GCMS-based evaluation, characterization and in silico analysis of antimicrobial metabolites in the crude extract of cold-adapted <i>Alcaligenes pakistanensis</i> LTP10

Imran Rabbani; Muhammad Rafiq; Suliman Shah; Tariq Ahmad; Muhammad Irfan; Aamer Ali Shah; Turki M. Dawoud; Fariha Hasan; Imran Rabbani; Muhammad Rafiq; Suliman Shah; Tariq Ahmad; Muhammad Irfan; Aamer Ali Shah; Turki M. Dawoud; Fariha Hasan

doi:10.3934/microbiol.2026011

AIMS Microbiology

2026, Volume 12, Issue 2: 252-281. doi: 10.3934/microbiol.2026011

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Research article

GCMS-based evaluation, characterization and in silico analysis of antimicrobial metabolites in the crude extract of cold-adapted Alcaligenes pakistanensis LTP10

1.
Department of Pharmacy, Kohat University of Science and Technology, Kohat, Pakistan
2.
Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
3.
Department of Microbiology, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
4.
Guizhou Key Laboratory of Microbiome and Infectious Disease Prevention and Control & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & School of Basic Medical Science & Institution of One Health Research, Guizhou Medical University, Gui'an New District, 561113, P.R. China
5.
FF Institute (Huzhou) Co., Ltd., Huzhou 313000, China
6.
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
7.
ASRT, Inc., Atlanta, Georgia, USA
8.
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia

Received: 17 December 2025 Revised: 06 April 2026 Accepted: 27 April 2026 Published: 06 May 2026

Antagonistic microorganisms from extreme environments have gained great attention from scientists due to increasing threat of global antimicrobial resistance. In this context, previously isolated cold-adapted isolate from Passu glacier Alcaligenes pakistanensis LTP10 was used to extract their antimicrobial metabolites with organic solvents. MIC and MBC assays of the extract were performed. The synergistic effect of LTP10 ethyl acetate extract was studied with known antibiotics against Staphylococcus aureus and Escherichia coli. The extract was analyzed by FTIR, GC-MS, and in silico studies. Ethyl acetate extract of LTP10 has shown a maximum activity of 20 ± 1.0 and 19.3 ± 1.2 mm against Staphylococcus epidermidis and S. aureus, respectively. MIC of the extract was 0.4 and 1.6 mg/mL against S. aureus and E. coli, respectively. FTIR analysis revealed the presesnce of functional groups belonging to alcohols, aliphatic hydrocarbons, and nitrogen containing organic compouns. GC-MS analysis confirmed the presence of important antimicrobial compounds Dodecanoic acid, 3-hydroxy-, 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione, and Pyrimidine-2,4(1H,3H)-dione in ethyl acetate extract of LTP10. A molecular docking study of these compounds has shown that 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione has strong binding affinity of -7.8 kcal/mol against dihydrofolate reductase. Moreover, an ADMET study of the compounds has predicted their good intestinal absorption and non-toxic nature. In this work, we uniquely identify and characterize antimicrobial metabolites of glacier-derived Alcaligenes, combining GC–MS profiling with in-silico analysis. It was concluded that Alcaligenes pakistanensis LTP10 could be considered a good source for antimicrobial compound production, which should be further characterized by analytical techniques.
- Alcaligenes pakistanensis,
- GC-MS,
- molecular docking,
- extreme environments,
- passu glacier,
- cold-adapted
Citation: Imran Rabbani, Muhammad Rafiq, Suliman Shah, Tariq Ahmad, Muhammad Irfan, Aamer Ali Shah, Turki M. Dawoud, Fariha Hasan. GCMS-based evaluation, characterization and in silico analysis of antimicrobial metabolites in the crude extract of cold-adapted Alcaligenes pakistanensis LTP10[J]. AIMS Microbiology, 2026, 12(2): 252-281. doi: 10.3934/microbiol.2026011

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Abstract

Antagonistic microorganisms from extreme environments have gained great attention from scientists due to increasing threat of global antimicrobial resistance. In this context, previously isolated cold-adapted isolate from Passu glacier Alcaligenes pakistanensis LTP10 was used to extract their antimicrobial metabolites with organic solvents. MIC and MBC assays of the extract were performed. The synergistic effect of LTP10 ethyl acetate extract was studied with known antibiotics against Staphylococcus aureus and Escherichia coli. The extract was analyzed by FTIR, GC-MS, and in silico studies. Ethyl acetate extract of LTP10 has shown a maximum activity of 20 ± 1.0 and 19.3 ± 1.2 mm against Staphylococcus epidermidis and S. aureus, respectively. MIC of the extract was 0.4 and 1.6 mg/mL against S. aureus and E. coli, respectively. FTIR analysis revealed the presesnce of functional groups belonging to alcohols, aliphatic hydrocarbons, and nitrogen containing organic compouns. GC-MS analysis confirmed the presence of important antimicrobial compounds Dodecanoic acid, 3-hydroxy-, 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione, and Pyrimidine-2,4(1H,3H)-dione in ethyl acetate extract of LTP10. A molecular docking study of these compounds has shown that 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione has strong binding affinity of -7.8 kcal/mol against dihydrofolate reductase. Moreover, an ADMET study of the compounds has predicted their good intestinal absorption and non-toxic nature. In this work, we uniquely identify and characterize antimicrobial metabolites of glacier-derived Alcaligenes, combining GC–MS profiling with in-silico analysis. It was concluded that Alcaligenes pakistanensis LTP10 could be considered a good source for antimicrobial compound production, which should be further characterized by analytical techniques.

Conflict of interest

Author Muhammad Rafiq and Muhammad Irfan were employed by the company FF Institute (Huzhou) Co., Ltd., Huzhou, China and ASRT, Inc., Atlanta, Georgia, USA respectively. All the remaining authors declare that they have no potential conflict of interest.

Author contributions

Conceptualization, I.R. and M.R; methodology, I.R, M.R. T.A, and S.S; validation, I.R, M.R, and A.A.S; formal analysis, I.R., S.S., T.A and T.M.D; investigation, I.R., and M.R; resources, F.H., T.M.D., and A.A.S; data curation, I.R., S.S., and M.I; writing—original draft preparation, I.R., M.R; writing—review and editing, A.A.S., T.M.D., M.I., and F.H; visualization, I.R., T.A., and M.I., supervision, F.H; funding acquisition, F.H, T.M.D; All authors have read and agreed to the published version of the manuscript.

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