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Febinia CA, Malik SG, Djuwita R, Weta IW, Wihandani DM, Maulida R, Sudoyo H, Holmes AJ. Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization. MICROBIAL ECOLOGY 2022; 83:798-810. [PMID: 34105009 DOI: 10.1007/s00248-021-01786-9] [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: 02/03/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.
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Affiliation(s)
- Clarissa A Febinia
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
- School of Life and Environmental Science and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Safarina G Malik
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Ratna Djuwita
- Department of Epidemiology, Faculty of Public Health, Universitas Indonesia, Depok, Indonesia
| | - I Wayan Weta
- Department of Public Health and Preventive Medicine / Clinical Nutrition, Faculty of Medicine, Universitas Udayana, Bali, Indonesia
| | - Desak Made Wihandani
- Department of Biochemistry, Faculty of Medicine, Universitas Udayana, Bali, Indonesia
| | - Rizka Maulida
- Department of Epidemiology, Faculty of Public Health, Universitas Indonesia, Depok, Indonesia
| | - Herawati Sudoyo
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Andrew J Holmes
- School of Life and Environmental Science and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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Thedja MD, Muljono DH, Ie SI, Sidarta E, Turyadi, Verhoef J, Marzuki S. Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific. PLoS One 2015; 10:e0132533. [PMID: 26162099 PMCID: PMC4498642 DOI: 10.1371/journal.pone.0132533] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 06/15/2015] [Indexed: 12/18/2022] Open
Abstract
Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates—East-Southeast Asia and Papua-Pacific—were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-.
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Affiliation(s)
- Meta Dewi Thedja
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Eijkman Winkler Institute, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - David Handojo Muljono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | | | - Erick Sidarta
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Turyadi
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Jan Verhoef
- Eijkman Winkler Institute, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Sangkot Marzuki
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Department of Medicine, Monash Medical Centre, Monash University, Clayton, Victoria, Australia
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Thedja MD, Muljono DH, Nurainy N, Sukowati CHC, Verhoef J, Marzuki S. Ethnogeographical structure of hepatitis B virus genotype distribution in Indonesia and discovery of a new subgenotype, B9. Arch Virol 2011; 156:855-68. [PMID: 21318309 PMCID: PMC3081436 DOI: 10.1007/s00705-011-0926-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 01/18/2011] [Indexed: 02/07/2023]
Abstract
The distribution of hepatitis B virus (HBV) in the populations of island Southeast Asia is of medical and anthropological interest and is associated with an unusually high genetic diversity. This study examined the association of this HBV genetic diversity with the ethnogeography of the populations of the Indonesian archipelago. Whole genome analysis of 21 HBV isolates from East Nusa Tenggara and Papua revealed two recently reported HBV/B subgenotypes unique to the former, B7 (7 isolates) and B8 (5 isolates), and uncovered a further novel subgenotype designated B9 (4 isolates). Further isolates were collected from 419 individuals with defined ethnic backgrounds representing 40 populations. HBV/B was predominant in Austronesian-language-speaking populations, whereas HBV/C was the major genotype in Papua and Papua-influenced populations of Moluccas; HBV/B3 was the predominant subgenotype in the western half of the archipelago (speakers of the Western Malayo-Polynesian [WMP] branch of Austronesian languages), whereas B7, B8 and B9 were specific to Nusa Tenggara (Central Malayo-Polynesian (CMP)). The result provides the first direct evidence that the distribution of HBV genotypes/subgenotypes in the Indonesian archipelago is related to the ethnic origin of its populations and suggests that the HBV distribution is associated with the ancient migratory events in the peopling of the archipelago.
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Affiliation(s)
- Meta Dewi Thedja
- Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430 Indonesia
- Eijkman Winkler Institute, Utrecht Medical Centre, Utrecht, The Netherlands
| | - David Handojo Muljono
- Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430 Indonesia
| | - Neni Nurainy
- Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430 Indonesia
- PT Bio Farma, Jl. Pasteur 28, Bandung, 40161 Indonesia
| | | | - Jan Verhoef
- Eijkman Winkler Institute, Utrecht Medical Centre, Utrecht, The Netherlands
| | - Sangkot Marzuki
- Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430 Indonesia
- Department of Medicine, Monash Medical Centre, Monash University, Clayton, VIC 3168 Australia
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Nurainy N, Muljono DH, Sudoyo H, Marzuki S. Genetic study of hepatitis B virus in Indonesia reveals a new subgenotype of genotype B in east Nusa Tenggara. Arch Virol 2008; 153:1057-65. [PMID: 18463783 DOI: 10.1007/s00705-008-0092-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 03/20/2008] [Indexed: 12/12/2022]
Abstract
The hepatitis B virus (HBV) genotype is associated with viral anthropological history, clinical outcome of disease and response to treatment. This study examines the HBV genotypes in Indonesia. HBV genotypes were determined by whole-genome sequencing and from the sequence of the Pre-S2 and S regions in a larger series. Two HBV genotypes, B (HBV/B) and C (HBV/C), were predominant. Three previously reported HBV/B subgenotypes were identified, with certain population association: HBV/B2 (HBV/Ba) was found mostly in Indonesians of Chinese ethnic origin, HBV/B3 was dominant among the Javanese, and HBV/B5, reported earlier from the Philippines, was also discovered, albeit at low frequency. Two other subgenotypes, HBV/B4 from Vietnam and HBV/B6, recently reported from the Arctic region, were not found. A novel subgenotype, HBV/B7, was recognized, associated with populations of the Nusa Tenggara islands in eastern Indonesia. Characteristic differences in HBsAg serotype and single nucleotide polymorphisms (SNPs) in the Pre-S2 region distinguish HBV/B7 from other HBV/B subgenotypes and further establish the new HBV subgenotype.
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Affiliation(s)
- Neni Nurainy
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia
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Sudoyo H, Widodo PT, Suryadi H, Lie YS, Safari D, Widjajanto A, Kadarmo DA, Hidayat S, Marzuki S. DNA analysis in perpetrator identification of terrorism-related disaster: suicide bombing of the Australian Embassy in Jakarta 2004. Forensic Sci Int Genet 2008; 2:231-7. [PMID: 19083826 DOI: 10.1016/j.fsigen.2007.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 12/10/2007] [Accepted: 12/14/2007] [Indexed: 11/30/2022]
Abstract
We report the strategy that we employed to identify the perpetrator of a suicide car bombing in front of the Australian Embassy in Jakarta, Indonesia, on 9 September 2004. The bomb was so massive that only small tissue pieces of the perpetrator could be recovered, preventing conventional approach to the identification of the bomber, necessitating the introduction of DNA analysis as the primary means for perpetrator identification. Crime scene investigation revealed the trajectory of the bomb blast, which was used to guide the collection of charred tissue fragments of the perpetrator. Mitochondrial DNA analysis was first conducted on 17 tissue fragments, recovered over large areas of the trajectory to, (a) confirm that they are of a common source, i.e. the perpetrator, and thus (b) establish the mtDNA HV1 sequence profile of the perpetrator. The mtDNA of the perpetrator matches that of a maternally related family member of one of four suspects. Standard autosomal STR analysis confirmed the identification. This case is of interest as an illustration of a successful application of DNA analysis as the primary means of disaster perpetrator identification.
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Affiliation(s)
- Herawati Sudoyo
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia.
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