Citrobacter portucalensis sp. nov., isolated from an aquatic sample

Ribeiro, Teresa Gonçalves; Gonçalves, Bruno Ribeiro; Silva, Mickael Santos Da; Novais, Ângela; Machado, Elisabete; Carriço, João André; Peixe, Luı́sa

doi:10.1099/ijsem.0.002154

Cited by 42 publications

(34 citation statements)

References 19 publications

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“…Multilocus sequence analysis has been increasingly used to identify and describe novel species ( Killer et al, 2014 , 2017 ; Chen et al, 2017 ; Doi et al, 2017 ; Liu et al, 2017 ; Ribeiro et al, 2017 ; Modesto et al, 2018 ). Mattarelli et al (2014) stated that a minimum of two additional phylogenetic markers should be used to accurately identify isolates, especially for describing novel species in the genera Bifidobacterium and Lactobacillus .…”

Section: Introductionmentioning

confidence: 99%

Identification and Classification for the Lactobacillus casei Group

Huang

et al. 2018

Front. Microbiol.

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Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.

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Section: Introductionmentioning

confidence: 99%

Identification and Classification for the Lactobacillus casei Group

Huang

et al. 2018

Front. Microbiol.

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“…Maximum-likelihood phylogenetic trees of 23 whole genome-sequences were reconstructed by applying IQ-Tree with 1000 bootstrap replicates. Alignments of 16S rRNA gene sequences downloaded from EZ-Taxon [18 ], concatenated partial fusA (protein synthesis elongation factor-G), leuS (leucine tRNA synthetase), pyrG (CTP synthetase) and rpoB (β-subunit of RNA polymerase) [19] as well as recN sequences (DNA repair) [2,20] used for recent description of new Citrobacter species extracted from available WGS data were done by clustal_w (BioEdit version 7.2.5) followed by phylogenetic treeing with RAxML and the GTR model in conjunction with GAMMA rates [21]. Trees were visualized using FigTree (version 1.4.3).…”

Section: Maldi-tof Axima System Assurance (Biomérieux;mentioning

confidence: 99%

“…Biochemical characteristics were analysed by the API 20E and VITEK2 systems and results are listed in Table 1 for all nine study isolates and closely related type strains of the genus Citrobacter [2,19,20,30]. Semi-quantitative analysis of enzymatic activities of all strains demonstrate positive reactions for l-pyrrolidonylarylamidase and β-galactosidase, but negative reactions for α-glucosidase, phosphatase, lipase, lysine decarboxylase, tryptophan deaminase, gelatinase, α-galactosidase, Glu-Gly-Arg-arylamidase, β-N-acetyl-galactosaminidase, β-xylosidase, β-alaninarylamidase-pNA and β-glucoronidase.…”

Section: Physiologymentioning

confidence: 99%

Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples

Oberhettinger

Schüle

Marschal

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Nine independent Gram-negative bacterial strains were isolated from rectal swabs or stool samples of immunocompromised patients from two different wards of a university hospital. All isolates were phylogenetically analysed based on their 16S rRNA gene sequence, housekeeping gene recN, multilocus sequence analysis of concatenated partial fusA, leuS, pyrG and rpoB sequences, and by whole genome sequencing data. The analysed strains of the new species cluster together and form a separate branch with Citrobacter werkmanii NBRC105721T as the most closely related species. An average nucleotide identity value of 95.9–96% and computation of digital DNA–DNA hybridization values separate the new species from all other type strains of the genus Citrobacter . Biochemical characteristics further delimit the isolates from closely related Citrobacter type strains. As a result of the described data, a new Citrobacter species is introduced, for which the name Citrobacter cronae sp. nov. is proposed. The type strain is Tue2-1T with a G+C DNA content of 52.2 mol%.

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“… Citrobacter portucalensis is a Gram-negative facultative anaerobic bacterium belonging to the family Enterobacteriaceae , and the type strain, Citrobacter portucalensis A60 T , was isolated from water in Portugal ( 1 ). Members of the genus Citrobacter occur in the intestines of humans and animals, and due to consequent fecal shedding, they can also be found in varied environments, such as water, soil, and sewage.…”

Section: Genome Announcementmentioning

confidence: 99%