Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut
by
, ,
Anchal Chaudhary
1,2, 
Omkar Avinash Ketkar
3,
Sayed Irfan
3,
Varnika Rana
1,
Praveen Rahi
3,
Rupesh Deshmukh
1
,
Jagdeep Kaur
2 and
Hena Dhar
1,* 1
National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
2
Department of Biotechnology, Panjab University, Chandigarh 160025, India
3
National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
*
Author to whom correspondence should be addressed.
Biology 2022, 11(5), 632; https://doi.org/10.3390/biology11050632
Submission received: 23 March 2022
/
Revised: 9 April 2022
/
Accepted: 12 April 2022
/
Published: 21 April 2022
(This article belongs to the Section Genetics and Genomics)
Simple Summary
The microbial production of health-beneficial omega-3 fatty acids has gained research attention due to the limitations of availability, sustainability, and contaminants associated with the conventional fish source. Among the marine bacteria, the Shewanella genus is well known for eicosapentaenoic acid (EPA) production along with bioremediation of organic and inorganic pollutants and bioelectricity generation. We report the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gut of a freshwater fish, Tilapia. Analysis of genomic data revealed a variety of antibiotic and stress-responsive genes, metal-reducing genes, and secondary metabolite genes. Overall, the study has provided an understanding of the biosynthetic gene cluster of omega-3 polyunsaturated fatty acids in addition to adaptation strategies of Shewanella sp. N2AIL and could be utilized in developing a strain for the commercial production of EPA.
Abstract
The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.
