tryptophan were also much lower expressed in pouchitis. After FMT, these activities transiently increased, and the overall metatranscriptome profiles closely mirrored those of the respective donors with notable fluctuations during the subsequent weeks. The levels of the clinical marker fecal calprotectin were concordant with the metatranscriptome data. Faecalibacterium prausnitzii represented the most active species contributing to butyrate synthesis via the acetyl-CoA pathway. Remission occurred after the last FMT in all patients and was characterized by a microbiota activity profile distinct from donors in two of the patients. CONCLUSIONS Our study demonstrates the clear but short-lived activity engraftment of donor microbiota, particularly the butyrate biosynthesis after each FMT. The data suggest that FMT triggers shifts in the activity of patient microbiota towards health which need to be repeated to reach critical thresholds. As a case study, these insights warrant cautious interpretation, and validation in larger cohorts is necessary for generalized applications. In the long run, probiotics with high taxonomic diversity consisting of well characterized strains could replace FMT to avoid the costly screening of donors and the risk of transferring unwanted genetic material. Video Abstract.
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Affiliation(s)
- Zhi-Luo Deng
- Group Computational Biology for Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany.
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Andreas Stallmach
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Arndt Steube
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Reck
- Group Microbial Communication, Helmholtz Center for Infection Research, Brunswick, Germany
- TÜV Rheinland, Cologne, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Brunswick, Germany
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11
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Ma X, Luo L, Karrar E, Zhang L, Li J. Comparative Study on the Absorption and Metabolism of Pinoresinol and Pinoresinol-4-O-β-D-Glucopyranoside in Mice. Mol Nutr Food Res 2023; 67:e2300536. [PMID: 37891711 DOI: 10.1002/mnfr.202300536] [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: 07/27/2023] [Revised: 09/20/2023] [Indexed: 10/29/2023]
Abstract
SCOPE Lignans are a group of phenolic compounds commonly found in plants, often in the form of glycosides. This study investigates the differences in the digestion, absorption, and metabolism of lignans and their glucosides using pinoresinol (PIN) and pinoresinol-4-O-β-D-glucopyranoside (PMG). METHODS AND RESULTS After oral administration mice PIN and PMG with a dose of 0.1 µmol kg-1 . The results showed that the stomach and small intestine rapidly absorbe PIN and PMG in their prototype form. After oral administration of 0.25 h, serum levels of PIN and PMG reach peak values of 61.14 and 52.97 ng mL-1 , respectively. This indicates a faster PIN absorption rate than PMG, likely due to the glycosides attach to the parent compound, with concentrations of 1574.14 and 876.75 ng g-1 , respectively. Pharmacokinetic analysis reveals that PIN has a greater area under the curve and a longer half-life than PMG in serum and liver. Moreover, mice in the PIN group exhibit higher metabolite levels in the serum and liver compared to those in the PMG group. CONCLUSION The deglycosylation process that occurs during the pickling of white radish facilitates the absorption and metabolism of the lignans fraction in the body.
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Affiliation(s)
- Xiaoyang Ma
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Lianzhong Luo
- Engineering Research Center of Marine Biopharmaceutical Resource, Fujian Province University, Xiamen Medical College, Xiamen, 361021, China
| | - Emad Karrar
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Lingyu Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Jian Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
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12
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Li J, Ma X, Luo L, Tang D, Zhang L. The What and Who of Dietary Lignans in Human Health: Special Attention to Estrogen Effects and Safety Evaluation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16419-16434. [PMID: 37870451 DOI: 10.1021/acs.jafc.3c02680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Lignans are a group of phenolic compounds found in plant-based diets. The human body can obtain lignans through diet, which are then metabolized into enterolignans. The enterolignans have been linked to several health benefits, including anticancer, anti-inflammatory, antioxidant effects, and estrogen effects. This review explores the relationship between the estrogenic effects of lignans and health. This review not only considers the estrogen-like activity of lignans but also discusses the safe dosage of lignans at different life stages. In addition, this review also identified other types of bioactive compounds that can act synergistically with lignans to promote health. Studies have shown that lignan administration during pregnancy and lactation reduces the risk of breast cancer in offspring. Further studies are needed to investigate the estrogenic safety effects of lignan on pregnant women and children. Whether lignans combine with other nutrients in complex food substrates to produce synergistic effects remains to be investigated. This review provides a basis for future studies on the safe dose of lignan and recommended dietary intake of lignan. We believe that the acquired as discussed here has implications for developing dietary therapies that can promote host nutrition and modulate estrogenic diseases.
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Affiliation(s)
- Jian Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xiaoyang Ma
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medical College, Xiamen 361023, China
| | - Danqing Tang
- The School of Foreign Languages of Jimei University, Xiamen 361021, China
| | - Lingyu Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
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13
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Kyaw TS, Upadhyay V, Tolstykh I, Van Loon K, Laffan A, Stanfield D, Gempis D, Kenfield SA, Chan JM, Piawah S, Atreya CE, Ng K, Venook A, Kidder W, Turnbaugh PJ, Van Blarigan EL. Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors. Am J Clin Nutr 2023; 118:518-529. [PMID: 37474105 PMCID: PMC10550847 DOI: 10.1016/j.ajcnut.2023.07.011] [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: 12/11/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Adherence to the American Cancer Society (ACS) guidelines of avoiding obesity, maintaining physical activity, and consuming a diet rich in fruits, vegetables, and whole grains is associated with longer survival in colorectal cancer (CRC) survivors. Dietary components of the ACS guidelines may act in part by changing the microbiome, which is implicated in CRC outcomes. OBJECTIVES We conducted a pilot cross-sectional study to explore associations between ACS guidelines and the gut microbiome. METHODS Stool samples and questionnaires were collected from 28 CRC survivors at the University of California, San Francisco from 2019 to 2020. ACS scores were calculated based on validated questionnaires. Gut microbial community structure from 16S amplicons and gene/pathway abundances from metagenomics were tested for associations with the ACS score and its components using ANOVA and general linear models. RESULTS The overall ACS score was not significantly associated with variations in the fecal microbiota. However, fruit and vegetable intake and alcohol intake accounted for 19% (P = 0.005) and 13% (P = 0.01) of variation in the microbiota, respectively. Fruit/vegetable consumption was associated with increased microbial diversity, increased Firmicutes, decreased Bacteroidota, and changes to multiple genes and metabolic pathways, including enriched pathways for amino acid and short-chain fatty acid biosynthesis and plant-associated sugar degradation. In contrast, alcohol consumption was positively associated with overall microbial diversity, negatively associated with Bacteroidota abundance, and associated with changes to multiple genes and metabolic pathways. The other components of the ACS score were not statistically significantly associated with the fecal microbiota in our sample. CONCLUSIONS These results guide future studies examining the impact of changes in the intake of fruits, vegetables, and alcoholic drinks on the gut microbiome of CRC survivors.
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Affiliation(s)
- Than S Kyaw
- Department of Microbiology and Immunology, University of California, San Francisco, CA, United States
| | - Vaibhav Upadhyay
- Department of Microbiology and Immunology, University of California, San Francisco, CA, United States; Department of Medicine, University of California, San Francisco, CA, United States
| | - Irina Tolstykh
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States
| | - Katherine Van Loon
- Department of Medicine, University of California, San Francisco, CA, United States; University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Angela Laffan
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Dalila Stanfield
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Daryll Gempis
- Department of Microbiology and Immunology, University of California, San Francisco, CA, United States
| | - Stacey A Kenfield
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States; Department of Urology, University of California, San Francisco, United States
| | - June M Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States; Department of Urology, University of California, San Francisco, United States
| | - Sorbarikor Piawah
- Department of Medicine, University of California, San Francisco, CA, United States; University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Chloe E Atreya
- Department of Medicine, University of California, San Francisco, CA, United States; University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Kimmie Ng
- Dana Farber Cancer Institute, Boston, MA, United States
| | - Alan Venook
- Department of Medicine, University of California, San Francisco, CA, United States; University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Wesley Kidder
- Department of Medicine, University of California, San Francisco, CA, United States; University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, United States
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California, San Francisco, CA, United States; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, United States.
| | - Erin L Van Blarigan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States; Department of Urology, University of California, San Francisco, United States.
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14
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Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol 2023; 21:e3002125. [PMID: 37205710 PMCID: PMC10234575 DOI: 10.1371/journal.pbio.3002125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/01/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. Our culture media formulations, atlas of metabolomics data, and genome-scale metabolic reconstructions form a freely available collection of resources to support further study of the biology of this prevalent gut bacterium.
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Affiliation(s)
- Cecilia Noecker
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Juan Sanchez
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Jordan E. Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Veronica Escalante
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Kai Trepka
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Yuanyuan Liu
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Dylan Dodd
- Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Microbiology & Immunology, Stanford University, Stanford, California, United States of America
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Brian C. DeFelice
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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15
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Beliaeva MA, Wilmanns M, Zimmermann M. Decipher enzymes from human microbiota for drug discovery and development. Curr Opin Struct Biol 2023; 80:102567. [PMID: 36963164 DOI: 10.1016/j.sbi.2023.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/26/2023]
Abstract
The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.
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Affiliation(s)
- Mariia A Beliaeva
- European Molecular Biology Laboratory, Heidelberg, Germany; European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@MariiaABeliaeva
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@WilmannsGroup
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16
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Sawane K, Nagatake T, Hosomi K, Kunisawa J. Anti-allergic property of dietary phytoestrogen secoisolariciresinol diglucoside through microbial and β-glucuronidase-mediated metabolism. J Nutr Biochem 2023; 112:109219. [PMID: 36375731 DOI: 10.1016/j.jnutbio.2022.109219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/03/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022]
Abstract
Phytoestrogens play pivotal roles in controlling not only the endocrine system but also inflammatory metabolic disorders. However, the effects of dietary phytoestrogens on allergic diseases and underlying mechanisms remain unclear. In this study, we revealed the unique metabolic conversion of phytoestrogen to exert anti-allergic properties, using an ovalbumin-induced allergic rhinitis mouse model. We found that dietary secoisolariciresinol diglucoside (SDG), a phytoestrogen abundantly present in flaxseed, alleviated allergic rhinitis by the microbial conversion to enterodiol (ED). We also found that ED circulated mainly in the glucuronide form (EDGlu) in blood, and deconjugation of EDGlu to ED aglycone occurred in the nasal passage; this activity was enhanced after the induction of allergic rhinitis, which was mediated by β-glucuronidase. We further found that IgE-mediated degranulation was inhibited by ED aglycone, but not by EDGlu, in a G protein-coupled receptor 30 (GPR30)-dependent manner. These results provide new insights into the anti-allergic properties of phytoestrogens and their metabolism in vivo for the development of novel therapeutic strategies against allergic rhinitis.
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Affiliation(s)
- Kento Sawane
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Takahiro Nagatake
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan; Laboratory of Functional Anatomy, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan; Laboratory of Gut Environmental System, Collaborative Research Center for Health and Medicine, NIBIOHN
| | - Koji Hosomi
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan; Laboratory of Gut Environmental System, Collaborative Research Center for Health and Medicine, NIBIOHN
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan; Laboratory of Gut Environmental System, Collaborative Research Center for Health and Medicine, NIBIOHN; Graduate School of Medicine, Graduate School of Science and Graduate School of Dentistry, Osaka University, Osaka, Japan; Division of Mucosal Immunology, Department of Microbiology and Immunology and International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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17
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Anderson BD, Bisanz JE. Challenges and opportunities of strain diversity in gut microbiome research. Front Microbiol 2023; 14:1117122. [PMID: 36876113 PMCID: PMC9981649 DOI: 10.3389/fmicb.2023.1117122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 02/19/2023] Open
Abstract
Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.
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Affiliation(s)
- Benjamin D Anderson
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Jordan E Bisanz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.,The Penn State Microbiome Center, Huck Institutes of the Life Sciences, University Park, PA, United States
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18
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Dong X, Guthrie BGH, Alexander M, Noecker C, Ramirez L, Glasser NR, Turnbaugh PJ, Balskus EP. Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nat Commun 2022; 13:7624. [PMID: 36494336 PMCID: PMC9734109 DOI: 10.1038/s41467-022-33576-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022] Open
Abstract
Eggerthella lenta is a prevalent human gut Actinobacterium implicated in drug, dietary phytochemical, and bile acid metabolism and associated with multiple human diseases. No genetic tools are currently available for the direct manipulation of E. lenta. Here, we construct shuttle vectors and develop methods to transform E. lenta and other Coriobacteriia. With these tools, we characterize endogenous E. lenta constitutive and inducible promoters using a reporter system and construct inducible expression systems, enabling tunable gene regulation. We also achieve genome editing by harnessing an endogenous type I-C CRISPR-Cas system. Using these tools to perform genetic knockout and complementation, we dissect the functions of regulatory proteins and enzymes involved in catechol metabolism, revealing a previously unappreciated family of membrane-spanning LuxR-type transcriptional regulators. Finally, we employ our genetic toolbox to study the effects of E. lenta genes on mammalian host biology. By greatly expanding our ability to study and engineer gut Coriobacteriia, these tools will reveal mechanistic details of host-microbe interactions and provide a roadmap for genetic manipulation of other understudied human gut bacteria.
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Affiliation(s)
- Xueyang Dong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ben G H Guthrie
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Cecilia Noecker
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Lorenzo Ramirez
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
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High polyphenolic cranberry beverage alters specific fecal microbiota but not gut permeability following aspirin challenge in healthy obese adults: A randomized, double-blind, crossover trial. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Koyama T, Murata J, Horikawa M, Satake H. Production of beneficial lignans in heterologous host plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1026664. [PMID: 36330251 PMCID: PMC9623879 DOI: 10.3389/fpls.2022.1026664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
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Ethanol Extract of Licorice Alleviates HFD-Induced Liver Fat Accumulation in Association with Modulation of Gut Microbiota and Intestinal Metabolites in Obesity Mice. Nutrients 2022; 14:nu14194180. [PMID: 36235833 PMCID: PMC9572531 DOI: 10.3390/nu14194180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
As a traditional Chinese medicine, licorice is often used in functional foods for its health benefits. However, the role of gut microbiota in the efficacy of licorice has not yet been fully elucidated. We hypothesized that the involvement of intestinal flora may be a key link in licorice ethanol extract (LEE)-induced health benefits. The aim of this study was to investigate whether LEE improves hepatic lipid accumulation in obese mice fed a high-fat diet (HFD) and whether the gut microbiota plays a key role in LEE treatment. Male C57BL/6J mice were fed HFD for liver fat accumulation and then treated with LEE. The same experiments were later performed using pseudo-sterile mice to verify the importance of gut flora. Supplementation with LEE improved the obesity profile, lipid profile and liver fat accumulation in HFD mice. In addition, LEE treatment improved intestinal flora dysbiosis caused by HFD in mice, as evidenced by a decrease in the percentage of Firmicutes/Bacteroidetes and an increase in the abundance of known anti-obesity-related bacteria. However, LEE failed to exhibit a therapeutic effect in pseudo-sterile mice. The results of the cellular assay showed that glycyrrhetic acid (GA), the main conversion product of glycyrrhizin (GL), was more effective in reducing fat accumulation and intracellular TG content in hepatocytes compared to GL. In conclusion, our data suggest that LEE attenuates obesity and hepatic fat accumulation in HFD mice, which may be associated with modulating the composition of gut microbiota and the conversion of LLE by the intestinal flora.
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22
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Zhao Y, Zhong X, Yan J, Sun C, Zhao X, Wang X. Potential roles of gut microbes in biotransformation of natural products: An overview. Front Microbiol 2022; 13:956378. [PMID: 36246222 PMCID: PMC9560768 DOI: 10.3389/fmicb.2022.956378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Natural products have been extensively applied in clinical practice, characterized by multi-component and multi-target, many pharmacodynamic substances, complex action mechanisms, and various physiological activities. For the oral administration of natural products, the gut microbiota and clinical efficacy are closely related, but this relationship remains unclear. Gut microbes play an important role in the transformation and utilization of natural products caused by the diversity of enzyme systems. Effective components such as flavonoids, alkaloids, lignans, and phenols cannot be metabolized directly through human digestive enzymes but can be transformed by enzymes produced by gut microorganisms and then utilized. Therefore, the focus is paid to the metabolism of natural products through the gut microbiota. In the present study, we systematically reviewed the studies about gut microbiota and their effect on the biotransformation of various components of natural products and highlighted the involved common bacteria, reaction types, pharmacological actions, and research methods. This study aims to provide theoretical support for the clinical application in the prevention and treatment of diseases and provide new ideas for studying natural products based on gut biotransformation.
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Affiliation(s)
- Yucui Zhao
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xinqin Zhong
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Junyuan Yan
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Congying Sun
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xin Zhao
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Xin Zhao,
| | - Xiaoying Wang
- Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Xiaoying Wang,
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23
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Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps. NPJ Biofilms Microbiomes 2022; 8:69. [PMID: 36038569 PMCID: PMC9424272 DOI: 10.1038/s41522-022-00328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 10–15% of the variation observed in the microbiome. Multiple mucosal brushings were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Mucosal aspirate sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 1–4% of the variance in the microbiome. Microbiome composition also enabled the accurate prediction of subject polyp types using Random Forest, which produced an area under curve values of 0.87–0.99. By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, our study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method’s practicality and effect on microbial community composition.
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24
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Rich BE, Jackson JC, de Ora LO, Long ZG, Uyeda KS, Bess EN. Alternative pathway for dopamine production by acetogenic gut bacteria that O-Demethylate 3-Methoxytyramine, a metabolite of catechol O-Methyltransferase. J Appl Microbiol 2022; 133:1697-1708. [PMID: 35737746 PMCID: PMC9544265 DOI: 10.1111/jam.15682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
Abstract
AIMS The gut microbiota modulates dopamine levels in vivo, but the bacteria and biochemical processes responsible remain incompletely characterized. A potential precursor of bacterial dopamine production is 3-methoxytyramine (3MT); 3MT is produced when dopamine is O-methylated by host catechol O-methyltransferase (COMT), thereby attenuating dopamine levels. This study aimed to identify whether gut bacteria are capable of reverting 3MT to dopamine. METHODS AND RESULTS Human faecal bacterial communities O-demethylated 3MT and yielded dopamine. Gut bacteria that mediate this transformation were identified as acetogens Eubacterium limosum and Blautia producta. Upon exposing these acetogens to propyl iodide, a known inhibitor of cobalamin-dependent O-demethylases, 3MT O-demethylation was inhibited. Culturing E. limosum and B. producta with 3MT afforded increased acetate levels as compared with vehicle controls. CONCLUSIONS Gut bacterial acetogens E. limosum and B. producta synthesized dopamine from 3MT. This O-demethylation of 3MT was likely performed by cobalamin-dependent O-demethylases implicated in reductive acetogenesis. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report that gut bacteria can synthesize dopamine by O-demethylation of 3MT. Owing to 3MT being the product of host COMT attenuating dopamine levels, gut bacteria that reverse this transformation-converting 3MT to dopamine-may act as a counterbalance for dopamine regulation by COMT.
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Affiliation(s)
- Barry E Rich
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Jayme C Jackson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Lizett Ortiz de Ora
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Zane G Long
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Kylie S Uyeda
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Elizabeth N Bess
- Department of Chemistry, University of California, Irvine, Irvine, California, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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25
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Li X, Xu E, Shi C, Qiao G, Chen S, Xu Y, Liu Y, Bao X. Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections. Pol J Microbiol 2022; 71:257-261. [PMID: 35716165 PMCID: PMC9252136 DOI: 10.33073/pjm-2022-024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/14/2022] [Indexed: 12/03/2022] Open
Abstract
The identification and antibiotic susceptibility of two clinical isolates of Eggerthella lenta from bloodstream infections were determined. This microorganism is rarely pathogenic, and the findings are presented here to promote the detection and awareness of this infection. The bacteria were obtained from one patient with pressure sores and another with a malignant gastric tumor. Smears were prepared, stained, and examined by microscopy. Single colonies were analyzed by Gram staining, MALDI-TOF MS, and the 16S rRNA gene sequencing. Antibiotic sensitivity was assessed by the agar dilution method. The bacilli were found to be Gram-positive, and the MS results showed 99.8% homology with E. lenta. It was confirmed by gene sequencing. Antibiotic susceptibility tests demonstrated that E. lenta was sensitive to piperacillin-tazobactam, ampicillin-sulbactam, imipenem, meropenem, metronidazole, clindamycin, and vancomycin. This study could increase awareness of this rare infection. ![]()
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Affiliation(s)
- Xiangyun Li
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Enjun Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Cuixiao Shi
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Guanhua Qiao
- Department of Laboratory Medicine, Anhui Medical University, Hefei, People's Republic of China
| | - Shuyi Chen
- Department of Laboratory Medicine, Anhui Medical University, Hefei, People's Republic of China
| | - Yuanhong Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China
| | - Yajing Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Anhui Medical University, Hefei, People's Republic of China
| | - Xundi Bao
- Department of Laboratory Medicine, Anhui Chest Hospital, Hefei, People's Republic of China
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26
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Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB. Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. BMC Microbiol 2022; 22:82. [PMID: 35350985 PMCID: PMC8966171 DOI: 10.1186/s12866-022-02495-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/17/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The conversion of plant lignans to bioactive enterolignans in the gastrointestinal tract is mediated through microbial processing. The goal of this study was to examine the relationships between lignan intake, plasma enterolactone concentrations, gut microbiome composition, and metabolic risk in free-living male adults. RESULTS In 303 men participating in the Men's Lifestyle Validation Study (MLVS), lignan intake was assessed using two sets of 7-day diet records, and gut microbiome was profiled through shotgun sequencing of up to 2 pairs of fecal samples (n = 911). A score was calculated to summarize the abundance of bacteria species that were significantly associated with plasma enterolactone levels. Of the 138 filtered species, plasma enterolactone levels were significantly associated with the relative abundances of 18 species at FDR < 0.05 level. Per SD increment of lignan intake was associated with 20.7 nM (SEM: 2.3 nM) higher enterolactone concentrations among participants with a higher species score, whereas the corresponding estimate was 4.0 nM (SEM: 1.7 nM) among participants with a lower species score (P for interaction < 0.001). A total of 12 plasma metabolites were also significantly associated with these enterolactone-predicting species. Of the association between lignan intake and metabolic risk, 19.8% (95%CI: 7.3%-43.6%) was explained by the species score alone, 54.5% (95%CI: 21.8%-83.7%) by both species score and enterolactone levels, and 79.8% (95%CI: 17.7%-98.6%) by further considering the 12 plasma metabolites. CONCLUSION We identified multiple gut bacteria species that were enriched or depleted at higher plasma levels of enterolactone in men. These species jointly modified the associations of lignan intake with plasma enterolactone levels and explained the majority of association between lignan intake and metabolic risk along with enterolactone levels and certain plasma metabolites.
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Affiliation(s)
- Yanping Li
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
| | - Fenglei Wang
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
| | - Jun Li
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
| | - Kerry L. Ivey
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA ,grid.430453.50000 0004 0565 2606Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000 Australia ,grid.1014.40000 0004 0367 2697Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, Australia
| | - Jeremy E. Wilkinson
- grid.38142.3c000000041936754X Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Dong D. Wang
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ruifeng Li
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
| | - Gang Liu
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
| | - Heather A. Eliassen
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Andrew T. Chan
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Clary B. Clish
- grid.66859.340000 0004 0546 1623Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Curtis Huttenhower
- grid.38142.3c000000041936754X Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Frank B. Hu
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Qi Sun
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Eric B. Rimm
- grid.38142.3c000000041936754XDepartment of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
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27
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Buttimer C, Bottacini F, Shkoporov AN, Draper LA, Ross P, Hill C. Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity. Microorganisms 2022; 10:195. [PMID: 35056644 PMCID: PMC8778435 DOI: 10.3390/microorganisms10010195] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 12/26/2022] Open
Abstract
Eggerthella lenta is an anaerobic, high GC, Gram-positive bacillus commonly found in the human digestive tract that belongs to the class Coriobacteriia of the phylum Actinobacteria. This species has been of increasing interest as an important player in the metabolism of xenobiotics and dietary compounds. However, little is known regarding its susceptibility to bacteriophage predation and how this may influence its fitness. Here, we report the isolation of seven novel E. lenta strains using cefotaxime and ceftriaxone as selective agents. We conducted comparative and pangenome analyses of these strains and those publicly available to investigate the diversity of prophages associated with this species. Prophage gene products represent a minimum of 5.8% of the E. lenta pangenome, comprising at least ten distantly related prophage clades that display limited homology to currently known bacteriophages. All clades possess genes implicated in virion structure, lysis, lysogeny and, to a limited extent, DNA replication. Some prophages utilise tyrosine recombinases and diversity generating retroelements to generate phase variation among targeted genes. The prophages have differing levels of sensitivity to the CRISPR/cas systems of their hosts, with spacers from 44 E. lenta isolates found to target only five out of the ten identified prophage clades. Furthermore, using a PCR-based approach targeting the prophage attP site, we were able to determine that several of these elements can excise from the host chromosome, thus supporting the notion that these are active prophages. The findings of this study provide further insights into the diversity of prophages infecting species of the phylum Actinobacteria.
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Affiliation(s)
- Colin Buttimer
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (C.B.); (A.N.S.); (L.A.D.); (P.R.)
| | - Francesca Bottacini
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland;
| | - Andrey N. Shkoporov
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (C.B.); (A.N.S.); (L.A.D.); (P.R.)
| | - Lorraine A. Draper
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (C.B.); (A.N.S.); (L.A.D.); (P.R.)
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (C.B.); (A.N.S.); (L.A.D.); (P.R.)
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (C.B.); (A.N.S.); (L.A.D.); (P.R.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
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28
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Shanmugam H, Ganguly S, Priya B. Plant food bioactives and its effects on gut microbiota profile modulation for better brain health and functioning in Autism Spectrum Disorder individuals: A review. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Haripriya Shanmugam
- Department of Nano Science and Technology Tamil Nadu Agricultural University Coimbatore India
| | | | - Badma Priya
- Molecular Biophysics Unit Indian Institute of Science Bangalore India
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29
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Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN. The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2. Trends Mol Med 2021; 27:1115-1134. [PMID: 34756546 PMCID: PMC8492747 DOI: 10.1016/j.molmed.2021.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) continues to exact a devastating global toll. Ascertaining the factors underlying differential susceptibility and prognosis following viral exposure is critical to improving public health responses. We propose that gut microbes may contribute to variation in COVID-19 outcomes. We synthesise evidence for gut microbial contributions to immunity and inflammation, and associations with demographic factors affecting disease severity. We suggest mechanisms potentially underlying microbially mediated differential susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These include gut microbiome-mediated priming of host inflammatory responses and regulation of endocrine signalling, with consequences for the cellular features exploited by SARS-CoV-2 virions. We argue that considering gut microbiome-mediated mechanisms may offer a lens for appreciating differential susceptibility to SARS-CoV-2, potentially contributing to clinical and epidemiological approaches to understanding and managing COVID-19.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Siobhán Harty
- Tandy Court, Spitalfields, Dublin 8, D08 RP20, Ireland
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Susan E Erdman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karl J Friston
- Wellcome Centre for Human Neuroimaging, University College London, London, UK
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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30
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Rashidi A, Ebadi M, Rehman TU, Elhusseini H, Nalluri H, Kaiser T, Holtan SG, Khoruts A, Weisdorf DJ, Staley C. Gut microbiota response to antibiotics is personalized and depends on baseline microbiota. MICROBIOME 2021; 9:211. [PMID: 34702350 PMCID: PMC8549152 DOI: 10.1186/s40168-021-01170-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/25/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND The magnitude of microbiota perturbations after exposure to antibiotics varies among individuals. It has been suggested that the composition of pre-treatment microbiota underpins personalized responses to antibiotics. However, this hypothesis has not been directly tested in humans. In this high-throughput amplicon study, we analyzed 16S ribosomal RNA gene sequences of 260 stool samples collected twice weekly from 39 patients with acute leukemia during their ~ 4 weeks of hospitalization for chemotherapy while they received multiple antibiotics. RESULTS Despite heavy and sustained antibiotic pressure, microbial communities in samples from the same patient remained more similar to one another than to those from other patients. Principal component mixed effect regression using microbiota and granular antibiotic exposure data showed that microbiota departures from baseline depend on the composition of the pre-treatment microbiota. Penalized generalized estimating equations identified 6 taxa within pre-treatment microbiota that predicted the extent of antibiotic-induced perturbations. CONCLUSIONS Our results indicate that specific species in pre-treatment microbiota determine personalized microbiota responses to antibiotics in humans. Thus, precision interventions targeting pre-treatment microbiota may prevent antibiotic-induced dysbiosis and its adverse clinical consequences. Video abstract.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, 14-100 PWB, MMC 480, 420 Delaware St. SE, Minneapolis, MN, 55455, USA.
| | - Maryam Ebadi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, 14-100 PWB, MMC 480, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | - Tauseef Ur Rehman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Heba Elhusseini
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, 14-100 PWB, MMC 480, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | - Harika Nalluri
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Thomas Kaiser
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Shernan G Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, 14-100 PWB, MMC 480, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, 14-100 PWB, MMC 480, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
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31
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Bishai JD, Palm NW. Small Molecule Metabolites at the Host-Microbiota Interface. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1725-1733. [PMID: 34544815 PMCID: PMC8500551 DOI: 10.4049/jimmunol.2100528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 01/15/2023]
Abstract
The trillions of bacteria that constitutively colonize the human gut collectively generate thousands of unique small molecules. These microbial metabolites can accumulate both locally and systemically and potentially influence nearly all aspects of mammalian biology, including immunity, metabolism, and even mood and behavior. In this review, we briefly summarize recent work identifying bioactive microbiota metabolites, the means through which they are synthesized, and their effects on host physiology. Rather than offering an exhaustive list of all known bioactive microbial small molecules, we select a few examples from each key class of metabolites to illustrate the diverse impacts of microbiota-derived compounds on the host. In addition, we attempt to address the microbial logic behind specific biotransformations. Finally, we outline current and emerging strategies for identifying previously undiscovered bioactive microbiota metabolites that may shape human health and disease.
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Affiliation(s)
- Jason D Bishai
- Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, CT; and
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
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32
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Langa S, Landete JM. Strategies to achieve significant physiological concentrations of bioactive phytoestrogens in plasma. Crit Rev Food Sci Nutr 2021; 63:2203-2215. [PMID: 34470513 DOI: 10.1080/10408398.2021.1971946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The benefits to health attributed to the intake of phytoestrogens (PEs) have been demonstrated in previous studies with significant physiological concentrations of bioactive PEs, such as genistein, equol, enterolignans and urolithins in plasma. However, the achievement of high bioactive PE levels in plasma is restricted to a select population group, mainly due to the low intake of plant PEs and/or the absence, or inhibition, of the microbiota capable of producing these bioactive forms. In this study, the intake of plant PEs, the concentration of bioactive PEs in plasma, the ability of the intestinal microbiota to produce bioactive PEs, as well as the different mechanisms used by GRAS bacteria to increase the level of bioactive PEs were evaluated concluding that the use of GRAS bacteria bioactive PE producers and the development of fermented foods enriched in bioactive PEs in addition to a high intake of plant PEs and taking care of the intestinal microbiota, are some of the different strategies to achieve significant physiological concentrations of bioactive PEs in the intestine and, subsequently, in plasma and targets organs which are essential to improve menopausal symptoms or reduce the risk of some pathologies such as breast and colon cancer, or cardiovascular disease.
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Affiliation(s)
- Susana Langa
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - José M Landete
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Boronat A, Rodriguez-Morató J, Serreli G, Fitó M, Tyndale RF, Deiana M, de la Torre R. Contribution of Biotransformations Carried Out by the Microbiota, Drug-Metabolizing Enzymes, and Transport Proteins to the Biological Activities of Phytochemicals Found in the Diet. Adv Nutr 2021; 12:2172-2189. [PMID: 34388248 PMCID: PMC8634308 DOI: 10.1093/advances/nmab085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/17/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022] Open
Abstract
The consumption of dietary phytochemicals has been associated with several health benefits and relevant biological activities. It is postulated that biotransformations of these compounds regulated by the microbiota, Phase I/II reactions, transport proteins, and deconjugating enzymes contribute not only to their metabolic clearance but also, in some cases, to their bioactivation. A number of factors (age, genetics, sex, physiopathological conditions, and the interplay with other dietary phytochemicals) modulating metabolic activities are important sources and contributors to the interindividual variability observed in clinical studies evaluating the biological activities of phytochemicals. In this review, we discuss all the processes that can affect the bioaccessibility and beneficial effects of these bioactive compounds. Herein, we argue that the role of these factors must be further studied to correctly understand and predict the effects observed following the intake of phytochemicals. This is, in particular, with regard to in vitro investigations, which have shown great inconsistency with preclinical and clinical studies. The complexity of in vivo metabolic activity and biotransformation should therefore be considered in the interpretation of results in vitro and their translation to human physiopathology.
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Affiliation(s)
- Anna Boronat
- Integrative Pharmacology and Systems Neurosciences Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jose Rodriguez-Morató
- Integrative Pharmacology and Systems Neurosciences Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain,Physiopathology of Obesity and Nutrition Networking Biomedical Research Centre (CIBEROBN), Madrid, Spain,Department of Experimental and Health Sciences (UPF-CEXS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gabriele Serreli
- Department of Biomedical Science, Pathology Section, Experimental Pathology Unit, University of Cagliari, Montserrato, Italy
| | - Montserrat Fitó
- Physiopathology of Obesity and Nutrition Networking Biomedical Research Centre (CIBEROBN), Madrid, Spain,Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute (CAMH), Toronto, Canada,Department of Pharmacology, Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Monica Deiana
- Department of Biomedical Science, Pathology Section, Experimental Pathology Unit, University of Cagliari, Montserrato, Italy
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Elucidation of an anaerobic pathway for metabolism of l-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria. Proc Natl Acad Sci U S A 2021; 118:2101498118. [PMID: 34362844 PMCID: PMC8364193 DOI: 10.1073/pnas.2101498118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient l-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent l-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the l-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis We identify a set of genes up-regulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a putative flavin cofactor to catalyze a redox-neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from l-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of l-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.
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Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 2021; 40:240-254. [PMID: 34304905 DOI: 10.1016/j.tibtech.2021.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.
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Discriminatory and cooperative effects within the mouse gut microbiota in response to flaxseed and its oil and lignan components. J Nutr Biochem 2021; 98:108818. [PMID: 34271098 DOI: 10.1016/j.jnutbio.2021.108818] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022]
Abstract
Gut microbial processing of dietary flaxseed (FS) contributes to its health benefits, but the relative effects of its bioactive components (lignans, omega-3 fatty acids, fiber) on the microbiota are unclear. We investigated the gut microbial compositional and functional responses to whole FS and its isolated components, FS oil (FSO) and secoisolariciresinol diglucoside (SDG) (precursor to microbial-derived enterolignans) to help understand their contribution to whole FS benefits. Cecum content and fecal samples were collected from C57BL/6 female mice fed a basal diet (AIN93G) or isocaloric diets containing 10% FS or 10% FS-equivalent amounts of FSO or SDG for 21 days. Cecal and fecal microbiota composition and predicted genomic functions, and their relationship with serum enterolignans were evaluated. Only FS modified the community structure. Shared- and diet-specific enriched taxa and functions were identified. Carbohydrate and protein processing functions were enriched in FS mice, and there was a positive correlation between select enriched taxa, encompassing fiber degraders and SDG metabolizers, and serum enterolignans. This was not observed in mice receiving isolated FSO and SDG, suggesting that FS fiber supports SDG microbial metabolism. In conclusion, the cooperative activities of a diverse microbiota are necessary to process FS components and, when administered at the amount present in FS, these components may act together to affect SDG-derived enterolignans production. This has implications for the use of FS, FSO and SDG in clinical practice.
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Tomás-Navarro M, Navarro JL, Vallejo F, Tomás-Barberán FA. Novel Urinary Biomarkers of Orange Juice Consumption, Interindividual Variability, and Differences with Processing Methods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4006-4017. [PMID: 33724826 DOI: 10.1021/acs.jafc.0c08144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Untargeted metabolomics identified urinary biomarkers able to discriminate between the intake of fresh hand-squeezed and industrially processed orange juices. Processing led to an upregulation in the excretion of hydroxy-polymethoxyflavone sulfates, abscisic acid, and sinapic acid 4'-glucuronide. The demethylated polymethoxyflavone metabolites were produced with a significant interindividual variability suggesting that they could originate from gut microbiota metabolism. No correlation between the excretion levels of flavanone and polymethoxyflavone metabolites was observed, showing that gut microbiota metabolism differences could be behind the interindividual variability. Subjects with a high excretion level of hesperetin conjugates could be low or high polymethoxyflavone excretors. Flavanone phase II metabolites were primarily glucuronides, while those of demethylated polymethoxyflavones were mainly sulfates. A comparative study with the available demethylated polymethoxyflavone standards suggested that the metabolites produced in humans could be tentatively 4'-hydroxy- and/or 3'-hydroxy-polymethoxyflavone sulfates. This study is the first to describe the bioavailability and metabolism of citrus juice polymethoxyflavones in humans.
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Affiliation(s)
- María Tomás-Navarro
- Laboratory of Food & Health, Research Group on Quality, Safety, and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, P. O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | | | - Fernando Vallejo
- Laboratory of Food & Health, Research Group on Quality, Safety, and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, P. O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | - Francisco A Tomás-Barberán
- Laboratory of Food & Health, Research Group on Quality, Safety, and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, P. O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
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McCann SE, Hullar MA, Tritchler DL, Cortes-Gomez E, Yao S, Davis W, O’Connor T, Erwin D, Thompson LU, Yan L, Lampe JW. Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry. Nutrients 2021; 13:nu13030919. [PMID: 33809130 PMCID: PMC8001909 DOI: 10.3390/nu13030919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/22/2022] Open
Abstract
Lignans are phytochemicals studied extensively as dietary factors in chronic disease etiology. Our goal was to examine associations between the gut microbiota and lignan metabolism and whether these associations differ by ethnicity. We conducted a flaxseed (FS) dietary intervention in 252 healthy, postmenopausal women of African ancestry (AA) and European ancestry (EA). Participants consumed ~10 g/d ground flaxseed for 6 weeks and provided overnight urine collections and fecal samples before and after intervention. The gut microbiota was characterized using 16S rRNA gene sequencing and differences in microbial community composition compared by ethnicity and intervention status. We observed a significant difference in the composition of the microbiota measured as beta diversity (p < 0.05) between AA and EA at baseline that was attenuated with FS consumption. Genera that were significantly associated with ENL production (e.g., Klebsiella, Lactobacillus, Slackia, Senegalimassilia) were unique to each group. Bacteria (e.g., Fusobacteria, Pyramidobacter and Odoribacter) previously associated with colorectal cancer and cardiovascular disease, both diet-related chronic diseases, were unique to either AA or EA and were significantly reduced in the FS intervention. This study suggests that ethnic variation in ENL metabolism may be linked to gut microbiota composition, and its impact on disease risk deserves future investigation.
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Affiliation(s)
- Susan E. McCann
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
- Correspondence: ; Tel.: +1-716-845-8842
| | - Meredith A.J. Hullar
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (M.A.J.H.); (J.W.L.)
| | - David L. Tritchler
- Department of Biostatistics, University at Buffalo, Buffalo, NY 14214, USA;
| | - Eduardo Cortes-Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (E.C.-G.); (L.Y.)
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Tracey O’Connor
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Deborah Erwin
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Lilian U. Thompson
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (E.C.-G.); (L.Y.)
| | - Johanna W. Lampe
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (M.A.J.H.); (J.W.L.)
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Hameed H, King EFB, Doleckova K, Bartholomew B, Hollinshead J, Mbye H, Ullah I, Walker K, Van Veelen M, Abou-Akkada SS, Nash RJ, Horrocks PD, Price HP. Temperate Zone Plant Natural Products-A Novel Resource for Activity against Tropical Parasitic Diseases. Pharmaceuticals (Basel) 2021; 14:227. [PMID: 33800005 PMCID: PMC7998250 DOI: 10.3390/ph14030227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
The use of plant-derived natural products for the treatment of tropical parasitic diseases often has ethnopharmacological origins. As such, plants grown in temperate regions remain largely untested for novel anti-parasitic activities. We describe here a screen of the PhytoQuest Phytopure library, a novel source comprising over 600 purified compounds from temperate zone plants, against in vitro culture systems for Plasmodium falciparum, Leishmania mexicana, Trypanosoma evansi and T. brucei. Initial screen revealed 6, 65, 15 and 18 compounds, respectively, that decreased each parasite's growth by at least 50% at 1-2 µM concentration. These initial hits were validated in concentration-response assays against the parasite and the human HepG2 cell line, identifying hits with EC50 < 1 μM and a selectivity index of >10. Two sesquiterpene glycosides were identified against P. falciparum, four sterols against L. mexicana, and five compounds of various scaffolds against T. brucei and T. evansi. An L. mexicana resistant line was generated for the sterol 700022, which was found to have cross-resistance to the anti-leishmanial drug miltefosine as well as to the other leishmanicidal sterols. This study highlights the potential of a temperate plant secondary metabolites as a novel source of natural products against tropical parasitic diseases.
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Affiliation(s)
- Hamza Hameed
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Department of Chemistry, College of Education for Pure Science, University of Mosul, Mosul, Iraq
| | - Elizabeth F. B. King
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | - Katerina Doleckova
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Department of Biology, Faculty of Life Sciences, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic
| | | | | | - Haddijatou Mbye
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- MRC Unit The Gambia at LSHTM, Atlantic Boulevard, Fajara, Banjul PO Box 273, The Gambia
| | - Imran Ullah
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Karen Walker
- School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK;
| | - Maria Van Veelen
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | | | - Robert J. Nash
- PhytoQuest Limited, Aberystwyth SY23 3EB, UK; (B.B.); (J.H.); (R.J.N.)
| | - Paul D. Horrocks
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | - Helen P. Price
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
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Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria. Nat Commun 2021; 12:790. [PMID: 33542233 PMCID: PMC7862272 DOI: 10.1038/s41467-021-20974-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbial transformations of flavonoids, an enormous class of polyphenolic compounds abundant in plant-based diets, are closely associated with human health. However, the enzymes that initiate the gut microbial metabolism of flavones and flavonols, the two most abundant groups of flavonoids, as well as their underlying molecular mechanisms of action remain unclear. Here, we discovered a flavone reductase (FLR) from the gut bacterium, Flavonifractor plautii ATCC 49531 (originally assigned as Clostridium orbiscindens DSM 6740), which specifically catalyses the hydrogenation of the C2–C3 double bond of flavones/flavonols and initiates their metabolism as a key step. Crystal structure analysis revealed the molecular basis for the distinct catalytic property of FLR. Notably, FLR and its widespread homologues represent a class of ene-reductases that has not been previously identified. Genetic and biochemical analyses further indicated the importance of FLR in gut microbial consumption of dietary and medicinal flavonoids, providing broader insight into gut microbial xenobiotic transformations and possible guidance for personalized nutrition and medicine. Flavonoids are abundant polyphenols in plants but it is not well understood how their metabolism is initiated by microbes in the human gut. Here, the authors identify and characterise an ene-reductase from the gut bacterium, Flavonifractor plautii ATCC 49531 that catalyses the hydrogenation of the C2–C3 double bond of flavones and flavonols and present its crystal structure.
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Bao R, Hesser LA, He Z, Zhou X, Nadeau KC, Nagler CR. Fecal microbiome and metabolome differ in healthy and food-allergic twins. J Clin Invest 2021; 131:141935. [PMID: 33463536 DOI: 10.1172/jci141935] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUNDThere has been a striking generational increase in the prevalence of food allergies. We have proposed that this increase can be explained, in part, by alterations in the commensal microbiome.METHODSTo identify bacterial signatures and metabolic pathways that may influence the expression of this disease, we collected fecal samples from a unique, well-controlled cohort of twins concordant or discordant for food allergy. Samples were analyzed by integrating 16S rRNA gene amplicon sequencing and liquid chromatography-tandem mass spectrometry metabolite profiling.RESULTSA bacterial signature of 64 operational taxonomic units (OTUs) distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. We detected significant enrichment in distinct metabolite pathways in each group. The enrichment of diacylglycerol in healthy twins is of particular interest for its potential as a readily measurable fecal biomarker of health. In addition, an integrated microbial-metabolomic analysis identified a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii, suggesting new possibilities for the development of live microbiome-modulating biotherapeutics.CONCLUSIONTwin pairs exhibited significant differences in their fecal microbiomes and metabolomes through adulthood, suggesting that the gut microbiota may play a protective role in patients with food allergies beyond the infant stage.TRIAL REGISTRATIONParticipants in this study were recruited as part of an observational study (ClinicalTrials.gov NCT01613885) at multiple sites from 2014 to 2018.FUNDINGThis work was supported by the Sunshine Charitable Foundation; the Moss Family Foundation; the National Institute of Allergy and Infectious Diseases (NIAID) (R56AI134923 and R01AI 140134); the Sean N. Parker Center for Allergy and Asthma Research; the National Heart, Lung, and Blood Institute (R01 HL 118612); the Orsak family; the Kepner family; and the Stanford Institute for Immunity, Transplant and Infection.
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Affiliation(s)
- Riyue Bao
- Department of Pediatrics, University of Chicago, Chicago, Illinois, USA.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA.,Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lauren A Hesser
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Ziyuan He
- Sean N. Parker Center for Allergy and Asthma Research
| | - Xiaoying Zhou
- Sean N. Parker Center for Allergy and Asthma Research
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research.,Division of Pulmonary and Critical Care Medicine, and.,Division of Allergy, Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Cathryn R Nagler
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA.,Department of Pathology, University of Chicago, Chicago, Illinois, USA
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Xin H, Ma T, Xu Y, Chen G, Chen Y, Villot C, Renaud DL, Steele MA, Guan LL. Characterization of fecal branched-chain fatty acid profiles and their associations with fecal microbiota in diarrheic and healthy dairy calves. J Dairy Sci 2020; 104:2290-2301. [PMID: 33358167 DOI: 10.3168/jds.2020-18825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022]
Abstract
Branched-chain fatty acids (BCFA) have recently been reported to play a role in human gut health during early life. However, little information is available on the fecal BCFA profiles in young ruminants and whether they are associated with the development of neonatal calf diarrhea. The objectives of this study were to (1) characterize BCFA profiles in feces collected from young calves, (2) compare the fecal BCFA composition between diarrheic and nondiarrheic dairy calves, and (3) explore the potential relationships between BCFA and microbiota in the feces. A total of 32 male Holstein dairy calves (13 ± 3 d old) with the same diet management were grouped as diarrheic (n = 16) or healthy (n = 16) based on fecal score (determined by liquid fecal consistency with some solid particles); diarrhea cases were defined as fecal score ≥2 for at least 2 d. Fecal samples were collected on the seventh day after calf arrival, and the fecal BCFA and microbial profiles were assessed using gas chromatograph and amplicon sequencing, respectively. In total, 7 BCFA were detected in the feces of all dairy calves; however, the concentrations of fecal BCFA differed between diarrheic and nondiarrheic calves. Specifically, the concentrations of iso-C16:0, iso-C17:0, anteiso-C17:0, and total even-chain BCFA were significantly higher in the feces of diarrheic calves. When the associations between BCFA and bacteria were studied, the relative abundance of Eggerthella was positively correlated with the concentrations of iso-C16:0 (ρ = 0.67), iso-17:0 (ρ = 0.77), anteiso-C17:0 (ρ = 0.73), and iso-C18:0 (ρ = 0.65), whereas the relative abundance of Subdoligranulum was positively correlated with the concentrations of iso-C14:0 (ρ = 0.62), iso-C15:0 (ρ = 0.78), and anteiso-C15:0 (ρ = 0.63). Use of random forest algorithm showed that BCFA such as anteiso-C15:0, iso-C16:0, iso-C17:0, iso-C18:0, and total even-chain BCFA could be used as biomarkers to differentiate diarrheic calves from healthy ones. Our findings generated fundamental knowledge on the potential roles of BCFA in neonatal calf gut health. Follow-up studies with larger animal populations are warranted to validate the feasibility of using BCFA as indicators of health status in neonatal calves.
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Affiliation(s)
- Hangshu Xin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tao Ma
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Clothilde Villot
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - David L Renaud
- Department of Population Medicine, University of Guelph, Guelph, ON, N1H 2W1, Canada
| | - Michael A Steele
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
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Rodrigues AMM, Estrela S, Brown SP. Community lifespan, niche expansion and the evolution of interspecific cooperation. J Evol Biol 2020; 34:352-363. [PMID: 33238064 DOI: 10.1111/jeb.13739] [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: 07/12/2020] [Revised: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 11/29/2022]
Abstract
Microbes live in dense and diverse communities where they deploy many traits that promote the growth and survival of neighbouring species, all the while also competing for shared resources. Because microbial communities are highly dynamic, the costs and benefits of species interactions change over the growth cycle of a community. How mutualistic interactions evolve under such demographic and ecological conditions is still poorly understood. Here, we develop an eco-evolutionary model to explore how different forms of helping with distinct fitness effects (rate-enhancing and yield-enhancing) affect the multiple phases of community growth, and its consequences for the evolution of mutualisms. We specifically focus on a form of yield-enhancing trait in which cooperation augments the common pool of resources, termed niche expansion. We show that although mutualisms in which cooperation increases partners growth rate are generally favoured at early stages of community growth, niche expansion can evolve at later stages where densities are high. Further, we find that niche expansion can promote the evolution of reproductive restraint, in which a focal species adaptively reduces its own growth rate to increase the density of partner species. Our findings suggest that yield-enhancing mutualisms are more prevalent in stable habitats with a constant supply of resources, and where populations typically live at high densities. In general, our findings highlight the need to integrate different components of population growth in the analysis of mutualisms to understand the composition and function of microbial communities.
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Affiliation(s)
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
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44
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Senizza A, Rocchetti G, Mosele JI, Patrone V, Callegari ML, Morelli L, Lucini L. Lignans and Gut Microbiota: An Interplay Revealing Potential Health Implications. Molecules 2020; 25:E5709. [PMID: 33287261 PMCID: PMC7731202 DOI: 10.3390/molecules25235709] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Plant polyphenols are a broad group of bioactive compounds characterized by different chemical and structural properties, low bioavailability, and several in vitro biological activities. Among these compounds, lignans (a non-flavonoid polyphenolic class found in plant foods for human nutrition) have been recently studied as potential modulators of the gut-brain axis. In particular, gut bacterial metabolism is able to convert dietary lignans into therapeutically relevant polyphenols (i.e., enterolignans), such as enterolactone and enterodiol. Enterolignans are characterized by various biologic activities, including tissue-specific estrogen receptor activation, together with anti-inflammatory and apoptotic effects. However, variation in enterolignans production by the gut microbiota is strictly related to both bioaccessibility and bioavailability of lignans through the entire gastrointestinal tract. Therefore, in this review, we summarized the most important dietary source of lignans, exploring the interesting interplay between gut metabolites, gut microbiota, and the so-called gut-brain axis.
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Affiliation(s)
- Alice Senizza
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
| | - Gabriele Rocchetti
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
| | - Juana I. Mosele
- Cátedra de Fisicoquímica, Departamento de Química Analítica y Fisicoquímica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires C1113AAD, Argentina;
| | - Vania Patrone
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
| | - Maria Luisa Callegari
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
| | - Lorenzo Morelli
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (V.P.); (M.L.C.); (L.M.); (L.L.)
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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46
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García-Villalba R, Beltrán D, Frutos MD, Selma MV, Espín JC, Tomás-Barberán FA. Metabolism of different dietary phenolic compounds by the urolithin-producing human-gut bacteria Gordonibacter urolithinfaciens and Ellagibacter isourolithinifaciens. Food Funct 2020; 11:7012-7022. [PMID: 32716447 DOI: 10.1039/d0fo01649g] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gordonibacter urolithinfaciens and Ellagibacter isourolithinifaciens are two human gut bacterial species that convert ellagic acid into urolithins. Urolithins are bioactive postbiotics produced by dehydroxylation reactions catalyzed by different catechol-dehydroxylases. The metabolic ability of these anaerobic bacteria on other dietary-phenolic compounds is unknown. In the present study, we evaluated the metabolism of flavonoids (quercetin, hesperetin, hesperidin, nobiletin, catechin, isoxanthohumol), isoflavonoids (daidzein), coumarins (esculetin, umbelliferone, scoparone), phenylpropanoids [caffeic acid; 3-(3',4'-dihydroxyphenyl)propanoic acid (dihydrocaffeic acid); rosmarinic acid, and chlorogenic acid], benzoic acid derivatives (gallic acid, ellagic acid), lignans (secoisolariciresinol diglucoside), stilbenes (resveratrol), and secoiridoids (oleuropein) by G. urolithinfaciens DSM 27213T and E. isourolithinifaciens DSM 104140T. Both strains metabolized ellagic acid leading to the characteristic urolithins. They also metabolized caffeic, dihydrocaffeic, rosmarinic, and chlorogenic acids. The rest of the phenolic compounds were not transformed. Catechol dehydroxylation and double bond reduction were prominent transformations observed during the incubations. The enzymatic activities seem to have a narrow substrate scope as many catechol- (quercetin, catechin, esculetin, gallic acid) and double bond-containing (resveratrol, esculetin, scoparone, umbelliferone) phenolics were not metabolized. The catechol-dehydroxylase activity was more efficient in E. isourolithinifaciens, while the reductase activity was more relevant in G. urolithinfaciens.
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Affiliation(s)
- Rocío García-Villalba
- Laboratory of Food & Health, Research Group on Quality, Safety, and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain.
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47
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Navarro SL, Levy L, Curtis KR, Elkon I, Kahsai OJ, Ammar HS, Randolph TW, Hong NN, Carnevale Neto F, Raftery D, Chapkin RS, Lampe JW, Hullar MAJ. Effect of a Flaxseed Lignan Intervention on Circulating Bile Acids in a Placebo-Controlled Randomized, Crossover Trial. Nutrients 2020; 12:E1837. [PMID: 32575611 PMCID: PMC7374341 DOI: 10.3390/nu12061837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Plant lignans and their microbial metabolites, e.g., enterolactone (ENL), may affect bile acid (BA) metabolism through interaction with hepatic receptors. We evaluated the effects of a flaxseed lignan extract (50 mg/day secoisolariciresinol diglucoside) compared to a placebo for 60 days each on plasma BA concentrations in 46 healthy men and women (20-45 years) using samples from a completed randomized, crossover intervention. Twenty BA species were measured in fasting plasma using LC-MS. ENL was measured in 24-h urines by GC-MS. We tested for (a) effects of the intervention on BA concentrations overall and stratified by ENL excretion; and (b) cross-sectional associations between plasma BA and ENL. We also explored the overlap in bacterial metabolism at the genus level and conducted in vitro anaerobic incubations of stool with lignan substrate to identify genes that are enriched in response to lignan metabolism. There were no intervention effects, overall or stratified by ENL at FDR < 0.05. In the cross-sectional analysis, irrespective of treatment, five secondary BAs were associated with ENL excretion (FDR < 0.05). In vitro analyses showed positive associations between ENL production and bacterial gene expression of the bile acid-inducible gene cluster and hydroxysteroid dehydrogenases. These data suggest overlap in community bacterial metabolism of secondary BA and ENL.
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Affiliation(s)
- Sandi L. Navarro
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Lisa Levy
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Keith R. Curtis
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Isaac Elkon
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Orsalem J. Kahsai
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Hamza S. Ammar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Timothy W. Randolph
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Natalie N. Hong
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Daniel Raftery
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; (N.N.H.); (F.C.N.)
| | - Robert S. Chapkin
- Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, TX 77843, USA;
| | - Johanna W. Lampe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
| | - Meredith A. J. Hullar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (I.E.); (O.J.K.); (H.S.A.); (T.W.R.); (D.R.); (J.W.L.); (M.A.J.H.)
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48
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Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ. A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe 2020; 27:1001-1013.e9. [PMID: 32348781 PMCID: PMC7292766 DOI: 10.1016/j.chom.2020.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.
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Affiliation(s)
- Jordan E Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Paola Soto-Perez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA
| | - Kathy N Lam
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elizabeth N Bess
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Henry J Haiser
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Than S Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Vayu M Rekdal
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Connie W Y Ha
- Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Suzanne Devkota
- Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA
| | - Emma Allen-Vercoe
- Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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49
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Seyed Hameed AS, Rawat PS, Meng X, Liu W. Biotransformation of dietary phytoestrogens by gut microbes: A review on bidirectional interaction between phytoestrogen metabolism and gut microbiota. Biotechnol Adv 2020; 43:107576. [PMID: 32531317 DOI: 10.1016/j.biotechadv.2020.107576] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Phytoestrogens are a class of plant produced polyphenolic compounds with diphenolic structure, which is similar to 17β-estradiol. These phytoestrogens preferentially bind to estrogen receptors, however, with weak affinity. Recently, many studies have found that these phytoestrogens can be transformed by gut microbiota through novel enzymatic reactions into metabolites with altered bioactivity. Recent studies have also implied that these metabolites could possibly modulate the host gut ecosystem, gene expression, metabolism and the immune system. Thus, isolating gut microbes capable of biotransforming phytoestrogens and characterizing the novel enzymatic reactions involved are principal to understand the mechanisms of beneficial effects brought by gut microbiota and their metabolism on phytoestrogens, and to provide the theoretical knowledge for the development of functional probiotics. In the present review, we summarized works on gut microbial biotransformation of phytoestrogens, including daidzin (isoflavone), phenylnaringenin (prenylflavonoid), lignans, resveratrol (stilbene) and ellagitannins. We mainly focus on gut bacterial isolation, metabolic pathway characterization, and the bidirectional interaction of phytoestrogens with gut microbes to illustrate the novel metabolic capability of gut microbiota and the methods used in these studies.
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Affiliation(s)
- Ahkam Saddam Seyed Hameed
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, PR China
| | - Parkash Singh Rawat
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, PR China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, PR China.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, PR China
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50
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Affiliation(s)
- Chloe E Atreya
- Department of Medicine, Division of Hematology and Oncology, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA
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