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Jung Y, Lee T, Oh HS, Hyun Y, Song S, Chun J, Kim HW. Gut microbial and clinical characteristics of individuals with autism spectrum disorder differ depending on the ecological structure of the gut microbiome. Psychiatry Res 2024; 335:115775. [PMID: 38503005 DOI: 10.1016/j.psychres.2024.115775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
Understanding the relationship between the gut microbiome and autism spectrum disorder (ASD) is challenging due to the heterogeneous nature of ASD. Here, we analyzed the microbial and clinical characteristics of individuals with ASD using enterotypes. A total of 456 individuals participated in the study, including 249 participants with ASD, 106 typically developing siblings, and 101 controls. The alpha and beta diversities of the ASD, sibling, and control groups did not show significant differences. Analysis revealed a negative association between the Bifidobacterium longum group and the Childhood Autism Rating Scale, as well as a negative association between the Streptococcus salivarus group and the Social Responsiveness Scale (SRS) within the ASD group. When clustered based on microbial composition, participants with ASD exhibited two distinct enterotypes, E1 and E2. In the E2 group, the SRS score was significantly higher, and the Vineland Adaptive Behavior Scale score was significantly lower compared to the E1 group. Machine learning results indicated that the microbial species predicting SRS scores were distinct between the two enterotypes. Our study suggests that the microbial composition in individuals with ASD exhibits considerable variability, and the patterns of associations between the gut microbiome and clinical symptoms may vary depending on the enterotype.
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Affiliation(s)
- Yeonjae Jung
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea; CJ Bioscience, Inc. Seoul, Korea
| | - Taeyeop Lee
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Yerin Hyun
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Jongsik Chun
- CJ Bioscience, Inc. Seoul, Korea; Department of Biological Sciences, Seoul National University, Seoul, Korea.
| | - Hyo-Won Kim
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Li X, Wang H, Wang H, Bullert AJ, Cui JY, Wang K, Lehmler HJ. Germ-free status but not subacute polychlorinated biphenyl (PCB) exposure altered hepatic phosphatidylcholine and ether-phosphatidylcholine levels in mice. Toxicology 2024; 504:153790. [PMID: 38552894 DOI: 10.1016/j.tox.2024.153790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants that pose a current ecosystem and human health concern. PCB exposure impacts the gut microbiome in animal models, suggesting a mechanistic link between PCB exposure and adverse health outcomes. The presence and absence of the microbiome and exposure to PCBs independently affect the lipid composition in the liver, which in turn affects the PCB disposition in target tissues, such as the liver. Here, we investigated microbiome × subacute PCB effects on the hepatic lipid composition of conventional and germ-free female mice exposed to 0, 6, or 30 mg/kg body weight of an environmental PCB mixture in sterile corn oil once daily for 3 consecutive days. Hepatic triacylglyceride and polar lipid levels were quantified using mass spectrometric methods following the subacute PCB exposure. The lipidomic analysis revealed no PCB effect on the hepatic levels. No microbiome effect was observed on levels of triacylglyceride and most polar lipid classes. The total hepatic levels of phosphatidylcholine (PC) and ether-phosphatidylcholine (ePC) lipids were lower in germ-free mice than the conventional mice from the same exposure group. Moreover, levels of several unsaturated PCs, such as PC(36:5) and PC(42:10), and ePCs, such as ePC(36:2) and ePC(4:2), were lower in germ-free than conventional female mice. Based on a KEGG pathway meta-analysis of RNA sequencing data, the ether lipid metabolism pathway is altered in the germ-free mouse liver. In contrast to the liver, extractable lipid levels, determined gravimetrically, differed in several tissues from naïve conventional vs. germ-free mice. Overall, microbiome × subacute PCB exposure effects on hepatic lipid composition are unlikely to affect PCB distribution into the mouse liver. Further studies are needed to assess how the different extractable lipid levels in other tissues alter PCB distribution in conventional vs. germ-free mice.
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Affiliation(s)
- Xueshu Li
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA
| | - Hui Wang
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA
| | - Hui Wang
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA
| | - Amanda J Bullert
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, University of Iowa, Iowa City, IA 52242, USA
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, University of Iowa, Iowa City, IA 52242, USA.
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Caenepeel C, Falony G, Machiels K, Verstockt B, Goncalves PJ, Ferrante M, Sabino J, Raes J, Vieira-Silva S, Vermeire S. Dysbiosis and Associated Stool Features Improve Prediction of Response to Biological Therapy in Inflammatory Bowel Disease. Gastroenterology 2024; 166:483-495. [PMID: 38096956 DOI: 10.1053/j.gastro.2023.11.304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/13/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND & AIMS Dysbiosis of the gut microbiota is considered a key contributor to inflammatory bowel disease (IBD) etiology. Here, we investigated potential associations between microbiota composition and the outcomes to biological therapies. METHODS The study prospectively recruited 296 patients with active IBD (203 with Crohn's disease, 93 with ulcerative colitis) initiating biological therapy. Quantitative microbiome profiles of pretreatment and posttreatment fecal samples were obtained combining flow cytometry with 16S amplicon sequencing. Therapeutic response was assessed by endoscopy, patient-reported outcomes, and changes in fecal calprotectin. The effect of therapy on microbiome variation was evaluated using constrained ordination methods. Prediction of therapy outcome was performed using logistic regression with 5-fold cross-validation. RESULTS At baseline, 65.9% of patients carried the dysbiotic Bacteroides2 (Bact2) enterotype, with a significantly higher prevalence among patients with ileal involvement (76.8%). Microbiome variation was associated with the choice of biological therapy rather than with therapeutic outcome. Only anti-tumor necrosis factor-α treatment resulted in a microbiome shift away from Bact2, concomitant with an increase in microbial load and butyrogen abundances and a decrease in potentially opportunistic Veillonella. Remission rates for patients hosting Bact2 at baseline were significantly higher with anti-tumor necrosis factor-α than with vedolizumab (65.1% vs 35.2%). A prediction model, based on anthropometrics and clinical data, stool features (microbial load, moisture, and calprotectin), and Bact2 detection predicted treatment outcome with 73.9% accuracy for specific biological therapies. CONCLUSION Fecal characterization based on microbial load, moisture content, calprotectin concentration, and enterotyping may aid in the therapeutic choice of biological therapy in IBD.
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Affiliation(s)
- Clara Caenepeel
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Kathleen Machiels
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Pfizer Biopharmaceuticals, Brussels, Belgium
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Pedro J Goncalves
- Machine Learning in Science, Excellence Cluster "Machine Learning," Tübingen University, Tübingen, Germany
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium.
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Qingbo L, Jing Z, Zhanbo Q, Jian C, Yifei S, Yinhang W, Shuwen H. Identification of enterotype and its predictive value for patients with colorectal cancer. Gut Pathog 2024; 16:12. [PMID: 38414077 PMCID: PMC10897996 DOI: 10.1186/s13099-024-00606-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Gut microbiota dysbiosis involved in the pathogenesis of colorectal cancer (CRC). The characteristics of enterotypes in CRC development have not been determined. OBJECTIVE To characterize the gut microbiota of healthy, adenoma, and CRC subjects based on enterotype. METHODS The 16 S rRNA sequencing data from 315 newly sequenced individuals and three previously published datasets were collected, providing total data for 367 healthy, 320 adenomas, and 415 CRC subjects. Enterotypes were analyzed for all samples, and differences in microbiota composition across subjects with different disease states in each enterotype were determined. The predictive values of a random forest classifier based on enterotype in distinguishing healthy, adenoma, and CRC subjects were evaluated and validated. RESULTS Subjects were classified into one of three enterotypes, namely, Bacteroide- (BA_E), Blautia- (BL_E), and Streptococcus- (S_E) dominated clusters. The taxonomic profiles of these three enterotypes differed among the healthy, adenoma, and CRC cohorts. BA_E group was enriched with Bacteroides and Blautia; BL_E group was enriched by Blautia and Coprococcus; S_E was enriched by Streptococcus and Ruminococcus. Relative abundances of these genera varying among the three human cohorts. In training and validation sets, the S_E cluster showed better performance in distinguishing among CRC patients, adenoma patients, and healthy controls, as well as between CRC and non-CRC individuals, than the other two clusters. CONCLUSION This study provides the first evidence to indicate that changes in the microbial composition of enterotypes are associated with disease status, thereby highlighting the diagnostic potential of enterotypes in the treatment of adenoma and CRC.
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Affiliation(s)
- Li Qingbo
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China
| | - Zhuang Jing
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No.1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province, 313000, People's Republic of China
| | - Qu Zhanbo
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No.1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province, 313000, People's Republic of China
| | - Chu Jian
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No.1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province, 313000, People's Republic of China
| | - Song Yifei
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China
| | - Wu Yinhang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China.
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, Zhejiang Province, People's Republic of China.
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No.1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province, 313000, People's Republic of China.
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, People's Republic of China.
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, Huzhou, Zhejiang Province, People's Republic of China.
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No.1558, Sanhuan North Road, Wuxing District, Huzhou, Zhejiang Province, 313000, People's Republic of China.
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Suvorov A, Zhao S, Leontieva G, Alekhina G, Yang J, Tsapieva A, Karaseva A, Smelova V, Guo D, Chen L. Evaluation of the Efficacy of Enterococcus faecium L3 as a Feed Probiotic Additive in Chicken. Probiotics Antimicrob Proteins 2023; 15:1169-1179. [PMID: 35904731 DOI: 10.1007/s12602-022-09970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
The study was devoted to the comparison of the probiotic effect of enterococcal Enterococcus faecium L3 to the antibiotic enramycin as a chicken feed additive. Two hundred and sixteen chickens were divided into three groups and tested by different parameters including weight gain, food consumption, blood biochemistry, immunology, and caecal microbiome at two checkpoints, 21 and 39 days after birth. By the end of the experiment, a group of chickens getting probiotic demonstrated weight gain of more than 100 g at the average relative to the control group with no additive in animal feed (P < 0.05). Blood serum biochemistry showed a significant increase in HDL level (P < 0.05) relative to the control group. The 16S RNA sequencing demonstrated the growth abundance of Lachnospiraceae and the decrease of Proteobacteria in probiotic fed group. On the contrary, the antibiotic fed group showed a noticeable increase in the abundance of Proteobacteria which included the genus Salmonella. Thus, probiotic E. faecium L3 being added to chicken food as a single additive may be considered as a possible replacement of antibiotic enramycin.
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Affiliation(s)
- Alexander Suvorov
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia.
- Saint Petersburg State University, University nab., 7-9, St. Petersburg, 199034, Russia.
| | - Shuangzhi Zhao
- Institute of Agro-Food Science and Technology & Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Galina Leontieva
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia
| | - Galina Alekhina
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia
| | - Jinyu Yang
- Institute of Agro-Food Science and Technology & Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Anna Tsapieva
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia
| | - Alena Karaseva
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia
| | - Valentina Smelova
- Institute of Experimental Medicine, Akademika Pavlova, 12, St. Petersburg, 197376, Russia
| | - Danyang Guo
- Institute of Agro-Food Science and Technology & Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Leilei Chen
- Institute of Agro-Food Science and Technology & Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Shandong Academy of Agricultural Sciences, Jinan, China
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Lai S, Yan Y, Pu Y, Lin S, Qiu JG, Jiang BH, Keller MI, Wang M, Bork P, Chen WH, Zheng Y, Zhao XM. Enterotypes of the human gut mycobiome. Microbiome 2023; 11:179. [PMID: 37563687 PMCID: PMC10416509 DOI: 10.1186/s40168-023-01586-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China. RESULTS We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging. CONCLUSIONS We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.
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Affiliation(s)
- Senying Lai
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yan Yan
- CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuchun Lin
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Jian-Ge Qiu
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Bing-Hua Jiang
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Marisa Isabell Keller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mingyu Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- College of Life Science, Henan Normal University, Xinxiang, Henan, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Zhejiang Province, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
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Fujitani T, Lyu Z, Sassa MH, Harada KH. Association between urinary zinc excretion and isoflavone-metabolizing enterotypes among Japanese females: a cross-sectional study. Environ Health Prev Med 2023; 28:63. [PMID: 37899210 PMCID: PMC10613555 DOI: 10.1265/ehpm.23-00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/30/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND Zinc absorption and competition among gut bacteria have been reported in animal studies. Thus, gut bacteria may modify zinc availability in humans. Metabolism of intestinal bacteria is known to be necessary for the activation of several phytoconstituents in the body. For example, equol, a typical substance of soybean isoflavone, is produced by intestinal bacteria metabolizing daidzein and the enterotype is one of distinct ones among Japanese population. The difference in the intestinal microflora can modify the bioavailability of zinc. In this study, we examined urinary zinc concentrations in adult female equol producers (EQPs). METHODS Urine samples from women participating in health examinations in Miyagi, Okinawa, Kyoto, Kochi, and Hokkaido prefectures were used; from total 17,484 samples, approximately 25 samples were randomly selected for each age group from 30 to 60 years per region (subsample: n = 520), and 520 samples with available urinary zinc concentration (determined by flame atomic absorption analysis) and enterobacterial type were analyzed. EQP was defined as log(equol/daidzein) ≥ -1.42, and urinary concentrations were corrected for creatinine concentration. Urinary zinc concentrations were compared by Student's t-test and multiple regression analyses. RESULTS The geometric mean urinary zinc concentration (µg/g-Cr) was lower in EQP than in non-EQP (p = 0.0136 by t-test after logarithm transformation). On the other hand, there was no correlation between urinary zinc concentration with daidzein (r = -0.0495, P = 0.436) and equol concentrations (r = -0.0721, P = 0.256). There was a significant negative association between urinary zinc concentration and EQP (β = -0.392, P = 0.0311) after adjusting with other potential confounding variables, such as daidzein intake. CONCLUSIONS The results suggest that gut bacteria that produce equol are involved in the metabolism of zinc. Based on previous studies, the bacteria that affect the metabolism of both substances are thought to be Enterococcus. Future studies are expected to identify specific intestinal bacteria for zinc availability and understand individual differences in the effects of micronutrients.
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Affiliation(s)
- Tomoko Fujitani
- Department of Health and Environmental Sciences, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Zhaoqing Lyu
- Department of Health and Environmental Sciences, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Mariko Harada Sassa
- Department of Health and Environmental Sciences, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Kouji H. Harada
- Department of Health and Environmental Sciences, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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Li Y, Cao W, Gao NL, Zhao XM, Chen WH. Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice. Genomics Proteomics Bioinformatics 2022; 20:382-393. [PMID: 34118462 PMCID: PMC9684084 DOI: 10.1016/j.gpb.2020.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 04/21/2020] [Accepted: 09/08/2020] [Indexed: 01/05/2023]
Abstract
Fecal microbiota transplantation (FMT) of human fecal samples into germ-free (GF) mice is useful for establishing causal relationships between the gut microbiota and human phenotypes. However, due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms, it may not be possible to replicate human phenotypes in mice through FMT; similarly, treatments that are effective in mouse models may not be effective in humans. In this study, we aimed to identify human gut microbes that undergo significant and consistent changes (i.e., in relative abundances) after transplantation into GF mice in multiple experimental settings. We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human-mouse pairs. Strikingly, on average, we found that only 47% of the human gut microbes could be re-established in mice at the species level, among which more than 1/3 underwent significant changes (referred to as "variable taxa"). Most of the human gut microbes that underwent significant changes were consistent across multiple human-mouse pairs and experimental settings. Consequently, about 1/3 of human samples changed their enterotypes, i.e., significant changes in their leading species after FMT. Mice fed with a controlled diet showed a lower enterotype change rate (23.5%) than those fed with a noncontrolled diet (49.0%), suggesting a possible solution for rescue. Most of the variable taxa have been reported to be implicated in human diseases, with some recognized as the causative species. Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes, provide useful information for researchers using mice in gut microbiota studies, and call for additional validations after FMT. An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.
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Affiliation(s)
- Yanze Li
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wenming Cao
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Na L Gao
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI), Fudan University, Shanghai 200433, China,Corresponding authors.
| | - Wei-Hua Chen
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China,College of Life Science, Henan Normal University, Xinxiang 453007, China,Corresponding authors.
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Abstract
Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis associated diseases, such as Clostridioides difficile infection (CDI) and inflammatory bowel disease (IBD). The engraftment of donor bacteria is essential for the effectiveness of FMT, which to some extent depends on the matching of donors and recipients. However, how different types of donor-derived bacteria affect FMT efficacy has not been fully dissected. We recruited two longitudinal IBD cohorts of 103 FMT recipients and further analyzed 1,280 microbiota datasets from 14 public CDI and IBD studies to uncover the effect of donor-derived microbiota in recipients. We found that two enterotypes, RCPT/E and RCPT/B (dominated by Enterobacteriaceae and Bacteroides, respectively), consistently exist in both CDI and IBD patients. Based on a time-course-based multi-cohort analysis of FMT fecal samples, we observed the interplay between recipient and donor-derived microbiota during FMT, in which the FMT outcome was significantly associated with the enterotype and microbiota distance between donor and recipient after FMT. We proposed a new measurement, the ratio of colonizers to residents after FMT (C2R), to quantify the engraftment of donor-derived bacteria in the recipients, and then constructed an enterotype-based statistical model for donor-recipient matching, which was validated by both cross-validation and an additional IBD FMT cohort (n = 42). We believe that with the accumulation of FMT multi-omics datasets, machine learning-based methods will be helpful for rational donor selection for improving efficacy and precision FMT practices.
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Affiliation(s)
- Ruiqiao He
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pan Li
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinfeng Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Bota Cui
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Faming Zhang
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
- CONTACT Faming Zhang Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu210011, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Fangqing Zhao Beijing Institutes of Life Science, Beijing Institutes of Life Science, Beijing, China
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10
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Si J, Lee G, You HJ, Joo SK, Lee DH, Ku BJ, Park S, Kim W, Ko G. Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease. Comput Struct Biotechnol J 2021; 19:5920-5930. [PMID: 34849196 PMCID: PMC8591343 DOI: 10.1016/j.csbj.2021.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/08/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is closely associated with type 2 diabetes mellitus (T2D), and these two metabolic diseases demonstrate bidirectional influences. The identification of microbiome profiles that are specific to liver injury or impaired glucose metabolism may assist understanding of the role of the gut microbiota in the relationship between NAFLD and T2D. Here, we studied a biopsy-proven Asian NAFLD cohort (n = 329; 187 participants with NAFLD, 101 with NAFLD and T2D, and 41 with neither) and identified Enterobacter, Romboutsia, and Clostridium sensu stricto as the principal taxa associated with the severity of NAFLD and T2D, whereas Ruminococcus and Megamonas were specific to NAFLD. In particular, the taxa that were associated with both severe liver pathology and T2D were also significantly associated with markers of diabetes, such as fasting blood glucose and Hb1Ac. Enterotype analysis demonstrated that participants with NAFLD had a significantly higher proportion of Bacteroides and a lower proportion of Ruminococcus than a Korean healthy twin cohort (n = 756). However, T2D could not be clearly distinguished from NAFLD. Analysis of an independent T2D cohort (n = 185) permitted us to validate the T2D-specific bacterial signature identified in the NAFLD cohort. Functional inference analysis revealed that endotoxin biosynthesis pathways were significantly enriched in participants with NAFLD and T2D, compared with those with NAFLD alone. These findings may assist with the development of effective therapeutic approaches for metabolic diseases that are associated with specific bacterial signatures.
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Key Words
- ALT, alanine aminotransferase
- BMI, body mass index
- Biomarker
- Enterotype
- FBS, fasting blood sugar
- FDR, false discovery rate
- FLI, fatty liver index
- Gut microbiome
- HbA1c, glycosylated hemoglobin
- LDL, low-density lipoprotein
- LPS, lipopolysaccharide
- MaAsLin2, microbiome multivariable association with linear models 2
- NAFL, non-alcoholic fatty liver
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- NASH-CRN, non-alcoholic steatohepatitis clinical research network
- Non-alcoholic fatty liver disease (NAFLD)
- PICRUSt2, phylogenetic investigation of communities by reconstruction of unobserved states 2
- T2D, type 2 diabetes mellitus
- Type 2 diabetes mellitus
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Affiliation(s)
- Jiyeon Si
- Medical Science Research Institute, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Giljae Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Ju You
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
| | - Sae Kyung Joo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Dong Hyeon Lee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Seoyeon Park
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Inc., Seoul 08826, Republic of Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Republic of Korea
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11
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Fu T, Pan L, Shang Q, Yu G. Fermentation of alginate and its derivatives by different enterotypes of human gut microbiota: Towards personalized nutrition using enterotype-specific dietary fibers. Int J Biol Macromol 2021; 183:1649-1659. [PMID: 34048831 DOI: 10.1016/j.ijbiomac.2021.05.135] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/08/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Alginate and its derivatives are widely used as food additives and dietary fibers. Previous studies indicated that alginate, polyguluronate (PG) and polymannuronate acid (PM) could be fermented by human gut microbiota. However, how different compositions of the microbiota may affect the fermentation outcomes of these polysaccharides remains unknown. Here we show that Bacteroides-dominated microbiota (Bacteroides enterotype) is more proficient at degrading and utilizing PG and PM as compared to Prevotella-dominated (Prevotella enterotype) and Escherichia-dominated microbiota (Escherichia enterotype). Enterotype dictates the fermentation outcomes of the three fibers and the amount of short-chain fatty acids (SCFAs) that are produced. Fermentation of alginate and PM by Bacteroides-dominated microbiota produced the highest amount of total SCFAs and butyrate. Our study demonstrates an enterotype-specific effect of microbiota on the fermentation of alginate and its derivatives and highlights that personalized nutrition using dietary fibers should be tailored according to individual's composition of the gut microbiome.
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Affiliation(s)
- Tianyu Fu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Lin Pan
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qingsen Shang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Qingdao Marine Biomedical Research Institute, Qingdao 266071, China.
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
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12
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Ren W, Yan H, Yu B, Walsh MC, Yu J, Zheng P, Huang Z, Luo J, Mao X, He J, Yan H, Chen D, Luo Y. Prevotella-rich enterotype may benefit gut health in finishing pigs fed diet with a high amylose-to-amylopectin ratio. ACTA ACUST UNITED AC 2021; 7:400-11. [PMID: 34258428 DOI: 10.1016/j.aninu.2020.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/06/2020] [Accepted: 08/13/2020] [Indexed: 01/10/2023]
Abstract
To investigate the influence of baseline enterotypes and dietary starch type on the concentration of short-chain fatty acids (SCFA), numbers of butyrate producing bacteria and the expression of genes related to intestinal barrier and inflammatory response in the colon of finishing pigs, a 60-d in vivo trial was conducted. A 2-wk pre-trial with 102 crossbred (Duroc × [Landrace × Yorkshire]) finishing barrows (90 d old) was conducted to screen enterotypes. Then, a total of 32 pigs (87.40 ± 2.76 kg) with high (HPBR, ≥ 14) and low (LPBR, ≤ 2) Prevotella-to-Bacteroides ratios (PBR) in equal measure were selected and randomly divided into 4 groups with 8 replicates per group and 1 pig per replicate. The trial was designed following a 2 (PBR) × 2 (amylose-to-amylopectin ratio, AMR) factorial arrangement. Pigs with different PBR were fed diets based on corn-soybean meal with high AMR (HAMR, 1.24) or low AMR (LAMR, 0.23), respectively. Results showed that neither PBR nor AMR influenced the growth performance of pigs. HPBR pigs fed HAMR diet had a higher number of colonic Clostridium cluster XIVa and higher gene expression of butyrate kinase compared to the LPBR pigs (P < 0.05). The HPBR pigs fed HAMR diets also had increased colonic concentrations of total SCFA and propionate compared to the LPBR pigs (P < 0.05). Comparing with other pigs, HPBR pigs fed HAMR diets showed a lower (P < 0.05) expression of histone deacetylases (HDAC) gene and higher (P < 0.05) expression of G protein-coupled receptor 43 gene (GPR 43) in the colonic mucosa. The interaction (P < 0.05) of HPBR and HAMR was also found to decrease the gene expression of interleukin (IL)-6, IL-12, IL-1β and tumor necrosis factor-α (TNF-α) in colonic mucosa. These findings show that HAMR diet increased the abundance and activity of butyrate-producing bacteria and the concentration and absorption of SCFA, which may be associated with the decreased gene expression of inflammatory cytokines in the colonic mucosa of pigs with Prevotella-rich enterotype. All these alterations are likely to have a positive effect on the intestinal health of finishing pigs.
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Liu W, Cheng M, Li J, Zhang P, Fan H, Hu Q, Han M, Su L, He H, Tong Y, Ning K, Long Y. Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock. Genomics Proteomics Bioinformatics 2021; 18:696-707. [PMID: 33607294 PMCID: PMC8377022 DOI: 10.1016/j.gpb.2020.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
The gut microbiota of intensive care unit (ICU) patients displays extreme dysbiosis associated with increased susceptibility to organ failure, sepsis, and septic shock. However, such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota. We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis. We collected 131 fecal samples from 64 ICU patients diagnosed with sepsis or septic shock and performed 16S rRNA gene sequencing to dissect their gut microbiota compositions. During the development of sepsis or septic shock and during various medical treatments, the ICU patients always exhibited two dysbiotic microbiota patterns, or ICU-enterotypes, which could not be explained by host properties such as age, sex, and body mass index, or external stressors such as infection site and antibiotic use. ICU-enterotype I (ICU E1) comprised predominantly Bacteroides and an unclassified genus of Enterobacteriaceae, while ICU-enterotype II (ICU E2) comprised predominantly Enterococcus. Among more critically ill patients with Acute Physiology and Chronic Health Evaluation II (APACHE II) scores > 18, septic shock was more likely to occur with ICU E1 (P = 0.041). Additionally, ICU E1 was correlated with high serum lactate levels (P = 0.007). Therefore, different patterns of dysbiosis were correlated with different clinical outcomes, suggesting that ICU-enterotypes should be diagnosed as independent clinical indices. Thus, the microbial-based human index classifier we propose is precise and effective for timely monitoring of ICU-enterotypes of individual patients. This work is a first step toward precision medicine for septic patients based on their gut microbiota profiles.
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Affiliation(s)
- Wanglin Liu
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinman Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Peng Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qinghe Hu
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Longxiang Su
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Huaiwu He
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yun Long
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing 100730, China.
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14
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Jiang Y, Yuan Z, Shen Y, Rosa BA, Martin J, Cao S, Zhou Y, Mitreva M, Cao J. Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection. ACTA ACUST UNITED AC 2021; 28:1. [PMID: 33416489 PMCID: PMC7792497 DOI: 10.1051/parasite/2020074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022]
Abstract
Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype.
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Affiliation(s)
- Yanyan Jiang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Zhongying Yuan
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - John Martin
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA
| | - Shengkui Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, 06023 CT, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St Louis, St Louis, 63001 MO, USA - Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, 63001 MO, USA
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 200025 Shanghai, PR China - Chinese Center for Tropical Diseases Research, 200025 Shanghai, PR China - World Health Organization Collaborating Centre for Tropical Diseases, 200025 Shanghai, PR China - Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, 200025 Shanghai, PR China
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15
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Li X, Liu Y, Martin JW, Cui JY, Lehmler HJ. Nontarget analysis reveals gut microbiome-dependent differences in the fecal PCB metabolite profiles of germ-free and conventional mice. Environ Pollut 2021; 268:115726. [PMID: 33032095 PMCID: PMC7746632 DOI: 10.1016/j.envpol.2020.115726] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 05/18/2023]
Abstract
Mammalian polychlorinated biphenyl (PCB) metabolism has not been systematically explored with nontarget high-resolution mass spectrometry (Nt-HRMS). Here we investigated the importance of the gut microbiome in PCB biotransformation by Nt-HRMS analysis of feces from conventional (CV) and germ-free (GF) adult female mice exposed to a single oral dose of an environmental PCB mixture (6 mg/kg or 30 mg/kg in corn oil). Feces were collected for 24 h after PCB administration, PCB metabolites were extracted from pooled samples, and the extracts were analyzed by Nt-HRMS. Twelve classes of PCB metabolites were detected in the feces from CV mice, including PCB sulfates, hydroxylated PCB sulfates (OH-PCB sulfates), PCB sulfonates, and hydroxylated methyl sulfone PCBs (OH-MeSO2-PCBs) reported previously. We also observed eight additional PCB metabolite classes that were tentatively identified as hydroxylated PCBs (OH-PCBs), dihydroxylated PCBs (DiOH-PCBs), monomethoxylated dihydroxylated PCBs (MeO-OH-PCBs), methoxylated PCB sulfates (MeO-PCB sulfates), mono-to tetra-hydroxylated PCB quinones ((OH)x-quinones, x = 1-4), and hydroxylated polychlorinated benzofurans (OH-PCDF). Most metabolite classes were also detected in the feces from GF mice, except for MeO-OH-PCBs, OH-MeSO2-PCBs, and OH-PCDFs. Semi-quantitative analyses demonstrate that relative PCB metabolite levels increased with increasing dose and were higher in CV than GF mice, except for PCB sulfates and MeO-PCB sulfates, which were higher in GF mice. These findings demonstrate that the gut microbiome plays a direct or indirect role in the absorption, distribution, metabolism, or excretion of PCB metabolites, which in turn may affect toxic outcomes following PCB exposure.
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Affiliation(s)
- Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, 52242-5000, USA
| | - Yanna Liu
- Division of Analytical and Environmental Toxicity, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, 114 18, Sweden
| | - Julia Yue Cui
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, 98105-6099, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, 52242-5000, USA.
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Christensen L, Sørensen CV, Wøhlk FU, Kjølbæk L, Astrup A, Sanz Y, Hjorth MF, Benítez-Páez A. Microbial enterotypes beyond genus level: Bacteroides species as a predictive biomarker for weight change upon controlled intervention with arabinoxylan oligosaccharides in overweight subjects. Gut Microbes 2020; 12:1847627. [PMID: 33319645 PMCID: PMC7781564 DOI: 10.1080/19490976.2020.1847627] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Recent studies indicate that microbial enterotypes may influence the beneficial effects of wholegrain enriched diets including bodyweight regulation. In a 4-week intervention trial, overweight subjects were randomized to consume either arabinoxylan-oligosaccharides (AXOS) (10.4 g/d) from wheat bran or polyunsaturated fatty acids (PUFA) (3.6 g/d). In the present study, we have stratified the subjects participating in the intervention (n = 29) according to the baseline Prevotella-to-Bacteroides (P/B) ratios through a post-hoc analysis and applied a linear mixed model analysis to identify the influence of this P/B ratio on the differences in weight changes in the intervention arms. Following AXOS consumption (n = 15), the high P/B group showed no bodyweight changes [-0.14 kg (95% CI: -0.67; 0.38, p = .59)], while the low P/B group gained 0.65 kg (95% CI: 0.16; 1.14, p = .009). Consequently, a difference of -0.79 kg was found between P/B groups (95% CI: -1.51; -0.08, p = .030). No differences were found between P/B groups following PUFA consumption (0.61 kg, 95% CI: -0.13; 1.35, p = .10). Among the Bacteroides species, B. cellulosilyticus relative abundance exhibited the highest positive rank correlation (Kendall's tau = 0.51, FDR p = .070) with 4-week weight change on AXOS, and such association was further supported by using supervised classification methods (Random Forest). We outlined several carbohydrate-active enzyme (CAZy) genes involved in xylan-binding and degradation to be enriched in B. cellulosilyticus genomes, as well as multiple accessory genes, suggesting a supreme AXOS-derived glycan scavenging role of such species. This post-hoc analysis, ensuring species and strain demarcation at the human gut microbiota, permitted to uncover the predictive role of Bacteroides species over P/B enterotype in weight gain during a fiber-based intervention. The results of this pilot trial pave the way for future assessments on fiber fermentation outputs from Bacteroides species affecting lipid metabolism in the host and with direct impact on adiposity, thus helping to design personalized interventions.
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Affiliation(s)
- Lars Christensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark,CONTACT Lars Christensen Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Claudia V. Sørensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Frederikke U. Wøhlk
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Louise Kjølbæk
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Mads F. Hjorth
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Alfonso Benítez-Páez
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain,Host-Microbe Interactions in Metabolic Health Laboratory, Príncipe Felipe Research Centre (CIPF), Valencia, Spain,Alfonso Benítez-Páez Host-Microbe Interactions in Metabolic Health Laboratory, Príncipe Felipe Research Center (CIPF). Valencia, Spain
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17
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Hosoda S, Nishijima S, Fukunaga T, Hattori M, Hamada M. Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation. Microbiome 2020; 8:95. [PMID: 32576288 PMCID: PMC7313204 DOI: 10.1186/s40168-020-00864-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/13/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the enterotype and assemblage is not well-understood. RESULTS In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized enterotypes. Conversely, the fourth assemblage corresponded to no enterotypes and emerged in all enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions. CONCLUSIONS We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an enterotype-independent assemblage. Video Abstract.
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Affiliation(s)
- Shion Hosoda
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169–8555 Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Suguru Nishijima
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169–8555 Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tsukasa Fukunaga
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169–8555 Japan
- Department of Computer Science, Graduate School of Information Science and Engineering, The University of Tokyo, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169–8555 Japan
- Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169–8555 Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
- Center for Data Science, Waseda University, Tokyo, Japan
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Hosfield BD, Pecoraro AR, Baxter NT, Hawkins TB, Markel TA. The Assessment of Fecal Volatile Organic Compounds in Healthy Infants: Electronic Nose Device Predicts Patient Demographics and Microbial Enterotype. J Surg Res 2020; 254:340-347. [PMID: 32526503 DOI: 10.1016/j.jss.2020.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND The assessment of fecal volatile organic compounds (VOCs) has emerged as a noninvasive biomarker in many different pathologies. Before assessing whether VOCs can be used to diagnose intestinal diseases, including necrotizing enterocolitis (NEC), it is necessary to measure the impact of variable infant demographic factors on VOC signals. MATERIALS AND METHODS Stool samples were collected from term infants at four hospitals in a large metropolitan area. Samples were heated, and fecal VOCs assessed by the Cyranose 320 Electronic Nose. Twenty-eight sensors were combined into an overall smellprint and were also assessed individually. 16s rRNA gene sequencing was used to categorize infant microbiomes. Smellprints were correlated to feeding type (formula versus breastmilk), sex, hospital of birth, and microbial enterotype. Overall smellprints were assessed by PERMANOVA with Euclidean distances, and individual sensors from each smellprint were assessed by Mann-Whitney U-tests. P < 0.05 was significant. RESULTS Overall smellprints were significantly different according to diet. Individual sensors were significantly different according to sex and hospital of birth, but overall smellprints were not significantly different. Using a decision tree model, two individual sensors could reliably predict microbial enterotype. CONCLUSIONS Assessment of fecal VOCs with an electronic nose is impacted by several demographic characteristics of infants and can be used to predict microbiome composition. Further studies are needed to design appropriate algorithms that are able to predict NEC based on fecal VOC profiles.
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Affiliation(s)
- Brian D Hosfield
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Anthony R Pecoraro
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | - Troy A Markel
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana.
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Ke S, Fang S, He M, Huang X, Yang H, Yang B, Chen C, Huang L. Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition. BMC Vet Res 2019; 15:172. [PMID: 31126262 PMCID: PMC6534858 DOI: 10.1186/s12917-019-1918-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs. Results Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis. Conclusions The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota. Electronic supplementary material The online version of this article (10.1186/s12917-019-1918-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shanlin Ke
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Xiaochang Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, People's Republic of China.
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Cheng M, Ning K. Stereotypes About Enterotype: the Old and New Ideas. Genomics Proteomics Bioinformatics 2019; 17:4-12. [PMID: 31026581 PMCID: PMC6521238 DOI: 10.1016/j.gpb.2018.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/27/2017] [Accepted: 02/09/2018] [Indexed: 12/21/2022]
Abstract
In 2011, the term “enterotype” first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view. We firstly illustrated the definition of the enterotype and various factors influencing enterotypes, such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis. Finally, we showed that the concept of enterotype has been extended to other ecological niches. Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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21
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Abstract
Background One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as “enterotype”, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease. Results We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease. Conclusion In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson’s disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).
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Affiliation(s)
- Ko Abe
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masaaki Hirayama
- School of Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8873, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.
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Rahayu ES, Utami T, Mariyatun M, Hasan PN, Kamil RZ, Setyawan RH, Pamungkaningtyas FH, Harahap IA, Wiryohanjoyo DV, Pramesi PC, Cahyanto MN, Sujaya IN, Juffrie M. Gut microbiota profile in healthy Indonesians. World J Gastroenterol 2019; 25:1478-1491. [PMID: 30948911 PMCID: PMC6441913 DOI: 10.3748/wjg.v25.i12.1478] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influencing gut microbiota such as age, diet, etc., area-based research is required. Indonesia has numerous different tribes and each of these tribes have different lifestyles. Hence, it is expected that each tribe has a specific gut microbiota. A deeper insight into the composition of gut microbiota can be used to determine the condition of gut microbiota in Indonesians and to consider which treatment may be suitable and effective to improve health status.
AIM To investigate the gut microbiota of Indonesian subjects represented by Javanese and Balinese tribes by analyzing fecal samples.
METHODS Fecal samples were collected from a total of 80 individuals with 20 in each of the young groups ranging from 25-45 years and the elderly group aged 70 years or more from two different regions, Yogyakarta and Bali. Fecal sample collection was performed at the end of the assessment period (day 14 ± 1 d) during which time the subjects were not allowed to consume probiotic or antibiotic products. The quantification of various Clostridium subgroups, Lactobacillus subgroups, Enterococcus, Streptococcus, Staphylococcus, Bacteroides fragilis group and Prevotella, Bifidobacterium and Atopobium cluster, Enterobacteriaceae and Pseudomonas was performed using the Yakult intestinal flora-scan (YIF-SCAN).
RESULTS The bacterial population in younger subjects’ feces was higher than that in the elderly population, with a total of approximately 10.0 – 10.6 log10 bacterial cells/g feces. The most abundant bacteria in all groups were Clostridium, followed by Prevotella, Atopobium, Bifidobacterium and Bacteroides. In the elderly, an increase in Enterobacteriaceae, Coliform and Escherichia coli was found. In terms of bacterial counts in Yogyakarta, total bacteria, Clostridium coccoides (C. coccoides) group, Bifidobacterium, Prevotella, Lactobacillus plantarum subgroup, and Streptococcus were significantly higher (P < 0.05) in younger than elderly subjects, while the Lactobacillus gasseri subgroup, Lactobacillus casei subgroup, and Lactobacillus reuteri subgroup counts were significantly lower (P < 0.05) in younger subjects. In Balinese subjects, total bacteria, C. coccoides group, Clostridium leptum subgroup, Bacteroides fragilis group, and Prevotella were significantly higher (P < 0.05) in younger compared to elderly individuals, while the Lactobacillus ruminis subgroup, and Enterobacteriaceae were significantly lower (P < 0.05) in younger subjects. The results also revealed that, besides the C. coccoides group and Clostridium leptum group being the most abundant gut microbiota in both Yogyakarta and Balinese people, the latter was indicated by a higher Clostridium perfringens count, which was almost 10 times that of Yogyakarta subjects. This may be a response to different lifestyles in the different tribes; however, this phenomenon requires further extensive study.
CONCLUSION Bacterial populations were higher in younger than in elderly subjects. Most abundant bacterial groups were Clostridium, Prevotella, Atopobium, Bifidobacterium, and Bacteroides. The level of Clostridium perfringens in Yogyakarta subjects was lower than that in Balinese subjects.
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Affiliation(s)
- Endang Sutriswati Rahayu
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Tyas Utami
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Mariyatun Mariyatun
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Pratama Nur Hasan
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Rafli Zulfa Kamil
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ryan Haryo Setyawan
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | | | - Iskandar Azmy Harahap
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Devin Varian Wiryohanjoyo
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Putrika Citta Pramesi
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Muhammad Nur Cahyanto
- Department of Food and Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - I Nengah Sujaya
- Department of Public Health, Udayana University, Denpasar 80234, Indonesia
| | - Mohammad Juffrie
- Department of Public Health, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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Zhong H, Penders J, Shi Z, Ren H, Cai K, Fang C, Ding Q, Thijs C, Blaak EE, Stehouwer CDA, Xu X, Yang H, Wang J, Wang J, Jonkers DMAE, Masclee AAM, Brix S, Li J, Arts ICW, Kristiansen K. Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children. Microbiome 2019; 7:2. [PMID: 30609941 PMCID: PMC6320620 DOI: 10.1186/s40168-018-0608-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/26/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children. RESULTS Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus. CONCLUSIONS Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.
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Affiliation(s)
- Huanzi Zhong
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism & Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Zhun Shi
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huahui Ren
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Kaiye Cai
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chao Fang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Qiuxia Ding
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Carel Thijs
- Department of Epidemiology, Care and Public Health Research Institute CAPHRI, Maastricht University, Maastricht, the Netherlands
| | - Ellen E Blaak
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Coen D A Stehouwer
- Department of Internal Medicine, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Daisy M A E Jonkers
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800, Kongens Lyngby, Denmark
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Ilja C W Arts
- Maastricht Centre for Systems Biology (MaCSBio) & Department of Epidemiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands.
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
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Mobeen F, Sharma V, Tulika P. Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions. Bioinformation 2018; 14:560-573. [PMID: 31223215 PMCID: PMC6563668 DOI: 10.6026/97320630014560] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/16/2018] [Accepted: 11/18/2018] [Indexed: 02/07/2023] Open
Abstract
Enterotypes are used for classifying individuals based on the gut microbiome. A number of studies are available to find the Enterotypes in healthy individuals; however, most of them lack comparisons at the world level. We analyzed the healthy human gut microbiomes of 495 datasets available in the European Nucleotide Archive (ENA) database derived from fifteen countries from four continents. Firmicutes and Bacteroidetes were the two most abundant phyla in the healthy human gut, worldwide. A high ratio of Proteobacteriato Actinobacteria and a low abundance of Prevotella were identified as the indicators of IBD. Prevotella, Bacteroides, and Bifidobacterium were identified as the Enterotypes in the inter-continental comparisons. At the intra-continental level, two (Bacteroides and Ruminococcaceae), four (Faecalibacterium, Bacteroides, Prevotella, and Clostridiales), and two (Prevotella, Bacteroides/Bifidobacterium) Enterotypes were identified in the American, European, and Asian continents, respectively. In addition, a high abundance of the unknown genus of Ruminococcaeae was observed in the Colombian human gut microbiome. A substantial impact of the geographical distance was observed on human gut microbiome variations, demonstrating a cumulative effect of factors, including dietary habits, genetics, lifestyle, environment, and climate, etc.
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Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Prakash Tulika
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
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25
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Yang H, Yang M, Fang S, Huang X, He M, Ke S, Gao J, Wu J, Zhou Y, Fu H, Chen C, Huang L. Evaluating the profound effect of gut microbiome on host appetite in pigs. BMC Microbiol 2018; 18:215. [PMID: 30547751 PMCID: PMC6295093 DOI: 10.1186/s12866-018-1364-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/02/2018] [Indexed: 12/21/2022] Open
Abstract
Background There are growing evidences showing that gut microbiota should play an important role in host appetite and feeding behavior. However, what kind of microbe(s) and how they affect porcine appetite remain unknown. Results In this study, 280 commercial Duroc pigs were raised in a testing station with the circadian feeding behavior records for a continuous period of 30–100 kg. We first analyzed the influences of host gender and genetics in porcine average daily feed intake (ADFI), but no significant effect was observed. We found that the Prevotella-predominant enterotype had a higher ADFI than the Treponema enterotype-like group. Furthermore, 12 out of the 18 OTUs positively associated with the ADFI were annotated to Prevotella, and Prevotella was the hub bacteria in the co-abundance network. These results suggested that Prevotella might be a keystone bacterial taxon for increasing host feed intake. However, some bacteria producing short-chain fatty acids (SCFAs) and lactic acid (e.g. Ruminococcaceae and Lactobacillus) showed negative associations with the ADFI. Predicted function capacity analysis showed that the genes for amino acid biosynthesis had significantly different enrichment between pigs with high and low ADFI. Conclusions The present study provided important information on the profound effect of gut microbiota on porcine appetite and feeding behavior. This will profit us to regulate porcine appetite through modulating the gut microbiome in the pig industry. Electronic supplementary material The online version of this article (10.1186/s12866-018-1364-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuff Co. Ltd., Xinxing, China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaochang Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shanlin Ke
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jun Gao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jinyuan Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yunyan Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hao Fu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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26
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Salem AE, Singh R, Ayoub YK, Khairy AM, Mullin GE. The gut microbiome and irritable bowel syndrome: State of art review. Arab J Gastroenterol 2018; 19:136-141. [PMID: 29935865 DOI: 10.1016/j.ajg.2018.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 12/14/2022]
Abstract
Irritable bowel syndrome (IBS) is a functional disorder of the gastrointestinal tract, the physiology of which is not very well understood. There are multiple factors and pathways involved in pathogenesis of this entity. Among all, dysmotility, dysregulation of the brain-gut axis, altered intestinal microbiota and visceral hypersensitivity play a major role. Over the last years, research has shown that the type of gut microbiome present in an individual plays a significant role in the pathophysiology of IBS. Multiple studies have consistently shown that subjects diagnosed with IBS have disruption in gut microbiota balance. It has been established that host immune system and its interaction with metabolic products of gut microbiota play an important role in the gastrointestinal tract. Therefore, probiotics, prebiotics and antibiotics have shown some promising results in managing IBS symptoms via modulating the interaction between the above. This paper discusses the various factors involved in pathophysiology of IBS, especially gut microbiota.
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Affiliation(s)
- Ahmed E Salem
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Division of Gastroenterology and Hepatology, Baltimore, MD, 21287 United States.
| | - Rajdeep Singh
- Department of Medicine, Sinai Hospital of Baltimore, Baltimore, MD, 21215 United States
| | - Younan K Ayoub
- Department of Endemic Medicine, Cairo University School of Medicine, Cairo, Egypt
| | - Ahmed M Khairy
- Department of Endemic Medicine, Cairo University School of Medicine, Cairo, Egypt
| | - Gerard E Mullin
- Johns Hopkins University School of Medicine, Division of Gastroenterology and Hepatology, Baltimore, MD, 21287 United States
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27
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Abstract
Psychological comorbidity is highly present in irritable bowel syndrome (IBS). Recent research points to a role of intestinal microbiota in visceral hypersensitivity, anxiety, and depression. Increased disease reactivity to psychological stress has been described too. A few clinical studies have attempted to identify features of dysbiosis in IBS. While animal studies revealed strong associations between stress and gut microbiota, studies in humans are rare. This review covers the most important studies on intestinal microbial correlates of psychological and clinical features in IBS, including stress, anxiety, and depression.
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Affiliation(s)
- Gabriele Moser
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, Vienna, 1090, Austria.
| | - Camille Fournier
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, Vienna, 1090, Austria
| | - Johannes Peter
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, Vienna, 1090, Austria
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28
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Li J, Fu R, Yang Y, Horz HP, Guan Y, Lu Y, Lou H, Tian L, Zheng S, Liu H, Shi M, Tang K, Wang S, Xu S. A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups. Syst Appl Microbiol 2017; 41:1-12. [PMID: 29129355 DOI: 10.1016/j.syapm.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.
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Affiliation(s)
- Jing Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Ruiqing Fu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Yaqun Guan
- Department of Biochemistry, Preclinical Medicine College, XinJiang Medical University, Urumqi 830011, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Haiyi Lou
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Lei Tian
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Zheng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Hongjiao Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Meng Shi
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
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29
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Wu Q, Pi X, Liu W, Chen H, Yin Y, Yu HD, Wang X, Zhu L. Fermentation properties of isomaltooligosaccharides are affected by human fecal enterotypes. Anaerobe 2017; 48:206-214. [PMID: 28882708 DOI: 10.1016/j.anaerobe.2017.08.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/02/2017] [Accepted: 08/31/2017] [Indexed: 01/16/2023]
Abstract
Isomaltooligosaccharides (IMOs) are enzymatically synthesized oligosaccharides that have potential prebiotic effects. Five IMO substrates with 2-16° of polymerization (DP) were studied for their fermentation capacities using human microbiomes in an in vitro batch fermentation model. Eleven fecal slurries belonging to three enterotypes, including the Bacteroides-, Prevotella- and Mixed-type, exhibited different degradation rates for long chain IMOs (DP 7 to 16). In contrast, the degradation rates for short chain IMOs (DP 2 to 6) were not affected by enterotypes. Both 16S rRNA gene sequencing and quantitative PCR demonstrated that, after fermentation, the Bifidobacterium growth with IMOs was primarily detected in the Bacteroides- and Mixed-type (non-Prevotella-type), and to a lesser degree in the Prevotella-type. Interestingly, the Prevotella-type microbiome had higher levels of propionic acid and butyric acid production than non-Prevotella-type microbiome after IMOs fermentation. Moreover, principal coordinate analysis (PCoA) of both denaturing gradient gel electrophoresis (DGGE) profiling and 16S rRNA sequencing data demonstrated that the microbiome community compositions were separately clustered based on IMO chain length, suggesting significant impact of DP on the bacterial community structure. The current results clearly demonstrated that the IMO chain length could modulate the structure and composition of the human colonic microbiome. Different responses to short and long chain IMOs were observed from three human enterotypes, indicating that IMOs may be used as therapeutic substrates for directly altering human colonic bacteria.
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Affiliation(s)
- Qinqin Wu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, PR China; State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Xiong'e Pi
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Wei Liu
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Huahai Chen
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Yeshi Yin
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Hongwei D Yu
- Department of Biomedical Sciences, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA; Progenesis Technologies, LLC, One John Marshall Drive, Robert C. Byrd Biotechnology Science Center, Suite 314, Huntington, WV 25755, USA
| | - Xin Wang
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Liying Zhu
- State Microbial Technology of Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China.
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30
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Liang C, Tseng HC, Chen HM, Wang WC, Chiu CM, Chang JY, Lu KY, Weng SL, Chang TH, Chang CH, Weng CT, Wang HM, Huang HD. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics 2017; 18:932. [PMID: 28198673 PMCID: PMC5310273 DOI: 10.1186/s12864-016-3261-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health. Results We obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively. Conclusions We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3261-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | - Hui-Mei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | | | | | - Kuan-Yi Lu
- Health GeneTech Corporation, Taoyuan, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Chao-Hsiang Chang
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | | | | | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
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