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Liu Y, Bai X, Wu H, Duan Z, Zhu C, Fu R, Fan D. Ginsenoside CK Alleviates DSS-Induced IBD in Mice by Regulating Tryptophan Metabolism and Activating Aryl Hydrocarbon Receptor via Gut Microbiota Modulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9867-9879. [PMID: 38602268 DOI: 10.1021/acs.jafc.4c00245] [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: 04/12/2024]
Abstract
Dysbiosis of gut microbiota is believed to be associated with inflammatory bowel disease (IBD). Ginsenoside compound K (CK), the main metabolite of Panax ginseng ginsenoside, has proven effective as an anti-inflammatory agent in IBD. However, the mechanisms by which CK modulates gut microbiota to ameliorate IBD remain poorly understood. Herein, CK demonstrated the potential to suppress the release of proinflammatory cytokines by gut microbiota modulation. Notably, supplementation with CK promoted the restoration of a harmonious balance in gut microbiota, primarily by enhancing the populations of Lactobacillus and Akkermansia. Furthermore, CK considerably elevated the concentrations of tryptophan metabolites derived from Lactobacillus that could activate the aryl hydrocarbon receptor. Overall, the promising alleviative efficacy of CK primarily stemmed from the promotion of Lactobacillus growth and production of tryptophan metabolites, suggesting that CK should be regarded as a prospective prebiotic agent for IBD in the future.
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Affiliation(s)
- Yuan Liu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Xue Bai
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Huanyan Wu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Zhiguang Duan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Rongzhan Fu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
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Zhu Y, Sun G, Cidan Y, Shi B, Tan Z, Zhang J, Basang W. Comprehensive Multi-Omic Evaluation of the Microbiota and Metabolites in the Colons of Diverse Swine Breeds. Animals (Basel) 2024; 14:1221. [PMID: 38672368 PMCID: PMC11047667 DOI: 10.3390/ani14081221] [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: 03/11/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Pigs stand as a vital cornerstone in the realm of human sustenance, and the intricate composition of their intestinal microbiota wields a commanding influence over their nutritional and metabolic pathways. We employed multi-omic evaluations to identify microbial evidence associated with differential growth performance and metabolites, thereby offering theoretical support for the implementation of efficient farming practices for Tibetan pigs and establishing a robust foundation for enhancing pig growth and health. In this work, six Duroc × landrace × yorkshi (DLY) pigs and six Tibetan pigs were used for the experiment. Following humane euthanasia, a comprehensive analysis was undertaken to detect the presence of short-chain fatty acids (SCFAs), microbial populations, and metabolites within the colonic environment. Additionally, metabolites present within the plasma were also assessed. The outcomes of our analysis unveiled the key variables affecting the microbe changes causing the observed differences in production performance between these two distinct pig breeds. Specifically, noteworthy discrepancies were observed in the microbial compositions of DLY pigs, characterized by markedly higher levels of Alloprevotella and Prevotellaceae_UCG-003 (p < 0.05). These disparities, in turn, resulted in significant variations in the concentrations of acetic acid, propionic acid, and the cumulative SCFAs (p < 0.05). Consequently, the DLY pigs exhibited enhanced growth performance and overall well-being, which could be ascribed to the distinct metabolite profiles they harbored. Conversely, Tibetan pigs exhibited a significantly elevated relative abundance of the NK4A214_group, which consequently led to a pronounced increase in the concentration of L-cysteine. This elevation in L-cysteine content had cascading effects, further manifesting higher levels of taurine within the colon and plasma. It is noteworthy that taurine has the potential to exert multifaceted impacts encompassing microbiota dynamics, protein and lipid metabolism, as well as bile acid metabolism, all of which collectively benefit the pigs. In light of this, Tibetan pigs showcased enhanced capabilities in bile acid metabolism. In summation, our findings suggest that DLY pigs excel in their proficiency in short-chain fatty acid metabolism, whereas Tibetan pigs exhibit a more pronounced competence in the realm of bile acid metabolism. These insights underscore the potential for future studies to leverage these breed-specific differences, thereby contributing to the amelioration of production performance within these two distinct pig breeds.
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Affiliation(s)
- Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China; (Y.Z.); (G.S.); (Y.C.); (B.S.)
| | - Guangming Sun
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China; (Y.Z.); (G.S.); (Y.C.); (B.S.)
| | - Yangji Cidan
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China; (Y.Z.); (G.S.); (Y.C.); (B.S.)
| | - Bin Shi
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China; (Y.Z.); (G.S.); (Y.C.); (B.S.)
| | - Zhankun Tan
- Faculty of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Jian Zhang
- Animal Husbandry and Veterinary Station, Gongbujiangda, Linzhi 860000, China;
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa 850009, China; (Y.Z.); (G.S.); (Y.C.); (B.S.)
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Morine Y, Utsunomiya T, Yamanaka-Okumura H, Saito Y, Yamada S, Ikemoto T, Imura S, Kinoshita S, Hirayama A, Tanaka Y, Shimada M. Essential amino acids as diagnostic biomarkers of hepatocellular carcinoma based on metabolic analysis. Oncotarget 2022; 13:1286-1298. [PMID: 36441784 DOI: 10.18632/oncotarget.28306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Metabolomics, defined as the comprehensive identification of all small metabolites in a biological sample, has the power to shed light on phenotypic changes associated with various diseases, including cancer. To discover potential metabolomic biomarkers of hepatocellular carcinoma (HCC), we investigated the metabolomes of tumor and non-tumor tissue in 20 patients with primary HCC using capillary electrophoresis-time-of-flight mass spectrometry. We also analyzed blood samples taken immediately before and 14 days after hepatectomy to identify associated changes in the serum metabolome. Marked changes were detected in the different quantity of 61 metabolites that could discriminate between HCC tumor and paired non-tumor tissue and additionally between HCC primary tumors and colorectal liver metastases. Among the 30 metabolites significantly upregulated in HCC tumors compared with non-tumor tissues, 10 were amino acids, and 7 were essential amino acids (leucine, valine, tryptophan, isoleucine, methionine, lysine, and phenylalanine). Similarly, the serum metabolomes of HCC patients before hepatectomy revealed a significant increase in 16 metabolites, including leucine, valine, and tryptophan. Our results reveal striking differences in the metabolomes of HCC tumor tissue compared with non-tumor tissue, and identify the essential amino acids leucine, valine, and tryptophan as potential metabolic biomarkers for HCC.
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Affiliation(s)
- Yuji Morine
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tohru Utsunomiya
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Hisami Yamanaka-Okumura
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yu Saito
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shinichiro Yamada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tetsuya Ikemoto
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Satoru Imura
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shohei Kinoshita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mitsuo Shimada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
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Yang S, Luo J, Chen Y, Wu R, Liu H, Zhou Z, Akhtar M, Xiao Y, Shi D. A buffalo rumen-derived probiotic (SN-6) could effectively increase simmental growth performance by regulating fecal microbiota and metabolism. Front Microbiol 2022; 13:935884. [PMID: 36386716 PMCID: PMC9649902 DOI: 10.3389/fmicb.2022.935884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/03/2022] [Indexed: 09/29/2023] Open
Abstract
Microorganisms play a key role in ruminal digestion, some of which can be used as probiotics to promote growth in ruminants. However, which potential bacteria are responsible for ruminant growth and how they potentiate the basic mechanism is unclear. In this study, three bacterial strains, Bacillus pumilus (SN-3), Bacillus paralicheniformis (SN-6), and Bacillus altitudinis (SN-20) with multiple digestive enzymes were isolated from the rumen of healthy buffaloes. Among these strains, SN-6 secreted cellulase, laccase, and amylase, and significantly inhibited Staphylococcus aureus ATCC25923 and Escherichia coli K99 in vitro. In addition, SN-6 exhibited strong tolerance to artificial gastric juice, intestinal juice, and high temperature. Antibiotic resistance test, virulence gene test, and mouse toxicity test confirmed the safety of SN-6. Further, SN-6 significantly increased the body weight (p < 0.01), affects the intestinal microbiota structure, and alters the metabolomic patterns of Simmental. There was a remarkable difference in the β diversity of fecal microflora between SN-6 and control groups (p < 0.05). Furthermore, SN-6 significantly increased the abundance of Clostridium_sensu_stricto_1, Bifidobacterium, Blautia, and Cellulolyticum, decreased the relative abundance of Monoglobus and norank_f_Ruminococcacea. Moreover, SN-6 feeding significantly enriched intestinal metabolites (i.e., 3-indoleacrylic acid, kynurenic acid) to maintain intestinal homeostasis. Finally, the microbial and metabolic functional analysis indicated that SN-6 could enhance amino acid metabolism (mainly tryptophan metabolism) and lipid metabolism pathways. Overall, these findings indicated that SN-6 could be used as a probiotic in ruminants.
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Affiliation(s)
- Shumin Yang
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ji Luo
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingying Chen
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Wu
- Suining Mubiao Agricultural Development Co., Ltd., Xuzhou, China
| | - Huazhen Liu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Akhtar
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuncai Xiao
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Deshi Shi
- State Key Laboratory of Agriculture Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Zhang R, Zhong Z, Ma H, Lin L, Xie F, Mao S, Irwin DM, Wang Z, Zhang S. Mucosal Microbiota and Metabolome in the Ileum of Hu Sheep Offered a Low-Grain, Pelleted or Non-pelleted High-Grain Diet. Front Microbiol 2021; 12:718884. [PMID: 34512596 PMCID: PMC8427290 DOI: 10.3389/fmicb.2021.718884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
Alterations in mucosal microbiota and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC/MS) to investigate mucosal microbiota and their metabolic profiles in the ileum of Hu sheep fed different diets. Here, we randomly allocated 15 Hu sheep to three diets, a non-pelleted low-grain diet (control diet; CON), a non-pelleted high-grain diet (HG), and a pelleted high-grain diet (HP). After 60 days of treatment, ileal mucosal samples were collected for microbiome and metabolome analysis. The results of principal coordinate analysis and permutation multivariate analysis showed that there was a tendency for microbial differentiation between the CON and HG groups (P < 0.1), although no significant difference between the HG and HP groups was observed (P > 0.05). Compared with the CON diet, the HG diet decreased (P < 0.05) the abundance of some probiotic species (e.g., Sphingomonas and Candidatus Arthromitus) and increased (P < 0.05) the abundance of acid-producing microbiota (e.g., Succiniclasticum, Nesterenkonia, and Alloprevotella) in the ileal mucosa. Compared with the HG diet, the HP diet decreased (P < 0.05) the abundance of Alloprevotella and increased (P < 0.05) the abundance of Mycoplasma in the ileal mucosa. Furthermore, partial least squares discriminant analysis and orthogonal partial least-squared discriminant analysis indicated that different dietary treatments resulted in different metabolic patterns in the ileal mucosa of the CON, HG, and HP groups. The HG diet altered (VIP > 1 and P < 0.05) the metabolic patterns of amino acids, fatty acids, and nucleotides/nucleosides (such as increased amounts of ornithine, tyrosine, cis-9-palmitoleic acid, and adenosine) compared with the CON diet. However, 10 differential metabolites (VIP > 1 and P < 0.05; including tyrosine, ornithine, and cis-9-palmitoleic acid) identified in the HG group exhibited a diametrically opposite trend in the HP group, suggesting that the HP diet could partially eliminate the changes brought upon by the HG diet. Collectively, our findings demonstrate that different diets altered the ileal mucosal microbiota and metabolites and provide new insight into the effects of high-grain diets on the intestinal health of ruminant animals.
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Affiliation(s)
- Ruiyang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiqiang Zhong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Huiting Ma
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Limei Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fei Xie
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Zhang Z, Chen X, Loh YJ, Yang X, Zhang C. The effect of calorie intake, fasting, and dietary composition on metabolic health and gut microbiota in mice. BMC Biol 2021; 19:51. [PMID: 33740961 PMCID: PMC7977615 DOI: 10.1186/s12915-021-00987-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Background Calorie restriction (CR) and intermittent fasting (IF) can promote metabolic health through a process that is partially mediated by gut microbiota modulation. To compare the effects of CR and IF with different dietary structures on metabolic health and the gut microbiota, we performed an experiment in which mice were subjected to a CR or IF regimen and an additional IF control (IFCtrl) group whose total energy intake was not different from that of the CR group was included. Each regimen was included for normal chow and high-fat diet. Results We showed that in normal-chow mice, the IFCtrl regimen had similar positive effects on glucose and lipid metabolism as the CR regimen, but the IF regimen showed almost no influence compared to the outcomes observed in the ad libitum group. IF also resulted in improvements, but the effects were less marked than those associate with CR and IFCtrl when the mice were fed a high-fat diet. Moreover, CR created a stable and unique gut microbial community, while the gut microbiota shaped by IF exhibited dynamic changes in fasting-refeeding cycles. At the end of each cycle, the gut microbiota of the IFCtrl mice was similar to that of the CR mice, and the gut microbiota of the IF mice was similar to that of the ad libitum group. When the abundance of Lactobacillus murinus OTU2 was high, the corresponding metabolic phenotype was improved regardless of eating pattern and dietary structure, which might be one of the key bacterial groups in the gut microbiota that is positively correlated with metabolic amelioration. Conclusion There are interactions among the amount of food intake, the diet structure, and the fasting time on metabolic health. The structure and composition of gut microbiota modified by dietary regimens might contribute to the beneficial effects on the host metabolism. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00987-5.
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Affiliation(s)
- Ziyi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuh Jiun Loh
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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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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Jiang D, He X, Valitutto M, Chen L, Xu Q, Yao Y, Hou R, Wang H. Gut microbiota composition and metabolomic profiles of wild and captive Chinese monals (Lophophorus lhuysii). Front Zool 2020; 17:36. [PMID: 33292307 PMCID: PMC7713318 DOI: 10.1186/s12983-020-00381-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. RESULTS The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. CONCLUSIONS There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.
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Affiliation(s)
- Dandan Jiang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Marc Valitutto
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
- EcoHealth Alliance, New York, NY, 10012, USA
| | - Li Chen
- Sichuan Fengtongzhai National Nature reserve administration, Yaan, 625700, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.
- Sichuan Academy of Giant Panda, Chengdu, 610081, China.
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Lindsay EC, Metcalfe NB, Llewellyn MS. The potential role of the gut microbiota in shaping host energetics and metabolic rate. J Anim Ecol 2020; 89:2415-2426. [PMID: 32858775 DOI: 10.1111/1365-2656.13327] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.
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Affiliation(s)
- Elle C Lindsay
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Neil B Metcalfe
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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Dietary Synbiotic Supplementation Protects Barrier Integrity of Hepatocytes and Liver Sinusoidal Endothelium in a Mouse Model of Chronic-Binge Ethanol Exposure. Nutrients 2020; 12:nu12020373. [PMID: 32023885 PMCID: PMC7071303 DOI: 10.3390/nu12020373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alcohol overconsumption disrupts the gut microbiota and intestinal barrier, which decreases the production of beneficial microbial metabolic byproducts and allows for translocation of pathogenic bacterial-derived byproducts into the portal-hepatic circulation. As ethanol is known to damage liver sinusoidal endothelial cells (LSEC), here we evaluated dietary supplementation with a previously studied synbiotic on gut microbial composition, and hepatocyte and LSEC integrity in mice exposed to ethanol. We tested a chronic-binge ethanol feeding mouse model in which C57BL/6 female mice were fed ethanol (5% vol/vol) for 10 days and provided a single ethanol gavage (5 g/kg body weight) on day 11, 6 h before euthanasia. An ethanol-treatment group also received oral supplementation daily with a synbiotic; and an ethanol-control group received saline. Control mice were pair-fed and isocalorically substituted maltose dextran for ethanol over the entire exposure period; they received a saline gavage daily. Ethanol exposure decreased gut microbial abundance and diversity. This was linked with diminished expression of adherens junction proteins in hepatocytes and dysregulated expression of receptors for advanced glycation end-products; and this coincided with reduced expression of endothelial barrier proteins. Synbiotic supplementation mitigated these effects. These results demonstrate synbiotic supplementation, as a means to modulate ethanol-induced gut dysbiosis, is effective in attenuating injury to hepatocyte and liver endothelial barrier integrity, highlighting a link between the gut microbiome and early stages of acute liver injury in ethanol-exposed mice.
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11
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Blatchford PA, Parkar SG, Hopkins W, Ingram JR, Sutton KH. Dose-Dependent Alterations to In Vitro Human Microbiota Composition and Butyrate Inhibition by a Supercritical Carbon Dioxide Hops Extract. Biomolecules 2019; 9:E390. [PMID: 31438572 PMCID: PMC6769549 DOI: 10.3390/biom9090390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
Hop cones (Humulus lupulus L.) have been used throughout history as an additive in beer brewing and as herbal supplements with medicinal and culinary properties. The objective of this study was to ascertain the effect of a range of concentrations of a supercritical CO2 extract of hops on the composition and metabolism of human gut bacterial communities using in vitro batch culture systems. Fermentations were conducted over 24 h using a mixed human fecal inoculum. Microbial metabolism was assessed by measuring organic acid production and microbial community alterations were determined by 16S rRNA gene sequencing. Butyrate, an important short chain fatty acid in maintaining colonic well-being, decreased at elevated concentrations of hops, which may partly be accounted for by the concomitant reduction of Eubacterium and Coprococcus, known butyrate-producing genera, and also the inhibition of Bifidobacterium, a beneficial organism that has a butyrogenic effect through metabolic cross-feeding with intestinal commensals. The hops compounds also caused dose-dependent increases in the potentially pathogenic Enterobacteriaceae and potentially beneficial Akkermansia. Thus, hops compounds had a significant impact on the structure of the bacterial consortium, which warrants further study including human clinical trials.
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Affiliation(s)
- Paul A Blatchford
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 11600, Palmerston North 4442, New Zealand
| | - Shanthi G Parkar
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 11600, Palmerston North 4442, New Zealand.
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12
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Locci E, Stocchero M, Noto A, Chighine A, Natali L, Napoli PE, Caria R, De-Giorgio F, Nioi M, d'Aloja E. A 1H NMR metabolomic approach for the estimation of the time since death using aqueous humour: an animal model. Metabolomics 2019; 15:76. [PMID: 31069551 DOI: 10.1007/s11306-019-1533-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
INTRODUCTION The estimation of the time since death, or post-mortem interval (PMI), still remains a main conundrum in forensic science. Several approaches have been so far proposed from either a qualitative or a quantitative point of view, but they still lack reliability and robustness. Recently, metabolomics has shown to be a potential tool to investigate the time-related post-mortem metabolite modifications in animal models. OBJECTIVES Here we propose, for the first time, the use of a 1H NMR metabolomic approach for the estimation of PMI from aqueous humour (AH) in an ovine model. METHODS AH samples were collected at different times after death (from 118 to 1429 min). 1H NMR experiments were performed and spectral data analysed by multivariate statistical tools. RESULTS A multivariate calibration model was built to estimate PMI on the basis of the metabolite content of the samples. The model was validated with an independent test set, obtaining a prediction error of 59 min for PMI < 500 min, 104 min for PMI from 500 to 1000 min, and 118 min for PMI > 1000 min. Moreover, the metabolomic approach suggested a picture of the mechanisms underlying the post-mortem biological modifications, highlighting the role played by taurine, choline, and succinate. CONCLUSION The time-related modifications of the 1H NMR AH metabolomic profile seem to be encouraging in addressing the issue of a reproducible and robust model to be employed for the estimation of the time since death.
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Affiliation(s)
- Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy.
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Antonio Noto
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Luca Natali
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | | | - Roberto Caria
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Fabio De-Giorgio
- Institute of Public Health, Section of Legal Medicine, Catholic University of Rome, Rome, Italy
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
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13
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Nho K, Kueider-Paisley A, MahmoudianDehkordi S, Arnold M, Risacher SL, Louie G, Blach C, Baillie R, Han X, Kastenmüller G, Jia W, Xie G, Ahmad S, Hankemeier T, van Duijn CM, Trojanowski JQ, Shaw LM, Weiner MW, Doraiswamy PM, Saykin AJ, Kaddurah-Daouk R. Altered bile acid profile in mild cognitive impairment and Alzheimer's disease: Relationship to neuroimaging and CSF biomarkers. Alzheimers Dement 2019; 15:232-244. [PMID: 30337152 PMCID: PMC6454538 DOI: 10.1016/j.jalz.2018.08.012] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/03/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Bile acids (BAs) are the end products of cholesterol metabolism produced by human and gut microbiome co-metabolism. Recent evidence suggests gut microbiota influence pathological features of Alzheimer's disease (AD) including neuroinflammation and amyloid-β deposition. METHOD Serum levels of 20 primary and secondary BA metabolites from the AD Neuroimaging Initiative (n = 1562) were measured using targeted metabolomic profiling. We assessed the association of BAs with the "A/T/N" (amyloid, tau, and neurodegeneration) biomarkers for AD: cerebrospinal fluid (CSF) biomarkers, atrophy (magnetic resonance imaging), and brain glucose metabolism ([18F]FDG PET). RESULTS Of 23 BAs and relevant calculated ratios after quality control procedures, three BA signatures were associated with CSF Aβ1-42 ("A") and three with CSF p-tau181 ("T") (corrected P < .05). Furthermore, three, twelve, and fourteen BA signatures were associated with CSF t-tau, glucose metabolism, and atrophy ("N"), respectively (corrected P < .05). DISCUSSION This is the first study to show serum-based BA metabolites are associated with "A/T/N" AD biomarkers, providing further support for a role of BA pathways in AD pathophysiology. Prospective clinical observations and validation in model systems are needed to assess causality and specific mechanisms underlying this association.
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Affiliation(s)
- Kwangsik Nho
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | | | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Guoxiang Xie
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, the Netherlands
| | | | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael W Weiner
- Center for Imaging of Neurodegenerative Diseases, Department of Radiology, San Francisco VA Medical Center/University of California San Francisco, San Francisco, CA, USA
| | - P Murali Doraiswamy
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, and the Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA.
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14
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Vernocchi P, Del Chierico F, Russo A, Majo F, Rossitto M, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paci P, Ercolini D, Marini F, Fiscarelli EV, Dallapiccola B, Lucidi V, Miccheli A, Putignani L. Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype. PLoS One 2018; 13:e0208171. [PMID: 30521551 PMCID: PMC6283533 DOI: 10.1371/journal.pone.0208171] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 11/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications. Objectives The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability. Methods Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1–6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis. Results The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection. Conclusions All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it’s possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children’s nutritional status and intestinal function.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Alessandra Russo
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabio Majo
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Martina Rossitto
- Diagnostics of Cystic Fibrosis, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Luca Casadei
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Antonietta La Storia
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Cristiano Rizzo
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cesare Manetti
- Department of Environmental Biology; Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- CNR-Institute for Systems Analysis and Computer Science (IASI), Rome, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Federico Marini
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alfredo Miccheli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Parasitology Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- * E-mail:
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15
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van der Hooft JJJ, Alghefari W, Watson E, Everest P, Morton FR, Burgess KEV, Smith DGE. Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose. Metabolomics 2018; 14:144. [PMID: 30830405 PMCID: PMC6208705 DOI: 10.1007/s11306-018-1438-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/04/2018] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Campylobacter jejuni is the leading cause of foodborne bacterial enteritis in humans, and yet little is known in regard to how genetic diversity and metabolic capabilities among isolates affect their metabolic phenotype and pathogenicity. OBJECTIVES For instance, the C. jejuni 11168 strain can utilize both L-fucose and L-glutamate as a carbon source, which provides the strain with a competitive advantage in some environments and in this study we set out to assess the metabolic response of C. jejuni 11168 to the presence of L-fucose and L-glutamate in the growth medium. METHODS To achieve this, untargeted hydrophilic liquid chromatography coupled to mass spectrometry was used to obtain metabolite profiles of supernatant extracts obtained at three different time points up to 24 h. RESULTS This study identified both the depletion and the production and subsequent release of a multitude of expected and unexpected metabolites during the growth of C. jejuni 11168 under three different conditions. A large set of standards allowed identification of a number of metabolites. Further mass spectrometry fragmentation analysis allowed the additional annotation of substrate-specific metabolites. The results show that C. jejuni 11168 upon L-fucose addition indeed produces degradation products of the fucose pathway. Furthermore, methionine was faster depleted from the medium, consistent with previously-observed methionine auxotrophy. CONCLUSIONS Moreover, a multitude of not previously annotated metabolites in C. jejuni were found to be increased specifically upon L-fucose addition. These metabolites may well play a role in the pathogenicity of this C. jejuni strain.
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Affiliation(s)
| | - Wejdan Alghefari
- King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
- Institute of Biological Chemistry, Biophysics & Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - Eleanor Watson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - Paul Everest
- School of Veterinary Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
| | - Fraser R Morton
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Karl E V Burgess
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics & Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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16
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Xu H, Li X, Zheng X, Xia Y, Fu Y, Li X, Qian Y, Zou J, Zhao A, Guan J, Gu M, Yi H, Jia W, Yin S. Pediatric Obstructive Sleep Apnea is Associated With Changes in the Oral Microbiome and Urinary Metabolomics Profile: A Pilot Study. J Clin Sleep Med 2018; 14:1559-1567. [PMID: 30176961 DOI: 10.5664/jcsm.7336] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 06/05/2018] [Indexed: 02/07/2023]
Abstract
STUDY OBJECTIVES Several cross-sectional studies have reported associations between oral diseases and obstructive sleep apnea (OSA). However, there have been no reports regarding the structure and composition of the oral microbiota with simultaneous evaluation of potential associations with perturbed metabolic profiles in pediatric OSA. METHODS An integrated approach, combining metagenomics based on high-throughput 16S rRNA gene sequencing, and metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and gas chromatography coupled with time-of-flight mass spectrometry, was used to evaluate the oral microbiome and the urinary metabolome. RESULTS 16S rRNA gene sequencing indicated that the oral microbiome composition was significantly perturbed in pediatric OSA compared with normal controls, especially with regard to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. Moreover, metabolomics profiling indicated that 57 metabolites, 5 of which were metabolites related to the microflora of the digestive tract, were differentially present in the urine of pediatric patients with OSA and controls. Co-inertia and correlation analyses revealed that several oral microbiome changes were correlated with urinary metabolite perturbations in pediatric OSA. However, this correlation relationship does not imply causality. CONCLUSIONS High-throughput sequencing revealed that the oral microbiome composition and function were significantly altered in pediatric OSA. Further studies are needed to confirm and determine the mechanisms underlying these findings.
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Affiliation(s)
- Huajun Xu
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyan Li
- Department of Otolaryngology-Head & Neck Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojiao Zheng
- Center for Translational Medicine, and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yunyan Xia
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiqun Fu
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Li
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjun Qian
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianyin Zou
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aihua Zhao
- Center for Translational Medicine, and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jian Guan
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meizhen Gu
- Department of Otolaryngology-Head & Neck Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hongliang Yi
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Jia
- Center for Translational Medicine, and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Shankai Yin
- Department of Otolaryngology Head and Neck Surgery and Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Chen T, You Y, Xie G, Zheng X, Zhao A, Liu J, Zhao Q, Wang S, Huang F, Rajani C, Wang C, Chen S, Ni Y, Yu H, Deng Y, Wang X, Jia W. Strategy for an Association Study of the Intestinal Microbiome and Brain Metabolome Across the Lifespan of Rats. Anal Chem 2018; 90:2475-2483. [PMID: 29353471 DOI: 10.1021/acs.analchem.7b02859] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is increased appreciation for the diverse roles of the microbiome-gut-brain axis on mammalian growth and health throughout the lifespan. Numerous studies have demonstrated that the gut microbiome and their metabolites are extensively involved in the communication between brain and gut. Association study of brain metabolome and gut microbiome is an active field offering large amounts of information on the interaction of microbiome, brain and gut but data size and complicated hierarchical relationships were found to be major obstacles to the formation of significant, reproducible conclusions. This study addressed a two-level strategy of brain metabolome and gut microbiome association analysis of male Wistar rats in the process of growth, employing several analytical platforms and various bioinformatics methods. Trajectory analysis showed that the age-related brain metabolome and gut microbiome had similarity in overall alteration patterns. Four high taxonomical level correlated pairs of "metabolite type-bacterial phylum", including "lipids-Spirochaetes", "free fatty acids (FFAs)-Firmicutes", "bile acids (BAs)-Firmicutes", and "Neurotransmitters-Bacteroidetes", were screened out based on unit- and multivariant correlation analysis and function analysis. Four groups of specific "metabolite-bacterium" association pairs from within the above high level key pairs were further identified. The key correlation pairs were validated by an independent animal study. This two-level strategy is effective in identifying principal correlations in big data sets obtained from the systematic multiomics study, furthering our understanding on the lifelong connection between brain and gut.
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Affiliation(s)
- Tianlu Chen
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Yijun You
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Guoxiang Xie
- University of Hawaii Cancer Center , Honolulu, Hawaii 96813, United States
| | - Xiaojiao Zheng
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Aihua Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Jiajian Liu
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Qing Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Shouli Wang
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Fengjie Huang
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
| | - Cynthia Rajani
- University of Hawaii Cancer Center , Honolulu, Hawaii 96813, United States
| | - Congcong Wang
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Shaoqiu Chen
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Yan Ni
- University of Hawaii Cancer Center , Honolulu, Hawaii 96813, United States
| | - Herbert Yu
- University of Hawaii Cancer Center , Honolulu, Hawaii 96813, United States
| | - Youping Deng
- Biostatistics and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii 96813, United States
| | - Xiaoyan Wang
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China.,University of Hawaii Cancer Center , Honolulu, Hawaii 96813, United States
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18
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Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology. J Bacteriol 2018; 200:JB.00376-17. [PMID: 28874411 DOI: 10.1128/jb.00376-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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Pereira-Fantini PM, Byars SG, Pitt J, Lapthorne S, Fouhy F, Cotter PD, Bines JE. Unravelling the metabolic impact of SBS-associated microbial dysbiosis: Insights from the piglet short bowel syndrome model. Sci Rep 2017; 7:43326. [PMID: 28230078 PMCID: PMC5322370 DOI: 10.1038/srep43326] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/11/2017] [Indexed: 12/16/2022] Open
Abstract
Liver disease is a major source of morbidity and mortality in children with short bowel syndrome (SBS). SBS-associated microbial dysbiosis has recently been implicated in the development of SBS-associated liver disease (SBS-ALD), however the pathological implications of this association have not been explored. In this study high-throughput sequencing of colonic content from the well-validated piglet SBS-ALD model was examined to determine alterations in microbial communities, and concurrent metabolic alterations identified in urine samples via targeted mass spectrometry approaches (GC-MS, LC-MS, FIA-MS) further uncovered impacts of microbial disturbance on metabolic outcomes in SBS-ALD. Multi-variate analyses were performed to elucidate contributing SBS-ALD microbe and metabolite panels and to identify microbe-metabolite interactions. A unique SBS-ALD microbe panel was clearest at the genus level, with discriminating bacteria predominantly from the Firmicutes and Bacteroidetes phyla. The SBS-ALD metabolome included important alterations in the microbial metabolism of amino acids and the mitochondrial metabolism of branched chain amino acids. Correlation analysis defined microbe-metabolite clustering patterns unique to SBS-ALD and identified a metabolite panel that correlates with dysbiosis of the gut microbiome in SBS.
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Affiliation(s)
- Prue M Pereira-Fantini
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia
| | - Sean G Byars
- Centre for Systems Genomics, School of Biosciences, The University of Melbourne, Parkville, Australia.,Department of Pathology, The University of Melbourne, Parkville, Australia
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Susan Lapthorne
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia
| | - Fiona Fouhy
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Julie E Bines
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, Australia
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Cheema AK, Maier I, Dowdy T, Wang Y, Singh R, Ruegger PM, Borneman J, Fornace AJ, Schiestl RH. Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis. PLoS One 2016; 11:e0151190. [PMID: 27073845 PMCID: PMC4830457 DOI: 10.1371/journal.pone.0151190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/24/2016] [Indexed: 11/18/2022] Open
Abstract
Intestinal microbiota play a significant role in nutrient metabolism, modulation of the immune system, obesity, and possibly in carcinogenesis, although the underlying mechanisms resulting in disease or impacts on longevity caused by different intestinal microbiota are mostly unknown. Herein we use isogenic Atm-deficient and wild type mice as models to interrogate changes in the metabolic profiles of urine and feces of these mice, which are differing in their intestinal microbiota. Using high resolution mass spectrometry approach we show that the composition of intestinal microbiota modulates specific metabolic perturbations resulting in a possible alleviation of a glycolytic phenotype. Metabolites including 3-methylbutyrolactone, kyneurenic acid and 3-methyladenine known to be onco-protective are elevated in Atm-deficient and wild type mice with restricted intestinal microbiota. Thus our approach has broad applicability to study the direct influence of gut microbiome on host metabolism and resultant phenotype. These results for the first time suggest a possible correlation of metabolic alterations and carcinogenesis, modulated by intestinal microbiota in A-T mice.
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Affiliation(s)
- Amrita K. Cheema
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Irene Maier
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tyrone Dowdy
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Yiwen Wang
- Department of Biostatistics, Biomathematics and Bioinformatics, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Rajbir Singh
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Paul M. Ruegger
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - Albert J. Fornace
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Robert H. Schiestl
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Radiation Oncology, Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
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22
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He X, Ji G, Jia W, Li H. Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanism and Application of Metabolomics. Int J Mol Sci 2016; 17:300. [PMID: 26999104 PMCID: PMC4813164 DOI: 10.3390/ijms17030300] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/14/2016] [Accepted: 02/17/2016] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota are intricately involved in the development of obesity-related metabolic diseases such as nonalcoholic fatty liver disease (NAFLD), type 2 diabetes, and insulin resistance. In the current review, we discuss the role of gut microbiota in the development of NAFLD by focusing on the mechanisms of gut microbiota-mediated host energy metabolism, insulin resistance, regulation of bile acids and choline metabolism, as well as gut microbiota-targeted therapy. We also discuss the application of a metabolomic approach to characterize gut microbial metabotypes in NAFLD.
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Affiliation(s)
- Xuyun He
- Center for Chinese Medical Therapy and Systems Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Guang Ji
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Wei Jia
- Center for Chinese Medical Therapy and Systems Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Center for Translational Medicine, and Shanghai Key Laboratory of Diabetes Mellitus, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Houkai Li
- Center for Chinese Medical Therapy and Systems Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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23
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Liu X, Cao S, Zhang X. Modulation of Gut Microbiota-Brain Axis by Probiotics, Prebiotics, and Diet. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7885-7895. [PMID: 26306709 DOI: 10.1021/acs.jafc.5b02404] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
There exists a bidirectional communication system between the gastrointestinal tract and the brain. Increasing evidence shows that gut microbiota can play a critical role in this communication; thus, the concept of a gut microbiota and brain axis is emerging. Here, we review recent findings in the relationship between intestinal microbes and brain function, such as anxiety, depression, stress, autism, learning, and memory. We highlight the advances in modulating brain development and behavior by probiotics, prebiotics, and diet through the gut microbiota-brain axis. A variety of mechanisms including immune, neural, and metabolic pathways may be involved in modulation of the gut microbiota-brain axis. We also discuss some future challenges. A deeper understanding of the relationship between the gut bacteria and their hosts is implicated in developing microbial-based therapeutic strategies for brain disorders.
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Affiliation(s)
- Xiaofei Liu
- College of Light Industry and Food Sciences, South China University of Technology , Guangzhou, China
| | - Shangqing Cao
- Department of Psychology, Sun Yat-Sen University , Guangzhou, China
- Library, South China University of Technology , Guangzhou, China
| | - Xuewu Zhang
- College of Light Industry and Food Sciences, South China University of Technology , Guangzhou, China
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24
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Shommu NS, Vogel HJ, Storey DG. Potential of metabolomics to reveal Burkholderia cepacia complex pathogenesis and antibiotic resistance. Front Microbiol 2015. [PMID: 26217312 PMCID: PMC4499752 DOI: 10.3389/fmicb.2015.00668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Burkholderia cepacia complex (Bcc) is a collection of closely related, genetically distinct, ecologically diverse species known to cause life-threatening infections in cystic fibrosis (CF) patients. By virtue of a flexible genomic structure and diverse metabolic activity, Bcc bacteria employ a wide array of virulence factors for pathogenesis in CF patients and have developed resistance to most of the commonly used antibiotics. However, the mechanism of pathogenesis and antibiotic resistance is still not fully understood. This mini review discusses the established and potential virulence determinants of Bcc and some of the contemporary strategies including transcriptomics and proteomics used to identify these traits. We also propose the application of metabolic profiling, a cost-effective modern-day approach to achieve new insights.
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Affiliation(s)
- Nusrat S Shommu
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada
| | - Douglas G Storey
- Microbiology Research Group, Department of Biological Sciences, University of Calgary , Calgary, AB, Canada
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25
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Abstract
Humans depend on our commensal bacteria for nutritive, immune-modulating, and metabolic contributions to maintenance of health. However, this commensal community exists in careful balance that, if disrupted, enters dysbiosis; this has been shown to contribute to the pathogenesis of colon, gastric, esophageal, pancreatic, laryngeal, breast, and gallbladder carcinomas. This development is closely tied to host inflammation, which causes and is aggravated by microbial dysbiosis and increases vulnerability to pathogens. Advances in sequencing technology have increased our ability to catalog microbial species associated with various cancer types across the body. However, defining microbial biomarkers as cancer predictors presents multiple challenges, and existing studies identifying cancer-associated bacteria have reported inconsistent outcomes. Combining metabolites and microbiome analyses can help elucidate interactions between gut microbiota, metabolism, and the host. Ultimately, understanding how gut dysbiosis impacts host response and inflammation will be critical to creating an accurate picture of the role of the microbiome in cancer.
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Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front Microbiol 2015; 6:209. [PMID: 25941514 PMCID: PMC4400912 DOI: 10.3389/fmicb.2015.00209] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/02/2015] [Indexed: 11/29/2022] Open
Abstract
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.
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Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Shane Nowack
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
- Department of Mathematical Sciences, Montana State UniversityBozeman, MT, USA
| | - Millie T. Olsen
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Isaac Klapper
- Department of Mathematical Sciences, Montana State UniversityBozeman, MT, USA
- Department of Mathematics, Temple UniversityPhiladelphia, PA, USA
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneyUltimo, NSW, Australia
| | - James K. Fredrickson
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
- Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
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Deusch S, Tilocca B, Camarinha-Silva A, Seifert J. News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals. Comput Struct Biotechnol J 2014; 13:55-63. [PMID: 26900430 PMCID: PMC4720016 DOI: 10.1016/j.csbj.2014.12.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 12/20/2022] Open
Abstract
Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about the investigated microbiota. In general, integration of the main Omics-technologies (genomics, transcriptomics, proteomics and metabolomics) in live science promises highly detailed information about the specific research object and helps to understand molecular changes in response to internal and external environmental factors. The microbial communities settled in the mammalian gastrointestinal tract are essential for the host metabolism and have a major impact on its physiology and health. The microbiotas of livestock like chicken, pig and ruminants are becoming a focus of interest for veterinaries, animal nutritionists and microbiologists. While pig is more often used as an animal model for human-related studies, the rumen microbiota harbors a diversity of enzymes converting complex carbohydrates into monomers which bears high potential for biotechnological applications. This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.
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Affiliation(s)
| | | | | | - Jana Seifert
- Corresponding author at: University of Hohenheim, Institute of Animal Nutrition, Emil-Wolff-Str. 10, 70599 Stuttgart, Germany.
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Xu YJ, Wang C, Ho WE, Ong CN. Recent developments and applications of metabolomics in microbiological investigations. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Bhattacharjee S, Lukiw WJ. Alzheimer's disease and the microbiome. Front Cell Neurosci 2013; 7:153. [PMID: 24062644 PMCID: PMC3775450 DOI: 10.3389/fncel.2013.00153] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/26/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Surjyadipta Bhattacharjee
- Departments of Neurology, Neuroscience and Ophthalmology, LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA
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