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Low A, Lee JKY, Gounot JS, Ravikrishnan A, Ding Y, Saw WY, Tan LWL, Moong DKN, Teo YY, Nagarajan N, Seedorf H. Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative. Microbiol Spectr 2022; 10:e0084922. [PMID: 35699469 PMCID: PMC9431525 DOI: 10.1128/spectrum.00849-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, Singapore
| | | | | | | | | | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik Ying Teo
- Genome Institute of Singapore, A*STAR, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
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Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, Seedorf H. Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans. J Antimicrob Chemother 2021; 75:3480-3484. [PMID: 32853333 DOI: 10.1093/jac/dkaa372] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on isolation and screening of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a cohort of healthy individuals in Singapore. METHODS MinION and Illumina sequencing was performed to obtain the complete genome sequences of Escherichia coli 2EC1-1 and 94EC. Subsequently, 109 human faecal samples were screened retrospectively for eravacycline-resistant Enterobacteriaceae strains, which were further tested for tet(X4) by PCR. The taxonomy of the isolated strains was determined by 16S rRNA gene PCR and Sanger sequencing. RESULTS Comparative genomic analysis of E. coli 2EC1-1 and 94EC revealed that both carry tet(X4), which is encoded by IncI1-type plasmids p2EC1-1 and p94EC-2, respectively. Retrospective screening of faecal samples collected from 109 healthy individuals showed that the faecal carriage rate of Tet(X4)-producing Enterobacteriaceae is 10.1% (95% CI = 5.1%-17.3%), suggesting that tet(X4) is widely distributed in the gut microbiota of healthy individuals in Singapore. CONCLUSIONS To the best of our knowledge, this is the first report on the prevalence of tet(X4) in the gut microbiota of a healthy human cohort, as well as the first description of this resistance mechanism outside of China. Our findings suggest that surveillance of tet(X4) in community settings is vital to monitor the spread of this resistance mechanism.
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Affiliation(s)
- Yichen Ding
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, 75 Commercial Rd, Melbourne, 3004, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore.,Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, 117546, Singapore.,Life Sciences Institute, National University of Singapore, 117456, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, 117558, Singapore
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Kassam I, Tan S, Gan FF, Saw WY, Tan LWL, Moong DKN, Soong R, Teo YY, Loh M. Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations. Hum Mol Genet 2021; 30:603-618. [PMID: 33547791 DOI: 10.1093/hmg/ddab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 12/12/2022] Open
Abstract
DNA methylation (DNAm) is an epigenetic modification that acts to regulate gene transcription, is essential for cellular processes and plays an important role in complex traits and disease. Variation in DNAm levels is influenced by both genetic and environmental factors. Several studies have examined the extent to which common genetic variation influences DNAm (i.e. mQTLs), however, an improved understanding of mQTLs across diverse human populations is needed to increase their utility in integrative genomic studies in order to further our understanding of complex trait and disease biology. Here, we systematically examine cis-mQTLs in three Southeast Asian populations in the Singapore Integrative Omics (iOmics) Study, comprised of Chinese (n = 93), Indians (n = 83) and Malays (n = 78). A total of 24 851 cis-mQTL probes were associated with at least one SNP in meta- and ethnicity-specific analyses at a stringent significance level. These cis-mQTL probes show significant differences in local SNP heritability between the ethnicities, enrichment in functionally relevant regions using data from the Roadmap Epigenomics Mapping Consortium and are associated with nearby genes and complex traits due to pleiotropy. Importantly, DNAm prediction performance and the replication of cis-mQTLs both within iOmics and between two independent mQTL studies in European and Bangladeshi individuals is best when the genetic distance between the ethnicities is small, with differences in cis-mQTLs likely due to differences in allele frequency and linkage disequilibrium. This study highlights the importance of, and opportunities from, extending investigation of the genetic control of DNAm to Southeast Asian populations.
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Affiliation(s)
- Irfahan Kassam
- Life Sciences Institute, National University of Singapore, Singapore 117456.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Sili Tan
- KK Research Centre, KK Women's and Children's Hospital, Singapore 229899
| | - Fei Fei Gan
- Department of NUH Tissue Repository, National University Health System, Singapore 119228
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne Victoria, Australia 3004
| | - Linda Wei-Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
| | - Yik-Ying Teo
- Life Sciences Institute, National University of Singapore, Singapore 117456.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232.,Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom W2 1PG.,Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (ASTAR), Singapore 138648
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Saw WY, Tantoso E, Begum H, Zhou L, Zou R, He C, Chan SL, Tan LWL, Wong LP, Xu W, Moong DKN, Lim Y, Li B, Pillai NE, Peterson TA, Bielawny T, Meikle PJ, Mundra PA, Lim WY, Luo M, Chia KS, Ong RTH, Brunham LR, Khor CC, Too HP, Soong R, Wenk MR, Little P, Teo YY. Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study. Nat Commun 2017; 8:653. [PMID: 28935855 PMCID: PMC5608948 DOI: 10.1038/s41467-017-00413-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 11/09/2022] Open
Abstract
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.The Singapore Genome Variation projects characterized the genetics of Singapore's Chinese, Malay, and Indian populations. The Singapore Integrative Omics Study introduced here goes further in providing multi-omic measurements in individuals from these populations, including genetic, transcriptome, lipidome, and lifestyle data, and will facilitate the study of common diseases in Asian communities.
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Affiliation(s)
- Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore.,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Erwin Tantoso
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Husna Begum
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Lihan Zhou
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Ruiyang Zou
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Cheng He
- MiRXES, Agency for Science, Technology and Research Singapore, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Sze Ling Chan
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research Singapore, 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Linda Wei-Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Lai-Ping Wong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Wenting Xu
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Yenly Lim
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Bowen Li
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Nisha Esakimuthu Pillai
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Trevor A Peterson
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Tomasz Bielawny
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Peter J Meikle
- Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21, 30 Flemington Road, Melbourne, VIC, 3010, Australia
| | - Piyushkumar A Mundra
- Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, Canada, R3E 0Z2.,National Microbiology Laboratory, 1015 Arlington St, Winnipeg, MB, Canada, R3E
| | - Kee-Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Liam R Brunham
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research Singapore, 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, 60 Biopolis St, Singapore, 138672, Singapore.,Singapore Eye Research Institute, 20 College Road, Singapore, 169856, Singapore
| | - Heng Phon Too
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,Molecular Engineering of Biological and Chemical System/Chemical Pharmaceutical Engineering, Singapore-Massachusetts Institute of Technology Alliance, 4 Engineering Drive 3, Singapore, 117576, Singapore.,Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research, Singapore), 20 Biopolis Way, Singapore, 138668, Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus R Wenk
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543, Singapore
| | - Peter Little
- Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore. .,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology and Research Singapore, 60 Biopolis St, Singapore, 138672, Singapore. .,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Department of Statistics and Applied Probability, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
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