Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Soutar, Craig D.; Stavrinides, John

doi:10.1099/ijsem.0.004542

“…A complex polyspecies microbiome has been found in necrotic lesion tissue. Three bacterial species, Gibbsiella quercinecans, Brenneria goodwinii, and Rahnella victoriana, have been consistently found, with Lonsdalea britannica sometimes present [15][16][17][18][19][20][21][22][23]. Comparisons of the genomes of these species with orthologous genes in canonical phytopathogens and nonpathogenic symbionts suggest that B. goodwinii and L. britannica have the genomic potential to cause tissue necrosis, with B. goodwinii the most likely to be the key causal necrogenic phytopathogen in AOD [16].…”

Section: Introductionmentioning

confidence: 99%

Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling

Gathercole

¹

,

Nocchi

²

,

Brown

³

et al. 2021

Forests

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Acute Oak Decline (AOD) is complex syndrome affecting Britain’s keystone native oak species, (Quercus robur L. and Q. petraea L. (Matt.) Liebl.), in some cases causing mortality within five years of symptom development. The most distinguishable symptom is weeping stem lesions, from which four species of bacteria have been isolated: Brenneria goodwinii, Gibbsiella quercinecans, Lonsdalea britannica and Rahnella victoriana. We do not yet know where else these bacteria exist, and little is known about the relationship of the wider oak leaf microbiome (phyllosphere) to acute oak decline. Here we investigate whether incidental evidence from a large oak genome re-sequencing dataset could be used to detect these bacteria in oak foliage, and whether bacterial incidence co-varied with AOD status or location. Oak leaves and buds were sampled from 421 trees at five sites in England. Whole genomic DNA from these samples was shot-gun sequenced with short reads. Non-oak reads were extracted from these data and queried to microbial databases. Reads uniquely matching AOD-associated bacterial genomes were found to be present on trees from all five sites and included trees with active lesions, trees with historic lesions and trees without AOD symptoms. The abundance of the AOD-associated bacteria did not differ between tree health categories but did differ among sites. We conclude that the AOD-associated bacteria may be members of the normal oak microbiome, whose presence on a tree is not sufficient to cause AOD symptoms.

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“…Among them, the family Enterobacteriaceae is the largest taxon in the order Enterobacteriales and contains over 30 genera including the genera assigned to incorrect family before the genomic era (https://lpsn.dsmz.de/family/enterobacteriaceae). Recently, several genera of this family were transferred to members of other families based on phylogenetic analysis using single-copy proteins [2].…”

Section: Full-textmentioning

confidence: 99%

Tenebrionicola larvae gen. nov., sp. nov., isolated from larvae of mealworm Tenebrio molitor L., and a proposal to transfer Erwinia teleogrylli Liu et al. 2016 to a new genus Entomohabitans as Entomohabitans teleogrylli comb. nov.

Lee

¹

,

Kim

²

,

Byeon

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two enterobacterial strains, designated YMB-R21T and YMB-R22, were isolated from larvae of mealworm Tenebrio molitor L. and examined for their taxonomic characteristics. A 16S rRNA gene-based neighbour-joining tree showed that the two isolates formed two distinct sublineages within the family Enterobacteriaceae and were separated from other genera of the family. The isolates showed 16S rRNA gene sequence similarity of 98.9 % to each other and ≤96.5 % to members of the order Enterobacteriales . The phylogenomic analysis based on 92 singly-copy core genes showed that the two isolates belonged to the family Enterobacteriaceae and formed a distinct sublineage at a position located remotely from the genera of the family. The loosely associated members were the type strain of Erwinia teleogrylli and members of the genus Shimwellia . Average nucleotide identity and digital DNA–DNA hybridization values showed that the isolates represented members of a novel species in the family Enterobacteriaceae . The values of amino acid identity between the two isolates and the closest relatives were 74.5–75.0 % with the type strain of E. teleogrylli and 74.5–74.8 % with the type strains of two Shimwellia species, while E. teleogrylli showed the amino acid identity values of 76.3–76.5 % with two Shimwellia species. Based on the results obtained here, we propose a new genus Tenebrionicola with the description of Tenebrionicola larvae sp. nov. (type strain YMB-R21T=KCTC 82597T=CCM 9152T and strain YMB-R22=KCTC 82598=CCM 9153), with the transfer of Erwinia teleogrylli Liu et al. 2016 to a new genus Entomohabitans as Entomohabitans teleogrylli comb. nov. (type strain SCU-B244T=CGMCC 1.12772T=DSM 28222T=KCTC 42022T).

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“…Among them, the family Budviciaceae is one of small groups and contains three genera with one or two species, Budvicia [2, 3], Liminorella [4] and Pragia [5]. The genus Limnobaculum [6], is a member of the family Enterobacteriaceae and contains the only and type species of the genus, was added to this family based on analysis of 32 single-copy core proteins [7]. Members of the family have been isolated from gut of milipede, clinical samples and well or lake water.…”

Section: Full-textmentioning

confidence: 99%

Jinshanibacter allomyrinae sp. nov., isolated from larvae of Allomyrina dichotoma, proposal of Insectihabitans xujianqingii gen. nov., comb. nov. and emended descriptions of the genera Jinshanibacter, Limnobaculum and Pragia

Lee

¹

,

Byeon

²

,

Kim

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Taxonomic positions of four Gram-negative bacterial strains, which were isolated from larvae of two insects in Jeju, Republic of Korea, were determined by a polyphasic approach. Strains CWB-B4, CWB-B41 and CWB-B43 were recovered from larvae of Protaetia brevitarsis seulensis, whereas strain BWR-B9T was from larvae of Allomyrina dichotoma. All the isolates grew at 10–37 °C, at pH 5.0–9.0 and in the presence of 4 % (w/v) NaCl. The 16S rRNA gene phylogeny showed that the four isolates formed two distinct sublines within the order Enterobacteriales and closely associated with members of the genus Jinshanibacter . The first group represented by strain CWB-B4 formed a tight cluster with Jinshanibacter xujianqingii CF-1111T (99.3 % sequence similarity), whereas strain BWR-B9T was most closely related to Jinshanibacter zhutongyuii CF-458T (99.5 % sequence similarity). The 92 core gene analysis showed that the isolates belonged to the family Budviciaceae and supported the clustering shown in 16S rRNA gene phylogeny. The genomic DNA G+C content of the isolates was 45.2 mol%. A combination of overall genomic relatedness and phenotypic distinctness supported that three isolates from Protaetia brevitarsis seulensis are different strains of Jinshanibacter xujianqingii , whereas one isolate from Allomyrina dichotoma represents a new species of the genus Jinshanibacter . On the basis of results obtained here, Jinshanibacter allomyrinae sp. nov. (type strain BWR-B9T=KACC 22153T=NBRC 114879T) and Insectihabitans xujianqingii gen. nov., comb. nov. are proposed, with the emended descriptions of the genera Jinshanibacter , Limnobaculum and Pragia .

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Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Cited by 29 publications

References 36 publications

Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling

Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling

Tenebrionicola larvae gen. nov., sp. nov., isolated from larvae of mealworm Tenebrio molitor L., and a proposal to transfer Erwinia teleogrylli Liu et al. 2016 to a new genus Entomohabitans as Entomohabitans teleogrylli comb. nov.

Jinshanibacter allomyrinae sp. nov., isolated from larvae of Allomyrina dichotoma, proposal of Insectihabitans xujianqingii gen. nov., comb. nov. and emended descriptions of the genera Jinshanibacter, Limnobaculum and Pragia

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