Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture

Ricardo Sánchez-Díaz; Zinnia Judith Molina-Garza; Lucía Elizabeth Cruz-Suárez; Joseph Selvin; George Seghal Kiran; Bruno Gómez-Gil; Lucio Galaviz-Silva; José Cuauhtémoc Ibarra-Gámez

doi:10.1016/j.jgar.2022.10.002

Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture

J Glob Antimicrob Resist. 2022 Dec:31:304-308. doi: 10.1016/j.jgar.2022.10.002. Epub 2022 Oct 19.

Authors

Ricardo Sánchez-Díaz¹, Zinnia Judith Molina-Garza², Lucía Elizabeth Cruz-Suárez², Joseph Selvin³, George Seghal Kiran⁴, Bruno Gómez-Gil⁵, Lucio Galaviz-Silva⁶, José Cuauhtémoc Ibarra-Gámez⁷

Affiliations

¹ Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México.
² Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico.
³ Department of Microbiology, Pondicherry University, Puducherry, India.
⁴ Department of Food Science and Technology, Pondicherry University, Puducherry, India.
⁵ Research Center for Food and Development (CIAD), Mazatlan Unit, Av. Sábalo Cerritos S/N, Mazatlán, Sinaloa, C.P. 82112. Mexico.
⁶ Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico. Electronic address: lucio.galavizsl@uanl.edu.mx.
⁷ Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México. Electronic address: jose.ibarra@itson.edu.mx.

PMID: 36272706
DOI: 10.1016/j.jgar.2022.10.002

Abstract

Objectives: This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VP_AHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico.

Methods: Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VP_AHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion Torrent^TM (PGM) and Illumina Miseq^TM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH.

Results: Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively.

Conclusions: The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.

Keywords: AHPND; Antibacterial; Bacillus pumilus; Bacillus safensis; Probiotic; Shrimp aquaculture.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Aquaculture
Bacillus pumilus*
Bacillus* / genetics
Penaeidae* / microbiology
Probiotics*
Vibrio parahaemolyticus* / genetics