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Gavzy SJ, Kensiski A, Saxena V, Lakhan R, Hittle L, Wu L, Iyyathurai J, Dhakal H, Lee ZL, Li L, Lee YS, Zhang T, Lwin HW, Shirkey MW, Paluskievicz CM, Piao W, Mongodin EF, Ma B, Bromberg JS. Early Immunomodulatory Program Triggered by Protolerogenic Bifidobacterium pseudolongum Drives Cardiac Transplant Outcomes. Transplantation 2024; 108:e91-e105. [PMID: 38587506 PMCID: PMC11188630 DOI: 10.1097/tp.0000000000004939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/24/2023] [Accepted: 11/20/2023] [Indexed: 04/09/2024]
Abstract
BACKGROUND Despite ongoing improvements to regimens preventing allograft rejection, most cardiac and other organ grafts eventually succumb to chronic vasculopathy, interstitial fibrosis, or endothelial changes, and eventually graft failure. The events leading to chronic rejection are still poorly understood and the gut microbiota is a known driving force in immune dysfunction. We previously showed that gut microbiota dysbiosis profoundly influences the outcome of vascularized cardiac allografts and subsequently identified biomarker species associated with these differential graft outcomes. METHODS In this study, we further detailed the multifaceted immunomodulatory properties of protolerogenic and proinflammatory bacterial species over time, using our clinically relevant model of allogenic heart transplantation. RESULTS In addition to tracing longitudinal changes in the recipient gut microbiome over time, we observed that Bifidobacterium pseudolongum induced an early anti-inflammatory phenotype within 7 d, whereas Desulfovibrio desulfuricans resulted in a proinflammatory phenotype, defined by alterations in leukocyte distribution and lymph node (LN) structure. Indeed, in vitro results showed that B pseudolongum and D desulfuricans acted directly on primary innate immune cells. However, by 40 d after treatment, these 2 bacterial strains were associated with mixed effects in their impact on LN architecture and immune cell composition and loss of colonization within gut microbiota, despite protection of allografts from inflammation with B pseudolongum treatment. CONCLUSIONS These dynamic effects suggest a critical role for early microbiota-triggered immunologic events such as innate immune cell engagement, T-cell differentiation, and LN architectural changes in the subsequent modulation of protolerant versus proinflammatory immune responses in organ transplant recipients.
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Affiliation(s)
- Samuel J. Gavzy
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Allison Kensiski
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Vikas Saxena
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Ram Lakhan
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Lauren Hittle
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD
| | - Long Wu
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Jegan Iyyathurai
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Hima Dhakal
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Zachariah L. Lee
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Lushen Li
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Young S. Lee
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Tianshu Zhang
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Hnin Wai Lwin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD
| | - Marina W. Shirkey
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Christina M. Paluskievicz
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Wenji Piao
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
| | - Emmanuel F. Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD
| | - Bing Ma
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD
| | - Jonathan S. Bromberg
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD
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2
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Long C, Wu J, Liu J. Microbiota in different digestive tract of paddlefish (Polyodon spathula) are related to their functions. PLoS One 2024; 19:e0302522. [PMID: 38758940 PMCID: PMC11101114 DOI: 10.1371/journal.pone.0302522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/07/2024] [Indexed: 05/19/2024] Open
Abstract
Paddlefish has high economic and ecological value. In this study, microbial diversity and community structure in intestine, stomach, and mouth of paddlefish were detected using high-throughput sequencing. The results showed that the diversity and richness indices decreased along the digestive tract, and significantly lower proportion of those were observed in intestine. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla. In top 10 phyla, there was no significant difference in mouth and stomach. But compared with intestine, there were significant differences in 8 of the 10 phyla, and Firmicutes and Bacteroidetes increased significantly, while Proteobacteria decreased significantly. There was no dominant genus in mouth and stomach, but Clostridium_sensu_stricto_1 and uncultured_bacterium_o_Bacteroidales was predominant in intestine. In conclusion, the species and abundance of microbiota in the mouth and stomach of paddlefish were mostly the same, but significantly different from those in intestine. Moreover, there was enrichment of the dominant bacteria in intestine.
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Affiliation(s)
- Chengxing Long
- Hunan University of Humanities, Science and Technology, Loudi, China
| | - Jieqi Wu
- Loudi Fisheries Science Research Institute, Loudi, China
| | - Jialin Liu
- Hunan University of Humanities, Science and Technology, Loudi, China
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3
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Zhang R, Qin X, Liu Y. Exploration of the intestinal flora to reveal the important contribution of Radix Astragali to Huangqi Jianzhong Tang in treating chronic atrophic gastritis rats. J Pharm Biomed Anal 2024; 242:116067. [PMID: 38417324 DOI: 10.1016/j.jpba.2024.116067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Radix Astragali (Huangqi in Chinese, HQ) is a commonly used Chinese herbal medicine for thousands of years. In this study, A classic prescription Huangqi Jianzhong tang (HQJZ) was selected to evaluate the important effect of HQ on rats with chronic atrophic gastritis (CAG) from the perspective of intestinal flora in cecal contents samples. Traditional pharmacological indicators, including weight change, pathological examination and biochemical indicators showed that HQ exerted favorable contribution to HQJZ against CAG, where the efficiencies of HQ and HQJZ were better than HY (HQJZ prepared without HQ). An accurate strategy was adopted to screen out the differential metabolites in the metabolomis analysis of intestinal flora in cecal contents samples based on the optimal screening factors, including VIP (importance of variables in projection), FC (fold change), AUROC (area under the receiver operating characteristic curve) and -ln(p-value), which were evaluated based on their interpreting, grouping, and predicting abilities of the performed orthogonal partial least-squares-discriminate analysis (OPLS-DA) models. Ten altered differential metabolites were obtained and associated with the intestinal flora, which HQ exerted the important metabolic contributions to HQJZ. The efficacy on the diversity of intestinal flora and their correlations with the altered metabolites further showed the important role of HQ in HQJZ composition. This work provided valuable approach for looking for potential biomarkers associated with metabolomics research with more accuracy, and provided new insights into the mechanisms to explain the efficacy of HQ contributing to HQJZ formula.
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Affiliation(s)
- Ruonan Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China.
| | - Yuetao Liu
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, PR China.
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4
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Liu Z, Zhang D, Chen S. Unveiling the gastric microbiota: implications for gastric carcinogenesis, immune responses, and clinical prospects. J Exp Clin Cancer Res 2024; 43:118. [PMID: 38641815 PMCID: PMC11027554 DOI: 10.1186/s13046-024-03034-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
High-throughput sequencing has ushered in a paradigm shift in gastric microbiota, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. Recent attention directed toward the composition and functionality of this 'community' has shed light on its potential relevance in cancer. The microbial composition in the stomach of health displays host specificity which changes throughout a person's lifespan and is subject to both external and internal factors. Distinctive alterations in gastric microbiome signature are discernible at different stages of gastric precancerous lesions and malignancy. The robust microbes that dominate in gastric malignant tissue are intricately implicated in gastric cancer susceptibility, carcinogenesis, and the modulation of immunosurveillance and immune escape. These revelations offer fresh avenues for utilizing gastric microbiota as predictive biomarkers in clinical settings. Furthermore, inter-individual microbiota variations partially account for differential responses to cancer immunotherapy. In this review, we summarize current literature on the influence of the gastric microbiota on gastric carcinogenesis, anti-tumor immunity and immunotherapy, providing insights into potential clinical applications.
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Affiliation(s)
- Zhiyi Liu
- Department of Oncology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, China
| | - Dachuan Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Siyu Chen
- Department of Oncology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, China.
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5
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Chen G, Yu Z, Zhang Y, Liu S, Chen C, Zhang S. Radiation-induced gastric injury during radiotherapy: molecular mechanisms and clinical treatment. JOURNAL OF RADIATION RESEARCH 2023; 64:870-879. [PMID: 37788485 PMCID: PMC10665304 DOI: 10.1093/jrr/rrad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/08/2023] [Indexed: 10/05/2023]
Abstract
Radiotherapy (RT) has been the standard of care for treating a multitude of cancer types. Radiation-induced gastric injury (RIGI) is a common complication of RT for thoracic and abdominal tumors. It manifests acutely as radiation gastritis or gastric ulcers, and chronically as chronic atrophic gastritis or intestinal metaplasia. In recent years, studies have shown that intracellular signals such as oxidative stress response, p38/MAPK pathway and transforming growth factor-β signaling pathway are involved in the progression of RIGI. This review also summarized the risk factors, diagnosis and treatment of this disease. However, the root of therapeutic challenges lies in the incomplete understanding of the mechanisms. Here, we also highlight the potential mechanistic, diagnostic and therapeutic directions of RIGI.
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Affiliation(s)
- Guangxia Chen
- Department of Gastroenterology, The First People’s Hospital of Xuzhou, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou 221200, China
| | - Zuxiang Yu
- Laboratory of Radiation Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuehua Zhang
- Laboratory of Radiation Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shiyu Liu
- Department of Gastroenterology, The First People’s Hospital of Xuzhou, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou 221200, China
| | - Chong Chen
- Department of Gastroenterology, The First People’s Hospital of Xuzhou, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou 221200, China
| | - Shuyu Zhang
- Laboratory of Radiation Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital , Chengdu 610051, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang 621099, China
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6
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Han Z, Min Y, Pang K, Wu D. Therapeutic Approach Targeting Gut Microbiome in Gastrointestinal Infectious Diseases. Int J Mol Sci 2023; 24:15654. [PMID: 37958637 PMCID: PMC10650060 DOI: 10.3390/ijms242115654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of Helicobacter pylori, Clostridium difficile, Vibrio cholerae, enteric viruses, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa Staphylococcus aureus, Candida albicans, and Giardia duodenalis. We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.
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Affiliation(s)
- Ziying Han
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
| | - Yiyang Min
- Peking Union Medical College, Beijing 100730, China
| | - Ke Pang
- Peking Union Medical College, Beijing 100730, China
| | - Dong Wu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
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7
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Komori E, Kato-Kogoe N, Imai Y, Sakaguchi S, Taniguchi K, Omori M, Ohmichi M, Nakamura S, Nakano T, Lee SW, Ueno T. Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota. Sci Rep 2023; 13:15863. [PMID: 37740058 PMCID: PMC10516953 DOI: 10.1038/s41598-023-43108-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
Gastric cancer is one of the leading causes of death worldwide, and resections are performed to cure the disease. We have previously reported the changes in the gastric microbiota after gastric cancer resection, which may be associated with the oral microbiota; however, the changes in the oral microbiota remain uncharacterized. This study aimed to characterize the changes in the salivary microbiota caused by gastric cancer resection and to evaluate their association with the gastric fluid microbiota. Saliva and gastric fluid samples were collected from 63 patients who underwent gastrectomy before and after surgery, and a 16S rRNA metagenomic analysis was performed to compare the microbiota composition. The number of bacterial species in the salivary microbiota decreased, and the bacterial composition changed after the resection of gastric cancer. In addition, we identified several bacterial genera that varied significantly in the salivary microbiota, some of which also showed similar changes in the gastric fluid microbiota. These findings indicate that changes in the gastric environment affect the oral microbiota, emphasizing the close association between the oral and gastric fluid microbiota. Our study signifies the importance of focusing on the oral microbiota in the perioperative period of gastrectomy in patients with gastric cancer.
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Affiliation(s)
- Eri Komori
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Nahoko Kato-Kogoe
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan.
| | - Yoshiro Imai
- Department of General and Gastroenterological Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Kohei Taniguchi
- Translational Research Program, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Michi Omori
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Mayu Ohmichi
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Sang-Woong Lee
- Department of General and Gastroenterological Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Takaaki Ueno
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
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8
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Bubeck AM, Urbain P, Horn C, Jung AS, Ferrari L, Ruple HK, Podlesny D, Zorn S, Laupsa-Borge J, Jensen C, Lindseth I, Lied GA, Dierkes J, Mellgren G, Bertz H, Matysik S, Krautbauer S, Liebisch G, Schoett HF, Dankel SN, Fricke WF. High-fat diet impact on intestinal cholesterol conversion by the microbiota and serum cholesterol levels. iScience 2023; 26:107697. [PMID: 37694136 PMCID: PMC10485154 DOI: 10.1016/j.isci.2023.107697] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
Cholesterol-to-coprostanol conversion by the intestinal microbiota has been suggested to reduce intestinal and serum cholesterol availability, but the relationship between intestinal cholesterol conversion and the gut microbiota, dietary habits, and serum lipids has not been characterized in detail. We measured conserved proportions of cholesterol high and low-converter types in individuals with and without obesity from two distinct, independent low-carbohydrate high-fat (LCHF) dietary intervention studies. Across both cohorts, cholesterol conversion increased in previous low-converters after LCHF diet and was positively correlated with the fecal relative abundance of Eubacterium coprostanoligenes. Lean cholesterol high-converters had increased serum triacylglycerides and decreased HDL-C levels before LCHF diet and responded to the intervention with increased LDL-C, independently of fat, cholesterol, and saturated fatty acid intake. Our findings identify the cholesterol high-converter type as a microbiome marker, which in metabolically healthy lean individuals is associated with increased LDL-C in response to LCHF.
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Affiliation(s)
- Alena M. Bubeck
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Paul Urbain
- Department of Medicine I, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cathrine Horn
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Science, University of Bergen, Bergen, Norway
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Anna S. Jung
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Lisa Ferrari
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Hannah K. Ruple
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Daniel Podlesny
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Stefanie Zorn
- Department of Medicine I, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johnny Laupsa-Borge
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Caroline Jensen
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Science, University of Bergen, Bergen, Norway
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | | | - Gülen Arslan Lied
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Jutta Dierkes
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gunnar Mellgren
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Science, University of Bergen, Bergen, Norway
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hartmut Bertz
- Department of Medicine I, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Silke Matysik
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Hans-Frieder Schoett
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Simon N. Dankel
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Science, University of Bergen, Bergen, Norway
- Mohn Nutrition Research Laboratory, Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - W. Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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9
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Huang H, Zhong W, Wang X, Yang Y, Wu T, Chen R, Liu Y, He F, Li J. The role of gastric microecological dysbiosis in gastric carcinogenesis. Front Microbiol 2023; 14:1218395. [PMID: 37583514 PMCID: PMC10423824 DOI: 10.3389/fmicb.2023.1218395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Gastric cancer (GC) is the leading cause of cancer-related death worldwide, and reducing its mortality has become an urgent public health issue. Gastric microecological dysbiosis (including bacteria, fungi, viruses, acid suppressants, antibiotics, and surgery) can lead to gastric immune dysfunction or result in a decrease in dominant bacteria and an increase in the number and virulence of pathogenic microorganisms, which in turn promotes development of GC. This review analyzes the relationship between gastric microecological dysbiosis and GC, elucidates dynamic alterations of the microbiota in Correa's cascade, and identifies certain specific microorganisms as potential biomarkers of GC to aid in early screening and diagnosis. In addition, this paper presents the potential of gastric microbiota transplantation as a therapeutic target for gastric cancer, providing a new direction for future research in this field.
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Affiliation(s)
- Hui Huang
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Wei Zhong
- Chengdu Medical College, Chengdu, Sichuan, China
| | | | - Ying Yang
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Tianmu Wu
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Runyang Chen
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Yanling Liu
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng He
- Chengdu Medical College, Chengdu, Sichuan, China
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Li
- Chengdu Medical College, Chengdu, Sichuan, China
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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10
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Vonaesch P, Billy V, Mann AE, Morien E, Habib A, Collard JM, Dédé M, Kapel N, Sansonetti PJ, Parfrey LW. The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status. MICROLIFE 2023; 4:uqad033. [PMID: 37680753 PMCID: PMC10481997 DOI: 10.1093/femsml/uqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023]
Abstract
Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Vincent Billy
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Allison E Mann
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Evan Morien
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Michel Dédé
- Laboratoire d’Analyse médicale, Institut Pasteur de Bangui, Avenue De Independence Bangui, 923 Central African Republic
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, Assistance Publique- Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 47-83 Bd de l’Hôpital, 75013 Paris, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
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11
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Xu X, Li G, Zhang D, Zhu H, Liu G, Zhang Z. Gut Microbiota is Associated with Aging-Related Processes of a Small Mammal Species under High-Density Crowding Stress. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205346. [PMID: 36965140 PMCID: PMC10190659 DOI: 10.1002/advs.202205346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/15/2023] [Indexed: 05/18/2023]
Abstract
Humans and animals frequently encounter high-density crowding stress, which may accelerate their aging processes; however, the roles of gut microbiota in the regulation of aging-related processes under high-density crowding stress remain unclear. In the present study, it is found that high housing density remarkably increases the stress hormone (corticosterone), accelerates aging-related processes as indicated by telomere length (in brain and liver cells) and DNA damage or inflammation (as revealed by tumor necrosis factor-α and interleukin-10 levels), and reduces the lifespan of Brandt's vole (Lasiopodomys brandtii). Fecal microbiota transplantation from donor voles of habitats with different housing densities induces similar changes in aging-related processes in recipient voles. The elimination of high housing density or butyric acid administration delays the appearance of aging-related markers in the brain and liver cells of voles housed at high-density. This study suggests that gut microorganisms may play a significant role in regulating the density-dependent aging-related processes and subsequent population dynamics of animals, and can be used as potential targets for alleviating stress-related aging in humans exposed to high-density crowding stress.
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Affiliation(s)
- Xiaoming Xu
- State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Da Zhang
- State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Hanyi Zhu
- State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Guang‐hui Liu
- Institute for Stem cell and RegenerationCASBeijing100049China
- State Key Laboratory of Membrane BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100101China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and RodentsInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
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12
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Peng X, Yao S, Huang J, Zhao Y, Chen H, Chen L, Yu Z. Alterations in bacterial community dynamics from noncancerous to Gastric cancer. Front Microbiol 2023; 14:1138928. [PMID: 36970687 PMCID: PMC10034189 DOI: 10.3389/fmicb.2023.1138928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Gastric microbiome has been shown to contribute to gastric carcinogenesis, understanding how alterations in gastric microbiome is helpful to the prevention and treatment of gastric cancer (GC). However, few studies have focused on the change of microbiome during the gastric carcinogenesis. In this study, the microbiome of gastric juice samples from healthy control (HC), gastric precancerous lesions (GPL) and gastric cancer (GC) was investigated by 16S rRNA gene sequencing. Our results showed that the alpha diversity of patients with GC was significantly lower than other groups. Compared to other groups, some genera in GC group were shown to be up-regulated (e.g., Lautropia and Lactobacillus) and down-regulated (e.g., Peptostreptococcus and Parvimonas). More importantly, the emergence of Lactobacillus was closely related to the occurrence and development of GC. Moreover, the microbial interactions and networks in GPL exhibited higher connectivity, complexity and lower clustering property, while GC showed the opposite trend. Taken together, we suggest that changes in the gastric microbiome are associated with GC and perform a key function in maintaining the tumor microenvironment. Therefore, our findings will provide new ideas and references for the treatment of GC.
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Affiliation(s)
- Xuan Peng
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Siqi Yao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jing Huang
- Department of Medical Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yiming Zhao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Hao Chen
- Department of Medical Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Liyu Chen
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- Liyu Chen,
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Zheng Yu,
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13
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Yang J, Xu J, Ling Z, Zhou X, Si Y, Liu X, Ji F. Prognostic effects of the gastric mucosal microbiota in gastric cancer. Cancer Sci 2023; 114:1075-1085. [PMID: 36403134 PMCID: PMC9986079 DOI: 10.1111/cas.15661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/22/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors with a high incidence and mortality. Microbiota play a significant role in human health and disease. We aimed to investigate the prognostic value of the gastric microbiota in different stomach microhabitats. We used our previously published 16S rRNA gene sequence data. We retrospectively enrolled a cohort of 132 patients with GC with complete prognostic information and selected 78 normal tissues, 49 peritumoral tissues, and 112 tumoral tissues for microbiota analysis. Patients with different prognoses showed different gastric microbiota compositions and diversity. The association network of the abundant gastric microbiota was more complicated in patients with poor prognoses. In the peritumoral microhabitat of patients with good prognoses, Helicobacter was significantly increased, whereas Halomonas and Shewanella were significantly decreased relative to that in the peritumoral microhabitat of patients with poor prognoses. PiCRUSt analysis revealed that the peritumoral microbiota had more different Kyoto Encyclopedia of Genes and Genomes pathways than did the tumoral and normal microbiota. This study evaluated the long-term prognostic value of the gastric mucosal microbiota in patients with GC. These findings suggested that the characteristic alterations of the gastric mucosal microbiota may be markers for clinical outcomes in these patients.
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Affiliation(s)
- Jinpu Yang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jiaren Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, Hangzhou, China
| | - Xinxin Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yongqiang Si
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaosun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
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14
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Wei Q, Zhang Q, Wu Y, Han S, Yin L, Zhang J, Gao Y, Shen H, Zhuang J, Chu J, Liu J, Wei Y. Analysis of bacterial diversity and community structure in gastric juice of patients with advanced gastric cancer. Discov Oncol 2023; 14:7. [PMID: 36662326 PMCID: PMC9860007 DOI: 10.1007/s12672-023-00612-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The occurrence and development of gastric cancer are related to microorganisms, which can be used as potential biomarkers of gastric cancer. OBJECTIVE To screen the microbiological markers of gastric cancer from the microorganisms of gastric juice. METHODS Gastric juice samples were collected from 61 healthy people and 78 patients with gastric cancer (48 cases of early gastric cancer and 30 cases of advanced gastric cancer). The bacterial 16 S rRNA V1-V4 region of gastric juice samples was sequenced. The Shannon index, Simpson index, Ace index and Chao index were used to analyze the diversity of gastric juice samples. The RDP classifier Bayesian algorithm was used to analyze the community structure of 97% OTU representative sequences with similar levels. Linear discriminant analysis and ST-test were used to analyze the differences. Six machine learning algorithms, including the logistic regression algorithm, random forest algorithm, neural network algorithm, support vector machine algorithm, Catboost algorithm and gradient lifting tree algorithm, were used to construct risk prediction models for gastric cancer and advanced gastric cancer. RESULTS The microbiota diversity and the abundance of bacteria was different in the healthy group, early gastric cancer and advanced gastric cancer (P < 0.05). The top five abundant bacteria among the three groups were Streptococcus, Rhodococcus, Prevotella, Pseudomonas and Helicobacter. Bacterial flora such as Streptococcus, Rhodococcus and Ochrobactrum were significantly different between the healthy group and the gastric cancer group. The accuracy of the random forest prediction model is the highest (82.73% correct). The bacteria with the highest predictive value included Streptococcus, Lactobacillus and Ochrobactrum. The abundance of bacteria such as Fusobacterium, Capnocytophaga, Atopobium, Corynebacterium was high in the advanced gastric cancer group. CONCLUSION Gastric juice bacteria can be used as potential biomarkers to predict the occurrence and development of gastric cancer.
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Affiliation(s)
- Qiang Wei
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Qi Zhang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Yinhang Wu
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuwen Han
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, People's Republic of China
| | - Lei Yin
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Jinyu Zhang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Yuhai Gao
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Hong Shen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Jing Zhuang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China
| | - Jian Chu
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Jiang Liu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China.
| | - Yunhai Wei
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Zhejiang Province, 313000, Huzhou, People's Republic of China.
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15
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Mannion A, Sheh A, Shen Z, Dzink-Fox J, Piazuelo MB, Wilson KT, Peek R, Fox JG. Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America. Gut Microbes 2023; 15:2186677. [PMID: 36907988 PMCID: PMC10026914 DOI: 10.1080/19490976.2023.2186677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.
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Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard Peek
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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16
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Koga Y. Microbiota in the stomach and application of probiotics to gastroduodenal diseases. World J Gastroenterol 2022; 28:6702-6715. [PMID: 36620346 PMCID: PMC9813937 DOI: 10.3748/wjg.v28.i47.6702] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/19/2022] Open
Abstract
The stomach is a hostile environment for most microbes because strong gastric acid kills indigenous microorganisms. Thus, the mass of indigenous microbes detected by traditional culturing method in a highly acidic stomach is reported to be very small. However, in a stomach with less acidity due to atrophic changes of the gastric mucosa, the number of live gastric microbiota dramatically increases and their composition changes. A probiotic is defined as a live microorganism that, when administered in adequate amounts, confers a health benefit on the host. The administration of probiotics to the stomach has thus far been considered impractical, mainly due to the strong acidity in the stomach. The identification of candidate probiotic strains with sufficient resistance to acidity and the ability to achieve close proximity to the gastric mucosa could enable the application of probiotics to the stomach. The utilization of probiotics alone for Helicobacter pylori (H. pylori) infection significantly improves gastric mucosal inflammation and decreases the density of H. pylori on the mucosa, although complete eradication of H. pylori has not yet been demonstrated. The use of probiotics in combination with antimicrobial agents significantly increases the H. pylori eradication rate, especially when the H. pylori strains are resistant to antimicrobial agents. While H. pylori has been considered the most important pathogenic bacterium for the development of gastric cancer, bacteria other than H. pylori are also suggested to be causative pathogens that promote the development of gastric cancer, even after the eradication of H. pylori. Increased non-H. pylori Gram-negative bacteria in the stomach with weak acidity accompanying atrophic gastritis may perpetuate gastric mucosal inflammation and accelerate carcinogenic progression, even after H. pylori eradication. Probiotics restore the acidity in this stomach environment and may therefore prevent the development of gastric cancer by termination of Gram-negative bacteria-induced inflammation. Functional dyspepsia (FD) is defined as the presence of symptoms that are thought to originate in the gastroduodenal region in the absence of any organic, systematic or metabolic diseases. Accumulating evidence has pointed out the duodenum as a target region underlying the pathophysiology of FD. A randomized placebo-controlled clinical trial using a probiotic strain (LG21) demonstrated a significant improving effect on major FD symptoms. One of the possible mechanisms of this effect is protection of the duodenal mucosa from injurious intestinal bacteria through the resolution of small intestinal bacterial over growth.
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Affiliation(s)
- Yasuhiro Koga
- Japanese Society for Probiotic Science, Isehara 259-1143, Japan
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17
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Ramai D, Salati M, Pomati G, Amoroso C, Facciorusso A, Botticelli A, Ghidini M. Antibiotics, the microbiome and gastrointestinal cancers: A causal interference? Curr Opin Pharmacol 2022; 67:102315. [PMID: 36351361 DOI: 10.1016/j.coph.2022.102315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022]
Abstract
Our understanding of the gut microbiota has significantly evolved over the last two decades. Advances in the analysis of the gut microbiome continues to reveal complex microbial communities and discoveries about their role in health and diseases, including cancer development, are continuously growing. In addition, research has demonstrated that the use of antibiotics can modulate the gut microbiota composition negatively and influence cancer treatment outcomes, suggesting that antibiotics should be avoided if possible. In this article, we review the role of the gut microbiota in the formation of GI cancers. We show that specific bacterial populations can positively or negatively affect cancer formation with specific attention given to gastric and colorectal cancer. We also review the role of microbial-targeted therapies on cancer treatment outcomes.
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Affiliation(s)
- Daryl Ramai
- Division of Gastroenterology and Hepatology, University of Utah Health, Salt Lake City, UT, USA
| | - Massimiliano Salati
- Department of Oncology and Hematology, Division of Oncology, University Hospital of Modena, Modena, Italy
| | - Giulia Pomati
- Department of Molecular Medicine, Sapienza University of Rome, Italy
| | - Chiara Amoroso
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Facciorusso
- Gastroenterology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Andrea Botticelli
- Department of Radiological, Oncological, Pathological Department, La Sapienza, University of Rome, Policlinico Umberto I, Rome, Italy
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
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18
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Li J, Chen D, Yu B, He J, Huang Z, Zheng P, Mao X, Li H, Yu J, Luo J, Yan H, Luo Y. Batch and sampling time exert a larger influence on the fungal community than gastrointestinal location in model animals: A meaningful case study. Front Nutr 2022; 9:1021215. [PMID: 36419550 PMCID: PMC9676510 DOI: 10.3389/fnut.2022.1021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Fungi play a fundamental role in the intestinal ecosystem and health, but our knowledge of fungal composition and distribution in the whole gastrointestinal tract (GIT) is very limited. The physiological similarity between humans and pigs in terms of digestive and associated metabolic processes places, the pig in a superior position over other non-primate models. Here, we aimed to characterize the diversity and composition of fungi in the GIT of pigs. Using high-throughput sequencing, we evaluated the fungal community in different locations of GIT of 11 pigs with 128.41 ± 1.25 kg body weight acquired successively. Among them, five pigs are sacrificed in April 2019 (Batch 1) and the other six are sacrificed in January 2020 (Batch 2). All subjects with similar genetic backgrounds, housing, management, and diet. Finally, no significant difference is found in the α-diversity (Richness) of the fungal community among all intestinal segments. Basidiomycota and Ascomycota are the two predominant fungal phyla, but Batch 1 harbored a notably high abundance of Basidiomycota and Batch 2 harbored a high abundance of Ascomycota. Moreover, the two batches harbored completely different fungal compositions and core fungal genera. FUNGuild (Fungal Functional Guild) analysis revealed that most of the fungal species present in the GIT are saprotroph, plant pathogen, and animal endosymbiont. Our study is the first to report that even under the same condition, large variations in fungal composition in the host GIT still occur from batch-to-batch and sampling time. The implications of our observations serve as references to the development of better models of the human gut.
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Gut Microbiota Dysbiosis in the Development and Progression of Gastric Cancer. JOURNAL OF ONCOLOGY 2022; 2022:9971619. [PMID: 36072968 PMCID: PMC9441395 DOI: 10.1155/2022/9971619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022]
Abstract
Objectives This study aims to explore gut microbiota dysbiosis in the histological stages of gastric cancer (GC). Methods Feces samples and clinical characteristics were collected from patients with different stages of GC, including 15 superficial gastritis (SG), 13 atrophic gastritis (AG), 8 gastric mucosal atypical hyperplasia (GMAH), and 15 advanced GC cases. The diversity and composition of gut microbiota among the four groups were determined by sequencing the V4 region of bacterial 16S rRNA genes. Results Reduced gut microbial alpha diversity and altered dissimilarity of the microbial community structure were found among the four groups. In addition, 18 species, 6 species, 6 species, and 16 species of bacteria were enriched in the SG, AG, GMAH, and GC groups, respectively, using the linear discriminant analysis (LDA) effect size (LEfSe) analyses. Besides, we found that two new genera, Scardovia and Halomonas, are associated with GC and the metabolic pathways of Genetic information processing and Circulatory System were more abundant in the GC group compared with noncancer groups. Conclusions We identified differences in microbial compositional changes across stages of GC. Six genera and two metabolic pathways were more abundant in the GC group than noncancer groups, suggesting that these findings may contribute to the therapy strategies in GC in the near feature.
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20
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Hosseini K, Ahangari H, Chapeland-leclerc F, Ruprich-Robert G, Tarhriz V, Dilmaghani A. Role of Fungal Infections in Carcinogenesis and Cancer Development: A Literature Review. Adv Pharm Bull 2022; 12:747-756. [PMID: 36415634 PMCID: PMC9675916 DOI: 10.34172/apb.2022.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/02/2021] [Accepted: 09/27/2021] [Indexed: 06/11/2024] Open
Abstract
Cancer is a serious debilitating disease and one of the most common causes of death. In recent decades the high risk of various cancers enforced scientists to discover novel prevention and treatment methods to diminish the mortality of this terrifying disease. Accordingly, its prevention can be possible in near future. Based on epidemiological evidence, there is a clear link between pathogenic fungal infections and cancer development. This association is often seen in people with weakened immune systems such as the elderly and people with acquired immunodeficiency (AIDS). Carcinoma in these people is first seen chronically and then acutely. Although the different genetic and environmental risk factors are involved in carcinogenesis, one of the most important risk factors is fungal species and infections associating with cancers etiology. Now it is known that microbial infection is responsible for initiating 2.2 million new cancer cases. In this way, many recent studies have focused on investigating the role and mechanism of fungal infections in diverse cancers occurrence. This review provides a comprehensive framework of the latest clinical findings and the association of fungal infections with versatile cancers including esophageal, gastric, colorectal, lung, cervical, skin, and ovarian cancer.
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Affiliation(s)
- Kamran Hosseini
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Ahangari
- Department of Food Science and Technology, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Florence Chapeland-leclerc
- Université de Paris, Faculté des Sciences, Laboratoire Interdiciplinaire des Energies de Demain (LIED), UMR 8236 CNRS, F-75013, Paris, France
| | - Gwenael Ruprich-Robert
- Université de Paris, Faculté des Sciences, Laboratoire Interdiciplinaire des Energies de Demain (LIED), UMR 8236 CNRS, F-75013, Paris, France
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Bio-Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Azita Dilmaghani
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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21
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Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ. Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling. Genome Res 2022; 32:1112-1123. [PMID: 35688483 DOI: 10.1101/gr.276482.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.
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Affiliation(s)
- Yichen Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Sheba Medical Center, Ramat Gan 52621, Israel
| | - Xiaochang Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Elaine Wolfe
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China.,Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen 518001, China.,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
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22
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Ferreira EO, Lagacé-Wiens P, Klein J. Campylobacter concisus gastritis masquerading as Helicobacter pylori on gastric biopsy. Helicobacter 2022; 27:e12864. [PMID: 34820966 DOI: 10.1111/hel.12864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/01/2021] [Accepted: 11/07/2021] [Indexed: 12/09/2022]
Abstract
OBJECTIVE Campylobacter concisus is a Gram-negative rod closely related to Helicobacter pylori. We sought to identify gastric biopsies positive for C. concisus that had been misdiagnosed as H. pylori gastritis in our routine surgical pathology practice. MATERIALS AND METHODS We performed a retrospective review of gastric biopsies in our regional microbiology and pathology electronic records to identify cases that were submitted for H. pylori testing in which C. consicus was identified on culture and how many had concurrent biopsies sent to pathology for histologic assessment over a two-year period (2017-2018). Pathologic findings in the gastric biopsies were reviewed and immunohistochemical staining for H. pylori was performed. RESULTS 50 of 2191 gastric biopsy specimens submitted to microbiology in 2017-18 grew C. concisus (2.3%), compared to 168 in which H. pylori was identified (7.7%). Twenty-eight cases had concurrent histology. A total of four cases (three from 2017 and one from 2018) demonstrated organisms morphologically identical to H. pylori in the H&E sections, of which all were H. pylori immunoreactive. CONCLUSIONS Our case series is the first to demonstrate that C. concisus can mimic H. pylori gastritis in routine biopsy pathology.
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Affiliation(s)
- Elizabeth O Ferreira
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philippe Lagacé-Wiens
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Julianne Klein
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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23
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Cui J, Hou S, Liu B, Yang M, Wei L, Du S, Li S. Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. BMC Med Genomics 2022; 15:60. [PMID: 35300688 PMCID: PMC8932003 DOI: 10.1186/s12920-022-01209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/01/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In traditional Chinese medicine, it is believed that the "tongue coating is produced by fumigation of stomach gas", and that tongue coating can reflect the health status of humans, especially stomach health. Therefore, studying the relationship between the microbiome of the tongue coating and the gastric fluid is of great significance for understanding the biological basis of tongue diagnosis. METHODS This paper detected the microbiomes of the tongue coating and the gastric fluid in 35 gastritis patients using metagenomic sequencing technology, systematically constructed the microbial atlas of tongue coating and gastric juice, and first described the similar characteristics between the two sites. RESULTS There was a significant correlation between tongue coating and gastric juice in terms of microbial species composition and overall diversity. In terms of species composition, it was found that the two sites were dominated by five phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, and that most of the gastric microbial species could be detected from the patient's own tongue coating. In terms of overall diversity, a significant correlation was found between the alpha diversity of the tongue coating microbiome and the gastric juice microbiome. Furthermore, in terms of abundance, 4 classes, 2 orders, 4 families, 18 genera and 46 species were found to significantly correlate between the tongue coating and the gastric fluid. CONCLUSIONS The results provide microbiome-based scientific evidence for tongue diagnosis, and offer a new perspective for understanding the biological basis of tongue diagnosis.
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Affiliation(s)
- Jiaxing Cui
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China.,China Industrial Control Systems Cyber Emergency Response Team, Beijing, 100040, China
| | - Siyu Hou
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Bing Liu
- Beijing Lotus BioMedical Technology Co., Ltd., Beijing, 102206, China
| | - Mingran Yang
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Shiyu Du
- China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China. .,School of Life Sciences and Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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24
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Role of Gastric Microorganisms Other than Helicobacter pylori in the Development and Treatment of Gastric Diseases. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6263423. [PMID: 35321071 PMCID: PMC8938066 DOI: 10.1155/2022/6263423] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 12/15/2022]
Abstract
The microenvironment in the stomach is different from other digestive tracts, mainly because of the secretion of gastric acid and digestive enzymes, bile reflux, special mucus barrier, gastric peristalsis, and so on, which all contribute to the formation of antibacterial environment. Microecological disorders can lead to gastric immune disorders or lead to the decrease of dominant bacteria and the increase of the abundance and virulence of pathogenic microorganisms and then promote the occurrence of diseases. The body performs its immune function through innate and adaptive immunity and maintains microbial balance through the mechanism of immune homeostasis. Microecological imbalance can lead to the invasion of pathogenic microorganisms and damage mucosal barrier and immune system. The coexistence of gastric microorganisms (including viruses and fungi) may play a synergistic or antagonistic role in the pathogenesis of gastric diseases. Probiotics have the ability to compete with intestinal pathogens, increase the secretion of immunoglobulin A (IgA), stimulate the production of mucin, bacteriocin, and lactic acid, regulate the expression and secretion of cytokines, and regulate the growth of microbiota, which all have beneficial effects on the host microbial environment. At present, most studies focused on Helicobacter pylori, ignoring other stomach microbes and the overall stomach microecology. So, in this article, we reviewed advances in human gastric microecology, the relationship between gastric microecology and immunity or gastric diseases, and the treatment of probiotics in gastric diseases, in order to explore new area for further study of gastric microorganisms and treatment of gastric diseases.
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25
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Lu Y, Liu H, Yang K, Mao Y, Meng L, Yang L, Ouyang G, Liu W. A comprehensive update: gastrointestinal microflora, gastric cancer and gastric premalignant condition, and intervention by traditional Chinese medicine. J Zhejiang Univ Sci B 2022; 23:1-18. [PMID: 35029085 DOI: 10.1631/jzus.b2100182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
With the recent upsurge of studies in the field of microbiology, we have learned more about the complexity of the gastrointestinal microecosystem. More than 30 genera and 1000 species of gastrointestinal microflora have been found. The structure of the normal microflora is relatively stable, and is in an interdependent and restricted dynamic equilibrium with the body. In recent years, studies have shown that there is a potential relationship between gastrointestinal microflora imbalance and gastric cancer (GC) and precancerous lesions. So, restoring the balance of gastrointestinal microflora is of great significance. Moreover, intervention in gastric premalignant condition (GPC), also known as precancerous lesion of gastric cancer (PLGC), has been the focus of current clinical studies. The holistic view of traditional Chinese medicine (TCM) is consistent with the microecology concept, and oral TCM can play a two-way regulatory role directly with the microflora in the digestive tract, restoring the homeostasis of gastrointestinal microflora to prevent canceration. However, large gaps in knowledge remain to be addressed. This review aims to provide new ideas and a reference for clinical practice.
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Affiliation(s)
- Yuting Lu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301608, China
| | - Huayi Liu
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin 300120, China.
| | - Kuo Yang
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin 300120, China
| | - Yijia Mao
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301608, China
| | - Lingkai Meng
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301608, China
| | - Liu Yang
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin 300120, China
| | - Guangze Ouyang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301608, China
| | - Wenjie Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301608, China
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26
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Yuan Z, Xiao S, Li S, Suo B, Wang Y, Meng L, Liu Z, Yin Z, Xue Y, Zhou L. The impact of Helicobacter pylori infection, eradication therapy, and probiotics intervention on gastric microbiota in young adults. Helicobacter 2021; 26:e12848. [PMID: 34448282 DOI: 10.1111/hel.12848] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/31/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND The impact of probiotics on non-Helicobacter pylori gastric microbiota and its role in microbial restoration after eradication were relatively unknown. We aimed to explore the effect of H. pylori eradication and probiotic intervention on gastric microbiota in young adults. METHODS Fifty-six H. pylori-negative and 95 H. pylori-positive subjects aged 19-30 were included in this study. H. pylori-infected individuals were randomly assigned to quadruple therapy, probiotics supplemented quadruple therapy, or probiotics monotherapy group. Gastric mucosa and gastric juice samples were collected before and 2 months after treatment for 16SrRNA gene sequencing. RESULTS The gastric microbial community structure and composition differed from H. pylori-negative subjects 2 months after successful H. pylori eradication. The α diversity of gastric mucosal microbiota significantly increased and was higher than H. pylori-negative subjects, while the α diversity of gastric juice microbiota decreased and was lower than the H. pylori-negative. After probiotics supplemented eradication treatment, Bifidobacterium was enriched in gastric mucosa, Lactobacillus was enriched in gastric juice, potentially pathogenic bacteria such as Fusobacterium and Campylobacter decreased, and the microbial diversity was closer to that of H. pylori-negative subjects compared to quadruple therapy group. Probiotics monotherapy significantly altered the diversity, community structure, and composition of gastric microbiota but showed no advantage in H. pylori inhibition and upregulating beneficial bacteria such as Bifidobacterium and Lactobacillus and related metabolism pathways. Certain potentially pathogenic bacteria such as Fusobacterium increased after probiotic monotherapy. CONCLUSION H. pylori eradication significantly disrupted gastric microbiota in young adults and could not be restored in a short time. Probiotics supplementation partially helped restore the gastric dysbiosis caused by eradication therapy, but it might be unnecessary for H. pylori-infected young adults to take probiotics alone.
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Affiliation(s)
- Ziying Yuan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Shiyu Xiao
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Sizhu Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Baojun Suo
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Ye Wang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Lingmei Meng
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Zuojing Liu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Zhihao Yin
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Yan Xue
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
| | - Liya Zhou
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, China
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27
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Li Q, Wu W, Gong D, Shang R, Wang J, Yu H. Propionibacterium acnes overabundance in gastric cancer promote M2 polarization of macrophages via a TLR4/PI3K/Akt signaling. Gastric Cancer 2021; 24:1242-1253. [PMID: 34076786 DOI: 10.1007/s10120-021-01202-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Eradication of Helicobacter pylori (H. pylori) could not completely prevent the progression of gastric cancer (GC), suggesting that non-H. pylori bacteria may participate in the carcinogenesis of GC. The dysbiosis of microbiota in the stomach of GC has gradually been investigated, while the detailed mechanism that promotes GC in this process has not been elucidated. We aimed to identify a non-H. pylori bacteria that contribute to GC. DESIGN GC tissues and adjacent normal tissues were collected to identify bacteria that significantly increased in GC tissues by 16S rRNA gene sequencing and fluorescence in situ hybridization (FISH) analysis. CCK8, wound healing assay, and trans-well assay were performed to analyze the tumor-promoting effect of this bacteria. Next, we detailed the mechanism for tumor-promoting effect of the bacteria by immunofluorescence, RT-qPCR, and western-blotting analysis. RESULTS Comparing the microbial community from GC tissues and adjacent normal tissues, we found that Propionibacterium acnes (P. acnes) significantly increased in GC tissues, especially in H. pylori-negative tissues. We further found that the abundance of P. acnes correlated with TNM stages of GC patients. Interestingly, condition medium (CM) from P. acnes-primed macrophages promoted migration of GC cells, while P. acnes only could not. We next proved that P. acnes triggers M2 polarization of macrophages via TLR4/PI3K/Akt signaling. CONCLUSIONS Together, our finding identified that P. acnes could be a possible agent for the progression of GC besides H. pylori. M2 polarization of macrophages could be promoted by P. acnes via TLR4/PI3K/Akt signaling, thus triggers the progression of GC.
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Affiliation(s)
- Qing Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Key Laboratory of Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision, Renmin Hospital of Wuhan University, Jiefang Rd. 238, Wuhan, 430060, People's Republic of China
| | - Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Dexin Gong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Key Laboratory of Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision, Renmin Hospital of Wuhan University, Jiefang Rd. 238, Wuhan, 430060, People's Republic of China
| | - Renduo Shang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Key Laboratory of Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision, Renmin Hospital of Wuhan University, Jiefang Rd. 238, Wuhan, 430060, People's Republic of China
| | - Jing Wang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Key Laboratory of Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.,Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision, Renmin Hospital of Wuhan University, Jiefang Rd. 238, Wuhan, 430060, People's Republic of China
| | - Honggang Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China. .,Hubei Key Laboratory of Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China. .,Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision, Renmin Hospital of Wuhan University, Jiefang Rd. 238, Wuhan, 430060, People's Republic of China.
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28
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Jiang Y, Meng F, Liu Y, Zheng L, Ye S, Zhang J. Does Helicobacter pylori infection affect the structure of bacteria in the gastric mucosa and fluid in patients with chronic antral gastritis? J GEN APPL MICROBIOL 2021; 67:179-185. [PMID: 34053980 DOI: 10.2323/jgam.2020.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study aimed to evaluate the composition of the gastric microbiota in the gastric mucosa and gastric fluid of patients with chronic antral gastritis. Specifically, we sought to determine whether Helicobacter pylori (Hp) infection changes the bacterial community in the gastric mucosa or alters the microbiota in the gastric fluid. The bacterial community at another site in the stomach was also investigated. DNA was extracted from 160 samples collected from 40 patients with chronic antral gastritis (20 Hp-positive and 20 Hp-negative cases). Three tissue samples of the gastric mucosa (gastric angle, body, and antral mucosa) and one tube of gastric fluid were collected from every patient. A 16S rRNA amplification library was created, and high-throughput sequencing was performed. A profile of the community composition was obtained using bioinformatics methods, including cluster, taxonomy, and diversity analyses. Analysis of the gastric bacterial community revealed that the community compositions of the gastric mucosa and gastric fluid of patients without Hp are similar to but show differences from those of Hp-positive patients. The microbiota in Hp-positive patients exhibited reduced microbial diversity, and the gastric fluid of these patients contained a small proportion of Hp. The richness of Leptotrichia in mucosal samples was greater than that in gastric fluid samples from Hp-negative patients with chronic antral gastritis. Hp changes the growth of other microbiota in the mucosa and affects the microbiota in the gastric fluid of patients with chronic antral gastritis. In addition to Hp, the presence of other bacteria might be related to the development of chronic antral gastritis.
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Affiliation(s)
- Yang Jiang
- Department of Science and Education, Tongde Hospital of Zhejiang Province
| | - Fei Meng
- Department of Research service, Zhiyuan Medical Inspection Institute CO., LTD
| | - Ying Liu
- Department of Basic Sciences, Zhejiang Tongji Vocational College of Science and Technology
| | - Liyun Zheng
- Department of Research service, Zhiyuan Medical Inspection Institute CO., LTD
| | - Shufang Ye
- Department of Gastroenterology, People's Hospital of Lishui City
| | - Jianmei Zhang
- Department of Gastroenterology, People's Hospital of Lishui City
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29
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Chen Y, Guo J, Chen C, Shi D, Fang D, Ji F, Li L. Characterization of the Gastric Mucosal Microbiota in Patients with Liver Cirrhosis and Its Associations with Gastrointestinal Symptoms. ENGINEERING 2021; 7:507-514. [DOI: 10.1016/j.eng.2020.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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30
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Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG, Sterbini FP, Masucci L, Cammarota G, Ianiro G, Spuul P, Schroeder M, Grill SW, Parsons BN, Pritchard DM, Posteraro B, Sanguinetti M, Gasbarrini G, Gasbarrini A, Cannistraci CV. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nat Commun 2021; 12:1926. [PMID: 33771992 PMCID: PMC7997970 DOI: 10.1038/s41467-021-22135-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
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Affiliation(s)
- Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum Munchen, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UK
| | - Antonio G Zippo
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Luca Masucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pirjo Spuul
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Stephan W Grill
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Brunella Posteraro
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany.
- Center for Complex Network Intelligence (CCNI) at Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, Beijing, China.
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Yang J, Zhou X, Liu X, Ling Z, Ji F. Role of the Gastric Microbiome in Gastric Cancer: From Carcinogenesis to Treatment. Front Microbiol 2021; 12:641322. [PMID: 33790881 PMCID: PMC8005548 DOI: 10.3389/fmicb.2021.641322] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/22/2021] [Indexed: 01/10/2023] Open
Abstract
The development of sequencing technology has expanded our knowledge of the human gastric microbiome, which is now known to play a critical role in the maintenance of homeostasis, while alterations in microbial community composition can promote the development of gastric diseases. Recently, carcinogenic effects of gastric microbiome have received increased attention. Gastric cancer (GC) is one of the most common malignancies worldwide with a high mortality rate. Helicobacter pylori is a well-recognized risk factor for GC. More than half of the global population is infected with H. pylori, which can modulate the acidity of the stomach to alter the gastric microbiome profile, leading to H. pylori-associated diseases. Moreover, there is increasing evidence that bacteria other than H. pylori and their metabolites also contribute to gastric carcinogenesis. Therefore, clarifying the contribution of the gastric microbiome to the development and progression of GC can lead to improvements in prevention, diagnosis, and treatment. In this review, we discuss the current state of knowledge regarding changes in the microbial composition of the stomach caused by H. pylori infection, the carcinogenic effects of H. pylori and non-H. pylori bacteria in GC, as well as the potential therapeutic role of gastric microbiome in H. pylori infection and GC.
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Affiliation(s)
- Jinpu Yang
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinxin Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaosun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Abstract
Within the last decade, our understanding of the role of the intestinal microbiota in health and disease has rapidly increased due to significant advances in next-generation sequencing technologies. Scientists have discovered more and more gut microbes with supposedly "beneficial" roles for human health and are starting to identify the underlying mechanisms. In this review, we summarize the latest knowledge about the human intestinal microbiota, including the intestinal bacteriome, virome and mycobiome. We discuss the function that recent studies attribute to the intestinal microbiota in preventing or controlling selected diseases and present recent research on biotherapeutic approaches to control these diseases.
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Affiliation(s)
- Pipat Piewngam
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
| | - François De Mets
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
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Bubeck AM, Preiss L, Jung A, Dörner E, Podlesny D, Kulis M, Maddox C, Arze C, Zörb C, Merkt N, Fricke WF. Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection. Sci Rep 2020; 10:13828. [PMID: 32796896 PMCID: PMC7427798 DOI: 10.1038/s41598-020-70535-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Wine is a globally produced, marketed and consumed alcoholic beverage, which is valued for its aromatic and qualitative complexity and variation. These properties are partially attributable to the bacterial involvement in the fermentation process. However, the organizational principles and dynamic changes of the bacterial wine microbiota remain poorly understood, especially in the context of red and white wine variations and environmental stress factors. Here, we determined relative and absolute bacterial microbiota compositions from six distinct cultivars during the first week of fermentation by quantitative and qualitative 16S rRNA gene amplification and amplicon sequencing. All wines harboured complex and variable bacterial communities, with Tatumella as the most abundant genus across all batches, but red wines were characterized by higher bacterial diversity and increased relative and absolute abundance of lactic and acetic acid bacteria (LAB/AAB) and bacterial taxa of predicted environmental origin. Microbial diversity was positively correlated with plant-derived DNA concentrations in the wine and Botrytis cinerea infection before harvest. Our findings suggest that exogenous factors, such as procedural differences between red and white wine production and environmental stress on grape integrity, can increase bacterial diversity and specific bacterial taxa in wine, with potential consequences for wine quality and aroma.
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Affiliation(s)
- Alena M Bubeck
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Lena Preiss
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Anna Jung
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Elisabeth Dörner
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Daniel Podlesny
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Marija Kulis
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Cynthia Maddox
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Personal Genome Diagnostics, Baltimore, MD, USA
| | - Cesar Arze
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Ring Therapeutics, Cambridge, MA, USA
| | - Christian Zörb
- Department of Plant Quality and Viticulture, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Nikolaus Merkt
- Department of Plant Quality and Viticulture, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany. .,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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The Role of Gastric Mucosal Immunity in Gastric Diseases. J Immunol Res 2020; 2020:7927054. [PMID: 32775468 PMCID: PMC7396052 DOI: 10.1155/2020/7927054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 12/17/2022] Open
Abstract
Gastric mucosa plays its immune function through innate and adaptive immunity by recruiting immune cells and releasing corresponding cytokines, which have an inseparable relationship with gastric diseases. Whether infective gastric diseases caused by Helicobacter pylori, Epstein-Barr virus or other microbe, noninfective gastric diseases, or gastric cancer, gastric mucosal immunity plays an important role in the occurrence and development of the disease. Understanding the unique immune-related tissue structure of the gastric mucosa and its role in immune responses can help prevent gastric diseases or treat them through immunotherapy. In this review, we summarize the basic feature of gastric mucosal immunity and its relationship with gastric diseases to track the latest progress of gastric mucosal immunity, update relevant knowledge and provide theoretical reference for the prevention and treatment of gastric diseases based on the gastric mucosal immunity.
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Immune status, and not HIV infection or exposure, drives the development of the oral microbiota. Sci Rep 2020; 10:10830. [PMID: 32616727 PMCID: PMC7331591 DOI: 10.1038/s41598-020-67487-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022] Open
Abstract
Even with antiretroviral therapy, children born to HIV-infected (HI) mothers are at a higher risk of early-life infections and morbidities including dental disease. The increased risk of dental caries in HI children suggest immune-mediated changes in oral bacterial communities, however, the impact of perinatal HIV exposure on the oral microbiota remains unclear. We hypothesized that the oral microbiota of HI and perinatally HIV-exposed-but-uninfected (HEU) children will significantly differ from HIV-unexposed-and-uninfected (HUU) children. Saliva samples from 286 child-participants in Nigeria, aged ≤ 6 years, were analyzed using 16S rRNA gene sequencing. Perinatal HIV infection was significantly associated with community composition (HI vs. HUU—p = 0.04; HEU vs. HUU—p = 0.11) however, immune status had stronger impacts on bacterial profiles (p < 0.001). We observed age-stratified associations of perinatal HIV exposure on community composition, with HEU children differing from HUU children in early life but HEU children becoming more similar to HUU children with age. Our findings suggest that, regardless of age, HIV infection or exposure, low CD4 levels persistently alter the oral microbiota during this critical developmental period. Data also indicates that, while HIV infection clearly shapes the developing infant oral microbiome, the effect of perinatal exposure (without infection) appears transient.
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Chicken Intestinal Mycobiome: Initial Characterization and Its Response to Bacitracin Methylene Disalicylate. Appl Environ Microbiol 2020; 86:AEM.00304-20. [PMID: 32358003 DOI: 10.1128/aem.00304-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal (GI) tract harbors a diverse population of microorganisms. While much work has been focused on the characterization of the bacterial community, very little is known about the fungal community, or mycobiota, in different animal species and chickens in particular. Here, we characterized the biogeography of the mycobiota along the GI tract of day 28 broiler chicks and further examined its possible shift in response to bacitracin methylene disalicylate (BMD), a commonly used in-feed antibiotic, through Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes. Out of 124 samples sequenced, we identified a total of 468 unique fungal features that belong to four phyla and 125 genera in the GI tract. Ascomycota and Basidiomycota represented 90% to 99% of the intestinal mycobiota, with three genera, i.e., Microascus, Trichosporon, and Aspergillus, accounting for over 80% of the total fungal population in most GI segments. Furthermore, these fungal genera were dominated by Scopulariopsis brevicaulis (Scopulariopsis is the anamorph form of Microascus), Trichosporon asahii, and two Aspergillus species. We also revealed that the mycobiota are more diverse in the upper than lower GI tract. The cecal mycobiota transitioned from being S. brevicaulis dominant on day 14 to T. asahii dominant on day 28. Furthermore, 2-week feeding of 55 mg/kg BMD tended to reduce the cecal mycobiota α-diversity. Taken together, we provided a comprehensive biogeographic view and succession pattern of the chicken intestinal mycobiota and its influence by BMD. A better understanding of intestinal mycobiota may lead to the development of novel strategies to improve animal health and productivity.IMPORTANCE The intestinal microbiota is critical to host physiology, metabolism, and health. However, the fungal community has been often overlooked. Recent studies in humans have highlighted the importance of the mycobiota in obesity and disease, making it imperative that we increase our understanding of the fungal community. The significance of this study is that we revealed the spatial and temporal changes of the mycobiota in the GI tract of the chicken, a nonmammalian species. To our surprise, the chicken intestinal mycobiota is dominated by a limited number of fungal species, in contrast to the presence of hundreds of bacterial taxa in the bacteriome. Additionally, the chicken intestinal fungal community is more diverse in the upper than the lower GI tract, while the bacterial community shows an opposite pattern. Collectively, this study lays an important foundation for future work on the chicken intestinal mycobiome and its possible manipulation to enhance animal performance and disease resistance.
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An anticonvulsive drug, valproic acid (valproate), has effects on the biosynthesis of fatty acids and polyketides in microorganisms. Sci Rep 2020; 10:9300. [PMID: 32518288 PMCID: PMC7283484 DOI: 10.1038/s41598-020-66251-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Valproic acid or valproate (VPA) is an anticonvulsive drug used for treatments of epilepsy, bipolar disorder, and migraine headaches. VPA is also an epigenetic modulator, inhibiting histone deacetylase, and it has been subjected to clinical study for cancer treatment. During the investigation of VPA on a metabolite profile in a fungus, we found that VPA has significant effects on the production of some fatty acids. Further exploration of VPA on fatty acid profiles of microorganisms, fungi, yeast, and bacteria, as well as representative gut microbiome, revealed that VPA could enhance or reduce the production of some fatty acids. VPA was found to induce the production of trans-9-elaidic acid, a fatty acid that was previously reported to have cellular effects in human macrophages. VPA could also inhibit the production of some polyketides produced by a model fungus. The present work suggests that the induction or inhibition of fatty acid biosynthesis by VPA (100 µM) in gut microbiome could give effects to patients treated with VPA because high doses of VPA oral administration (up to 600 mg to 900 mg) are used by patients; the concentration of VPA in the human gut may reach a concentration of 100 µM, which may give effects to gut microorganisms.
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Mucosa microbiome of gastric lesions: Fungi and bacteria interactions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:195-213. [PMID: 32475522 DOI: 10.1016/bs.pmbts.2020.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many components of the gastric non-Helicobacter pylori microbiota have been identified recently thanks to advances in DNA sequencing techniques. Several lines of evidence support the hypothesis that the gastric microbiome is essential for gastric disorders such as gastric cancer. Microbial interactions impact the pathophysiology of various gastric disorders. This chapter provides an overview of recent findings regarding general gastric microbial community profiling, microbial interactions in the stomach, and microbial characteristics in various gastric disorders.
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Gastric cancer: genome damaged by bugs. Oncogene 2020; 39:3427-3442. [PMID: 32123313 PMCID: PMC7176583 DOI: 10.1038/s41388-020-1241-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death worldwide. The role of the microorganisms in gastric tumorigenesis attracts much attention in recent years. These microorganisms include bacteria, virus, and fungi. Among them, Helicobacter pylori (H. pylori) infection is by far the most important risk factor for GC development, with special reference to the early-onset cases. H. pylori targets multiple cellular components by utilizing various virulence factors to modulate the host proliferation, apoptosis, migration, and inflammatory response. Epstein–Barr virus (EBV) serves as another major risk factor in gastric carcinogenesis. The virus protein, EBER noncoding RNA, and EBV miRNAs contribute to the tumorigenesis by modulating host genome methylation and gene expression. In this review, we summarized the related reports about the colonized microorganism in the stomach and discussed their specific roles in gastric tumorigenesis. Meanwhile, we highlighted the therapeutic significance of eradicating the microorganisms in GC treatment.
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Rajilic-Stojanovic M, Figueiredo C, Smet A, Hansen R, Kupcinskas J, Rokkas T, Andersen L, Machado JC, Ianiro G, Gasbarrini A, Leja M, Gisbert JP, Hold GL. Systematic review: gastric microbiota in health and disease. Aliment Pharmacol Ther 2020; 51:582-602. [PMID: 32056247 DOI: 10.1111/apt.15650] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/09/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Helicobacter pylori is the most infamous constituent of the gastric microbiota and its presence is the strongest risk factor for gastric cancer and other gastroduodenal diseases. Although historically the healthy stomach was considered a sterile organ, we now know it is colonised with a complex microbiota. However, its role in health and disease is not well understood. AIM To systematically explore the literature on the gastric microbiota in health and disease as well as the gut microbiota after bariatric surgery. METHODS A systematic search of online bibliographic databases MEDLINE/EMBASE was performed between 1966 and February 2019 with screening in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Randomised controlled trials, cohort studies and observational studies were included if they reported next-generation sequencing derived microbiota analysis on gastric aspirate/tissue or stool samples (bariatric surgical outcomes). RESULTS Sixty-five papers were eligible for inclusion. With the exception of H pylori-induced conditions, overarching gastric microbiota signatures of health or disease could not be determined. Gastric carcinogenesis induces a progressively altered microbiota with an enrichment of oral and intestinal taxa as well as significant changes in host gastric mucin expression. Proton pump inhibitors usage increases gastric microbiota richness. Bariatric surgery is associated with an increase in potentially pathogenic proteobacterial species in patient stool samples. CONCLUSION While H pylori remains the single most important risk factor for gastric disease, its capacity to shape the collective gastric microbiota remains to be fully elucidated. Further studies are needed to explore the intricate host/microbial and microbial/microbial interplay.
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Wang J, Xiong Y, Zhang J, Lu X, Wei G. Naturally selected dominant weeds as heavy metal accumulators and excluders assisted by rhizosphere bacteria in a mining area. CHEMOSPHERE 2020; 243:125365. [PMID: 31759218 DOI: 10.1016/j.chemosphere.2019.125365] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 05/04/2023]
Abstract
Managers need more practical and promising plants for use in heavy metal phytoremediation. Although previous studies have identified the potential of some weeds and microbial strains in phytoremediation, the potential of dominant weeds and the relationship between weeds and their rhizosphere bacterial strains are still unknown. In our study, we examined dominant weeds in the Dabaoshan mine located in Guangdong province, China to test their abilities as heavy metal accumulators and excluders. Results suggest that Ludwigia prostrata exhibited the highest potential for accumulating Cu, Pb and Zn compared with the other plants. Specifically, L. prostrata accumulated 71.58, 130.76 and 454.72 mg kg-1 of Cu, Pb and Zn, respectively; the species' translocation factor of Zn was 2.04, indicating a high accumulation of Zn. In contrast, the Cd translocation factor (TF) of Digitaria sanguinalis was 0.18, significantly lower than that of other plant species examined. Our results suggest that Ludwigia prostrata hyperaccumulates Zn and may also serve as a potential candidate remediation plant for Cu and Pb due to its high absolute accumulation amount of Cu and Pb, while Digitaria sanguinalis may be a potential candidate as a Cd excluder. We also found that rhizosphere bacterial communities were shaped by individual dominant plant species. Chloroflexi was the most dominant phylum in accumulator plant such as Fimbristylis miliacea, while Cyanobacteria was the most dominant phylum in excluder plant such as Digitaria sanguinalis. Our study provides insights for selecting new weedy forbs and grasses, rhizosphere bacterial species and developing approaches for phytoremediation and phytostabilization.
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Affiliation(s)
- Jiaxin Wang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, PR China
| | - Yue Xiong
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, PR China
| | - Jiaen Zhang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, PR China; Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangzhou, 510642, PR China; Guangdong Engineering Research Center for Modern Eco-agriculture and Circular Agriculture, Guangzhou, PR China.
| | - Xuening Lu
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, PR China
| | - Guangchang Wei
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, PR China
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Abstract
Gastric environment has long been considered sterile, but the discovery of Helicobacter pylori (H. pylori) changed such concept in 1982. Over the past few decades, modern techniques have provided insight into microbial communities in the stomach and the interactions between communities, ranging from methods that rely on bacterial culture to the application of macrogenomics and high-throughput sequencing techniques. H. pylori is an important risk factor for gastric disease, but there may be other bacteria involved in the occurrence of gastric disease. This review summarizes the current progress in the understanding of the relationship between gastric microflora and gastric disease.
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Affiliation(s)
- Fang Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Enviroesnment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi Province, China
| | - Tian Liang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Enviroesnment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi Province, China
| | - Yan-Song Li
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Enviroesnment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi Province, China
| | - Su Bai
- Department of Digestive Medicine, Affiliated Hospital of Tibet University for Nationalities, Xianyang 712082, Shaanxi Province, China
| | - Long-Li Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Enviroesnment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi Province, China
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Cui J, Cui H, Yang M, Du S, Li J, Li Y, Liu L, Zhang X, Li S. Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade. Protein Cell 2019; 10:496-509. [PMID: 30478535 PMCID: PMC6588651 DOI: 10.1007/s13238-018-0596-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023] Open
Abstract
The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.
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Affiliation(s)
- Jiaxing Cui
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Hongfei Cui
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Mingran Yang
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Shiyu Du
- China-Japan Friendship Hospital, Beijing, 100029, China
| | - Junfeng Li
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Yingxue Li
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Liyang Liu
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences and Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
| | - Shao Li
- MOE Key Laboratory of Bioinformatics and TCM-X center/Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences and Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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Shen X, Yao YF, Li JY, Li Y. [Human mycobiome and diseases]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2019; 37:314-319. [PMID: 31218869 DOI: 10.7518/hxkq.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing applications, the structure and composition of mycobiome in the mouth, lung, gut, vagina, and skin have been analyzed, and the role of microbiome in diseases has been investigated. Mycobiome also influences the composition of bacteriome and includes key species that maintain the structure and function of microbial communities. Fungi also influence host immune responses. In this review, we summarized the mycobiome com-position at various sites and different diseases and the interactions between fungi-bacteria and fungi-host.
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Affiliation(s)
- Xin Shen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yu-Fei Yao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ji-Yao Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yan Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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The effect of pyridostigmine on small intestinal bacterial overgrowth (SIBO) and plasma inflammatory biomarkers in HIV-associated autonomic neuropathies. J Neurovirol 2019; 25:551-559. [PMID: 31098925 DOI: 10.1007/s13365-019-00756-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Indexed: 01/08/2023]
Abstract
Small intestinal bacterial overgrowth (SIBO) is common among patients with HIV-associated autonomic neuropathies (HIV-AN) and may be associated with increased bacterial translocation and elevated plasma inflammatory biomarkers. Pyridostigmine is an acetylcholinesterase inhibitor which has been used to augment autonomic signaling. We sought preliminary evidence as to whether pyridostigmine could improve proximal gastrointestinal motility, reduce SIBO, reduce plasma sCD14 (a marker of macrophage activation and indirect measure of translocation), and reduce the inflammatory cytokines IL-6 and TNFα in patients with HIV-AN. Fifteen participants with well-controlled HIV, HIV-AN, and SIBO were treated with 8 weeks of pyridostigmine (30 mg PO TID). Glucose breath testing for SIBO, gastric emptying studies (GES) to assess motility, plasma sCD14, IL-6, and TNFα, and gastrointestinal autonomic symptoms were compared before and after treatment. Thirteen participants (87%) experienced an improvement in SIBO following pyridostigmine treatment; with an average improvement of 50% (p = 0.016). There was no change in gastrointestinal motility; however, only two participants met GES criteria for gastroparesis at baseline. TNFα and sCD14 levels declined by 12% (p = 0.004) and 19% (p = 0.015), respectively; there was no significant change in IL-6 or gastrointestinal symptoms. Pyridostigmine may ameliorate SIBO and reduce levels of sCD14 and TNFα in patients with HIV-AN. Larger placebo-controlled studies are needed to definitively delineate how HIV-AN affects gastrointestinal motility, SIBO, and systemic inflammation in HIV, and whether treatment improves clinical outcomes.
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Zhang S, Shi D, Li M, Li Y, Wang X, Li W. The relationship between gastric microbiota and gastric disease. Scand J Gastroenterol 2019; 54:391-396. [PMID: 30945954 DOI: 10.1080/00365521.2019.1591499] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Traditionally, the stomach was believed to be a sterile organ unsuitable for microbiota growth. However, the discovery of H. pylori subverted this conception. With the development of molecular techniques, an abundance of microbiota of great diversity was found in the stomach. In addition, various lines of evidence suggest that the gastric microbiota plays a critical role in the development and progression of the gastric disease.The gastrointestinal microbiome plays an important role in various physiologic and pathologic processes.
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Affiliation(s)
- Shuyi Zhang
- a Endoscopy Center, Tianjin Union Medical Center , Tianjin , China
| | - Dan Shi
- b Tianjin Medical University Graduate School , Tianjin , China
| | - Muran Li
- c Department of gastroenterology , Tianjin Union Medical Center , Tianjin , China
| | - Yanru Li
- a Endoscopy Center, Tianjin Union Medical Center , Tianjin , China
| | - Ximo Wang
- d Tianjin Clinical Medicine Research Centre for ITCWM Acute abdomen Tianjin Hospital of ITCWM Nankai Hospital , Tianjin , China
| | - Wen Li
- a Endoscopy Center, Tianjin Union Medical Center , Tianjin , China.,b Tianjin Medical University Graduate School , Tianjin , China
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Han HS, Lee SY, Oh SY, Moon HW, Cho H, Kim JH. Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis. J Clin Med 2019; 8:E312. [PMID: 30841591 PMCID: PMC6462939 DOI: 10.3390/jcm8030312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
Mucosal inflammation is characterized by neutrophil and mononuclear cell infiltration. This study aimed to determine the gastric and duodenal microbiota associated with histological, endoscopic, and symptomatic gastritis. Dyspeptic adults who presented for evaluation were included. Subjects with either comorbidities or recent drug intake were excluded. Three endoscopic biopsies were obtained from the antrum, body, and duodenum. Next-generation sequencing for 16S ribosomal RNA V1⁻V2 hypervariable regions was performed. The correlation between the composition of microbiota and the degree of inflammatory cell infiltration, endoscopic findings, and Patient Assessment of Gastrointestinal Disorders Symptom Severity Index (PAGI-SYM) score was analyzed. In 98 included subjects, microbial communities in the antrum and body showed Bray⁻Curtis similarity; however, those in the duodenum showed dissimilarity. Histological and endoscopic gastritis was associated with the abundance of Helicobacter pylori and that of commensal bacteria in the stomach. The abundances of Variovorax paradoxus and Porphyromonas gingivalis were correlated with histological gastritis, but not with endoscopic or symptomatic gastritis. The total PAGI-SYM score showed a stronger correlation with the duodenal microbiota (Prevotella nanceiensis and Alloprevotella rava) than with the gastric microbiota (H. pylori, Neisseria elongate, and Corynebacterium segmentosum). Different correlations of the gastric and duodenal microbiota with histological, endoscopic, and symptomatic gastritis were observed for the first time at the species level. H. pylori-negative gastritis is not associated with endoscopic or symptomatic gastritis. Only H. pylori-induced endoscopic gastritis requires gastric cancer surveillance. Owing to the weak correlation with H. pylori, symptomatic gastritis should be assessed separately from histological and endoscopic gastritis.
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Affiliation(s)
- Hye Seung Han
- Department of Pathology, Konkuk University School of Medicine, Seoul 05030, Korea.
| | - Sun-Young Lee
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul 05030, Korea.
| | - Seo Young Oh
- Department of Pathology, Konkuk University School of Medicine, Seoul 05030, Korea.
| | - Hee Won Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul 05030, Korea.
| | - Hyunseok Cho
- R&D Center, BioCore. Co. Ltd., Seoul 08511, Korea.
| | - Ji-Hoon Kim
- R&D Center, BioCore. Co. Ltd., Seoul 08511, Korea.
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Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer. EBioMedicine 2018; 40:336-348. [PMID: 30584008 PMCID: PMC6412016 DOI: 10.1016/j.ebiom.2018.12.034] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development. METHODS A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats. FINDINGS GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota. INTERPRETATION Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.
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Hu YL, Pang W, Huang Y, Zhang Y, Zhang CJ. The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics. Front Cell Infect Microbiol 2018; 8:433. [PMID: 30619779 PMCID: PMC6299874 DOI: 10.3389/fcimb.2018.00433] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022] Open
Abstract
Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.
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Affiliation(s)
- Yuan-Liang Hu
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wei Pang
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yun Huang
- Department of General Surgery, Navy General Hospital, Beijing, China
| | - Yan Zhang
- Department of General Surgery, Navy General Hospital, Beijing, China
| | - Chao-Jun Zhang
- Graduate School, Third Military Medical University (Army Medical University), Chongqing, China.,Department of General Surgery, Navy General Hospital, Beijing, China
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Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils. mSystems 2018; 3:mSystems00262-18. [PMID: 30505943 PMCID: PMC6247015 DOI: 10.1128/msystems.00262-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
Clinical stomach interventions, such as acid inhibition or bypass surgery, have been linked to fecal microbiota alterations. We demonstrate that the stomach microbiota largely overlaps those of adjacent gastrointestinal locations and identify gradual decreases and increases in the relative abundances of specific bacteria within the stomach, suggesting selective enrichment and depletion. Moreover, similarities between stomach and esophagus samples are proportional to the concentrations of Streptococcus (Firmicutes) in the stomach. The relative abundance of Firmicutes in the stomach, compared to that of Bacteroidetes, is increased in RNA relative to DNA, indicating higher transcriptional activity. Moreover, increased absolute bacterial loads are associated with decreased relative abundance of Firmicutes and higher relative abundance of Bacteroidetes. Our findings characterize the stomach microbiota as influenced by Bacteroidetes influx against a background of transcriptionally more active Firmicutes. Human, mouse, and gerbil stomach microbiotas differ at lower taxonomic levels, which might affect the utility of these model organisms. Clinical interventions in the stomach have been linked to fecal microbiota alterations, suggesting a function of the stomach in gastrointestinal (GI) homeostasis. We sought to determine the taxonomic bacterial biogeography of the upper GI tract, including different sites within the human stomach (cardia, corpus, and antrum), adjacent upstream (esophagus) and downstream (duodenum) locations, and luminal contents (aspirate), as well as whole-stomach samples from mice and gerbils. Qualitative and quantitative DNA- and RNA-based taxonomic microbiota analyses were combined to study the relationship of relative and absolute bacterial abundances and transcriptionally active bacterial microbiota components in the stomach of humans and mice. Stomach microbiota compositions resembled those of esophagus and duodenum. However, along the descending GI tract, the relative abundances of specific oropharyngeal commensals decreased (Streptococcus) or increased (Rothia mucilaginosa, Porphyromonas, and Lachnospiraceae). Furthermore, the compositional similarity (weighted UniFrac) between stomach aspirates and esophageal biopsy samples increased with gastric Streptococcus relative abundance. In both human aspirate and mouse stomach samples, Firmicutes were more abundant among transcriptionally active bacteria than Bacteroidetes. The relative abundance of Firmicutes in the stomach was negatively correlated and that of Bacteroidetes was positively correlated with absolute bacterial abundance, suggesting a disproportionate increase of Bacteroidetes over Firmicutes at higher bacterial densities. Human, mouse, and gerbil stomach samples showed similarities at higher taxonomic levels but differences at lower taxonomic levels. Our findings suggest selective enrichment and depletion of specific bacterial taxa in the stomach and Firmicutes being transcriptionally more active than Bacteroidetes that increase in relative abundance with total bacterial load. IMPORTANCE Clinical stomach interventions, such as acid inhibition or bypass surgery, have been linked to fecal microbiota alterations. We demonstrate that the stomach microbiota largely overlaps those of adjacent gastrointestinal locations and identify gradual decreases and increases in the relative abundances of specific bacteria within the stomach, suggesting selective enrichment and depletion. Moreover, similarities between stomach and esophagus samples are proportional to the concentrations of Streptococcus (Firmicutes) in the stomach. The relative abundance of Firmicutes in the stomach, compared to that of Bacteroidetes, is increased in RNA relative to DNA, indicating higher transcriptional activity. Moreover, increased absolute bacterial loads are associated with decreased relative abundance of Firmicutes and higher relative abundance of Bacteroidetes. Our findings characterize the stomach microbiota as influenced by Bacteroidetes influx against a background of transcriptionally more active Firmicutes. Human, mouse, and gerbil stomach microbiotas differ at lower taxonomic levels, which might affect the utility of these model organisms.
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