Corynebacterium confusum sp. nov., isolated from human clinical specimens

Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease

Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes. IMPORTANCE Corynebacterium are commonly found bacteria on the human skin. In this study, we perform comparative genomics to gain insight into genetic traits which differentiate a phylogenetically related group of Corynebacterium, the Corynebacterium tuberculostearicum species complex, that includes the most prevalent species from the genus in skin microbiomes. After resolving the presence of distinct species within the complex, we applied metagenomic analysis to uncover biogeographic associations of individual species within the complex with specific body sites and discovered that one species, commonly found in the nares of individuals, increases in abundance across multiple body sites during atopic dermatitis flares.

Isolation and characterization of Corynebacterium spp. from bulk tank raw cow's milk of different dairy farms in Germany

We detected Corynebacterium spp. in raw milk samples of three farms by means of a selective, tellurite-containing medium. The isolated strains were identified based on full 16S rRNA gene sequences and partial rpoB gene sequences as C. xerosis, C. variabile, C. lactis, C. callunae, C. confusum, C. glutamicum and C. crudilactis. The identification based on 16S rRNA and rpoB sequences was not reliable for isolates of C. xerosis. Chemotaxonomic markers of the isolates, fatty acids, acyl type of peptidoglycan, presence and length of mycolic acids, quinone patterns, and polar lipids, were in accord with the known characteristics of these species. Biochemical profiles, analyzed with the API Coryne system, were able to differentiate all groups, but were unable to identify the strains due to an inappropriate database for raw-milk associated corynebacteria. Most of the tested isolates showed a single-substance resistance against oxacillin, but three single isolates were classified as multidrug resistant.

Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744(T.)

Corynebacterium timonense strain 5401744^T is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. It was isolated from the blood of a patient with endocarditis. In this work, we describe a set of features of this organism, together with the complete genome sequence and annotation. The 2,553,575 bp long genome contains 2,401 protein-coding genes and 55 RNA genes, including between 5 and 6 rRNA operons.

Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid

Gram-positive, facultatively anaerobic, rod-shaped bacteria were isolated from the blood of a patient with endocarditis (strain 5401744T) and from the hip joint fluid of a patient with an infected orthopaedic prosthesis (strain 5402485T). These strains were characterized by using a polyphasic taxonomic approach. Based on cellular morphology and biochemical criteria the two isolates were tentatively assigned to the genus Corynebacterium, although they did not correspond to any recognized species. The predominant fatty acids were a mix of C18:2omega6,9c and anteiso-C18:0 (32.1% of the total), C16:0 (26.3%) and C18:1omega9c (22.5%) for strain 5402485T and C18:1omega9c (36.4%), C17:1omega9c (27.1%) and C16:0 (10.9%) for strain 5401744T. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 5401744T was closely related to the type strains of Corynebacterium auris, Corynebacterium capitovis, Corynebacterium lipophiloflavum and Corynebacterium mycetoides (97.0, 96.6, 96.5 and 96.3% similarity, respectively) and strain 5402485T was closely related to the type strains of Corynebacterium macginleyi, Corynebacterium accolens, Corynebacterium tuberculostearicum, Corynebacterium confusum, Corynebacterium mastitidis and Corynebacterium renale (95.6, 95.3, 95.3, 94.5, 94.0 and 93.5%, respectively). On the basis of phenotypic data and phylogenetic inference, these isolates are considered to represent two novel species of the genus Corynebacterium, for which the names Corynebacterium timonense sp. nov. (type strain, 5401744T=CSUR P20T=CIP 109424T=CCUG 53856T) and Corynebacterium massiliense sp. nov. (type strain, 5402485T=CSUR P19T=CIP 109423T=CCUG 53857T) are proposed.

Corynebacterium ureicelerivorans sp. nov., a lipophilic bacterium isolated from blood culture

A lipophilic coryneform bacterium isolated from a blood culture from a patient with signs of septicaemia was characterized by means of phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids, which are consistent with the genus Corynebacterium. The isolate was characterized biochemically by the very rapid (approx. 60 s) positive result that was obtained in a urease test in the API Coryne system. Comparative 16S rRNA gene sequencing demonstrated that the isolate belonged phylogenetically to the genus Corynebacterium. The values for sequence divergence (⩾1.4 %) with respect to known Corynebacterium species, together with phenotypic differences, show that the unidentified bacterium represents a novel member of this genus. On the basis of both the phenotypic and phylogenetic data, this isolate should be classified within a novel species of the genus Corynebacterium, for which the name Corynebacterium ureicelerivorans sp. nov. is proposed. The type strain is IMMIB RIV-2301T (=DSM 45051T=CCUG 53377T).

Corynebacterium ciconiae sp. nov., isolated from the trachea of black storks (Ciconia nigra)

Eight unidentified Gram-positive, rod-shaped organisms were recovered from the tracheas of apparently healthy black storks (Ciconia nigra) and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria the isolates were tentatively assigned to the genus Corynebacterium, although three of the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that all of the isolates were phylogenetically members of the genus Corynebacterium. Five strains were genotypically identified as representing Corynebacterium falsenii, whereas the remaining three strains represented a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium mastitidis and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from black storks represent a novel species within the genus Corynebacterium, for which the Corynebacterium ciconiae sp. nov. is proposed. The type strain is CECT 5779T (=BS13T=CCUG 47525T).

Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov

Nine unidentified Gram-positive, lipophilic corynebacteria were isolated from clinical and food samples and subjected to a polyphasic taxonomic analysis. The bacteria were distinguished from Corynebacterium species with validly published names by biochemical tests, fatty acid content and whole-cell protein analysis. Comparative 16S rRNA gene sequence analysis demonstrated unambiguously that the nine strains were related phylogenetically to the species ‘Corynebacterium tuberculostearicum’ and represented a distinct subline within the genus Corynebacterium. On the basis of both phenotypic and phylogenetic evidence, the formal description of Corynebacterium tuberculostearicum sp. nov. is proposed. The type strain of C. tuberculostearicum is Medalle XT (=LDC-20T=CIP 107291T=CCUG 45418T=ATCC 35529T).

Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica)

A previously unknown Gram-positive, non-spore-forming, non-lipophilic, catalase-positive, irregular rod-shaped bacterium (M/106/00/5T) was isolated, in mixed culture, from the penis of a Caspian seal (Phoca caspica). The strain was a facultative anaerobe that was able to grow at 22 and 42 °C. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of more than 5 % from other described Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium isolated from a Caspian seal (strain M/106/00/5T=CCUG 44566T=CIP 107965T) be classified as the type strain of a novel species of the genus Corynebacterium, Corynebacterium caspium sp. nov.

Isolation of Corynebacterium falsenii and description of Corynebacterium aquilae sp. nov., from eagles

Biochemical, molecular chemical and molecular genetic studies were performed on seven unidentified gram-positive, rod-shaped organisms recovered from eagles. The strains were provisionally identified as Corynebacterium jeikeium with the commercial API Coryne system, but they were able to grow under anaerobic conditions and were non-lipophilic. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates belonged phylogenetically to the genus Corynebacterium. Three strains were identified genotypically as Corynebacterium falsenii; the remaining four strains corresponded to a hitherto unknown lineage within the genus Corynebacterium, associated with a small subcluster of species that included Corynebacterium diphtheriae and its close relatives. The unknown bacterial strains were readily distinguished from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterial strains from eagles should be classified as Corynebacterium aquilae sp. nov. (type strain is S-613T = CECT 5993T = CCUG 46511T).

Corynebacterium sphenisci sp. nov., isolated from wild penguins

Six unidentified gram-positive, rod-shaped organisms recovered from the cloacae of apparently healthy wild penguins were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types, consistent with the genus Corynebacterium. Corynomycolic acids, which are characteristic of the genus, were also detected, albeit in small amounts. Comparative 16S rRNA gene sequencing studies showed that the unidentified organisms were phylogenetically related to corynebacteria and represent a novel subline associated with a small subcluster of species that includes Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium freneyi. The unknown isolates were readily distinguished from their closest phylogenetic relatives and all other Corynebacterium species with validly published names by using a combination of biochemical and chemotaxonomic criteria. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown isolates recovered from penguins be classified as a novel species in the genus Corynebacterium, Corynebacterium sphenisci sp. nov. The type strain is CECT 5990T (= CCUG 46398T).

Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins

Twenty unidentified Gram-positive, rod-shaped organisms were recovered from the cloacae of apparently healthy wild penguins (Spheniscus magellanicus) and subjected to a polyphasic taxonomic analysis. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Corynebacterium, although the organisms did not appear to correspond to any recognized species. Lipid studies confirmed this generic placement, and comparative 16S rRNA gene sequencing showed that the unidentified organisms represent a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium diphtheriae and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from penguins be classified in the genus Corynebacterium, as Corynebacterium spheniscorum sp. nov. The type strain is strain PG 39T (=CCUG 45512T =CECT 5986T).

Characteristics of rare or recently described corynebacterium species recovered from human clinical material in Canada

Nineteen new Corynebacterium species or taxa described since 1995 have been associated with human disease. We report the characteristics of 72 strains identified as or most closely resembling 14 of these newer, medically relevant Corynebacterium species or taxa, as well as describe in brief an isolate of Corynebacterium bovis, a rare pathogen for humans. The bacteria studied in this report were nearly all derived from human clinical specimens and were identified by a polyphasic approach. Most were characterized by nearly full 16S rRNA gene sequence analysis. Some isolates were recovered from previously unreported sources and exhibited unusual phenotypes or represented the first isolates found outside Europe. Products of fermentation, with emphasis on the presence or absence of propionic acid, were also studied in order to provide an additional characteristic with which to differentiate among phenotypically similar species.

Isolation and characterization of a black-pigmented Corynebacterium sp. from a woman with spontaneous abortion

An unusual black-pigmented coryneform bacterium was isolated from the urogenital tract of a woman who experienced a spontaneous abortion during month 6 of pregnancy. Biochemical and chemotaxonomic analyses demonstrated that the unknown bacterium belonged to the genus Corynebacterium. Phylogenetic analysis based on 16S rRNA sequences (GenBank accession no. AF220220) revealed that the organism was a member of a distinct subline which includes uncultured Corynebacterium MTcory 1P (GenBank accession no. AF115934), derived from prostatic fluid, and Corynebacterium CDC B8037 (GenBank accession no. AF033314), an uncharacterized black-pigmented coryneform bacterium. On the basis of chemotaxonomic and phylogenetic evidence, this organism probably represents a new species and is most closely related to the uncharacterized Centers for Disease Control and Prevention group 4 coryneforms. Our strain is designated CN-1 (ATCC 700975).

Phenotypic and phylogenetic characterization of a new Corynebacterium species from dogs: description of Corynebacterium auriscanis sp. nov

Six strains of a previously undescribed catalase-positive coryneform bacterium isolated from clinical specimens from dogs were characterized by phenotypic and molecular genetic methods. Biochemical and chemotaxonomic studies revealed that the unknown bacterium belonged to the genus Corynebacterium sensu stricto. Comparative 16S rRNA gene sequencing showed that the six strains were genealogically highly related and constitute a new subline within the genus Corynebacterium; this subline is close to but distinct from C. falsenii, C. jeikeium, and C. urealyticum. The unknown bacterium from dogs was distinguished from all currently validated Corynebacterium species by phenotypic tests including electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as a new species, Corynebacterium auriscanis. The type strain of C. auriscanis is CCUG 39938(T).

Ribosomal DNA sequencing as a tool for identification of bacterial pathogens

Conventional methods for the identification and characterization of clinical isolates of bacterial pathogens sometimes fall short when such isolates exhibit unusual phenotypic profiles. Recent advances in DNA sequencing technology have greatly enhanced the ability of the microbiologist to determine the identity of a bacterial isolate. Given the relative objectivity of DNA sequence information and growing availability of sequence information databases, a significant movement is now afoot to use molecular methods for the identification of clinical pathogens.