Farzanfar, A. The use of probiotics in shrimp aquaculture. FEMS Immunol. Med. Microbiol. 48, 149–158 (2006).
Google Scholar
Lakshmi, B., Viswanath, B. & Sai Gopal, D. V. R. Probiotics as Antiviral Agents in Shrimp Aquaculture. J. Pathog. 2013, 1–3 (2013).
Sanchez Ortiz, A. C. et al. Isolation and characterization of potential probiotic bacteria from pustulose ark (Anadara tuberculosa) suitable for shrimp farming. Lat. Am. J. Aquat. Res. 43, 123–136 (2015).
Dawood, M. A. O., Koshio, S., Abdel-Daim, M. M. & Van Doan, H. Probiotic application for sustainable aquaculture. Rev. Aquac. 11, 907–924 (2019).
Google Scholar
Giatsis, C. et al. Probiotic legacy effects on gut microbial assembly in tilapia larvae. Sci. Rep. 6, 1 (2016).
Google Scholar
Kumar, V., Roy, S., Meena, D. K. & Sarkar, U. K. Application of probiotics in shrimp aquaculture: Importance, mechanisms of action, and methods of administration. Rev. Fish. Sci. Aquacult. 24, 342–368 (2016).
Google Scholar
Zommiti, M. et al. In vitroassessment of the probiotic properties and bacteriocinogenic potential of pediococcus pentosaceus MZF16 isolated from artisanal tunisian meat “dried ossban. Front. Microbiol. 9, 1 (2018).
Google Scholar
Martino, M. E. et al. Genotypic and phenotypic diversity of Pediococcus pentosaceus strains isolated from food matrices and characterisation of the penocin operon. Antonie Van Leeuwenhoek 103, 1149–1163 (2013).
Google Scholar
Truc, L. N. T. et al. Effects of feed mixed with lactic acid bacteria and carbon, nitrogen, phosphorus supplied to the water on the growth and survival rate of white leg shrimp (penaeus vannamei) infected with acute hepatopancreatic necrosis disease caused by vibrio parahaemolyticus. Biology 10 (2021).
Adel, M., Yeganeh, S., Dawood, M. A. O., Safari, R. & Radhakrishnan, S. Effects of Pediococcus pentosaceus supplementation on growth performance, intestinal microflora and disease resistance of white shrimp, Litopenaeus vannamei. Aquac. Nutr. 23, 1401–1409 (2017).
Google Scholar
Scientific Opinion on the efficacy of Bactocell (Pediococcus acidilactici) when used as a feed additive for fish. EFSA Journal 10, (2012)
Pérez-Sánchez, T., Ruiz-Zarzuela, I., de Blas, I. & Balcázar, J. L. Probiotics in aquaculture: A current assessment. Rev. Aquac. 6, 133–146 (2014).
Google Scholar
Havarstein, L. S., Holo, H. & Nes, I. F. The leader peptide of colicin V shares consensus sequences with leader peptides that are common among peptide bacteriocins produced by Gram-positive bacteria. Microbiology 140, 2383–2389 (1994).
Google Scholar
McCormick, J. K., Klaenhammer, T. R. & Stiles, M. E. Colicin V can be produced by lactic acid bacteria. Lett. Appl. Microbiol. 29, 37–41 (1999).
Google Scholar
Dai, G. et al. A ferritin-like protein with antioxidant activity in Ureaplasma urealyticum. BMC Microbiol. 15, 1 (2015).
Google Scholar
Coppo, L., Montano, S. J., Padilla, A. C. & Holmgren, A. Determination of glutaredoxin enzyme activity and protein S-glutathionylation using fluorescent eosin-glutathione. Anal. Biochem. 499, 24–33 (2016).
Google Scholar
Duan, Y. et al. Oxidative stress response of the black tiger shrimp Penaeus monodon to Vibrio parahaemolyticus challenge. Fish Shellfish Immunol. 46, 354–365 (2015).
Google Scholar
Won, S. et al. Evaluation of potential probiotics bacillus subtilis WB60, Pediococcus pentosaceus, and Lactococcus lactis on growth performance, immune response, gut histology and immune-related genes in whiteleg shrimp, Litopenaeus vannamei. Microorganisms 8, (2020).
Chai, P. C., Song, X. L., Chen, G. F., Xu, H. & Huang, J. Dietary supplementation of probiotic Bacillus PC465 isolated from the gut of Fenneropenaeus chinensis improves the health status and resistance of Litopenaeus vannamei against white spot syndrome virus. Fish Shellfish Immunol. 54, 602–611 (2016).
Google Scholar
Wang, Y. B. Effect of probiotics on growth performance and digestive enzyme activity of the shrimp Penaeus vannamei. Aquaculture 6, 327–332 (2007).
Google Scholar
Zokaeifar, H. et al. Effects of Bacillus subtilis on the growth performance, digestive enzymes, immune gene expression and disease resistance of white shrimp, Litopenaeus vannamei. Fish Shellfish Immunol. 33, 683–689 (2012).
Lovett, D. L. & Felder, D. L. Ontogenetic change in digestive enzyme activity of larval and postlarval white shrimp Penaeus setiferus (Crustacea, Decapoda, Penaeidae). Biol. Bull. 178, 144–159 (1990).
Google Scholar
Castex, M., Lemaire, P., Wabete, N. & Chim, L. Effect of probiotic Pediococcus acidilactici on antioxidant defences and oxidative stress of Litopenaeus stylirostris under Vibrio nigripulchritudo challenge. Fish Shellfish Immunol. 28, 622–631 (2010).
Google Scholar
Gamboa-Delgado, J., Molina-Poveda, C. & Cahu, C. Digestive enzyme activity and food ingesta in juvenile shrimp Litopenaeus vannamei (Boone, 1931) as a function of body weight. Aquac. Res. 34, 1403–1411 (2003).
Google Scholar
Thongprajukaew, K. et al. Effects of dietary modified palm kernel meal on growth, feed utilization, radical scavenging activity, carcass composition and muscle quality in sex reversed Nile tilapia (Oreochromis niloticus). Aquaculture 439, 45–52 (2015).
Google Scholar
Kamarudin, M. S., Jones, D. A., le Vay, L. & Abidin, A. Z. Ontogenetic change in digestive enzyme activity during larval development of Macrobrachium rosenbergii. Aquaculture 123, 323–333 (1994).
Google Scholar
Zhou, X. X., Wang, Y. B., & Li, W. fen. Effect of probiotic on larvae shrimp (Penaeus vannamei) based on water quality, survival rate and digestive enzyme activities. Aquaculture 287, 349–353 (2009).
Zhang, Q. et al. Dietary administration of Bacillus (B. licheniformis and B. subtilis) and isomaltooligosaccharide influences the intestinal microflora, immunological parameters and resistance against Vibrio alginolyticus in shrimp, Penaeus japonicus (Decapoda: Penaeidae). Aquac. Res. 42, 943–952 (2011).
Chiu, C. H., Guu, Y. K., Liu, C. H., Pan, T. M. & Cheng, W. Immune responses and gene expression in white shrimp, Litopenaeus vannamei, induced by Lactobacillus plantarum. Fish Shellfish Immunol. 23, 364–377 (2007).
Google Scholar
Chen, L. et al. Intestinal immune function, antioxidant status and tight junction proteins mRNA expression in young grass carp (Ctenopharyngodon idella) fed riboflavin deficient diet. Fish Shellfish Immunol. 47, 470–484 (2015).
Google Scholar
Duan, Y. et al. Effect of dietary poly-β-hydroxybutyrate (PHB) on growth performance, intestinal health status and body composition of Pacific white shrimp Litopenaeus vannamei (Boone, 1931). Fish Shellfish Immunol. 60, 520–528 (2017).
Google Scholar
Daniels, C. L. et al. Effect of dietary Bacillus spp. and mannan oligosaccharides (MOS) on European lobster (Homarus gammarus L.) larvae growth performance, gut morphology and gut microbiota. Aquaculture 304, 49–57 (2010).
Martin, G. G. & Graves, B. L. Fine structure and classification of shrimp hemocytes. J. Morphol. 185, 339–348 (1985).
Google Scholar
Kawai, T. & Akira, S. The role of pattern-recognition receptors in innate immunity: Update on toll-like receptors. Nat. Immunol. 11, 373–384 (2010).
Google Scholar
Wang, X. W. & Wang, J. X. Pattern recognition receptors acting in innate immune system of shrimp against pathogen infections. Fish Shellfish Immunol. 34, 981–989 (2013).
Google Scholar
Sánchez-Ortiz, A. C. et al. Effect of mixed-Bacillus spp isolated from pustulose ark Anadara tuberculosa on growth, survival, viral prevalence and immune-related gene expression in shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 59, 95–102 (2016).
Google Scholar
Maningas, M. B. B., Kondo, H., Hirono, I., Saito-Taki, T. & Aoki, T. Essential function of transglutaminase and clotting protein in shrimp immunity. Mol. Immunol. 45, 1269–1275 (2008).
Google Scholar
Fagutao, F. F., Maningas, M. B. B., Kondo, H., Aoki, T. & Hirono, I. Transglutaminase regulates immune-related genes in shrimp. Fish Shellfish Immunol. 32, 711–715 (2012).
Google Scholar
Senan, S., Prajapati, J. B. & Joshi, C. G. Whole-genome based validation of the adaptive properties of Indian origin probiotic Lactobacillus helveticus MTCC 5463. J. Sci. Food Agric. 95, 321–328 (2015).
Google Scholar
Grover, S., Rashmi, H. M., Srivastava, A. K. & Batish, V. K. Probiotics for human health -new innovations and emerging trends. Gut Pathogens 8, 2233–1859 (2012).
Ocaña, V. & Nader-Macías, M. E. Adhesion of Lactobacillus vaginal strains with probiotic properties to vaginal epithelial cells. Biocell 25, 265–273 (2001).
Google Scholar
Botes, M., Loos, B., Van Reenen, C. A. & Dicks, L. M. T. Adhesion of the probiotic strains Enterococcus mundtii ST4SA and Lactobacillus plantarum 423 to Caco-2 cells under conditions simulating the intestinal tract, and in the presence of antibiotics and anti-inflammatory medicaments. Arch. Microbiol. 190, 573–584 (2008).
Google Scholar
Xu, H., Jeong, H. S., Lee, H. Y. & Ahn, J. Assessment of cell surface properties and adhesion potential of selected probiotic strains. Lett. Appl. Microbiol. 49, 434–442 (2009).
Google Scholar
Ton-That, H., Marraffini, L. A. & Schneewind, O. Protein sorting to the cell wall envelope of Gram-positive bacteria. Biochim. Biophys. Acta, Mol. Cell Res. 1694, 269–278 (2004).
Remus, D. M. et al. Impact of Lactobacillus plantarum sortase on target protein sorting, gastrointestinal persistence, and host immune response modulation. J. Bacteriol. 195, 502–509 (2013).
Google Scholar
Douillard, F. P. et al. Functional identification of conserved residues involved in Lactobacillus rhamnosus strain GG sortase specificity and pilus biogenesis. J. Biol. Chem. 289, 15764–15775 (2014).
Google Scholar
Westermann, C. et al. Exploring the genome sequence of Bifidobacterium bifidum S17 for potential players in host-microbe interactions. Symbiosis 58, 191–200 (2012).
Google Scholar
Lebeer, S., Vanderleyden, J. & De Keersmaecker, S. C. J. Genes and Molecules of Lactobacilli Supporting Probiotic Action. Microbiol. Mol. Biol. Rev. 72, 728–764 (2008).
Google Scholar
Lorca, G. L., Raya, R. R., Taranto, M. P. & De Valdez, G. F. Adaptive acid tolerance response in Lactobacillus acidophilus. Biotechnol. Lett. 20, 239–241 (1998).
Google Scholar
Pfeiler, E. A., Azcarate-Peril, M. A. & Klaenhammer, T. R. Characterization of a novel bile-inducible operon encoding a two-component regulatory system in Lactobacillus acidophilus. J. Bacteriol. 189, 4624–4634 (2007).
Google Scholar
Zacharof, M. P. & Lovitt, R. W. Bacteriocins Produced by Lactic Acid Bacteria a Review Article. APCBEE Proc. 2, 50–56 (2012).
Google Scholar
Garsa, A. K., Kumariya, R., Sood, S. K., Kumar, A. & Kapila, S. Bacteriocin production and different strategies for their recovery and purification. Probiot. Antimicrob. Prot. 6, 47–58 (2014).
Google Scholar
Dicks, L. M. T. et al. Medical and Personal Care Applications of Bacteriocins Produced by Lactic Acid Bacteria. In Prokaryotic Antimicrobial Peptides 391–421 (2011).
Foulquié Moreno, M. R., Rea, M. C., Cogan, T. M. & De Vuyst, L. Applicability of a bacteriocin-producing Enterococcus faecium as a co-culture in Cheddar cheese manufacture. Int. J. Food Microbiol. 81, 73–84 (2003).
López-Cuellar, M. del R., Rodríguez-Hernández, A. I. & Chavarría-Hernández, N. LAB bacteriocin applications in the last decade. Biotechnol. and Biotechnol. Equip. 30, 1039–1050 (2016).
Nilsen, T., Nes, I. F. & Holo, H. Enterolysin A, a cell wall-degrading bacteriocin from Enterococcus faecalis LMG 2333. Appl. Environ. Microbiol. 69, 2975–2984 (2003).
Google Scholar
Jiang, J. et al. Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System. Front. Microbiol. 11, 253 (2020).
Google Scholar
Vandecraen, J., Chandler, M., Aertsen, A. & Van Houdt, R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43, 709–730 (2017).
Google Scholar
Deutscher, J., Francke, C. & Postma, P. W. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol. Mol. Biol. Rev. 70, 939–1031 (2006).
Google Scholar
Jamal, Z. et al. Distribution and functions of phosphotransferase system genes in the genome of the lactic acid bacterium Oenococcus oeni. Appl. Environ. Microbiol. 79, 3371–3379 (2013).
Google Scholar
Abe, K. & Uchida, K. Correlation between depression of catabolite control of xylose metabolism and a defect in the phosphoenolpyruvate: Mannose phosphotransferase system in Pediococcus halophilus. J. Bacteriol. 171, 1793–1800 (1989).
Google Scholar
Monedero, V. et al. The phosphotransferase system of Lactobacillus casei: Regulation of carbon metabolism and connection to cold shock response. J. Mol. Microbiol. Biotechnol. 12, 20–32 (2006).
Google Scholar
Stevens, M. J. A., Molenaar, D., De Jong, A., De Vos, W. M. & Kleerebezem, M. Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance. Appl. Environ. Microbiol. 76, 3748–3752 (2010).
Google Scholar
Houot, L., Chang, S., Pickering, B. S., Absalon, C. & Watnick, P. I. The phosphoenolpyruvate phosphotransferase system regulates Vibrio cholerae biofilm formation through multiple independent pathways. J. Bacteriol. 192, 3055–3067 (2010).
Google Scholar
Prabhurajeshwar, C. & Chandrakanth, R. K. Probiotic potential of Lactobacilli with antagonistic activity against pathogenic strains: An in vitro validation for the production of inhibitory substances. Biomed. J. 40, 270–283 (2017).
Google Scholar
Del Re, B., Sgorbati, B., Miglioli, M. & Palenzona, D. Adhesion, autoaggregation and hydrophobicity of 13 strains of Bifidobacterium longum. Lett. Appl. Microbiol. 31, 438–442 (2000).
Google Scholar
Lowry. Lowry Protein Assay. J. Biol. Chem. 265–275 (1951).
Rungruangsak-Torrissen, K., Moss, R., Andresen, L. H., Berg, A. & Waagbø, R. Different expressions of trypsin and chymotrypsin in relation to growth in Atlantic salmon (Salmo salar L.). Fish Physiol. Biochem. 32, 7–23 (2006).
Areekijseree, M. et al. Temperature and pH characteristics of amylase and proteinase of adult freshwater pearl mussel, Hyriopsis (Hyriopsis) bialatus Simpson 1900. Aquaculture 234, 575–587 (2004).
Google Scholar
Xue, X. M. et al. Characterisation of cellulase activity in the digestive system of the redclaw crayfish (Cherax quadricarinatus). Aquaculture 180, 373–386 (1999).
Google Scholar
Stuckmann, M. & Winkler, U. K. Glycogen, hyaluronate, and some other polysaccharides greatly enhance the formation of exolipase by Serratia marcescens. J. Bacteriol. 138, 663–670 (1979).
Google Scholar
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. bioRxiv 071282, (2016).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Walker, B. J. et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, (2014).
Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679 (2007).
Google Scholar
Lukashin, A. V. & Borodovsky, M. GeneMark.hmm: New solutions for gene finding. Nucl. Acids Res. 26, 1107–1115 (1998).
Besemer, J. & Borodovsky, M. Heuristic approach to deriving models for gene finding. Nucl. Acids Res. 27, 3911–3920 (1999).
Google Scholar
Besemer, J., Lomsadze, A. & Borodovsky, M. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucl. Acids Res. 29, 2607–2618 (2001).
Aziz, R. K. et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genom. 9, 75 (2008).
Google Scholar
Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucl. Acids Res. 42, D206-214 (2014).
Google Scholar
Lowe, T. M. & Chan, P. P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucl. Acids Res. 44, W54-57 (2016).
Google Scholar
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955–964 (1997).
Google Scholar
Schattner, P., Brooks, A. N. & Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl. Acids Res. 33, W686-689 (2005).
Google Scholar
Lagesen, K. et al. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucl. Acids Res. 35, 3001–3008 (2007).
Google Scholar
Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J. & Wishart, D. S. PHAST: A Fast Phage Search Tool. Nucl. Acids Res. 39, W347-352 (2011).
Google Scholar
Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats. Nucl. Acids Res. 35, W52-57 (2007).
Google Scholar
Grant, J. R. & Stothard, P. The CGView Server: a comparative genomics tool for circular genomes. Nucl. Acids Res. 36, W181-184 (2008).
Google Scholar
Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).
Google Scholar
Surachat, K., Sangket, U., Deachamag, P. & Chotigeat, W. In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases. PLoS One 12, e0183548 (2017).
de Jong, A., van Hijum, S. A. F. T., Bijlsma, J. J. E., Kok, J. & Kuipers, O. P. BAGEL: A web-based bacteriocin genome mining tool. Nucl. Acids Res. 34, W273-276 (2006).
Google Scholar
Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32, 1792–1797 (2004).
Google Scholar

