Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia
Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Meka, Abu Feyisa [verfasserIn] Bekele, Gessesse Kebede [verfasserIn] Abas, Musin Kelel [verfasserIn] Gemeda, Mesfin Tafesse [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2024 |
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| Schlagwörter: |
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| Anmerkung: |
© The Author(s) 2024 |
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| Übergeordnetes Werk: |
Enthalten in: Discover applied sciences - Springer International Publishing, 2024, 6(2024), 8 vom: 24. Juli |
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| Übergeordnetes Werk: |
volume:6 ; year:2024 ; number:8 ; day:24 ; month:07 |
| Links: |
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| DOI / URN: |
10.1007/s42452-024-06110-x |
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SPR05671999X |
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| 520 | |a Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. | ||
| 520 | |a Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. | ||
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10.1007/s42452-024-06110-x doi (DE-627)SPR05671999X (SPR)s42452-024-06110-x-e DE-627 ger DE-627 rakwb eng Meka, Abu Feyisa verfasserin aut Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. Bioactive compound (dpeaa)DE-He213 Functional gene (dpeaa)DE-He213 Microbial genomes (dpeaa)DE-He213 Sof Umer cave (dpeaa)DE-He213 Bekele, Gessesse Kebede verfasserin aut Abas, Musin Kelel verfasserin aut Gemeda, Mesfin Tafesse verfasserin aut Enthalten in Discover applied sciences Springer International Publishing, 2024 6(2024), 8 vom: 24. Juli Online-Ressource (DE-627)1882945751 (DE-600)3181295-8 3004-9261 nnns volume:6 year:2024 number:8 day:24 month:07 https://dx.doi.org/10.1007/s42452-024-06110-x X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_2050 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2024 8 24 07 |
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10.1007/s42452-024-06110-x doi (DE-627)SPR05671999X (SPR)s42452-024-06110-x-e DE-627 ger DE-627 rakwb eng Meka, Abu Feyisa verfasserin aut Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. Bioactive compound (dpeaa)DE-He213 Functional gene (dpeaa)DE-He213 Microbial genomes (dpeaa)DE-He213 Sof Umer cave (dpeaa)DE-He213 Bekele, Gessesse Kebede verfasserin aut Abas, Musin Kelel verfasserin aut Gemeda, Mesfin Tafesse verfasserin aut Enthalten in Discover applied sciences Springer International Publishing, 2024 6(2024), 8 vom: 24. Juli Online-Ressource (DE-627)1882945751 (DE-600)3181295-8 3004-9261 nnns volume:6 year:2024 number:8 day:24 month:07 https://dx.doi.org/10.1007/s42452-024-06110-x X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_2050 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2024 8 24 07 |
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10.1007/s42452-024-06110-x doi (DE-627)SPR05671999X (SPR)s42452-024-06110-x-e DE-627 ger DE-627 rakwb eng Meka, Abu Feyisa verfasserin aut Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. Bioactive compound (dpeaa)DE-He213 Functional gene (dpeaa)DE-He213 Microbial genomes (dpeaa)DE-He213 Sof Umer cave (dpeaa)DE-He213 Bekele, Gessesse Kebede verfasserin aut Abas, Musin Kelel verfasserin aut Gemeda, Mesfin Tafesse verfasserin aut Enthalten in Discover applied sciences Springer International Publishing, 2024 6(2024), 8 vom: 24. Juli Online-Ressource (DE-627)1882945751 (DE-600)3181295-8 3004-9261 nnns volume:6 year:2024 number:8 day:24 month:07 https://dx.doi.org/10.1007/s42452-024-06110-x X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_2050 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2024 8 24 07 |
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10.1007/s42452-024-06110-x doi (DE-627)SPR05671999X (SPR)s42452-024-06110-x-e DE-627 ger DE-627 rakwb eng Meka, Abu Feyisa verfasserin aut Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. Bioactive compound (dpeaa)DE-He213 Functional gene (dpeaa)DE-He213 Microbial genomes (dpeaa)DE-He213 Sof Umer cave (dpeaa)DE-He213 Bekele, Gessesse Kebede verfasserin aut Abas, Musin Kelel verfasserin aut Gemeda, Mesfin Tafesse verfasserin aut Enthalten in Discover applied sciences Springer International Publishing, 2024 6(2024), 8 vom: 24. Juli Online-Ressource (DE-627)1882945751 (DE-600)3181295-8 3004-9261 nnns volume:6 year:2024 number:8 day:24 month:07 https://dx.doi.org/10.1007/s42452-024-06110-x X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_2050 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2024 8 24 07 |
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10.1007/s42452-024-06110-x doi (DE-627)SPR05671999X (SPR)s42452-024-06110-x-e DE-627 ger DE-627 rakwb eng Meka, Abu Feyisa verfasserin aut Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. Bioactive compound (dpeaa)DE-He213 Functional gene (dpeaa)DE-He213 Microbial genomes (dpeaa)DE-He213 Sof Umer cave (dpeaa)DE-He213 Bekele, Gessesse Kebede verfasserin aut Abas, Musin Kelel verfasserin aut Gemeda, Mesfin Tafesse verfasserin aut Enthalten in Discover applied sciences Springer International Publishing, 2024 6(2024), 8 vom: 24. Juli Online-Ressource (DE-627)1882945751 (DE-600)3181295-8 3004-9261 nnns volume:6 year:2024 number:8 day:24 month:07 https://dx.doi.org/10.1007/s42452-024-06110-x X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_2050 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2024 8 24 07 |
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Meka, Abu Feyisa |
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Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia |
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Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. © The Author(s) 2024 |
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Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. © The Author(s) 2024 |
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Abstract Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds.The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites.Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways. © The Author(s) 2024 |
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