Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov. Issue 4 (20th April 2023)

• Record Type: Journal Article
• Authors: Dong, Kui; Pu, Ji; Yang, Jing; Zhou, Guohong; Gao, Yuqian; Kang, Zhiming; Lei, Wenjing; Ji, Xuan; Min, Guowen; Li, Hong; Li, Junqin; Sun, Bin; Xu, Jianguo
• Is Part Of: International journal of systematic and evolutionary microbiology. Volume 73:Issue 4(2023)
• Publication Date: 2023-04-20
• Subjects: healthy human eye -- phylogenetic analysis -- Paracoccus -- novel species -- sequence analysis -- whole-genome sequencing; Microbiology -- Periodicals; Microbiology -- Classification -- Periodicals; 579
• DOI: 10.1099/ijsem.0.005838
• Languages: English
• ISSNs: 1466-5026

Abstract

Abstract : Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398 T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398 T and DK608 were members of Paracoccus, most similar to Paracoccus laeviglucosivorans 43P T (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05 T (98.34 and 98.41 %), and Paracoccus limmosus NB88 T (98.21 and 98.29 %). Phenotypic analysis showed that DK398 T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β -glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0 . The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398 T . The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22 %) average nucleotide identity, digital DNA–DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398 T represents a novel species of the genus Paracoccus, for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398 T (=CGMCC 1.17227 T =JCM 33719 T ).