Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives

Bansal, Kanika; Kaur, Amandeep; Singh, Anu; Patil, Prabhu B.

doi:10.1101/2021.08.22.457248

Cited by 3 publications

(1 citation statement)

References 77 publications

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“…Because of their phenotypic and genotypic diversity, the taxonomic status of the genus Stenotrophomonas and S. maltophilia has changed several times. Besides the species in the Stenotrophomonas maltophilia complex (SMc), S. maltophilia ( Chang et al., 2015 ; Patil et al., 2018 ; Bansal et al., 2021 ; Brooke, 2021 ) and S. sepilia ( Gautam et al., 2021 ), only S. pavanii ( Iebba et al., 2018 ), S. acidaminiphila ( Ježek et al., 2020 ; Zhang et al., 2022 ) and S. rhizophila ( Chao et al., 2022 ) have been isolated from human samples. The clinically important species S. africana ( Coenye et al., 2004 ) is classified as a synonym of S. maltophilia , whereas S. pavanii has been removed from SMc ( Rouf et al., 2011 ; Patil et al., 2018 ; Maturana and Cardenas, 2021 ; Deng et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

A novel pathogenic species of genus Stenotrophomonas: Stenotrophomonas pigmentata sp. nov

Li,

Yu,

Fan

et al. 2024

Front. Cell. Infect. Microbiol.

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IntroductionStenotrophomonas is a prominent genus owing to its dual nature. Species of this genus have many applications in industry and agriculture as plant growth-promoting rhizobacteria and microbial biological control agents, whereas species such as Stenotrophomonas maltophilia are considered one of the leading gram-negative multi-drug-resistant bacterial pathogens because of their high contribution to the increase in crude mortality and significant clinical challenge. Pathogenic Stenotrophomonas species and most clinical isolates belong to the Stenotrophomonas maltophilia complex (SMc). However, a strain highly homologous to S. terrae was isolated from a patient with pulmonary tuberculosis (TB), which aroused our interest, as S. terrae belongs to a relatively distant clade from SMc and there have been no human association reports.MethodsThe pathogenicity, immunological and biochemical characteristics of 610A2T were systematically evaluated.Results610A2T is a new species of genus Stenotrophomonas, which is named as Stenotrophomonas pigmentata sp. nov. for its obvious brown water-soluble pigment. 610A2T is pathogenic and caused significant weight loss, pulmonary congestion, and blood transmission in mice because it has multiple virulence factors, haemolysis, and strong biofilm formation abilities. In addition, the cytokine response induced by this strain was similar to that observed in patients with TB, and the strain was resistant to half of the anti-TB drugs.ConclusionsThe pathogenicity of 610A2T may not be weaker than that of S. maltophilia. Its isolation extended the opportunistic pathogenic species to all 3 major clades of the genus Stenotrophomonas, indicating that the clinical importance of species of Stenotrophomonas other than S. maltophilia and potential risks to biological safety associated with the use of Stenotrophomonas require more attention.

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Section: Introductionmentioning

confidence: 99%

A novel pathogenic species of genus Stenotrophomonas: Stenotrophomonas pigmentata sp. nov

Li,

Yu,

Fan

et al. 2024

Front. Cell. Infect. Microbiol.

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Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri

Bansal

Patil

2022

Phytopathology®

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Based on phylo-taxonogenomics criteria, we present amended descriptions for twenty pathovars to Xanthomonas citri. Incidentally, eighteen were first reported from India. Seven out of twenty are currently classified as X. axonopodis, twelve out of twenty as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining sixteen were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. The present proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants.

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Systematic hyper-variation and evolution at a lipopolysaccharide locus in the population of Xanthomonas species that infect rice and sugarcane

Singh

Bansal

Patil

2022

Preprint

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Advent of high throughput sequencing and population genomics is enabling researchers to investigate selection pressure at hyper-variable genomic loci encoding pathogen-associated molecular patter (PAMP) molecules like lipopolysaccharide (LPS) in an unprecedented manner. Xanthomonas is a model group of phytopathogenic bacteria that infects host in tissue-specific manner. Our in-depth investigation revealed that the successful emergence of lineages infecting major cereals and grasses like rice, sugarcane, and wheat was mediated by acquisition and later replacement of an ancestral type (BXO8) of LPS cassette by distinct one. In the population of the rice xylem pathogen, X. oryzae pv. oryzae (Xoo), the BXO8 is replaced by a distinct BXO1 type of cassette. Alternatively, in diverse Xanthomonas species that infect sugarcane, the BXO8 ancestral cassette has been replaced by yet another kind of Xvv type of LPS cassette, suggesting convergent evolution at an LPS locus mediated by horizontal gene transfer (HGT) events. Aside from xylem, two closely related lineages of X. oryzae that infect parenchyma tissue of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect citrus, walnut, and strawberry parenchyma, indicating yet another instance of parallel evolution facilitated by HGT. Our targeted and mega-population-based genome dynamic studies revealed potential role of acquisition of specific types of LPS cassettes in the emergence and evolution of tissue specificity in Xanthomonas. Additional cellular, molecular, genetic, and plant studies will help us figure out how a distinct type of LPS help Xanthomonas pathovars and lineages adapt to parenchyma and xylem tissues.

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Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives

Cited by 3 publications

References 77 publications

A novel pathogenic species of genus Stenotrophomonas: Stenotrophomonas pigmentata sp. nov

A novel pathogenic species of genus Stenotrophomonas: Stenotrophomonas pigmentata sp. nov

Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri

Systematic hyper-variation and evolution at a lipopolysaccharide locus in the population of Xanthomonas species that infect rice and sugarcane

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