1
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Zheng S, Qin W, Chen T, Ouyang R, Wang X, Li Q, Zhao Y, Liu X, Wang D, Zhou L, Xu G. Strategy for Comprehensive Detection and Annotation of Gut Microbiota-Related Metabolites Based on Liquid Chromatography-High-Resolution Mass Spectrometry. Anal Chem 2024; 96:2206-2216. [PMID: 38253323 DOI: 10.1021/acs.analchem.3c05219] [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: 01/24/2024]
Abstract
Gut microbiota, widely populating the mammalian gastrointestinal tract, plays an important role in regulating diverse pathophysiological processes by producing bioactive molecules. Extensive detection of these molecules contributes to probing microbiota function but is limited by insufficient identification of existing analytical methods. In this study, a systematic strategy was proposed to detect and annotate gut microbiota-related metabolites on a large scale. A pentafluorophenyl (PFP) column-based liquid chromatography-high-resolution mass spectrometry (LC-HRMS) method was first developed for high-coverage analysis of gut microbiota-related metabolites, which was verified to be stable and robust with a wide linearity range, high sensitivity, satisfactory recovery, and repeatability. Then, an informative database integrating 968 knowledge-based microbiota-related metabolites and 282 sample-sourced ones defined by germ-free (GF)/antibiotic-treated (ABX) models was constructed and subsequently used for targeted extraction and annotation in biological samples. Using pooled feces, plasma, and urine of mice for demonstration application, 672 microbiota-related metabolites were annotated, including 21% neglected by routine nontargeted peak detection. This strategy serves as a useful tool for the comprehensive capture of the intestinal flora metabolome, contributing to our deeper understanding of microbe-host interactions.
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Affiliation(s)
- Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wangshu Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Tiantian Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runze Ouyang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Ying Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Difei Wang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang 110022, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [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] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
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Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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3
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Elucidating gut microbiota and metabolite patterns shaped by goat milk-based infant formula feeding in mice colonized by healthy infant feces. Food Chem 2023; 410:135413. [PMID: 36623461 DOI: 10.1016/j.foodchem.2023.135413] [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: 06/30/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
The gut microbiota plays an evolutionarily conserved role in host metabolism, which is influenced by diet. Here, we investigated differences in shaping the gut microbiota and regulating metabolism in cow milk-based infant formula, goat milk-based infant formula, and mix milk-based infant formula compared with pasteurized human milk. 16S rRNA results showed that goat milk-based infant formula selectively increased the relative abundance of Blautia, Roseburia, Alistites and Muribaculum in the gut compared to other infant formulas. Metabolomics identification indicated that goat milk-based infant formula mainly emphasized bile acid biosynthesis, arachidonic acid metabolism and steroid biosynthesis metabolic pathways. Metabolites associated with these metabolic pathways were positively associated with increased microorganisms in goat milk-based infant formula, particularly Alistipes. Furthermore, we found a deficiency of Akkermansia abundance in three infant formula-fed compared to pasteurizedhuman milk-fed. This study presents new insights into the improvement and application of goat milk-based infant formulas in terms of intestinal microecology.
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4
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Implication of gut microbes and its metabolites in colorectal cancer. J Cancer Res Clin Oncol 2023; 149:441-465. [PMID: 36572792 DOI: 10.1007/s00432-022-04422-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/14/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer with a significant impact on loss of life. In 2020, nearly 1.9 million new cases and over 9,35,000 deaths were reported. Numerous microbes that are abundant in the human gut benefit host physiology in many ways. Although the underlying mechanism is still unknown, their association appears to be crucial in the beginning and progression of CRC. Diet has a significant impact on the microbial composition and may increase the chance of getting CRC. Increasing evidence points to the gut microbiota as the primary initiator of colonic inflammation, which is connected to the development of colonic tumors. However, it is unclear how the microbiota contributes to the development of CRCs. Patients with CRC have been found to have dysbiosis of the gut microbiota, which can be identified by a decline in commensal bacterial species, such as those that produce butyrate, and a concurrent increase in harmful bacterial populations, such as opportunistic pathogens that produce pro-inflammatory cytokines. We believe that using probiotics or altering the gut microbiota will likely be effective tools in the fight against CRC treatment. PURPOSE In this review, we revisited the association between gut microbiota and colorectal cancer whether cause or effect. The various factors which influence gut microbiome in patients with CRC and possible mechanism in relation with development of CRC. CONCLUSION The clinical significance of the intestinal microbiota may aid in the prevention and management of CRC.
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5
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Xu R, Lee J, Zhang S, Chen L, Zhu J. Structure similarity and molecular networking analysis for the discovery of polyphenol biotransformation products of gut microbes. Anal Chim Acta 2022; 1221:340145. [PMID: 35934377 PMCID: PMC10324525 DOI: 10.1016/j.aca.2022.340145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/21/2022] [Accepted: 07/03/2022] [Indexed: 11/26/2022]
Abstract
Intestinal bacteria can metabolize polyphenols into highly bioavailable derivatives, which provide potential health-promoting effects to the host. However, the metabolic pathways and related products in this process are still largely unclear. Polyphenols are generally characterized by the presence of many phenolic structural units, which makes it possible to explore correlations among compounds based on similar molecular networks. In this study, we developed a standard-oriented/database-assisted molecular networking (SODA-MN) method for iterative compound annotation analysis to explore the metabolic profiles of polyphenol-rich black raspberry extract metabolized by representative gut bacteria. Starting from a group of polyphenol metabolites, the SODA-MN method predicted the possible polyphenol derivatives by adding or deducting common biotransformation groups and iterative annotating of structure similarity based on fragmentation spectra. Our results showed that 48 polyphenol derivatives in the first round of analysis alone (fragmentation match≥5, spec score >0.5) can be annotated, which were associated with 13 detected polyphenol standards that served as seed compounds. Meanwhile, this method was applied to a time-course study to show the time-dependent changes of polyphenols metabolized by a mix of gut bacteria. In addition, the metabolic capabilities of polyphenols among four representative gut bacteria were compared via our newly developed method and differential polyphenol metabolites were detected. In summary, the SODA-MN method provides a new approach for the annotation of unknown compounds by structure similarity and molecular networking analysis. Our analysis results could provide identification of key polyphenol derivatives that may contribute to the mechanistic investigations of their functions and assist our understanding of how polyphenols and gut bacteria interact to promote human health.
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Affiliation(s)
- Rui Xu
- Human Nutrition Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jisun Lee
- Human Nutrition Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Shiqi Zhang
- Human Nutrition Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Li Chen
- Human Nutrition Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiangjiang Zhu
- Human Nutrition Program, The Ohio State University, Columbus, OH, 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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6
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Jia X, Xu W, Zhang L, Li X, Wang R, Wu S. Impact of Gut Microbiota and Microbiota-Related Metabolites on Hyperlipidemia. Front Cell Infect Microbiol 2021; 11:634780. [PMID: 34490132 PMCID: PMC8417472 DOI: 10.3389/fcimb.2021.634780] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Hyperlipidemia, defined as the presence of excess fat or lipids in the blood, has been considered as a high-risk factor and key indicator of many metabolic diseases. The gut microbiota has been reported playing a vital role in regulating host lipid metabolism. The pathogenic role of gut microbiota in the development of hyperlipidemia has been revealed through fecal microbiota transplantation experiment to germ-free mice. The effector mechanism of microbiota-related metabolites such as bile acids, lipopolysaccharide, and short-chain fatty acids in the regulation of hyperlipidemia has been partially unveiled. Moreover, studies on gut-microbiota-targeted hyperlipidemia interventions, including the use of prebiotics, probiotics, fecal microbiota transplantation, and natural herbal medicines, also have shown their efficacy in the treatment of hyperlipidemia. In this review, we summarize the relationship between gut microbiota and hyperlipidemia, the impact of gut microbiota and microbiota-related metabolites on the development and progression of hyperlipidemia, and the potential therapeutic management of hyperlipidemia targeted at gut microbiota.
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Affiliation(s)
- Xiaokang Jia
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Wen Xu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lei Zhang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoyan Li
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Ruirui Wang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuisheng Wu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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7
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Dalal N, Jalandra R, Bayal N, Yadav AK, Sharma M, Makharia GK, Kumar P, Singh R, Solanki PR, Kumar A. Gut microbiota-derived metabolites in CRC progression and causation. J Cancer Res Clin Oncol 2021; 147:3141-3155. [PMID: 34273006 DOI: 10.1007/s00432-021-03729-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/04/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities. PURPOSE In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development. CONCLUSION Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Nitin Bayal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Amit K Yadav
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, 110029, India
| | - Pramod Kumar
- Sri Aurobindo College, Delhi University, New Delhi, 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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8
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Jaimes JD, Slavíčková A, Hurych J, Cinek O, Nichols B, Vodolánová L, Černý K, Havlík J. Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling. PLoS One 2021; 16:e0247378. [PMID: 33765008 PMCID: PMC7993802 DOI: 10.1371/journal.pone.0247378] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Characterization of metabolites and microbiota composition from human stool provides powerful insight into the molecular phenotypic difference between subjects with normal weight and those with overweight/obesity. The aim of this study was to identify potential metabolic and bacterial signatures from stool that distinguish the overweight/obesity state in children/adolescents. Using 1H NMR spectral analysis and 16S rRNA gene profiling, the fecal metabolic profile and bacterial composition from 52 children aged 7 to 16 was evaluated. The children were classified into three groups (16 with normal-weight, 17 with overweight, 19 with obesity). The metabolomic analysis identified four metabolites that were significantly different (p < 0.05) among the study groups based on one-way ANOVA testing: arabinose, butyrate, galactose, and trimethylamine. Significantly different (p < 0.01) genus-level taxa based on edgeR differential abundance tests were genus Escherichia and Tyzzerella subgroup 3. No significant difference in alpha-diversity was detected among the three study groups, and no significant correlations were found between the significant taxa and metabolites. The findings support the hypothesis of increased energy harvest in obesity by human gut bacteria through the growing observation of increased fecal butyrate in children with overweight/obesity, as well as an increase of certain monosaccharides in the stool. Also supported is the increase of trimethylamine as an indicator of an unhealthy state.
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Affiliation(s)
- José Diógenes Jaimes
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Andrea Slavíčková
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jakub Hurych
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Ondřej Cinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic.,Department of Paediatrics, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Ben Nichols
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Lucie Vodolánová
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Karel Černý
- Olivova Children's Medical Institution, Říčany, Czech Republic
| | - Jaroslav Havlík
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czech Republic
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9
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Peng Y, Nie Y, Yu J, Wong CC. Microbial Metabolites in Colorectal Cancer: Basic and Clinical Implications. Metabolites 2021; 11:metabo11030159. [PMID: 33802045 PMCID: PMC8001357 DOI: 10.3390/metabo11030159] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading cancers that cause cancer-related deaths worldwide. The gut microbiota has been proved to show relevance with colorectal tumorigenesis through microbial metabolites. By decomposing various dietary residues in the intestinal tract, gut microbiota harvest energy and produce a variety of metabolites to affect the host physiology. However, some of these metabolites are oncogenic factors for CRC. With the advent of metabolomics technology, studies profiling microbiota-derived metabolites have greatly accelerated the progress in our understanding of the host-microbiota metabolism interactions in CRC. In this review, we briefly summarize the present metabolomics techniques in microbial metabolites researches and the mechanisms of microbial metabolites in CRC pathogenesis, furthermore, we discuss the potential clinical applications of microbial metabolites in cancer diagnosis and treatment.
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Affiliation(s)
- Yao Peng
- Department of Gastroenterology, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou 510180, China; (Y.P.); (Y.N.)
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou 510180, China; (Y.P.); (Y.N.)
- Department of Gastroenterology, The Second Affiliated Hospital, Medical School, South China University of Technology, Guangzhou 510180, China
| | - Jun Yu
- Department of Gastroenterology, The Second Affiliated Hospital, Medical School, South China University of Technology, Guangzhou 510180, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence: (J.Y.); (C.C.W.)
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence: (J.Y.); (C.C.W.)
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10
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Jain A, Correia MSP, Meistermann H, Vujasinovic M, Löhr JM, Globisch D. Comparison of two arylsulfatases for targeted mass spectrometric analysis of microbiota-derived metabolites. J Pharm Biomed Anal 2020; 195:113818. [PMID: 33342568 DOI: 10.1016/j.jpba.2020.113818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Sulfation of metabolites is the second highest phase II modification in humans, which plays a critical role in the xenobiotics clearance process and gut microbiota-host co-metabolism. Besides the main function to remove xenobiotics from the body, sulfated metabolites have also been linked to inflammation, bacterial pathogenesis and metabolic disorders. A better understanding of how these metabolites impact the human body has turned into an important research area. Analytical methods for selective identification of this metabolite class are scarce. We have recently developed an assay utilizing the arylsulfatase from Helix pomatia due to a high substrate promiscuity combined with state-of-the-art metabolomics bioinformatic analysis for the selective identification of O-sulfated metabolites in human samples. This enzyme requires a multistep purification process as highest purity is needed for the developed mass spectrometric assay. In this study, we have utilized a new and recombinant overexpressed arylsulfatase (ASPC) for the selective identification of organic sulfate esters in human urine samples. We have compared the substrate conversion in urine samples and substrate specificity of this enzyme with purified arylsulfatase from Helix pomatia. Our analysis of urine samples revealed that both enzymes can be utilized for the selective analysis and discovery of sulfated metabolites with high promiscuity as demonstrated by equal hydrolysis of 108 substrates including sulfated conjugates of 27 metabolites of microbial origin. Importantly, we also identified 21 substrates in human urine samples that are exclusively hydrolyzed by ASPC and application of this enzyme increases the discovery of unknown sulfated metabolites with a higher scaffold diversity.
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Affiliation(s)
- Abhishek Jain
- Dept. Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 599, SE-75124 Uppsala, Sweden
| | - Mario S P Correia
- Dept. Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 599, SE-75124 Uppsala, Sweden
| | - Hannes Meistermann
- Dept. Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 599, SE-75124 Uppsala, Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
| | - Daniel Globisch
- Dept. Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 599, SE-75124 Uppsala, Sweden.
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11
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Correia MSP, Lin W, Aria AJ, Jain A, Globisch D. Rapid Preparation of a Large Sulfated Metabolite Library for Structure Validation in Human Samples. Metabolites 2020; 10:metabo10100415. [PMID: 33081284 PMCID: PMC7603051 DOI: 10.3390/metabo10100415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolomics analysis of biological samples is widely applied in medical and natural sciences. Assigning the correct chemical structure in the metabolite identification process is required to draw the correct biological conclusions and still remains a major challenge in this research field. Several metabolite tandem mass spectrometry (MS/MS) fragmentation spectra libraries have been developed that are either based on computational methods or authentic libraries. These libraries are limited due to the high number of structurally diverse metabolites, low commercial availability of these compounds, and the increasing number of newly discovered metabolites. Phase II modification of xenobiotics is a compound class that is underrepresented in these databases despite their importance in diet, drug, or microbiome metabolism. The O-sulfated metabolites have been described as a signature for the co-metabolism of bacteria and their human host. Herein, we have developed a straightforward chemical synthesis method for rapid preparation of sulfated metabolite standards to obtain mass spectrometric fragmentation pattern and retention time information. We report the preparation of 38 O-sulfated alcohols and phenols for the determination of their MS/MS fragmentation pattern and chromatographic properties. Many of these metabolites are regioisomers that cannot be distinguished solely by their fragmentation pattern. We demonstrate that the versatility of this method is comparable to standard chemical synthesis. This comprehensive metabolite library can be applied for co-injection experiments to validate metabolites in different human sample types to explore microbiota-host co-metabolism, xenobiotic, and diet metabolism.
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12
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Yu Z, Shi D, Liu W, Meng Y, Meng F. Metabolome responses of Enterococcus faecium to acid shock and nitrite stress. Biotechnol Bioeng 2020; 117:3559-3571. [PMID: 32662876 DOI: 10.1002/bit.27497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
Abstract
Enterococcus faecium is gaining increasing interest due to its virulence and tolerance to a range of stresses (e.g., acid shock and nitrite stress in human stomach). The chemical taxonomy and basic structural features of cellular metabolite can provide us a deeper understanding of bacterial tolerance at molecular level. Here, we used hierarchical classification and molecular composition analysis to investigate the metabolome responses of E. faecium to acid shock and nitrite stress. Our results showed that considerable high biodegradable compounds (e.g., dipeptides) were produced by E. faecium under acid shock, while nitrite stress induced the accumulations of some low biodegradable compounds (e.g., organoheterocyclic compounds and benzenoids). Complete genome analysis and metabolic pathway profiling suggested that E. faecium produced high biodegradable metabolites responsible for the proton-translocation and biofilm formation, which increase its tolerance to acid shock. Yet, the presence of low biodegradable metabolites due to the nitrite exposure could disturb the bacterial productions of surface proteins, and thus inhibiting biofilm formation. Our approach uncovered the hidden interactions between intracellular metabolites and exogenous stress, and will improve the understanding of host-microbe interactions.
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Affiliation(s)
- Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Dongchen Shi
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Wencong Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
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13
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Lin W, Conway LP, Block A, Sommi G, Vujasinovic M, Löhr JM, Globisch D. Sensitive mass spectrometric analysis of carbonyl metabolites in human urine and fecal samples using chemoselective modification. Analyst 2020; 145:3822-3831. [PMID: 32393929 DOI: 10.1039/d0an00150c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Metabolites with ketone or aldehyde functionalities comprise a large proportion of the human metabolome, most notably in the form of sugars. However, these reactive molecules are also generated through oxidative stress or gut microbiota metabolism and have been linked to disease development. The discovery and structural validation of this class of metabolites over the large concentration range found in human samples is crucial to identify their links to pathogenesis. Herein, we have utilized an advanced chemoselective probe methodology alongside bioinformatic analysis to identify carbonyl-metabolites in urine and fecal samples. In total, 99 metabolites were identified in urine samples and the chemical structure for 40 metabolites were unambiguously validated using a co-injection procedure. We also describe the preparation of a metabolite-conjugate library of 94 compounds utilized to efficiently validate these ketones and aldehydes. This method was used to validate 33 metabolites in a pooled fecal sample extract to demonstrate the potential for rapid and efficient metabolite detection over a wide metabolite concentration range. This analysis revealed the presence of six metabolites that have not previously been detected in either sample type. The constructed library can be utilized for straightforward, large-scale, and expeditious analysis of carbonyls in any sample type.
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Affiliation(s)
- Weifeng Lin
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
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14
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Huang JF, Zhao Q, Dai MY, Xiao XR, Zhang T, Zhu WF, Li F. Gut microbiota protects from triptolide-induced hepatotoxicity: Key role of propionate and its downstream signalling events. Pharmacol Res 2020; 155:104752. [DOI: 10.1016/j.phrs.2020.104752] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/16/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
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15
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Abstract
The intestinal tract harbors a diverse community of microbes that have co-evolved with the host immune system. Although many of these microbes execute functions that are critical for host physiology, the host immune system must control the microbial community so that the dynamics of this interdependent relationship is maintained. To facilitate host homeostasis, the immune system ensures that the microbial load is tolerated, but anatomically contained, while remaining reactive to microbial invasion. Although the microbiota is required for intestinal immune development, immune responses regulate the structure and composition of the intestinal microbiota by evolving unique immune adaptations that manage this high-bacterial load. The immune mechanisms work together to ensure that commensal bacteria rarely breach the intestinal barrier and that any that do invade should be killed rapidly to prevent penetration to systemic sites. The communication between microbiota and the immune system is mediated by the interaction of bacterial components with pattern recognition receptors expressed by intestinal epithelium and various antigen-presenting cells resulting in activation of both innate and adaptive immune responses. Interaction between the microbial community and host plays a crucial role in the mucosal homeostasis and health status of the host. In addition to providing a home to numerous microbial inhabitants, the intestinal tract is an active immunological organ, with more resident immune cells than anywhere else in the body, organized in lymphoid structures called Peyer's patches and isolated lymphoid follicles such as the cecal tonsils. Macrophages, dendritic cells, various subsets of T cells, B cells and the secretory immunoglobulin A (IgA) they produce, all contribute to the generation of a proper immune response to invading pathogens while keeping the resident microbial community in check without generating an overt inflammatory response to it. IgA-producing plasma cells, intraepithelial lymphocytes, and γδT cell receptor-expressing T cells are lymphocytes that are uniquely present in the mucosa. In addition, of the γδT cells in the intestinal lamina propria, there are significant numbers of IL-17-producing T cells and regulatory T cells. The accumulation and function of these mucosal leukocytes are regulated by the presence of intestinal microbiota, which regulate these immune cells and enhance the mucosal barrier function allowing the host to mount robust immune responses against invading pathogens, and simultaneously maintains immune homeostasis.
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Affiliation(s)
- Michael H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, 77845 USA.
| | - Annah Lee
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, 77845 USA; Department of Poultry Science, Texas A&M University, College Station, TX, 77845 USA
| | - Elizabeth Santin
- Universidade Federal Do Paraná, Department of Veterinary Medicine, Curitiba, 80035-050 Brazil
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16
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Wu WK, Hsu CC, Sheen LY, Wu MS. Measurement of gut microbial metabolites in cardiometabolic health and translational research. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 1:e8537. [PMID: 31344762 DOI: 10.1002/rcm.8537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/07/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
The human gut microbiota is a functioning endocrine organ and stands at the intersection between dietary components and health or disease. There are very many microbial metabolites with numerous structures and functions arising from the gut microbial fermentation of foods and become signals for biological communication in the human body. These small molecules can be absorbed and delivered to distant organs through the circulatory system to build the gut-systemic axis. The gut microbial metabolomes are thus believed to play important roles in regulating cardiometabolic health and provide opportunities in mechanistic research and new drug discovery. Measurement of these novel microbial metabolites in clinical samples may serve as a tool for investigating disease biomarkers. In the past decade, the development of untargeted and targeted metabolomics approaches using NMR, LC/MS, and GC/MS has contributed to the exploration of gut microbial metabolomes in cardiometabolic health and disease. Some important targets are currently being translated into clinical applications. In this review article, we introduce an oral carnitine challenge test developed as an example to demonstrate the potential applications in personalized nutrition based on the function of gut microbiota. It is a method taking the gut microbiota as a bioreactor and provides fermentable materials as inputs and measures the outputs of targeted microbial byproducts in the blood or urine. This challenge test may be extended to measure metabolites from microbial fermentation related to other endocrinological or inflammatory diseases. We review current gut metabolome research approaches and propose a gut microbial functional measurement using a challenge test. We suggest that the maturation in measuring gut microbial metabolites may provide an important piece to complete the puzzle of precision medicine.
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Affiliation(s)
- Wei-Kai Wu
- Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Lee-Yan Sheen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ming-Shiang Wu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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17
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Luan H, Wang X, Cai Z. Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders. MASS SPECTROMETRY REVIEWS 2019; 38:22-33. [PMID: 29130504 DOI: 10.1002/mas.21553] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/12/2017] [Indexed: 05/10/2023]
Abstract
Metabolomics seeks to take a "snapshot" in a time of the levels, activities, regulation and interactions of all small molecule metabolites in response to a biological system with genetic or environmental changes. The emerging development in mass spectrometry technologies has shown promise in the discovery and quantitation of neuroactive small molecule metabolites associated with gut microbiota and brain. Significant progress has been made recently in the characterization of intermediate role of small molecule metabolites linked to neural development and neurodegenerative disorder, showing its potential in understanding the crosstalk between gut microbiota and the host brain. More evidence reveals that small molecule metabolites may play a critical role in mediating microbial effects on neurotransmission and disease development. Mass spectrometry-based metabolomics is uniquely suitable for obtaining the metabolic signals in bidirectional communication between gut microbiota and brain. In this review, we summarized major mass spectrometry technologies including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and imaging mass spectrometry for metabolomics studies of neurodegenerative disorders. We also reviewed the recent advances in the identification of new metabolites by mass spectrometry and metabolic pathways involved in the connection of intestinal microbiota and brain. These metabolic pathways allowed the microbiota to impact the regular function of the brain, which can in turn affect the composition of microbiota via the neurotransmitter substances. The dysfunctional interaction of this crosstalk connects neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease and Huntington's disease. The mass spectrometry-based metabolomics analysis provides information for targeting dysfunctional pathways of small molecule metabolites in the development of the neurodegenerative diseases, which may be valuable for the investigation of underlying mechanism of therapeutic strategies.
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Affiliation(s)
- Hemi Luan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
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18
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Wang L, Ravichandran V, Yin Y, Yin J, Zhang Y. Natural Products from Mammalian Gut Microbiota. Trends Biotechnol 2018; 37:492-504. [PMID: 30392727 DOI: 10.1016/j.tibtech.2018.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 02/08/2023]
Abstract
The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.
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Affiliation(s)
- Leli Wang
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, 410081, Changsha, China; These authors contributed equally to this work
| | - Vinothkannan Ravichandran
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235, Qingdao, China; These authors contributed equally to this work
| | - Yulong Yin
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, 410081, Changsha, China; Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, 410125, Changsha, China
| | - Jia Yin
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, 410081, Changsha, China; Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235, Qingdao, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235, Qingdao, China.
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19
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Cai J, Nichols RG, Koo I, Kalikow ZA, Zhang L, Tian Y, Zhang J, Smith PB, Patterson AD. Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity. mSystems 2018; 3:e00123-18. [PMID: 30417115 PMCID: PMC6222046 DOI: 10.1128/msystems.00123-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effect on the gut microbiota. The microbiota was isolated from mouse cecum and was exposed to tempol for 4 h under strict anaerobic conditions. The flow cytometry data suggested that short-term tempol exposure to the microbiota is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short-chain fatty acids, branched-chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating that the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology, and metabolism and a comparison of in vitro and in vivo exposures with tempol, suggest that physiologic and metabolic phenotyping can provide unique insight into gut microbiota toxicity. IMPORTANCE The gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global metabolomics with flow cytometry to evaluate the direct effect of tempol on the microbiota. This approach may be useful in deciphering how other xenobiotics directly influence the microbiota.
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Affiliation(s)
- Jingwei Cai
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Robert G. Nichols
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Imhoi Koo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Zachary A. Kalikow
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Limin Zhang
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS), Wuhan, China
| | - Yuan Tian
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS), Wuhan, China
| | - Jingtao Zhang
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Philip B. Smith
- Metabolomics Facility, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew D. Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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20
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Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption ionization mass spectrometry. Anal Bioanal Chem 2018; 411:147-156. [PMID: 30377739 DOI: 10.1007/s00216-018-1436-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/06/2018] [Accepted: 10/17/2018] [Indexed: 01/30/2023]
Abstract
A high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI)-MS-based metabolomics platform was developed using a pre-fabricated microarray of nanoparticles and organic matrices. Selected organic matrices, inorganic nanoparticle (NP) suspensions, and sputter coated metal NPs, as well as various additives, were tested for metabolomics analysis of the turkey gut microbiome. Four NPs and one organic matrix were selected as the optimal matrix set: α-cyano-4-hydroycinnamic acid, Fe3O4 and Au NPs in positive ion mode with 10 mM sodium acetate, and Cu and Ag NPs in negative ion mode with no additive. Using this set of five matrices, over two thousand unique metabolite features were reproducibly detected across intestinal samples from turkeys fed a diet amended with therapeutic or sub-therapeutic antibiotics (200 g/ton or 50 g/ton bacitracin methylene disalicylate (BMD), respectively), or non-amended feed. Among the thousands of unique features, 56 of them were chemically identified using MALDI-MS/MS, with the help of in-parallel liquid chromatography (LC)-MS/MS analysis. Lastly, as a proof of concept application, this protocol was applied to 52 turkey cecal samples at three different time points from the antibiotic feed trial. Statistical analysis indicated variations in the metabolome of turkeys with different ages or treatments. Graphical abstract ᅟ.
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21
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Garg N, Conway LP, Ballet C, Correia MSP, Olsson FKS, Vujasinovic M, Löhr J, Globisch D. Chemoselective Probe Containing a Unique Bioorthogonal Cleavage Site for Investigation of Gut Microbiota Metabolism. Angew Chem Int Ed Engl 2018; 57:13805-13809. [PMID: 30168889 DOI: 10.1002/anie.201804828] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Neeraj Garg
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Louis P. Conway
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Caroline Ballet
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Mario S. P. Correia
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Frida K. S. Olsson
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department of Clinical ScienceIntervention and Technology (CLINTEC) and Department for Digestive DiseasesKarolinska Institute and Karolinska University Hospital Stockholm Sweden
| | - J.‐Matthias Löhr
- Department of Clinical ScienceIntervention and Technology (CLINTEC) and Department for Digestive DiseasesKarolinska Institute and Karolinska University Hospital Stockholm Sweden
| | - Daniel Globisch
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
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22
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Garg N, Conway LP, Ballet C, Correia MSP, Olsson FKS, Vujasinovic M, Löhr J, Globisch D. Chemoselective Probe Containing a Unique Bioorthogonal Cleavage Site for Investigation of Gut Microbiota Metabolism. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Neeraj Garg
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Louis P. Conway
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Caroline Ballet
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Mario S. P. Correia
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Frida K. S. Olsson
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department of Clinical ScienceIntervention and Technology (CLINTEC) and Department for Digestive DiseasesKarolinska Institute and Karolinska University Hospital Stockholm Sweden
| | - J.‐Matthias Löhr
- Department of Clinical ScienceIntervention and Technology (CLINTEC) and Department for Digestive DiseasesKarolinska Institute and Karolinska University Hospital Stockholm Sweden
| | - Daniel Globisch
- Department of Medicinal ChemistryScience for Life LaboratoryUppsala University Box 574 75123 Uppsala Sweden
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23
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Ballet C, Correia MSP, Conway LP, Locher TL, Lehmann LC, Garg N, Vujasinovic M, Deindl S, Löhr JM, Globisch D. New enzymatic and mass spectrometric methodology for the selective investigation of gut microbiota-derived metabolites. Chem Sci 2018; 9:6233-6239. [PMID: 30090311 PMCID: PMC6063053 DOI: 10.1039/c8sc01502c] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/27/2018] [Indexed: 12/18/2022] Open
Abstract
Gut microbiota significantly impact human physiology through metabolic interaction. Selective investigation of the co-metabolism of bacteria and their human host is a challenging task and methods for their analysis are limited. One class of metabolites associated with this co-metabolism are O-sulfated compounds. Herein, we describe the development of a new enzymatic assay for the selective mass spectrometric investigation of this phase II modification class. Analysis of human urine and fecal samples resulted in the detection of 206 sulfated metabolites, which is three times more than reported in the Human Metabolome Database. We confirmed the chemical structure of 36 sulfated metabolites including unknown and commonly reported microbiota-derived sulfated metabolites using synthesized internal standards and mass spectrometric fragmentation experiments. Our findings demonstrate that enzymatic sample pre-treatment combined with state-of-the-art metabolomics analysis represents a new and efficient strategy for the discovery of unknown microbiota-derived metabolites in human samples. Our described approach can be adapted for the targeted investigation of other metabolite classes as well as the discovery of biomarkers for diseases affected by microbiota.
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Affiliation(s)
- Caroline Ballet
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
| | - Mário S P Correia
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
| | - Louis P Conway
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
| | - Theresa L Locher
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
| | - Laura C Lehmann
- Department of Cell and Molecular Biology , Science for Life Laboratory , Uppsala University , Box 596 , SE-75124 Uppsala , Sweden
| | - Neeraj Garg
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
| | - Miroslav Vujasinovic
- Department for Digestive Diseases , Karolinska University Hospital , Stockholm , Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology , Science for Life Laboratory , Uppsala University , Box 596 , SE-75124 Uppsala , Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases , Karolinska University Hospital , Stockholm , Sweden
- Department of Clinical Science , Intervention and Technology (CLINTEC) , Karolinska Institute , Stockholm , Sweden
| | - Daniel Globisch
- Department of Medicinal Chemistry , Science for Life Laboratory , Uppsala University , Box 574 , SE-75123 Uppsala , Sweden .
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24
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Yan S, Zhu C, Yu T, Huang W, Huang J, Kong Q, Shi J, Chen Z, Liu Q, Wang S, Jiang Z, Chen Z. Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets. Front Microbiol 2017; 8:1812. [PMID: 28983290 PMCID: PMC5613163 DOI: 10.3389/fmicb.2017.01812] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 12/26/2022] Open
Abstract
This study was conducted to compare the microbiome and metabolome differences in the colon lumen from two pig breeds with different genetic backgrounds. Fourteen weaned piglets at 30 days of age, including seven Landrace piglets (a lean-type pig breed with a fast growth rate) and seven Meihua piglets (a fatty-type Chinese local pig breed with a slow growth rate), were fed the same diets for 35 days. Untargeted metabolomics analyses showed that a total of 401 metabolites differed between Landrace and Meihua. Seventy of these 401 metabolites were conclusively identified. Landrace accumulated more short-chain fatty acids (SCFAs) and secondary bile acids in the colon lumen. Moreover, expression of the SCFAs transporter (solute carrier family 5 member 8, SLC5A8) and receptor (G protein-coupled receptor 41, GPR41) in the colon mucosa was higher, while the bile acids receptor (farnesoid X receptor, FXR) had lower expression in Landrace compared to Meihua. The relative abundances of 8 genera and 16 species of bacteria differed significantly between Landrace and Meihua, and were closely related to the colonic concentrations of bile acids or SCFAs based on Pearson's correlation analysis. Collectively, our results demonstrate for the first time that there were differences in the colonic microbiome and metabolome between Meihua and Landrace piglets, with the most profound disparity in production of SCFAs and secondary bile acids.
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Affiliation(s)
- Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Cui Zhu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Ting Yu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Jianfeng Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China.,Brain Science Institute, South China Normal UniversityGuangzhou, China
| | - Qian Kong
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Jingfang Shi
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Qinjian Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Shaolei Wang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Zongyong Jiang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China.,Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science, Institute of Animal Science, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Zhuang Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
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