Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

Wallner, Adrian; King, Eoghan; Ngonkeu, Eddy Léonard Mangaptché; Moulin, Lionel; Béna, Gilles

doi:10.1186/s12864-019-6186-z

Cited by 47 publications

(51 citation statements)

References 103 publications

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“…Burkholderia has also been reported to infect the brain [ 44 , 45 ]. Of particular interest, Burkholderia species encode the rate-limiting enzyme for secondary bile acid synthesis (bile-acid dehydratase) [ 46 ], highlighting the fact that the appendix microbiome of PD sufferers has an enrichment of microbiota that metabolize bile acids.…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease

Killinger

Ensink

et al. 2021

Metabolites

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The gut microbiome can impact brain health and is altered in Parkinson’s disease (PD). The vermiform appendix is a lymphoid tissue in the cecum implicated in the storage and regulation of the gut microbiota. We sought to determine whether the appendix microbiome is altered in PD and to analyze the biological consequences of the microbial alterations. We investigated the changes in the functional microbiota in the appendix of PD patients relative to controls (n = 12 PD, 16 C) by metatranscriptomic analysis. We found microbial dysbiosis affecting lipid metabolism, including an upregulation of bacteria responsible for secondary bile acid synthesis. We then quantitatively measure changes in bile acid abundance in PD relative to the controls in the appendix (n = 15 PD, 12 C) and ileum (n = 20 PD, 20 C). Bile acid analysis in the PD appendix reveals an increase in hydrophobic and secondary bile acids, deoxycholic acid (DCA) and lithocholic acid (LCA). Further proteomic and transcriptomic analysis in the appendix and ileum corroborated these findings, highlighting changes in the PD gut that are consistent with a disruption in bile acid control, including alterations in mediators of cholesterol homeostasis and lipid metabolism. Microbially derived toxic bile acids are heightened in PD, which suggests biliary abnormalities may play a role in PD pathogenesis.

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Section: Discussionmentioning

confidence: 99%

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease

Killinger

Ensink

et al. 2021

Metabolites

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“…Taxonomic proposals based on borderline values, such as many values obtained in the present study, are inevitably subjective. Small-scale comparisons of well-selected strains undoubtedly would allow to find some unique strains with a genomic divergence clearly beyond the threshold values and with a distinctive phenotype and would facilitate a straightforward description of several novel Burkholderia species (like for instance in reference Wallner et al, 2019 ). Yet, the complexity of the natural diversity as presented in this comprehensive dataset of taxon K bacteria argues against such practices.…”

Section: Discussionmentioning

confidence: 99%

Burkholderia cepacia Complex Taxon K: Where to Split?

et al. 2020

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The objective of the present study was to provide an updated classification for Burkholderia cepacia complex (Bcc) taxon K isolates. A representative set of 39 taxon K isolates were analyzed through multilocus sequence typing (MLST) and phylogenomic analyses. MLST analysis revealed the presence of at least six clusters of sequence types (STs) within taxon K, two of which contain the type strains of Burkholderia contaminans (ST-102) and Burkholderia lata (ST-101), and four corresponding to the previously defined taxa Other Bcc groups C, G, H and M. This clustering was largely supported by a phylogenomic tree which revealed three main clades. Isolates of B. contaminans and of Other Bcc groups C, G, and H represented a first clade which generally shared average nucleotide identity (ANI) and average digital DNA-DNA hybridization (dDDH) values at or above the 95-96% ANI and 70% dDDH thresholds for species delineation. A second clade consisted of Other Bcc group M bacteria and of four B. lata isolates and was supported by average ANI and dDDH values of 97.2 and 76.1% within this clade and average ANI and dDDH values of 94.5 and 57.2% toward the remaining B. lata isolates (including the type strain), which represented a third clade. We therefore concluded that isolates known as Other Bcc groups C, G, and H should be classified as B. contaminans, and propose a novel species, Burkholderia aenigmatica sp. nov., to accommodate Other Bcc M and B. lata ST-98, ST-103, and ST-119 isolates. Optimized MALDI-TOF MS databases for the identification of clinical Burkholderia isolates may provide correct species-level identification for some of these bacteria but would identify most of them as B. cepacia complex. MLST facilitates species-level identification of many taxon K strains but some may require comparative genomics for accurate species-level assignment. Finally, the inclusion of Other Bcc groups C, G, and H into B. contaminans affects the phenotype of this species minimally and the proposal to classify Other Bcc group M and B. lata ST-98, ST-103, and ST-119 strains as a novel Burkholderia species is supported by a distinctive phenotype, i.e., growth at 42 • C and lysine decarboxylase activity.

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“…Burkholderia are a very diverse group of Gram-negative bacteria found in wide-ranging environments including soil, water and in association with plants, fungi, animals and humans [8]. The genus has undergone extensive taxonomic revision since its definition in 1992 [9], and has recently been split into six genera, Burkholderia sensu stricto, Paraburkholderia, Caballeronia, Trinickia, Mycetohabitans and Robbsia [10]. There are currently more than 30 Burkholderia species, 22 of which belong to the Burkholderia cepacia complex (Bcc) [10].…”

Section: Introductionmentioning

confidence: 99%

“…The genus has undergone extensive taxonomic revision since its definition in 1992 [9], and has recently been split into six genera, Burkholderia sensu stricto, Paraburkholderia, Caballeronia, Trinickia, Mycetohabitans and Robbsia [10]. There are currently more than 30 Burkholderia species, 22 of which belong to the Burkholderia cepacia complex (Bcc) [10]. Members of the Bcc are opportunistic pathogens linked with life-threatening lung infections in individuals with cystic fibrosis (CF) [11] and are problematic contaminants of industrial products [12].…”

Section: Introductionmentioning

confidence: 99%

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Weiser

Yap

Otter

et al. 2020

Viruses

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Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.

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Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

Cited by 47 publications

References 103 publications

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease

Burkholderia cepacia Complex Taxon K: Where to Split?

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

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