Search tips
Search criteria 


Logo of genannJournal InfoAuthorsPermissionsJournals.ASM.orggenomeA ArticleGenome Announcements
Genome Announc. 2017 September; 5(37): e00975-17.
Published online 2017 September 14. doi:  10.1128/genomeA.00975-17
PMCID: PMC5597766

Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9


Corynebacterium amycolatum ICIS 9 was isolated from a vaginal smear of a healthy woman. Here, we report the draft genome sequence of C. amycolatum ICIS 9, which will be useful for further studies of specific genetic features of this strain and for understanding its probiotic properties.


Vaginal microbiocenosis is an open complex multicomponent system that exists in a state of dynamic equilibrium. It is widely known that lactobacilli play a major role in protecting the vaginal environment from nonindigenous and potentially harmful microorganisms (1, 2). Using culture-independent techniques, several investigators have demonstrated that a significant proportion (7 to 33%) of healthy women lacks appreciable numbers of Lactobacillus spp. in the vagina (3, 4), which may be replaced by other lactic acid-producing bacteria such as Atopobium vaginae and Megasphaera, Leptotrichia, and Corynebacterium spp. (5). Therefore, in the absence of lactobacilli, these organisms are probably involved in protecting the vaginal biotope from infection.

We carried out a pilot study to determine the biological properties of vaginal isolates of microorganisms of the genus Corynebacterium. We found that Corynebacterium spp. that are isolated from healthy women have potential probiotic properties. Metabolites of these strains significantly increased antagonistic activity of the peroxide-producing lactobacilli (6), inhibited growth and biofilm formation, and destroyed 1-day-old (24-h-grown) pathogenic and opportunistic microorganisms (7). Here, we report the draft genome sequence of Corynebacterium amycolatum ICIS 9, which will be useful for further studies of specific genetic features of this strain and for understanding its probiotic properties.

The strain was grown in tryptic soy broth (Sigma-Aldrich Co., USA) at 37°C. Genomic DNA was extracted from an overnight culture using the phenol-chloroform method. The preparation of DNA libraries and sequencing were carried out at the Center of Shared Equipment “Persistence of Microorganisms” at the Institute for Cellular and Intracellular Symbiosis, UrB RAS (Orenburg, Russia). Library preparation was performed using the Nextera XT DNA library preparation kit (Illumina, USA) according to the manufacturer’s instructions. Sequencing was performed on an Illumina MiSeq platform using a MiSeq version 3 reagent kit (Illumina). The reads were quality trimmed using the sliding window mode of the Trimmomatic program (8). De novo genome assembly was performed using a SPAdes genome assembler (St. Petersburg genome assembler version 3.9.0) (9). The draft sequence consists of 181 contigs of more than 200 bp, with an average coverage of 22.0×, an N50 length of 45,496 bp, and an L50 value of 18 bp. It has a G+C content of 58.67% and a total length of 2,587,830 bp. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (, which identified 2,392 coding sequences, including 2,330 proteins, 53 pseudogenes, and 6 rRNAs (3 complete rRNAs [5S, 16S, and 23S] and 3 partial rRNAs [5S]).

Genome sequence analysis of C. amycolatum ICIS 9 showed the presence of genes that are responsible for the biosynthesis of vitamins (biotin, riboflavin, and pyridoxine), folate, lipoic acid, and other cofactors; a large number of genes of stress response systems, including those related to oxidative stress, heat shock, and cold shock; and a number of genes that contribute to antibiotic resistance (vancomycin, fluoroquinolones, tetracycline, and beta-lactam) and heavy-metal resistance (arsenic, mercury, and cobalt-zinc-cadmium). A number of genes are responsible for the synthesis of possible biosurfactants, such as phospholipids, triacylglycerols, fatty acids, and neutral lipids.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MTPT00000000. The version described in this paper is the first version, MTPT01000000.


We thank Darуa Poshvina for the technical assistance in preparing the DNA library.

This work was carried out in the framework of fundamental research at the Ural Branch of the Russian Academy of Sciences, project 15-4-4-28. This research was supported by a 2017 grant from the Orenburg Region: “Certification of Bacteria and Protozoa, Having Medical and Biotechnological Significance, Based on Full-Genome Sequencing.”


Citation Gladysheva IV, Khlopko YA, Cherkasov SV. 2017. Draft genome sequence of the vaginal isolate Corynebacterium amycolatum ICIS 9. Genome Announc 5:e00975-17.


1. Klebanoff SJ, Hillier SL, Eschenbach DA, Waltersdorph AM 1991. Control of the microbial flora of the vagina by H2O2-generating lactobacilli. J Infect Dis 164:94–100. doi:.10.1093/infdis/164.1.94 [PubMed] [Cross Ref]
2. Kaewnopparat S, Dangmanee N, Kaewnopparat N, Srichana T, Chulasiri M, Settharaksa S 2013. In vitro probiotic properties of Lactobacillus fermentum SK5 isolated from vagina of a healthy woman. Anaerobe 22:6–13. doi:.10.1016/j.anaerobe.2013.04.009 [PubMed] [Cross Ref]
3. Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J, Van Simaey L, De Ganck C, Temmerman M, Vaneechoutte M 2004. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol 4:16. doi:.10.1186/1471-2180-4-16 [PMC free article] [PubMed] [Cross Ref]
4. Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW 2005. Microbes on the human vaginal epithelium. Proc Natl Acad Sci U S A 102:7952–7957. doi:.10.1073/pnas.0503236102 [PubMed] [Cross Ref]
5. Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, Foster JA, Forney LJ 2007. Differences in the composition of vaginal microbial communities found in healthy caucasian and black women. ISME J 1:121–133. doi:.10.1038/ismej.2007.12 [PubMed] [Cross Ref]
6. Cherkasov SV, Gladysheva IV, Bukharin OV 2012. Symbiotic interactions of corynebacteria and lactobacilli in realization of oxidative mechanisms of antagonism. Zh Mikrobiol Epidemiol Immunobiol 6:13–16. [PubMed]
7. Gladysheva IV, Cherkasov SV, Khlopko YA 2017. Antibacterial activities of metabolites from Corynebacterium spp. strains isolated from reproductive tract of a healthy woman against human pathogenic bacteria. Int J Pharm Biol Sci 8:549–556.
8. Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:.10.1093/bioinformatics/btu170 [PMC free article] [PubMed] [Cross Ref]
9. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)