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Taha SFM, Bhassu S, Omar H, Raju CS, Rajamanikam A, Govind SKP, Mohamad SB. Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach. 3 Biotech 2023; 13:275. [PMID: 37457869 PMCID: PMC10338424 DOI: 10.1007/s13205-023-03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03671-3.
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Affiliation(s)
- Siti Fatimah Mohd Taha
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chandramati Samudi Raju
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Arutchelvan Rajamanikam
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Suresh Kumar P. Govind
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Chakaroun RM, Olsson LM, Bäckhed F. The potential of tailoring the gut microbiome to prevent and treat cardiometabolic disease. Nat Rev Cardiol 2023; 20:217-235. [PMID: 36241728 DOI: 10.1038/s41569-022-00771-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 12/12/2022]
Abstract
Despite milestones in preventive measures and treatment, cardiovascular disease (CVD) remains associated with a high burden of morbidity and mortality. The protracted nature of the development and progression of CVD motivates the identification of early and complementary targets that might explain and alleviate any residual risk in treated patients. The gut microbiota has emerged as a sentinel between our inner milieu and outer environment and relays a modified risk associated with these factors to the host. Accordingly, numerous mechanistic studies in animal models support a causal role of the gut microbiome in CVD via specific microbial or shared microbiota-host metabolites and have identified converging mammalian targets for these signals. Similarly, large-scale cohort studies have repeatedly reported perturbations of the gut microbial community in CVD, supporting the translational potential of targeting this ecological niche, but the move from bench to bedside has not been smooth. In this Review, we provide an overview of the current evidence on the interconnectedness of the gut microbiome and CVD against the noisy backdrop of highly prevalent confounders in advanced CVD, such as increased metabolic burden and polypharmacy. We further aim to conceptualize the molecular mechanisms at the centre of these associations and identify actionable gut microbiome-based targets, while contextualizing the current knowledge within the clinical scenario and emphasizing the limitations of the field that need to be overcome.
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Affiliation(s)
- Rima Mohsen Chakaroun
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Mukherji S, Imchen M, Mondal S, Bhattacharyya A, Siddhardha B, Kumavath R, Ghosh A. Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban. CHEMOSPHERE 2022; 309:136806. [PMID: 36220439 DOI: 10.1016/j.chemosphere.2022.136806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Sangita Mondal
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anish Bhattacharyya
- School of Biological Sciences, Division of Genomics and Evolution, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periye P.O., Kasaragod, Kerala, 671316, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014 India.
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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4
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Rosso AD, Aguilera P, Quesada S, Mascardi F, Mascuka SN, Cimolai MC, Cerezo J, Spiazzi R, Conlon C, Milano C, Iraola GM, Penas-Steinhardt A, Belforte FS. Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context. Microorganisms 2022; 10:2190. [PMID: 36363782 PMCID: PMC9698371 DOI: 10.3390/microorganisms10112190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible host. IBD includes ulcerative colitis (UC) and Crohn's disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.
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Affiliation(s)
- Ayelén D. Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Ciudad Autónoma de Buenos Aires C1199, Argentina
| | - Sebastian N. Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - María C. Cimolai
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Jimena Cerezo
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Renata Spiazzi
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Carolina Conlon
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Claudia Milano
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Gregorio M. Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay
- Centro de Biología Integrativa, Universidad Mayor, Santiago 7510041, Chile
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire CB10 1SA, UK
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires 1127, Argentina
| | - Fiorella S. Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
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5
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Shao L, Liao J, Qian J, Chen W, Fan X. MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. BMC Microbiol 2021; 21:263. [PMID: 34592929 PMCID: PMC8485520 DOI: 10.1186/s12866-021-02321-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations introduced during data generation and processing limit the comparisons among independent studies in respect of interpretability. Although multiple databases have been constructed as platforms for data reuse, they are of limited value since only raw sequencing files are considered. DESCRIPTION Here, we present MetaGeneBank, a standardized database that provides details on sample collection and sequencing, and abundances of genes, microbiota and molecular functions for 4470 raw sequencing files (over 12 TB) collected from 16 studies covering over 10 types of diseases and 14 countries using a unified data-processing pipeline. The incorporation of tools that enable browsing and searching with descriptive attributes, gene sequences, microbiota and functions makes the database user-friendly. We found that the source of specimen contributes more than sequencing centers or platforms to the variations of microbiota. Special attention should be paid when re-analyzing sequencing files from different countries. CONCLUSIONS Collectively, MetaGeneBank provides a gateway to utilize the untapped potential of gut metagenomic data in helping fighting against human diseases. With the continuous updating of the database in terms of data volume, data types and sample types, MetaGeneBank would undoubtedly be the benchmarking database in the future in respect of data reuse, and would be valuable in translational science.
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Affiliation(s)
- Li Shao
- Hangzhou Normal University, Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,iMedicine Lab, Alibaba-Zhejiang University Joint Research Center for Future Digital Health , Hangzhou, 310018, Zhejiang, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310003, China
| | - Jingyang Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310003, China
| | - Wenbin Chen
- The First Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou, 310003, Zhejiang, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310003, China. .,iMedicine Lab, Alibaba-Zhejiang University Joint Research Center for Future Digital Health , Hangzhou, 310018, Zhejiang, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou , Hangzhou, 310058, China.
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6
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Murphy K, O'Donovan AN, Caplice NM, Ross RP, Stanton C. Exploring the Gut Microbiota and Cardiovascular Disease. Metabolites 2021; 11:metabo11080493. [PMID: 34436434 PMCID: PMC8401482 DOI: 10.3390/metabo11080493] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular disease (CVD) has been classified as one of the leading causes of morbidity and mortality worldwide. CVD risk factors include smoking, hypertension, dyslipidaemia, obesity, inflammation and diabetes. The gut microbiota can influence human health through multiple interactions and community changes are associated with the development and progression of numerous disease states, including CVD. The gut microbiota are involved in the production of several metabolites, such as short-chain fatty acids (SCFAs), bile acids and trimethylamine-N-oxide (TMAO). These products of microbial metabolism are important modulatory factors and have been associated with an increased risk of CVD. Due to its association with CVD development, the gut microbiota has emerged as a target for therapeutic approaches. In this review, we summarise the current knowledge on the role of the gut microbiome in CVD development, and associated microbial communities, functions, and metabolic profiles. We also discuss CVD therapeutic interventions that target the gut microbiota such as probiotics and faecal microbiota transplantation.
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Affiliation(s)
- Kiera Murphy
- Teagasc Food Research Centre, Moorepark, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
| | - Aoife N O'Donovan
- Teagasc Food Research Centre, Moorepark, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Co. Cork P61 C996, Ireland
| | - Noel M Caplice
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- Centre for Research in Vascular Biology, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Co. Cork P61 C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Co. Cork P61 C996, Ireland
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Imchen M, Kumavath R. Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment. FEMS Microbiol Ecol 2021; 96:5897355. [PMID: 32845305 DOI: 10.1093/femsec/fiaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
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8
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Imchen M, Kumavath R. Metagenomic insights into the antibiotic resistome of mangrove sediments and their association to socioeconomic status. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115795. [PMID: 33068846 DOI: 10.1016/j.envpol.2020.115795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Mangrove sediments are prone to anthropogenic activities that could enrich antibiotics resistance genes (ARGs). The emergence and dissemination of ARGs are of serious concern to public health worldwide. Therefore, a comprehensive resistome analysis of global mangrove sediment is of paramount importance. In this study, we have implemented a deep machine learning approach to analyze the resistome of mangrove sediments from Brazil, China, Saudi Arabia, India, and Malaysia. Geography (RANOSIM = 39.26%; p < 0.005) as well as human intervention (RANOSIM = 16.92%; p < 0.005) influenced the ARG diversity. ARG diversity was also inversely correlated to the human development index (HDI) of the host country (R = -0.53; p < 0.05) rather than antibiotics consumption (p > 0.05). Several genes including multidrug efflux pumps were significantly (p < 0.05) enriched in the sites with human intervention. Resistome was consistently dominated by rpoB2 (19.26 ± 0.01%), multidrug ABC transporter (10.40 ± 0.23%), macB (8.84 ± 0.36n%), tetA (4.13 ± 0.35%), mexF (3.26 ± 0.19%), CpxR (2.93 ± 0.2%), bcrA (2.38 ± 0.24%), acrB (2.37 ± 0.18%), mexW (2.19 ± 0.17%), and vanR (1.99 ± 0.11%). Besides, mobile ARGs such as vanA, tet(48), mcr, and tetX were also detected in the mangrove sediments. Comparative analysis against terrestrial and ocean resistomes showed that the ocean ecosystem harbored the lowest ARG diversity (Chao1 = 71.12) followed by mangroves (Chao1 = 258.07) and terrestrial ecosystem (Chao1 = 294.07). ARG subtypes such as abeS and qacG were detected exclusively in ocean datasets. Likewise, rpoB2, multidrug ABC transporter, and macB, detected in mangrove and terrestrial datasets, were not detected in the ocean datasets. This study shows that the socioeconomic factors strongly determine the antibiotic resistome in the mangrove. Direct anthropogenic intervention in the mangrove environment also enriches antibiotic resistome.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala, 671320, India.
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9
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Džunková M, Lipták R, Vlková B, Gardlík R, Čierny M, Moya A, Celec P. Salivary microbiome composition changes after bariatric surgery. Sci Rep 2020; 10:20086. [PMID: 33208788 PMCID: PMC7674438 DOI: 10.1038/s41598-020-76991-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary microbiome composition and body weight is unclear. Herein we investigate this relation by analyzing saliva samples from 35 adult patients with obesity undergoing bariatric surgery. Our aim was to describe salivary microbiome changes during body weight loss on an individual-specific level, and to elucidate the effect of bariatric surgery on the salivary microbiome which has not been studied before. Analysis of samples collected before and 1 day after surgery, as well as 3 and 12 months after surgery, showed that the salivary microbiome changed in all study participants, but these changes were heterogeneous. In the majority of participants proportions of Gemella species, Granulicatella elegans, Porphyromonas pasteri, Prevotella nanceiensis and Streptococcus oralis decreased, while Veillonella species, Megasphaera micronuciformis and Prevotella saliva increased. Nevertheless, we found participants deviating from this general trend which suggests that a variety of individual-specific factors influence the salivary microbiome composition more effectively than the body weight dynamics alone. The observed microbiome alternations could be related to dietary changes. Therefore, further studies should focus on association with altered taste preferences and potential oral health consequences.
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Affiliation(s)
- Mária Džunková
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Róbert Lipták
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Roman Gardlík
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Michal Čierny
- Department of Bariatric Surgery, Břeclav Hospital, Břeclav, Czech Republic
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO-Public Health), Valencia, Spain.
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain.
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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Santoro A, Zhao J, Wu L, Carru C, Biagi E, Franceschi C. Microbiomes other than the gut: inflammaging and age-related diseases. Semin Immunopathol 2020; 42:589-605. [PMID: 32997224 PMCID: PMC7666274 DOI: 10.1007/s00281-020-00814-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022]
Abstract
During the course of evolution, bacteria have developed an intimate relationship with humans colonizing specific body sites at the interface with the body exterior and invaginations such as nose, mouth, lung, gut, vagina, genito-urinary tract, and skin and thus constituting an integrated meta-organism. The final result has been a mutual adaptation and functional integration which confers significant advantages to humans and bacteria. The immune system of the host co-evolved with the microbiota to develop complex mechanisms to recognize and destroy invading microbes, while preserving its own bacteria. Composition and diversity of the microbiota change according to development and aging and contribute to humans' health and fitness by modulating the immune system response and inflammaging and vice versa. In the last decades, we experienced an explosion of studies on the role of gut microbiota in aging, age-related diseases, and longevity; however, less reports are present on the role of the microbiota at different body sites. In this review, we describe the key steps of the co-evolution between Homo sapiens and microbiome and how this adaptation can impact on immunosenescence and inflammaging. We briefly summarized the role of gut microbiota in aging and longevity while bringing out the involvement of the other microbiota.
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Affiliation(s)
- Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72703, USA
| | - Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ciriaco Carru
- Department of Biomedical Sciences, University Hospital (AOU) - University of Sassari, Sassari, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology (FABIT), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
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Al-Nbaheen MS. Impact of weight loss predictors in severe-morbid obesity patients in the Saudi population. Saudi J Biol Sci 2020; 27:2509-2513. [PMID: 32994706 PMCID: PMC7499111 DOI: 10.1016/j.sjbs.2020.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/08/2020] [Indexed: 12/26/2022] Open
Abstract
Universally, obesity has been affected more than 650 million and converts as global health problem. Obesity is equally affecting starting from children to elder population. Obese subjects are converting into severe obese and then into morbid obesity. Body mass index is proning from 30 to 50 kg/m2 in the adult population. Obesity is connected with the future complications of hypertension, type 2 diabetes mellitus, cardiovascular, stroke, osteoarthritis, obstructive sleep apnea and liver diseases. Loosing of body fat is the only option to avoid obesity and this could be achieved with routine physical activity and diet modifications. Obesity subjects may fail to achieve the daily routine activities or insufficient activity may be involved and finally fail to lose the body fat after the medical course. Then these severe or morbidity obese can be lose with the existing surgery. Currently, Bariatric Surgery (BS) has become the active treatment for long-term weight loss. Various types (Roux-en-Y gastric bypass, sleeve gastrectomy and duodenal switch and the jejunoileal bypass) of BS are performed on the gastrointestinal tract. Throughout the world population, BS has found to be safe in losing the weight and avoiding the future and long-term complications. The prevalence of overweight and obesity in Saudi Arabia is an issue in terms of incidence and health consequences. Maximum obesity studies involved in Saudi Arabia has proven to be develop the long-term complications in the future involving from child to morbid obesity. Limited bariatric studies carried out in the Saudi subjects confirmed as effective tool in lowering the body fat and avoiding the life-threatened complications of human diseases. So, this review recommends BS as effective and safe surgical treatment to lose body fat in the Saudi population. However, post-operative monitoring is mandatory to follow-up.
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De R, Mukhopadhyay AK, Dutta S. Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter. Gut Pathog 2020; 12:32. [PMID: 32655699 PMCID: PMC7339541 DOI: 10.1186/s13099-020-00371-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut. RESULTS 16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or "microbial dark matter" occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs. CONCLUSIONS This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
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Villette R, Kc P, Beliard S, Salas Tapia MF, Rainteau D, Guerin M, Lesnik P. Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Front Pharmacol 2020; 11:278. [PMID: 32308619 PMCID: PMC7145900 DOI: 10.3389/fphar.2020.00278] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption in cholesterol metabolism, particularly hypercholesterolemia, is a significant cause of atherosclerotic cardiovascular disease. Large interindividual variations in plasma cholesterol levels are traditionally related to genetic factors, and the remaining portion of their variance is accredited to environmental factors. In recent years, the essential role played by intestinal microbiota in human health and diseases has emerged. The gut microbiota is currently viewed as a fundamental regulator of host metabolism and of innate and adaptive immunity. Its bacterial composition but also the synthesis of multiple molecules resulting from bacterial metabolism vary according to diet, antibiotics, drugs used, and exposure to pollutants and infectious agents. Microbiota modifications induced by recent changes in the human environment thus seem to be a major factor in the current epidemic of metabolic/inflammatory diseases (diabetes mellitus, liver diseases, inflammatory bowel disease, obesity, and dyslipidemia). Epidemiological and preclinical studies report associations between bacterial communities and cholesterolemia. However, such an association remains poorly investigated and characterized. The objectives of this review are to present the current knowledge on and potential mechanisms underlying the host-microbiota dialogue for a better understanding of the contribution of microbial communities to the regulation of cholesterol homeostasis.
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Affiliation(s)
- Remy Villette
- INSERM, UMRS U1166, "Integrative Biology of Atherosclerosis" and Sorbonne Université, Paris, France
| | - Pukar Kc
- INSERM, UMRS U1166, "Integrative Biology of Atherosclerosis" and Sorbonne Université, Paris, France
| | - Sophie Beliard
- Aix-Marseille Université, INSERM U1263, INRA, C2VN, Marseille, France.,APHM, La Conception Hospital, Marseille, France
| | | | - Dominique Rainteau
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, AP-HP, Hôpital Saint Antoine, Département de Métabolomique Clinique, Paris, France
| | - Maryse Guerin
- INSERM, UMRS U1166, "Integrative Biology of Atherosclerosis" and Sorbonne Université, Paris, France
| | - Philippe Lesnik
- INSERM, UMRS U1166, "Integrative Biology of Atherosclerosis" and Sorbonne Université, Paris, France
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Farin W, Oñate FP, Plassais J, Bonny C, Beglinger C, Woelnerhanssen B, Nocca D, Magoules F, Le Chatelier E, Pons N, Cervino ACL, Ehrlich SD. Impact of laparoscopic Roux-en-Y gastric bypass and sleeve gastrectomy on gut microbiota: a metagenomic comparative analysis. Surg Obes Relat Dis 2020; 16:852-862. [PMID: 32360114 DOI: 10.1016/j.soard.2020.03.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Bariatric surgery is an effective therapeutic procedure for morbidly obese patients. The 2 most common interventions are sleeve gastrectomy (SG) and laparoscopic Roux-en-Y gastric bypass (LRYGB). OBJECTIVES The aim of this study was to compare microbiome long-term microbiome after SG and LRYGB surgery in obese patients. SETTING University Hospital, France; University Hospital, United States; and University Hospital, Switzerland. METHODS Eighty-nine and 108 patients who underwent SG and LRYGB, respectively, were recruited. Stools were collected before and 6 months after surgery. Microbial DNA was analyzed with shotgun metagenomic sequencing (SOLiD 5500 xl Wildfire). MSPminer, a novel innovative tool to characterize new in silico biological entities, was used to identify 715 Metagenomic Species Pan-genome. One hundred forty-eight functional modules were analyzed using GOmixer and KEGG database. RESULTS Both interventions resulted in a similar increase of Shannon's diversity index and gene richness of gut microbiota, in parallel with weight loss, but the changes of microbial composition were different. LRYGB led to higher relative abundance of aero-tolerant bacteria, such as Escherichia coli and buccal species, such as Streptococcus and Veillonella spp. In contrast, anaerobes, such as Clostridium, were more abundant after SG, suggesting better conservation of anaerobic conditions in the gut. Enrichment of Akkermansia muciniphila was also observed after both surgeries. Function-level changes included higher potential for bacterial use of supplements, such as vitamin B12, B1, and iron upon LRYGB. CONCLUSION Microbiota changes after bariatric surgery depend on the nature of the intervention. LRYGB induces greater taxonomic and functional changes in gut microbiota than SG. Possible long-term health consequences of these alterations remain to be established.
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Affiliation(s)
| | - Florian Plaza Oñate
- Data Science, Enterome, Paris, France; Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Christoph Beglinger
- Department of Biomedicine, University of Basel and Department of Research, St. Claraspital, Basel, Switzerland
| | - Bettina Woelnerhanssen
- Department of Biomedicine, University of Basel and Department of Research, St. Claraspital, Basel, Switzerland
| | - David Nocca
- Digestive Surgery, Saint-Eloi University Hospital of Montpellier, Montpellier, France
| | | | | | | | | | - S Dusko Ehrlich
- Université Paris-Saclay, Jouy en Josas, France; Centre for Host Microbiome Interaction, Dental Institute, King's College London, London, United Kingdom
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