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Handayani DP, Isnansetyo A, Istiqomah I. New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56. BMC Genomics 2024; 25:364. [PMID: 38615000 PMCID: PMC11015633 DOI: 10.1186/s12864-024-10266-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/15/2024] Open
Abstract
Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425-CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA-DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.
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Affiliation(s)
- Desy Putri Handayani
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alim Isnansetyo
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Indah Istiqomah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Handayani DP, Isnansetyo A, Istiqomah I, Jumina J. New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment. Mar Biotechnol (NY) 2022; 24:190-202. [PMID: 35166965 DOI: 10.1007/s10126-022-10096-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The marine bacterium Pseudoalteromonas xiamenensis STKMTI.2 was isolated from a mangrove soil sediment on Setokok Island, Batam, Indonesia. The genome of this bacterium consisted of 4,563,326 bp (GC content: 43.2%) with 1 chromosome, 2 circular plasmids, 2 linear plasmids, 4,824 protein-coding sequences, 25 rRNAs, 104 tRNAs, 4 ncRNAs, and 1 clustered, regularly interspaced, short palindromic repeated (CRISPR). This strain possessed cluster genes which are responsible for the production of brominated marine pyrroles/phenols (bmp), namely, bmp8 and bmp9. Other gene clusters responsible for the synthesis of secondary metabolites were identified using antiSMASH and BAGEL4, which yielded five results, namely, non-ribosomal peptides, polyketide-like butyrolactone, Lant class I, and RiPP-like, detected in chromosome 1, while prodigiosin was detected in the unnamed plasmid 5. This suggests that these whole genome data will be of remarkable importance for the improved understanding of the biosynthesis of industrially important bioactive and antibacterial compounds produced by P. xiamenensis STKMTI.2.
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Affiliation(s)
- Desy Putri Handayani
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alim Isnansetyo
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Indah Istiqomah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jumina Jumina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Gaafar AY, Yamashita H, Istiqomah I, Kawato Y, Ninomiya K, Younes A, Nakai T. Comparative immunohistological study on using capsaicin, piperine, and okadaic acid for the transepithelial passage of the inactivated viral and bacterial vaccines in fish. Microsc Res Tech 2020; 83:979-987. [PMID: 32282995 DOI: 10.1002/jemt.23491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022]
Abstract
The practical difficulty of parenteral application of fish vaccines against devastating fish diseases diverted the interest toward oral vaccination. Search for effective methods to enhance the oral uptake of viral and bacterial vaccines is continuing. The current research focus on a new role of mucosal fish vaccine adjuvants inducing the antigen uptake by enhancing vascularity or increasing intestinal permeability. Some inflammatory substances cause reversible pathology to the intestinal epithelium, which could be employed for the transepithelial passage of vaccine particles. The natural inflammatory substances used were capsaicin, piperine, and okadaic acid as 1 mg, 2 mg, and 1 μg/fish, respectively. Two inactivated vaccines were used as antigens to test the effect of these inflammatory substances in two different fish hosts. Tested vaccines were inactivated redspotted grouper nervous necrosis virus vaccine in sevenband grouper (Epinephelus septemfasciatus) and inactivated Edwardsiella tarda vaccine in red sea bream (Pagrus major) fish models. The inflammatory substances and each vaccine were anally intubated to fish. Capsaicin proved to be effectively aiding the transepithelial passage of vaccine particles more than piperine, while okadaic acid had no detectable effect.
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Affiliation(s)
| | - Hirofumi Yamashita
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Ehime, Japan
| | - Indah Istiqomah
- Laboratory of Fish Diseases, Department of Fisheries, Faculty of Agriculture, Yogyakarta, Indonesia
| | - Yasuhiko Kawato
- National Research Institute of Fisheries Science, Fisheries Research Agency, Minamiise, Japan
| | - Kanae Ninomiya
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Abdelgayed Younes
- Veterinary Research Division, National Research Centre, Cairo, Egypt
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
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Basir B, Isnansetyo A, Istiqomah I, Jabbar FBA. Toksisitas Daun Miana (Coleus scutellarioides (L) Benth) Sebagai Antibakteri Pada Udang Vannamei (Litopenaeus vannamei). SIGANUS: JFMS 2020; 1:56-61. [DOI: 10.31605/siganus.v1i2.653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Tujuan Penelitian ini untuk menganalisis toksisitas daun miana sebagai antibakteri pada udang vanamei. Penelitian ini dilaksanakan pada Maret sampai Oktober 2019, di Laboratorium Sekolah Tinggi Teknologi Kelautan (STITEK) Makassar. Sampel daun miana berasal dari beberapa daerah di Sulawesi Selatan. Uji aktivitas antibakteri ekstrak daun miana dengan tiga fraksi, yaitu ethanol, n-hexane, dan chloroform menggunakan metode difusi kertas cakram dengan konsentrasi ekstrak 500 µg/mL dan 1000 µg/mL, sebanyak tiga kali ulangan. Uji toksisitas metode BST (LC70) dengan konsentrasi uji 2500, 1250, 625, 312.5, 156.25, 78.125 µg/mL. Data yang diperoleh dianalisis secara deskriptif. Hasil penelitian menunjukkan bahwa uji aktivitas ekstrak daun miana tertinggi pada fraksi chloroform, dengan diameter hambat 28 mm. Sementara pada antibiotik oxytetracycline diameter hambat sebesar 31 mm. Nilai toksisitas pada tingkat mortalitas 30% pada konsentrasi 1250 µg/mL. Ekstrak daun miana fraksi chloroform mampu menggantikan peran antibiotic oxytetracycline dengan penggunaan konsentrasi dibawah 1250 µg/mL.
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Kawato Y, Istiqomah I, Gaafar AY, Hanaoka M, Ishimaru K, Yasuike M, Nishiki I, Nakamura Y, Fujiwara A, Nakai T. A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages. Arch Virol 2019; 165:303-311. [PMID: 31786689 DOI: 10.1007/s00705-019-04485-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/26/2019] [Indexed: 01/21/2023]
Abstract
A novel jumbo bacteriophage (myovirus) is described. The lytic phage of Tenacibaculum maritimum, which is the etiological agent of tenacibaculosis in a variety of farmed marine fish worldwide, was plaque-isolated from seawater around a fish aquaculture field in Japan. The phage had an isometric head 110-120 nm in diameter, from which several 50- to 100-nm-long flexible fiber-like appendages emanate, and a 150-nm-long rigid contractile tail. The full genomes of the two representative phages (PTm1 and PTm5) were 224,680 and 226,876 bp long, respectively, both with 29.7% GC content, and the number of predicted open reading frames (ORFs) was 308 and 306, respectively. The average nucleotide sequence identity between PTm1 and PTm5 was 99.95%, indicating they are quite similar to each other. A genetic relationship was found in 15.0-16.6% of the predicted ORFs among the T. maritimum phages PTm1 and PTm5, the Tenacibaculum spp. phage pT24, and the Sphingomonas paucimobilis phage PAU. Phylogenetic analysis based on the terminase large subunit genes revealed that these four phages (PTm1, PTm5, pT24 and PAU) are more closely related than the other 10 jumbo myoviruses that have similar genome sizes. Transmission electron microscopy observations suggest that the head fibers of the T. maritimum phage function as tentacles to search and recognize the host cell surface to facilitate infection.
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Affiliation(s)
- Yasuhiko Kawato
- Nansei Main Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, Japan
| | - Indah Istiqomah
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Fisheries, Faculty of Agriculture, Gadjah Mada University, Yogyakarta, Indonesia
| | - Alkhateib Y Gaafar
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Veterinary Research Division, National Research Centre, Cairo, Egypt
| | - Makoto Hanaoka
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Katsuya Ishimaru
- Aquaculture Research Institute, Kindai University, Wakayama, Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.
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Isnansetyo A, Istiqomah I, Muhtadi, Sinansari S, Hernawan RK, Triyanto, Widada J. A potential bacterial biocontrol agent, strain S2V2 against pathogenic marine Vibrio in aquaculture. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-9992-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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