Evaluation Of Prophages and Anti-Microbial Resistance Profile of Bacillus Subtilis Using in Silico Approach

Bacteriophages or phages are bacterial viruses that can disrupt bacterial metabolism. The antibacterial potential of bacteriophages has been documented [1]. The emergence of antibiotic resistant pathogenic microbes is a global threat to public health. The development of alternative antimicrobial agents is therefore one of the important priorities of medical research. The threat of antimicrobial resistance to human health has become recognized globally, it is associated with death of millions of people annually [2]. The urgent need for alternative and effective antibiotics has generated interest in prophages as alternative means of treatment of infections caused by antibiotic resistant bacteria. Large number of phages are reported to be present in the digestive system and may play a significant role in modifying the immune functions [3]. Prophages are capable of bypassing epithelial layer thereby influencing immune responses in different parts of the body

Studies have indicated that prophages do not exert significant harmful effects on mammalian cells. Apart from antibacterial action, phages are reported to have anti-inflammatory and immune modulatory effects [4]. The use of bacteriophages to combat antimicrobial resistance most comply with quality assurance and safety measures including eliminating the risk of prophage contamination with resistant bacterial cells. Bacterial lines used for the manufacture of bacteriophages must be assessed for phages and antimicrobial resistant genes in order to prevent transfer of virulent genes and antimicrobial resistance to other bacterial strains in the patient. The main objective of this study was to identify prophages and antimicrobial resistant genes in Bacillus subtilis strain using computational methods.

Data retrieval and genome assembly

Data on Bacillus subtilis was retrieved from Sequence Raw Achieve (SRA) of National Centre for Biotechnology Information. The retrieved sequence was submitted for genome assembly using the database of Bacterial Viral Bioinformatic Resource Centre (BVBRC). The database is an information system designed to support research on bacteria and infectious diseases [5].

Prophage identification using PHASTER server

The assembled genome file obtained from BV-BRC was submitted for prophage identification using Phage Search Tool Enhanced Release. The PHASTER database is reliable for rapid identification and annotation of prophage sequences within bacterial genomes and plasmids [6].

Evaluation of antimicrobial resistance profile

Identification of antimicrobial resistance gene was done using the resistance gene identifier protocol of the Comprehensive Antimicrobial Resistance Database (CARD). It is a bioinformatic database of resistance genes, their products and associated phenotypes [7]. The database combines antibiotic resistance ontology with curated antimicrobial resistance genes sequences and mutations that provide a framework for annotation and interpretation of resistomes.

The prophages and antimicrobial resistance profile of bacillus subtilis evaluated are shown in Table 1 and Table 2. The high rate of development of antimicrobial resistance compared to the level of antibiotic discovery represents a global public health challenge [8]. There is, therefore, a need to give special at represent so the development of phages as potential therapeutic antimicrobial agents against antimicrobial resistant pathogens. One of the advantages of bacteriophage is that very few doses are required because of the increase concentration of bacteriophage at site of infection after the initial administration, their effects are also limited to the site of infection [9]. A significant reduction in the cost of treatment has also been associated with the use of bacteriophages. Prophages induce antimicrobial resistance and increase pathogenicity in bacterial species leading to renewed interest in identification of prophage sequences in bacterial genomes [10,11].

Table 1:Prophage sequences of Bacillus subtilis identified using Phaster server.

Note: Intact score > 90, Questionable (score 70-90), incomplete (score < 70)
Region Length: The length of the sequence of that region (in bp).
Score: The score of the region based on the above criteria.
Region Position: The start and end positions of the region on the bacterial chromosome.
Most Common Phage: The phage(s) with the highest number of proteins most similar to those in the region.
GC %: The percentage of GC nucleotides of the region.

Table 2:Antimicrobial resistance profile Bacillus subtilis strain.

1. Memon MA, Shmalberg J, Adair HS, Allweiler S, Bryan JN, et al. (2016) Integrative veterinary medical education and consensus guidelines for an integrative veterinary medicine curriculum within veterinary colleges. Open Vet J 6(1): 44-56.
2. Caneschi A, Bardhi A, Barbarossa A, Zaghini A (2023) The use of antibiotics and antimicrobial resistance in veterinary medicine, a complex phenomenon: A narrative review. Antibiotics 12(3): 487.
3. Arlt S, Heuwieser W (2010) Evidence-based complementary and alternative veterinary medicine-a contradiction in terms? Berl Munch Tierarztl Wochenschr 123(9-10): 377-384.
4. Pun JK (2020) An integrated review of the role of communication in veterinary clinical practice. BMC Vet Res 16(1): 394.
5. Gyles C (2020) Complementary and alternative veterinary medicine. Can Vet J 61(4): 345-346.
6. Mills DS (2022) Clinical animal behaviour: Paradigms, problems and practice. Animals 12(22): 3103.
7. Mahmoudi S, Jafari E, Nasrabadi HA, Liaghatdar MJ (2012) Holistic education: An approach for 21^st Int Educ Stud 5(2): 178.
8. Saad M, Medeiros R, Mosini AC (2017) Are we ready for a true biopsychosocial-spiritual model? The many meanings of "spiritual". Medicines 4(4): 79.
9. Galbadage T, Peterson BM, Wang DC, Wang JS, Gunasekera RS (2020) Biopsychosocial and spiritual implications of patients with COVID-19 dying in isolation. Front Psychol 11: 588623.
10. Young CE, Roncisvalle CA (2001) Expenditures, investment and financing for sustainable development in Brazil. Economic Commission for Latin America and the Caribbean (ECLAC).
11. Dwivedi YK, Hughes L, Baabdullah AM, Navarrete SR, Giannakis M, et al. (2022) Metaverse beyond the hype: Multidisciplinary perspectives on emerging challenges, opportunities and agenda for research, practice and policy. Int J Inf Manag 66: 102542.
12. Al-Riyami H, Al-Maskari A, Nadar SK, Almaskari M (2023) Knowledge, attitudes and practices regarding traditional and complimentary medicine in Oman. Sultan Qaboos Univ Med J 23(1):90-98.
13. Alikhani S, Nummi P, Ojala A (2021) Urban wetlands: A review on ecological and cultural values. Water 13(22): 3301.
14. Harrison TM, Churgin SM (2022) Acupuncture and traditional Chinese veterinary medicine in zoological and exotic animal medicine: A review and introduction of methods. Vet Sci 9(2): 74.
15. Khazaei R, Seidavi A, Bouyeh M (2022) A review on the mechanisms of the effect of silymarin in milk thistle (Silybum marianum) on some laboratory animals. Vet Med Sci 8(1): 289-301.
16. Maltese PE, Michelini S, Baronio M, Bertelli M (2019) Molecular foundations of chiropractic therapy. Acta Biomed 90(10-S): 93-102.
17. Marotti I, Betti L, Bregola V, Bosi S, Trebbi G, et al. (2014) Transcriptome profiling of wheat seedlings following treatment with ultrahigh diluted arsenic trioxide. Evid Based Complement Alternat Med 2014: 851263.
18. Cencic A, Chingwaru W (2010) The role of functional foods, nutraceuticals, and food supplements in intestinal health. Nutrients 2(6): 611-625.
19. Mille MA, McClement J, Lauer S (2022) Physiotherapeutic strategies and their current evidence for canine osteoarthritis. Vet Sci 10(1): 2.
20. Formenton MR, Pereira MAA, Fantoni DT (2017) Small animal massage therapy: A brief review and relevant observations. Top Companion Anim Med 32(4): 139-145.
21. Tabish SA (2008) Complementary and alternative healthcare: is it evidence-based? Int J Health Sci (Qassim) 2(1): V-IX.
22. Chiappelli F, Prolo P, Rosenblum M, Edgerton M, Cajulis OS (2006) Evidence-based research in complementary and alternative medicine II: the process of evidence-based research. Evid Based Complement Alternat Med 3(1): 3-12.
23. Ventola CL (2010) Current issues regarding Complementary and Alternative Medicine (CAM) in the United States: Part 1: The widespread use of CAM and the need for better-informed health care professionals to provide patient counseling 35(8): 461-468.
24. Quain A, Ward MP, Mullan S (2021) Ethical challenges posed by advanced veterinary care in companion animal veterinary practice. Animals (Basel) 11(11): 3010.
25. Rösch T, Schaper E, Tipold A, Fischer M, Dilly M, et al. (2014) Clinical skills of veterinary students-a cross-sectional study of the self-concept and exposure to skills training in Hannover, Germany. BMC Vet Res 21:10: 969.
26. Nadareishvili I, Pkhakadze G, Japiashvili N, Lunze K (2021) Regulatory environment for complementary and alternative medicine in Georgia-a health policy analysis. Int J Health Plann Manage 36(4): 1038-1051.