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Complete genome sequence of Streptomyces sp. MMS22-DDSA8, a soil actinobacterium exhibiting antifungal activity
Korean J. Microbiol. 2024;60(2):92-94
Published online June 30, 2024
© 2024 The Microbiological Society of Korea.

Jae Ha Lee1, Young Soo Hong2, and Seung Bum Kim1*

1Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
2Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
Correspondence to: *E-mail:;
Tel.: +82-42-821-6412; Fax: +82-42-822-7367
Received February 1, 2024; Revised April 8, 2024; Accepted April 12, 2024.
Streptomyces sp. MMS22-DDSA8 is a Gram-positive, aerobic, filamentous and spore-forming actinobacterium isolated from soil. Strain MMS22-DDSA8 exhibited antimicrobial activity against filamentous fungi. In this study, the whole genome sequence of strain MMS22-DDSA8 was determined, and a single contig consisting of 8.22 Mb in length with a G + C content of 71.2% was obtained. The 16S rRNA gene and genome-based analyses indicated that strain MMS22-DDSA8 shared highest similarities with Streptomyces lydicamycinicus NBRC 110027T. The in silico genome analysis indicated presence of 26 biosynthetic gene clusters for secondary metabolite production, including those related to antimicrobial activity. The detailed analysis of genome indicated a high potential of strain MMS22-DDSA8 as a novel producer of antimicrobial compounds.
Keywords : Streptomyces lydicamycinicus, antifungal activity, biosynthetic gene cluster, whole genome

Actinobacteria are aerobic, Gram-positive bacteria with high DNA G + C contents, and widely distributed in terrestrial and aquatic environments. They are also well known for producing a wide range of secondary metabolites, including antibiotics, enzymes, pigments, plant growth facilitators and flavoring agents (Ranjani et al., 2016). The genus Streptomyces is not only the representative group of actinobacteria, but also the largest genus among prokaryotes, as the genus encompasses more than 700 valid species (Kämpfer, 2015; Parte et al., 2020). Streptomyces is a well-known producer of antibiotic compounds, and it is estimated that about two-thirds of known antibiotics have been originated from this genus (Alam et al., 2022). These compounds include antifungal agents, as reported in a number of studies (Olanrewaju and Babalola, 2019; Pacios-Michelena et al., 2021; Alam et al., 2022).

In this study, an actinobacterial isolate designated strain MMS22-DDSA8, showing antifungal activity against filamentous fungi, was subjected to genome based analysis. Strain MMS22-DDSA8 was isolated from soil as described previously (Lee, 2023). The whole genome analysis was performed with a hybrid sequencing technology using the MiSeq (Illumina) and MinION sequencing platforms (Oxford Nanopore Technologies) by the service of KNU NGS center (, and the obtained reads were assembled using Flye ver. 2.8.3-b1695 (Kolmogorov et al., 2019) and Pilon ver. 1.23 (Walker et al., 2014). The assembled sequence was then annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP; (Tatusova et al., 2016). Taxonomic identification based on 16S rRNA gene was performed using EzBioCloud (Yoon et al., 2017), and digital DNA-DNA hybridization (dDDH) values were also calculated using the Type Strain Genome Server (TYGS) (Meier-Kolthoff and Göker, 2019). Potential biosynthetic gene clusters (BGCs) for secondary metabolite production were predicted using antiSMASH bacterial version (Blin et al., 2023).

The obtained genome data of strain MMS22-DDSA8 consisted of a single contig with a total length of 8,223,489 bp and a DNA G + C content of 71.20%. The total number of genes were 7,429, the coding sequences (CDS) were 7,342, and protein coding genes were 6,116. The number of RNA genes were 87, which include 18 copies of rRNAs (6 copies each of 5S, 16S and 23S subumits), 66 tRNAs, and 3 ncRNAs. A total of 5 CRISPR arrays were also found within the genome. The detailed features of whole genome are given in Table 1.

Main features of the genome of strain MMS22-DDSA8

Feature MMS22-DDSA8
BioProject no. PRJNA844529
BioSample no. SAMN28822300
Accession no. CP098437
Size (Mb) 8.22
G + C content (%) 71.20
No. of contigs 1
Total genes 7,430
CDS 7,343
CDS with protein 6,084
Pseudogenes 1,259
RNA genes 87
rRNAs (5S, 16S, 23S) 6, 6, 6
tRNAs 66
ncRNAs 3
CRISPR arrays 5

The 16S rRNA gene sequence-based analysis indicated that strain MMS22-DDSA8 was mostly related to S. lydicamycinicus NBRC 110027T with a sequence similarity of 99.93%, then to Streptomyces angustmyceticus NRRL B-2347T with 99.86% similarity. The comparison of dDDH also indicated that strain MMS22-DDSA8 shared highest relatedness of 95.1% with S. lydicamycinicus NBRC 110027T, thus confirming that MMS22-DDSA8 could be assigned to S. lydicamycinicus.

The prediction of BGCs for secondary metabolites yielded 26 clusters for various compounds. Those BGCs included those for several antibiotics, in particular a lassopeptide type BGC for citrulassin D (locus tag NGC97_09810–09880) sharing 100% gene content similarity with that from Streptomyces katrae (MIBiG accession no. BGC0001550), a hybrid of type I polyketide synthase (T1PKS)-non-ribosomal peptide synthetase (NRPS) type BGC for lydicamycin (locus tag NGC97_33090 – 33410) sharing 96% similarity with that from Streptomyces sp. ID38640 (MIBiG no. BGC0001477), and a type II PKS (T2PKS) BGC for oxytetracycline (locus tag NGC97_04610 – 04945) sharing 95% similarity with that from Streptomyces rimosus (MIBiG no. BGC0000254). A BGC for antipain (locus tag NGC97_02465–02705), an oligopeptide acting as a protease inhibitor of trypsin and papain (Suda et al., 1972), was also predicted, which shared 100% similarity with that from Streptomyces sp. (MIBiG no. BGC0002051). The overall profile of the predicted BGCs were fairly similar to that of S. lydicamycinicus NBRC 110027T, but a siderophore type BGC for synechobactin (locus tag NGC97_10220–10335), albeit with low similarity, was found only in strain MMS22-DDSA8. It is also notable that S. lydicamycinicus NBRC 110027T was isolated from deep sea environment (Komaki et al., 2020), which is in contrast to strain MMS22-DDSA8, an isolate from soil.

In this study, a high quality genome of Streptomyces sp. MMS22-DDSA8, a soil actinobacterium exhibiting antifungal activity, was obtained and the resultant data confirmed that the strain can also be a producer of various antibacterial agents such as lydicamycin, oxytetracycline and citrulassin D, which shows a high potential of strain MMS22-DDSA8 as a producer of various bioactive metabolites.

Nucleotide sequence accession numbers

Streptomyces sp. strain MMS22-DDSA8 was deposited at the Korean Collection for Type Cultures (KCTC) under the accession number KCTC 59216. The GenBank accession number for the whole genome sequence of strain MMS22-DDSA8 is CP098437. The relevant BioProject and BioSample numbers are PRJNA844529 and SAMN28822300, respectively.

적 요

사상성 진균류에 대한 항균활성을 보이는 방선균주를 분리하여 Streptomyces sp. MMS22-DDSA8로 명명하였고, 전장유전체를 분석한 결과 총 연장 8.22 Mb, G + C 함량 71.2%의 단일 염색체 정보를 얻었다. MMS22-DDSA8는 16S rRNA 유전자 및 전장유전체 기반 동정 결과 Streptomyces lydicamycinicus NBRC 110027T와 가장 가까운 것으로 나타났다. 유전체 기반 in silico 분석으로부터 총 26개의 이차대사산물 생합성 유전자군을 확인했으며, 그 중에 다수의 항균활성물질 생산 유전자이 발견되었다. 이 연구로부터 MMS22-DDSA8 균주가 유용물질 생산자로서 높은 잠재력을 가진 것을 확인할 수 있었다.


This research was supported by a research grant of Chungnam National University (2021–2022).

Conflict of Interest

The authors declare that there is no conflict of interest.

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