Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the Burkholderia pseudomallei Response to Different Niches

Ghazali, Ahmad-Kamal; Firdaus-Raih, Mohd; Kumar, Asqwin Uthaya; Lee, Wei-Kang; Hoh, Chee-Choong; Nathan, Sheila

doi:10.1128/spectrum.03835-22

Cited by 7 publications

(7 citation statements)

References 86 publications

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“…Siderophores have been reported to exist in BCC. A comparative transcriptome study of B. pseudomallei reported on the induction of siderophores that were able to adapt and survive in the host ( Ghazali et al, 2023 ). However, in antiSMASH results, species belonging to group B did not show the presence of siderophore-related clans.…”

Section: Resultsmentioning

confidence: 99%

Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus

Kim,

Han,

Lee

et al. 2024

Front. Microbiol.

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Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.

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Section: Resultsmentioning

confidence: 99%

Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus

Kim,

Han,

Lee

et al. 2024

Front. Microbiol.

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“…For environmental conditions, K96243 was exposed to water 47 , while UKMD286 and UKMH10 were cultivated in a soil extract medium 48,49 to mimic B. pseudomallei in the environment. For infection conditions, K96243 and UKMD286 were used in murine challenges 47,48 and isolated from mice organs, while UKMH10 was subjected to human plasma 49 to simulate host infection. This approach facilitated the comparison of differentially expressed lineage-specific genes between environmental and infection conditions.…”

Section: Resultsmentioning

confidence: 99%

“…This analysis focused on the expression profile of a strain UKMD286, representative of lineage 2. RNAseq data was obtained from an experiment conducted by Ghazali et al 48 and accessed through the European Nucleotide Archive (ENA) (E-MTAB-11200).…”

Section: Methodsmentioning

confidence: 99%

“…To delve deeper into the functionality of dominant lineage-specific genes, we explored their expression patterns across both environmental and infection conditions. We selected representative strains -"K96243" (lineage 1 -sub-lineage 1.1), "UKMD286" (lineage 2 -sublineage 2.1), and "UKMH10" (lineage 3 -sub-lineage 3.2) -all are clinical isolates with preexisting gene expression profiles under infection and environmental conditions [47][48][49] . For environmental conditions, K96243 was exposed to water 47 , while UKMD286 and UKMH10 were cultivated in a soil extract medium 48,49 to mimic B. pseudomallei in the environment.…”

Section: Lineage-specific Genes Were Selectively Expressedmentioning

confidence: 99%

“…We selected representative strains -"K96243" (lineage 1 -sub-lineage 1.1), "UKMD286" (lineage 2 -sublineage 2.1), and "UKMH10" (lineage 3 -sub-lineage 3.2) -all are clinical isolates with preexisting gene expression profiles under infection and environmental conditions [47][48][49] . For environmental conditions, K96243 was exposed to water 47 , while UKMD286 and UKMH10 were cultivated in a soil extract medium 48,49 to mimic B. pseudomallei in the environment. For infection conditions, K96243 and UKMD286 were used in murine challenges 47,48 and isolated from mice organs, while UKMH10 was subjected to human plasma 49 to simulate host infection.…”

Section: Lineage-specific Genes Were Selectively Expressedmentioning

confidence: 99%

See 2 more Smart Citations

Genetic diversity, determinants, and dissemination ofBurkholderia pseudomalleilineages implicated in melioidosis in northeast Thailand

Seng

Tandhavanant

Saiprom

et al. 2023

Preprint

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Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of disease-causing bacterial lineages, dissemination, and their adaptive mechanisms remains limited. To address this, we conducted comprehensive genomic analysis of 1,265 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, presenting the most densely sampled collection to date. Our study identified four dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific co-colonisation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analysis of a representative isolate from one lineage revealed upregulation of lineage-specific genes under nutrient-depletion. Our study also demonstrated the impact of river systems, monsoons, and typhoons in shaping the geographical dispersal of B. pseudomallei. Collectively, our findings underscore the importance of bacterial persistence in the environment as a prelude to exposure and infection, thereby providing insights for melioidosis prevention and control strategies.

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Diabetes and Infectious Diseases with a Focus on Melioidosis

Uthaya Kumar,

Ahmad Zan,

et al. 2024

Curr Microbiol

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Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the Burkholderia pseudomallei Response to Different Niches

Cited by 7 publications

References 86 publications

Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus

Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus

Genetic diversity, determinants, and dissemination ofBurkholderia pseudomalleilineages implicated in melioidosis in northeast Thailand

Diabetes and Infectious Diseases with a Focus on Melioidosis

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