Using Core Genome Alignments to Assign Bacterial Species

Chung, Matthew; Munro, James B.; Hotopp, Julie C. Dunning

doi:10.1101/328021

Cited by 3 publications

(2 citation statements)

References 69 publications

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“…In addition to 'R. monacensis' species, all other Rickettsia species in the spotted fever group are classified as the second Rickettsia species (Chung et al, 2018). Our conclusion that 'R.…”

Section: Resultsmentioning

confidence: 78%

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Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus

Alowaysi

Jun-yan

Stark

et al. 2019

Ticks and Tick-borne Diseases

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A rickettsial isolate was obtained from a partially engorged Ixodes pacificus female, which was collected from Humboldt County, California. The isolate was provisionally named Rickettsia endosymbiont Ixodes pacificus (REIP). The REIP isolate displayed the highest nucleotide sequence identity to Rickettsia species phylotype G021 in I. pacificus (99%, 99%, and 100% for ompA, 16S rRNA, and gltA, respectively), a bacterium that was previously identified in I. pacifiucs by PCR. Analysis of sequences from complete opening frames of five genes, 16S rRNA, gltA, ompA, ompB, and sca4, provided inference to the bacteria's classification among other Rickettsia species. The REIP isolate displayed 99.8%, 99.4%, 99.2%, 99.5%, and 99.6% nucleotide sequence identity for 16S rRNA, gltA, ompA, ompB, and sca4 gene, respectively, with genes of 'R. monacensis' str. IrR/Munich, indicating the REIP isolate is closely related to 'R. monacensis'. Our suggestion was further supported by phylogenetic analysis using concatenated sequences of 16S rRNA, gltA, ompA, ompB, and sca4 genes, concatenated sequences of dksA-xerC, mppA-purC, and rpmE-tRNA fMet intergenic spacer regions. Both phylogenetic trees implied that the REIP isolate is most closely related to 'R. monacensis' str. IrR/Munich. We propose the bacterium be considered as 'Rickettsia monacensis' str. Humboldt for its closest phylogenetic relative (=DSM 103975T =ATCC TSD-94T).

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Section: Resultsmentioning

confidence: 78%

“…monacensis' str. IrR/Munich is 99.6% (Chung et al, 2018). In addition, the different genome content between the two strains is reflected by unique plasmids that exist in their genomes.…”

Section: Resultsmentioning

confidence: 95%

Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus

Alowaysi

Jun-yan

Stark

et al. 2019

Ticks and Tick-borne Diseases

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Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

Leducq

Sneddon

Santos

et al. 2022

Preprint

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Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfers. We showed that Methylobacterium contains four evolutionary distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition of recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), which early branching in Methylobacterium history was heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandon of Methylorubrum.

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A biosafety level-2 dose-dependent lethal mouse model of spotted fever rickettsiosis: Rickettsia parkeri Atlantic Rainforest-like isolate

Londoño

Mendell

Walker

et al. 2018

Preprint

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12 13 Background 14 15The species of the Rickettsia genus is separated into four groups: the ancestral group, 16 typhus group, transitional group and spotted fever group. Rickettsia parkeri, a spotted 17 fever group Rickettsia, has been reported across the American continents as infecting 18 several tick species and is associated with a relatively mild human disease characterized 19 by eschar formation at the tick feeding site, fever, myalgia and rash. Currently several 20 mouse models that provide a good approach to study the acute lethal disease caused by 21 Rickettsia, but these models can only be performed in an animal biosafety level 3 22 laboratory. We present an alternative mouse model for acute lethal rickettsial disease, 2 23 using R. parkeri and C3H/HeN mice, with the advantage that this model can be studied 24 in an animal biosafety level 2 laboratory. 25 26 Principal findings 27 28 In the C3H/HeN mouse model, we determined that infection with 1x10 6 and 1x10 7 viable 29 R. parkeri Atlantic Rainforest-like isolate produced dose-dependent severity, whereas 30 infection with 1x10 8 viable bacteria resulted in a lethal illness. The animals became 31 moribund on day five or six post-infection. The lethal disease was characterized by ruffled 32 fur, erythema, labored breathing, decreased activity, and hunched back, which began on 33 day three post-infection (p.i.) and coincided with the peak bacterial loads. Significant 34 splenomegaly (on days three and five p.i.), neutrophilia (on days three and five p.i.), and 35 thrombocytopenia (on days one, three and five p.i.) were observed. 36 37 Significance 38 39The greatest advantage of this inbred mouse model is the ability to investigate immunity 40 and pathogenesis of rickettsiosis with all the tools available at biosafety level 2. 41 42 Author summary 43 44Rickettsia is a bacterial genus that contains distinct species that are transmitted by 45 arthropods. Many of these agents produce infection and disease in humans. The illness 3 46 can range from very aggressive, such as Rocky Mountain spotted fever caused by 47 Rickettsia rickettsii, to mild human disease characterized by eschar formation at the tick 48 feeding site and less severe symptoms caused by Rickettsia parkeri. To study these 49 diseases, animal models are invaluable, and mouse models offer the best advantages. 50Several mouse models are most useful for study of the acute lethal disease produced by 51 these bacteria, providing the opportunity to test different treatments and vaccine 52 candidates. However, work with these models requires an animal biosafety level 3 53 laboratory. In this report, we present an alternative mouse model to study acute lethal 54 spotted fever group rickettsial disease with the advantage that experiments can be 55 performed at biosafety level 2. 56 57 63 64 Rickettsia parkeri, a member of the SFG, has been reported across the American 65 continents as infecting several tick species including the Amblyomma maculatum 66 complex (A. maculatum, A. triste, A. tig...

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Using Core Genome Alignments to Assign Bacterial Species

Cited by 3 publications

References 69 publications

Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus

Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus

Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

A biosafety level-2 dose-dependent lethal mouse model of spotted fever rickettsiosis: Rickettsia parkeri Atlantic Rainforest-like isolate

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