| Literature DB >> 30586413 |
Gabriele Margos1, Alex Gofton2, Daniel Wibberg3, Alexandra Dangel1, Durdica Marosevic1, Siew-May Loh2, Charlotte Oskam2, Volker Fingerle1.
Abstract
The genus Borrelia, originally described by Swellengrebel in 1907, contains tick- or louse-transmitted spirochetes belonging to the relapsing fever (RF) group of spirochetes, the Lyme borreliosis (LB) group of spirochetes and spirochetes that form intermittent clades. In 2014 it was proposed that the genus Borrelia should be separated into two genera; Borrelia Swellengrebel 1907 emend. Adeolu and Gupta 2014 containing RF spirochetes and Borreliella Adeolu and Gupta 2014 containing LB group of spirochetes. In this study we conducted an analysis based on a method that is suitable for bacterial genus demarcation, the percentage of conserved proteins (POCP). We included RF group species, LB group species and two species belonging to intermittent clades, Borrelia turcica Güner et al. 2004 and Candidatus Borrelia tachyglossi Loh et al. 2017. These analyses convincingly showed that all groups of spirochetes belong into one genus and we propose to emend, and re-unite all groups in, the genus Borrelia.Entities:
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Year: 2018 PMID: 30586413 PMCID: PMC6306154 DOI: 10.1371/journal.pone.0208432
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1Phylogenetic reconstruction of Borrelia species based on 791 aligned protein homologs built with the PEPR pipeline and FastTree2 with 100 jackknifed resampling replicates.
All node support values are 100 except where indicated.
Borrelia species and strains included in study.
| type strain | strain included | sequence source/GB accession number | available at culture collection | ||||
|---|---|---|---|---|---|---|---|
| ATCC | DSMZ | CIP | JCM | ||||
| VS461T | PKo | NC_008277 | DSM-10508 | CIP 103469 | |||
| SCW41T | SCW41 T | SAMN05328445 | BAA-1877 | DSM-22541 | |||
| PBi T | PBi T | CP028872 | BAA-2496 | DSM-23469 | |||
| DN127 T | DN127 T | NC_015921 | DSM-17990 | CIP 109136 | |||
| B31 T | B31 T | NC_001318 | 35210 | DSM-4680 | |||
| CA446 T | CA446 T | SAMN05328472 | BAA-2689 | DSM-17989 | CIP 109133 | ||
| SCW22 T | SCW22 T | SAMN05328473 | BAA-1773 | DSM-22119 | |||
| VA1 | VA1 | CP009910 | |||||
| SV1 | SV1 | NZ_ABJZ00000000 | |||||
| 20047 T | 20047 T | CP028861 | 51383 | DSM-10534 | |||
| HO14 T | HO14 T | SAMN05328497 | 51557 | JCM 8951 | |||
| 25015 T | 25015 | SAMN05328498 | BAA-2495 | DSM-26572 | |||
| PotiB2 T | PotiB2 T | SAMN05328499 | DSM-107168 | CIP 105366 | |||
| MN14-1420 T | MN14-1420 T | NZ_CP015780 | BAA-2743 | DSM-102811 | |||
| PC-Eq17 T | A14S | NZ_ABKB00000000 | DSM-16813 | CIP 108855 | |||
| VS116 T | VS116 T | SAMN02436326 | DSM-21467 | CIP 105367 | |||
| Okinawa-CW62 T | Okinawa-CW62 T | SAMN08904503 | DSM-24625 | JCM 17189 | |||
| IST7 T | IST7 T | CP028884-91 | DSM-16138 | ||||
| 1268-Bc-F10 | CP025785-90 | ||||||
| nd | BA2 | NZ_CP005829 | |||||
| nd | Co53 | NZ_CP005745 | ATCC 43381 | ||||
| nd | Achema | NC_017808 | |||||
| nd | Ly | NC_011229 | |||||
| nd | HS1 | NZ_CP014349 | BAA-2821 | DSM 4682 | CIP 104209 | ||
| nd | CRI | NZ_AYOU00000000 | |||||
| HT31T | LB-2001 | NC_022079 | |||||
| nd | SLO | NZ_CP005851 | |||||
| nd | No12 | NZ_AYOT00000000 | |||||
| nd | A1 | NC_011244 | |||||
| nd | 91E135 | NC_008710 | |||||
GB = GenBank; ATCC = American Type Culture Collection; DSMZ = Deutsche Stammsammlung für Mikroorganismen und Zellkulturen; JCM = Japan Collection of Microoranisms; nd = no data
*sample ID
Fig 2Boxplot of inter- and intra-specific POCP values.
Inter-specific and intra-specific comparisons included Lyme borreliosis (LB) and relapsing-fever species (RF), reptile-associated species (REP) including the echnida-associated species ‘Candidatus B. tachyglossi’. The inter-genera comparison included the members of the genera Borrelia, Brachyspira, Leptospira, Spirochaeta, and Treponema.
Fig 3Percentage of conserved proteins (POCP) matrix generated by the method described in [18].
POCP values of species belonging to the LB group, RF group of spirochetes, the reptile-associated species B. turcica and echnida-associated species B. tachyglossi are above the genus threshold of 50%, indicating that all belong into one bacterial genus, Borrelia.
Fig 4Partial amino acid alignment of (A) a putative lipoprotein (GI: 1195064) and (B) a hypothetical protein (GI: 1194969) showing a CSI in which the form of the indel in ‘Candidatus Borrelia tachyglossi’ and B. turcica matches that in LB species.
Designation of LB and RF-differentiating CSIs in ‘Candidatus Borrelia tachyglossi’ and B. turcica genomes.
| Gene | Size of CSI (aa) | ‘ | |
|---|---|---|---|
| 1 | RF | RF | |
| Nicotinamide-nucleotide adenylyltransferase | 1 | LB | LB |
| Hypothetical protein (BB0838) | 3 | LB | LB |
| Trigger factor | 2 | RF | RF |
| Chemotaxis protein | 1 | RF | RF |
| DNA polymerase III subunit beta | 1 | RF | RF |
| Translation factor Sua5 | 2 | N/A | RF |
| Ferrous iron transporter | 1 | RF | RF |
| Glucose-6-phosphate isomerase | 1 | RF | RF |
| Hypothetical protein (BRE16) | 3 | RF | RF |
| Hypothetical protein (BDU327) | 6 | RF | RF |
| Hypothetical protein (BT0471) | 1 | LB | LB |
| L-latcate permease | 1 | RF | RF |
| 1-phosphofructokinase | 1 | RF | RF |
| GTP-binding protein | 2 | RF | RF |
| Sodium/panthothenate symporter | 1 | LB | LB |
| Hypothetical protein (BRE32) | 2 | RF | RF |
| Hypothetical protein (Q7M33) | 1 | RF | RF |
| Hypothetical protein (BRE47) | 5 | RF | RF |
| L-proline transport system ATP-binding protein | 1 | RF | RF |
| Penicillin-binding protein | 1 | RF | RF |
| Hypothetical protein (Q7M131) | 1 | RF | RF |
| Hypothetical protein (BT0110) | 2 | RF | RF |
| Hypothetical protein (BB0110) | 2 | RF | RF |
| Glutamate racemase | 6 | RF | RF |
| 16S riboisonal RNA methyltransferase | 1 | RF | RF |
| DNA mismatch repair protein | 3 | RF | RF |
| Putative lipoprotein | 3 | LB | LB |
| Membrane protein | 1 | LB | RF |
| Hypothetical protein (BRE314) | 1 | RF | RF |
| Methylgalactoside ABC transporter ATP-binding protein | 1 | RF | RF |
| Hypothetical protein (BRE355) | 1 | LB | LB |
| Sensor transduction histidine kinase | 1 | RF | RF |
| DNA polymerase III subunit delta | 2 | LB | RF |
| Hypothetical protein (Q7M860) | 2 | RF | RF |
| Hypothetical protein (KK90081) | 1 | RF | RF |
| Hypothetical protein (Q7M140) | 2 | LB | LB |
| Hypothetical protein (BG0159) | 1 | LB | LB |
| Outer membrane protein | 1 | RF | RF |
| Transglycosylase SLT domain-containing protein | 1 | RF | RF |
| Cell division protein | 1 | RF | RF |
| Excinuclease ABC subunit C | 1 | RF | RF |
| Hypothetical protein (BG0519) | 1 | RF | RF |
| Hypothetical protein (BBIDN1270545) | 5 | RF | RF |
| Hypothetical protein (BBUN400354) | 3 | RF | RF |
| Hypothetical protein (BBUZS70553) | 1 | RF | RF |
| Hypothetical protein (BB0554) | 1 | RF | RF |
| Hypothetical protein (BB0554) | 2 | RF | RF |
| Hypothetical protein (BBUCA803285) | 1 | RF | RF |
| Methyl-accepting chemotaxis protein | 2 | LB | LB |
| Chemotaxis protein | 1 | RF | RF |
| Chemotaxis protein | 1 | RF | RF |
| Hypothetical protein (L14403475) | 1 | RF | RF |