Molecular phylogeny of Burkholderia pseudomallei from a remote region of Papua New Guinea
- Baker, Anthony, Pearson, Talima, Price, Erin, Dale, Julia, Keim, Paul, Hornstra, Heidie, Greenhill, Andrew, Padilla, Gabriel, Warner, Jeffrey
- Authors: Baker, Anthony , Pearson, Talima , Price, Erin , Dale, Julia , Keim, Paul , Hornstra, Heidie , Greenhill, Andrew , Padilla, Gabriel , Warner, Jeffrey
- Date: 2011
- Type: Text , Journal article
- Relation: PLoS ONE Vol. 6, no. 3 (2011), p.
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- Description: Background: The island of New Guinea is located midway between the world's two major melioidosis endemic regions of Australia and Southeast Asia. Previous studies in Papua New Guinea have demonstrated autochthonous melioidosis in Balimo, Western province. In contrast to other regions of endemicity, isolates recovered from both environmental and clinical sources demonstrate narrow genetic diversity over large spatial and temporal scales. Methodology/Principal Findings: We employed molecular typing techniques to determine the phylogenetic relationships of these isolates to each other and to others worldwide to aid in understanding the origins of the Papua New Guinean isolates. Multi-locus sequence typing of the 39 isolates resolved three unique sequence types. Phylogenetic reconstruction and Structure analysis determined that all isolates were genetically closer to those from Australia than those from Southeast Asia. Gene cluster analysis however, identified a Yersinia-like fimbrial gene cluster predominantly found among Burkholderia pseudomallei derived from Southeast Asia. Higher resolution VNTR typing and phylogenetic reconstruction of the Balimo isolates resolved 24 genotypes with long branch lengths. These findings are congruent with long term persistence in the region and a high level of environmental stability. Conclusions/Significance: Given that anthropogenic influence has been hypothesized as a mechanism for the dispersal of B. pseudomallei, these findings correlate with limited movement of the indigenous people in the region. The palaeogeographical and anthropogenic history of Australasia and the results from this study indicate that New Guinea is an important region for the further study of B. pseudomallei origins and dissemination.
- Authors: Baker, Anthony , Pearson, Talima , Price, Erin , Dale, Julia , Keim, Paul , Hornstra, Heidie , Greenhill, Andrew , Padilla, Gabriel , Warner, Jeffrey
- Date: 2011
- Type: Text , Journal article
- Relation: PLoS ONE Vol. 6, no. 3 (2011), p.
- Full Text:
- Reviewed:
- Description: Background: The island of New Guinea is located midway between the world's two major melioidosis endemic regions of Australia and Southeast Asia. Previous studies in Papua New Guinea have demonstrated autochthonous melioidosis in Balimo, Western province. In contrast to other regions of endemicity, isolates recovered from both environmental and clinical sources demonstrate narrow genetic diversity over large spatial and temporal scales. Methodology/Principal Findings: We employed molecular typing techniques to determine the phylogenetic relationships of these isolates to each other and to others worldwide to aid in understanding the origins of the Papua New Guinean isolates. Multi-locus sequence typing of the 39 isolates resolved three unique sequence types. Phylogenetic reconstruction and Structure analysis determined that all isolates were genetically closer to those from Australia than those from Southeast Asia. Gene cluster analysis however, identified a Yersinia-like fimbrial gene cluster predominantly found among Burkholderia pseudomallei derived from Southeast Asia. Higher resolution VNTR typing and phylogenetic reconstruction of the Balimo isolates resolved 24 genotypes with long branch lengths. These findings are congruent with long term persistence in the region and a high level of environmental stability. Conclusions/Significance: Given that anthropogenic influence has been hypothesized as a mechanism for the dispersal of B. pseudomallei, these findings correlate with limited movement of the indigenous people in the region. The palaeogeographical and anthropogenic history of Australasia and the results from this study indicate that New Guinea is an important region for the further study of B. pseudomallei origins and dissemination.
Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR
- Greenhill, Andrew, Tsuji, Hirokazu, Ogata, Kiyohito, Natsuhara, Kazumi, Morita, Ayako, Soli, Kevin, Larkins, Jo-Ann, Tadokoro, Kiyoshi, Odani, Shingo, Baba, Jun, Naito, Yuichi, Tomitsuka, Eriko, Nomoto, Kriko, Siba, Peter, Horwood, Paul, Umezaki, Masahiro
- Authors: Greenhill, Andrew , Tsuji, Hirokazu , Ogata, Kiyohito , Natsuhara, Kazumi , Morita, Ayako , Soli, Kevin , Larkins, Jo-Ann , Tadokoro, Kiyoshi , Odani, Shingo , Baba, Jun , Naito, Yuichi , Tomitsuka, Eriko , Nomoto, Kriko , Siba, Peter , Horwood, Paul , Umezaki, Masahiro
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS ONE Vol. 10, no. 2 (2015), p. 1-15
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- Description: There has been considerable interest in composition of gut microbiota in recent years, leading to a better understanding of the role the gut microbiota plays in health and disease. Most studies have been limited in their geographical and socioeconomic diversity to high-income settings, and have been conducted using small sample sizes. To date, few analyses have been conducted in low-income settings, where a better understanding of the gut microbiome could lead to the greatest return in terms of health benefits. Here, we have used quantitative real-time polymerase chain reaction targeting dominant and sub-dominant groups of microorganisms associated with human gut microbiome in 115 people living a subsistence lifestyle in rural areas of Papua New Guinea. Quantification of Clostridium coccoides group, C. leptum subgroup, C. perfringens, Bacteroides fragilis group, Bifidobacterium, Atopobium cluster, Prevotella, Enterobacteriaceae, Enterococcus, Staphylococcus, and Lactobacillus spp. was conducted. Principle coordinates analysis (PCoA) revealed two dimensions with Prevotella, clostridia, Atopobium, Enterobacteriaceae, Enterococcus and Staphylococcus grouping in one dimension, while B. fragilis, Bifidobacterium and Lactobacillus grouping in the second dimension. Highland people had higher numbers of most groups of bacteria detected, and this is likely a key factor for the differences revealed by PCoA between highland and lowland study participants. Age and sex were not major determinants in microbial population composition. The study demonstrates a gut microbial composition with some similarities to those observed in other low-income settings where traditional diets are consumed, which have previously been suggested to favor energy extraction from a carbohydrate rich diet. © 2015 PLOS ONE.
- Authors: Greenhill, Andrew , Tsuji, Hirokazu , Ogata, Kiyohito , Natsuhara, Kazumi , Morita, Ayako , Soli, Kevin , Larkins, Jo-Ann , Tadokoro, Kiyoshi , Odani, Shingo , Baba, Jun , Naito, Yuichi , Tomitsuka, Eriko , Nomoto, Kriko , Siba, Peter , Horwood, Paul , Umezaki, Masahiro
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS ONE Vol. 10, no. 2 (2015), p. 1-15
- Full Text:
- Reviewed:
- Description: There has been considerable interest in composition of gut microbiota in recent years, leading to a better understanding of the role the gut microbiota plays in health and disease. Most studies have been limited in their geographical and socioeconomic diversity to high-income settings, and have been conducted using small sample sizes. To date, few analyses have been conducted in low-income settings, where a better understanding of the gut microbiome could lead to the greatest return in terms of health benefits. Here, we have used quantitative real-time polymerase chain reaction targeting dominant and sub-dominant groups of microorganisms associated with human gut microbiome in 115 people living a subsistence lifestyle in rural areas of Papua New Guinea. Quantification of Clostridium coccoides group, C. leptum subgroup, C. perfringens, Bacteroides fragilis group, Bifidobacterium, Atopobium cluster, Prevotella, Enterobacteriaceae, Enterococcus, Staphylococcus, and Lactobacillus spp. was conducted. Principle coordinates analysis (PCoA) revealed two dimensions with Prevotella, clostridia, Atopobium, Enterobacteriaceae, Enterococcus and Staphylococcus grouping in one dimension, while B. fragilis, Bifidobacterium and Lactobacillus grouping in the second dimension. Highland people had higher numbers of most groups of bacteria detected, and this is likely a key factor for the differences revealed by PCoA between highland and lowland study participants. Age and sex were not major determinants in microbial population composition. The study demonstrates a gut microbial composition with some similarities to those observed in other low-income settings where traditional diets are consumed, which have previously been suggested to favor energy extraction from a carbohydrate rich diet. © 2015 PLOS ONE.
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