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Ren Y, Chen L, Guo R, Ma S, Li S, Zhang Y, Jiang H, Shi H, Zhang P. Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes. J Transl Med 2024; 22:202. [PMID: 38403655 PMCID: PMC10894479 DOI: 10.1186/s12967-024-05004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/18/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored. METHODS In this study, we compared the gut fungal populations of 223 ESRD patients and 69 healthy controls (HCs) based on shotgun metagenomic sequencing data, and analyzed their associations with host serum and fecal metabolites. RESULTS Our findings revealed that ESRD patients had a higher diversity in the gut mycobiome compared to HCs. Dysbiosis of the gut mycobiome in ESRD patients was characterized by a decrease of Saccharomyces cerevisiae and an increase in various opportunistic pathogens, such as Aspergillus fumigatus, Cladophialophora immunda, Exophiala spinifera, Hortaea werneckii, Trichophyton rubrum, and others. Through multi-omics analysis, we observed a substantial contribution of the gut mycobiome to host serum and fecal metabolomes. The opportunistic pathogens enriched in ESRD patients were frequently and positively correlated with the levels of creatinine, homocysteine, and phenylacetylglycine in the serum. The populations of Saccharomyces, including the HC-enriched Saccharomyces cerevisiae, were frequently and negatively correlated with the levels of various toxic metabolites in the feces. CONCLUSIONS Our results provided a comprehensive understanding of the associations between the gut mycobiome and the development of ESRD, which had important implications for guiding future therapeutic studies in this field.
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Affiliation(s)
- Yi Ren
- Department of Critical Care Nephrology and Blood Purification, the First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, People's Republic of China
- Department of Nephrology, People's Hospital of Longhua, Shenzhen, 518109, People's Republic of China
| | - Lei Chen
- Department of Critical Care Nephrology and Blood Purification, the First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, People's Republic of China
| | - Shiyang Ma
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi, People's Republic of China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, 710004, Shaanxi, People's Republic of China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, 710004, Shaanxi, People's Republic of China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, 710004, People's Republic of China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, People's Republic of China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430076, People's Republic of China
| | - Hongli Jiang
- Department of Critical Care Nephrology and Blood Purification, the First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, People's Republic of China.
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi, People's Republic of China.
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, 710004, Shaanxi, People's Republic of China.
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, 710004, Shaanxi, People's Republic of China.
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, 710004, People's Republic of China.
| | - Pan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xi'an, 710004, Shaanxi, People's Republic of China.
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, 710004, Shaanxi, People's Republic of China.
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, 710004, Shaanxi, People's Republic of China.
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, 710004, People's Republic of China.
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Gao Q, Li D, Wang Y, Zhao C, Li M, Xiao J, Kang Y, Lin H, Wang N. Analysis of intestinal flora and cognitive function in maintenance hemodialysis patients using combined 16S ribosome DNA and shotgun metagenome sequencing. Aging Clin Exp Res 2024; 36:28. [PMID: 38334873 PMCID: PMC10857965 DOI: 10.1007/s40520-023-02645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
BACKGROUND Cognitive impairment is widely prevalent in maintenance hemodialysis (MHD) patients, and seriously affects their quality of life. The intestinal flora likely regulates cognitive function, but studies on cognitive impairment and intestinal flora in MHD patients are lacking. METHODS MHD patients (36) and healthy volunteers (18) were evaluated using the Montreal Cognitive Function Scale, basic clinical data, and 16S ribosome DNA (rDNA) sequencing. Twenty MHD patients and ten healthy volunteers were randomly selected for shotgun metagenomic analysis to explore potential metabolic pathways of intestinal flora. Both16S rDNA sequencing and shotgun metagenomic sequencing were conducted on fecal samples. RESULTS Roseburia were significantly reduced in the MHD group based on both 16S rDNA and shotgun metagenomic sequencing analyses. Faecalibacterium, Megamonas, Bifidobacterium, Parabacteroides, Collinsella, Tyzzerella, and Phascolarctobacterium were positively correlated with cognitive function or cognitive domains. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included oxidative phosphorylation, photosynthesis, retrograde endocannabinoid signaling, flagellar assembly, and riboflavin metabolism. CONCLUSION Among the microbiota, Roseburia may be important in MHD patients. We demonstrated a correlation between bacterial genera and cognitive function, and propose possible mechanisms.
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Affiliation(s)
- Qiuyi Gao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dianshi Li
- Centre for Empirical Legal Studies, Faculty of Law, University of Macau, Macau, China
| | - Yue Wang
- Department of Nephrology, Binzhou Medical University Affiliated Shengli Oilfield Central Hospital, Binzhou, China
| | - Chunhui Zhao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Mingshuai Li
- School of Graduate, Dalian Medical University, Dalian, China
| | - Jingwen Xiao
- School of Graduate, Dalian Medical University, Dalian, China
| | - Yan Kang
- School of Graduate, Dalian Medical University, Dalian, China
| | - Hongli Lin
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Nan Wang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
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de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet 2021; 11:575592. [PMID: 33537056 PMCID: PMC7848172 DOI: 10.3389/fgene.2020.575592] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
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Affiliation(s)
- Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - José Perdigão
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - Sintia Almeida
- Central de Genômica e Bioinformática (CeGenBio), Núcleo de Pesquisa e Desenvolvimento de Medicamentos (NPDM), Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil
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Wongsurawat T, Nakagawa M, Atiq O, Coleman HN, Jenjaroenpun P, Allred JI, Trammel A, Puengrang P, Ussery DW, Nookaew I. An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients. J Microbiol Methods 2019; 166:105739. [PMID: 31626891 DOI: 10.1016/j.mimet.2019.105739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022]
Abstract
Gut metagenome profiling using the Oxford Nanopore Technologies (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species. IT better detected low-abundance species through amplification, when material was limited.
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Affiliation(s)
- Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Mayumi Nakagawa
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Omar Atiq
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Hannah N Coleman
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - James I Allred
- Cancer Clinical Trials and Regulatory Affairs Office, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Angela Trammel
- Cancer Clinical Trials and Regulatory Affairs Office, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Pantakan Puengrang
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - David W Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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Lu GH, Hua XM, Cheng J, Zhu YL, Wang GH, Pang YJ, Yang RW, Zhang L, Shou H, Wang XM, Qi J, Yang YH. Impact of Glyphosate on the Rhizosphere Microbial Communities of An EPSPS-Transgenic Soybean Line ZUTS31 by Metagenome Sequencing. Curr Genomics 2018; 19:36-49. [PMID: 29491731 PMCID: PMC5817875 DOI: 10.2174/1389202918666170705162405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/17/2016] [Accepted: 10/30/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The worldwide use of glyphosate has dramatically increased, but also has been raising concern over its impact on mineral nutrition, plant pathogen, and soil microbiota. To date, the bulk of previous studies still have shown different results on the effect of glyphosate application on soil rhizosphere microbial communities. OBJECTIVE This study aimed to clarify whether glyphosate has impact on nitrogen-fixation, pathogen or disease suppression, and rhizosphere microbial community of a soybean EPSPS-transgenic line ZUTS31 in one growth season. METHOD Comparative analysis of the soil rhizosphere microbial communities was performed by 16S rRNA gene amplicons sequencing and shotgun metagenome sequencing analysis between the soybean line ZUTS31 foliar sprayed with diluted glyphosate solution and those sprayed with water only in seed-filling stage. RESULTS There were no significant differences of alpha diversity but with small and insignificant difference of beta diversity of soybean rhizosphere bacteria after glyphosate treatment. The significantly enriched Gene Ontology (GO) terms were cellular, metabolic, and single-organism of biological process together with binding, catalytic activity of molecular function. The hits and gene abundances of some functional genes being involved in Plant Growth-Promoting Traits (PGPT), especially most of nitrogen fixation genes, significantly decreased in the rhizosphere after glyphosate treatment. CONCLUSION Our present study indicated that the formulation of glyphosate-isopropylamine salt did not significantly affect the alpha and beta diversity of the rhizobacterial community of the soybean line ZUTS31, whereas it significantly influenced some functional genes involved in PGPT in the rhizosphere during the single growth season.
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Affiliation(s)
- Gui-Hua Lu
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing210095, China
| | - Xiao-Mei Hua
- Nanjing Institute of Environmental Sciences, MEP, Nanjing210042, China
| | - Jing Cheng
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Yin-Ling Zhu
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Gu-Hao Wang
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Yan-Jun Pang
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Rong-Wu Yang
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Lei Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei230031, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310003, China
| | - Xiao-Ming Wang
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Jinliang Qi
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
| | - Yong-Hua Yang
- NJU–NJFU Joint Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing210093, China
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