Proteus faecis sp. nov., and Proteus cibi sp. nov., two new species isolated from food and clinical samples in China

Dai, Hongyue; Chen, Aiping; Wang, Yubao; Lu, Binghuai; Wang, Yonglu; Chen, Jianhui; Huang, Ying; Li, Zhenpeng; Fang, Yujie; Xiao, Tao; Cai, Hongyan; Du, Zong‐Jun; Wei, Qiang; Kan, Biao; Wang, Duochun

doi:10.1099/ijsem.0.003248

Cited by 22 publications

(14 citation statements)

References 21 publications

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“…Meier-Kolthoff et al [34] proposed a 79 % dDDH threshold for the subspecies level. By comparing the physiological characteristics of both type strains, a few differences were found that support a subspecies status [14]. Both species differ in the acid formation from d -fructose and l -rhamnose.…”

Section: Full-textmentioning

confidence: 99%

“…Species of the genus Proteus are physiologically very similar and a differentiation between species is only possible on the basis of a set of features. Nevertheless, the type strains of the proposed subspecies and the reference strain of the genomic species share characteristics which enable them to be distinguished from the other type strains [14].…”

Section: Full-textmentioning

confidence: 99%

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Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

Behrendt

Wende

Kolb

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae . The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA–DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae . Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.

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Section: Full-textmentioning

confidence: 99%

Section: Full-textmentioning

confidence: 99%

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

Behrendt

Wende

Kolb

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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“…Except for P. mirabilis ATCC 29906 T , all of the other test Proteus strains' whole genome sequences were sequenced by our group, and these data were deposited into the NCBI database. The GenBank accession numbers are listed below in Table 2 [7,8,9]. Figure S1.…”

Section: Genomic Relatedness Among Isolates Of Different Speciesmentioning

confidence: 99%

“…Genospecies 3 can be distinguished from Proteus genospecies 4, 5 and 6 because it is negative for Jordan's tartrate utilization and was named by the species of P. hauseri, while genospecies 4, 5 and 6 remained unnamed due to their undistinguishable phenotypic differentiation [4]. In addition, six newly de ned species, i.e., P. terrae and P. cibarius, P. alimentorum, P. columbae, P. faecis and P. cibi, were proposed recently based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses [5][6][7][8][9]. Thus, the genus Proteus comprises ten validly published species and three unnamed genospecies to date (4, 5 and 6).…”

Section: Introductionmentioning

confidence: 99%

Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015

Dai

et al. 2020

Preprint

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Background: Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. Results: Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. Conclusions: This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.

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“…remained unnamed due to their undistinguishable phenotypic differentiation [4]. In addition, six newly defined species, i.e, P. terrae and P. cibarius, P. alimentorum, P. columbae, P. faecis and P. cibi were proposed recently based on phylogenetic, phenotypic, chemotaxonomic and genotypic analysis [5][6][7][8][9].…”

mentioning

confidence: 99%

A multilocus sequence analysis for the taxonomic update and identification of the genus Proteus

Dai¹,

Lu²,

Li³

et al. 2020

Preprint

Self Cite

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Background: The members of the genus Proteus are commonly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species are remain unelucidated. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within genus of Proteus. Results: Of all 223 Proteus strains collected in current study, phylogenetic tree of concatenated five HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided into eleven clusters, which representative of their counterpart species. Meanwhile, phylogenetic trees of the five individual HKGs were also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intra-species distance of HKGs concatenation, all inter-species indicated more significant different distances than those of intra-species, which revealed these HKGs concatenation can be used as gene marker to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA and each of eleven clusters were congruent with eleven different Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus, and found that P. mirabilis is the most species of Proteus. However, the top second is P. terrae, but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, three species, P. terrae, P. cibarius and Proteus genospecies 5 should be regarded as the heterotypic synonyms.Conclusions: Our data suggested the MLSA was a powerful method for the discrimination and classification of the Proteus at species level. The MLSA scheme provides a rapid, economical and precise identification of Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in clinical diagnosis and treatment of Proteus infection.

show abstract

Proteus faecis sp. nov., and Proteus cibi sp. nov., two new species isolated from food and clinical samples in China

Cited by 22 publications

References 21 publications

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015

A multilocus sequence analysis for the taxonomic update and identification of the genus Proteus

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