Chryseobacterium carnipullorum sp. nov., isolated from raw chicken

Abstract

Three Gram-staining-negative, rod-shaped, non-spore-forming, non-motile, oxidase-positive, yellow pigmented and aerobic bacterial isolates designated 8_R23573, 9_R23581 T and 10_R23577 were isolated from raw chicken at a broiler processing plant in Bloemfontein, South Africa. A polyphasic taxonomic approach was used to determine their exact taxonomic identities. Phylogenetic analysis of the 16S rRNA gene sequences showed that the three strains belonged to the genus Chryseobacterium, exhibiting the highest similarities to Chryseobacterium shigense DSM 17126 T (98.6-99.2 %) and Chryseobacterium luteum DSM 18605 T (98.3-98.7 %). The most abundant quinone was menaquinone MK-6 and the predominant cellular fatty acids were iso-15 : 0, iso-17 : 1v9c, iso-17 : 0 3-OH and summed feature 3 (iso-16 : 1v7c and/or iso-15 : 0 2-OH), which supported the affiliation of the strains to the genus Chryseobacterium. The DNA G+C contents of the strains were 36.9, 36.7 and 36.6 mol% respectively. The DNA-DNA hybridization results gave relatedness values ranging from 78.8 to 87.2 % among the three strains and 23.4 to 56.1 % to the two nearest phylogenetic neighbours C. shigense DSM 17126 T and C. luteum LMG 23785 T . On the basis of the data from this polyphasic study, the three strains are concluded to represent a novel species of the genus Chryseobacterium for which the name Chryseobacterium carnipullorum sp. nov. is proposed. The type strain is 9_R23581 T (5LMG 26732 T 5DSM 25581 T ).The genus Chryseobacterium belongs to the family Flavobacteriaceae (Bernardet et al., 2002;Bernardet, 2011). It was described by Vandamme et al. (1994) to accommodate six species formerly classified within the genus Flavobacterium, namely Chryseobacterium balustinum, Chryseobacterium gleum, Chryseobacterium indologenes, Chryseobacterium indoltheticum, Chryseobacterium meningosepticum and Chryseobacterium scophthalmum and was later amended (Kämpfer et al., 2009). The type species is C. gleum. Members of the genus Chryseobacterium include psychrotolerant and proteolytic spoilage micro-organisms that are widely distributed in food sources such as milk, fish, meat and poultry (Hugo et al., 2003;de Beer et al., 2005 de Beer et al., , 2006 and occur in a variety of ecological niches such as soil, water, sludge, plants, and human and fish clinical specimens (Hugo et al., 2003;Bernardet et al., 2005Bernardet et al., , 2011Hugo & Jooste, 2012).In 2006 the genus Chryseobacterium consisted of only 10 validly named species. Since then the genus has undergone significant and rapid expansion and, at the time of writing, it comprises 61 species with validly published names (Bernardet et al., 2006) and more continue to be described (Euzéby, 2012). This can be ascribed to the readily available and improved phenotypic, chemotaxonomic and molecular identification methods used in the polyphasic taxonomic approach.During the course of the characterization of chryseobacterial strains isolated from raw chicken in a previous study (de Beer, 2005) at a poultry processing plan...

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

“…Organisms may have 16S rRNA gene sequences over 99 % similar or even identical and still belong to different species, with DDH values below 70 % and ANI values less than 95 %. For example, the type strains of Chryseobacterium shigense [60] and Chryseobacterium carnipullorum [61] share 99.3 % identity in their 16S rRNA gene sequences, which could indicate they belong to the same species, but genome comparisons suggest otherwise (DNA–DNA hybridization <44 % [62, 63] and ANIb <91 %). The 16S rRNA gene sequences of Chryseobacterium jejuense are also very similar to those of Chryseobacterium nakagawai and Chryseobacterium lactis (98.9 and 98.8% identical, respectively), but the ANIb values from genome comparisons (averaging <87 and<82 %, respectively) confirm that all are separate species.…”

Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense

“…Members of the genus Chryseobacterium, described by Vandamme et al (1994), have been isolated from a wide variety of samples, such as the plant rhizosphere (Park et al, 2006;Kämpfer et al, 2014), compost (Kämpfer et al, 2010), soil (Shen et al, 2005;Weon et al, 2008;Hoang et al, 2013), meat (de Beer et al, 2005;Charimba et al, 2013), a newt tank (Kirk et al, 2013), desert soil (Peng et al, 2009), milk (Hantsis-Zacharov et al, 2008), diseased fish (Bernardet et al, 2005;Ilardi et al, 2009), a beer-bottling plant (Herzog et al, 2008), fresh water (Kim et al, 2005, a dairy environment (Hugo et al, 2003), wastewater (Kämpfer et al, 2003) and clinical samples (Vaneechoutte et al, 2007;Kämpfer et al, 2009). The members of the genus Chryseobacterium are Gramnegative and aerobic.…”

分离自成都大熊猫兽舍空气中的一株金黄杆菌属新种的鉴定

“…Strain 25-1 T showed less than 96.4% sequence similarity to the type strains of all recognized species in the genus Chryseobacterium. The highest 16S rRNA sequence similarity was found with C. carnis NCTC 13525 T (96.4%) (Holmes et al, 2013), followed by C. lathyri RBA2-6 T (95.8%), C. zeae JM1085 T (95.8%) (Kämpfer et al, 2014b), C. shigense GUM kaji T (95.8%) (Shimomura et al, 2005), C. gwangjuense THG A-18 T (95.7%) (Park et al, 2013), and C. carnipullorum 9-R23581 T (95.7%) (Charimba et al, 2013), as determined using the EzTaxon server 2.1. Strain 25-1 T was included in a cluster containing the type strains of C. carnis and C. chaponense, forming a distinct phylogenetic lineage within the genus Chryseobacterium in the neighborjoining phylogenetic tree (Fig.…”