Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces
BackgroundNumerous studies have demonstrated that Akkermansia is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. Akkermansia spp. exhibit potential as probiotics under specific...
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Frontiers Media S.A.
2024-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1500886/full |
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| author | Wenjing Lu Biqing Zha Jie Lyu Chenxi LingHu Jing Chen Sisi Deng Xiangling Zhang Liang Li Guoqing Wang |
| author_facet | Wenjing Lu Biqing Zha Jie Lyu Chenxi LingHu Jing Chen Sisi Deng Xiangling Zhang Liang Li Guoqing Wang |
| author_sort | Wenjing Lu |
| collection | DOAJ |
| description | BackgroundNumerous studies have demonstrated that Akkermansia is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. Akkermansia spp. exhibit potential as probiotics under specific conditions. However, the gene accumulation curve derived from pan-genome analysis suggests that the genome of Akkermansia strains remains open. Consequently, current genome mining efforts are insufficient to fully capture the intraspecific and interspecific characteristics of Akkermansia, necessitating continuous exploration of the genomic and phenotypic diversity of new isolates.MethodsBased on this finding, we sequenced, assembled, and functionally annotated the whole genomes of four new human isolates from our laboratory: AKK-HX001, AKK-HX002, AKK-HX003, and AKK-HX004.ResultsPhylogenetic analysis revealed that all four isolates belonged to the AmII phylogroup, whereas the type strain DSM 22959 is classified within the AmI phylogroup. Moreover, 2,184 shared homologous genes were identified among the four isolates. Functional annotation using the COG, KEGG, and CAZy databases indicated that the functional genes of the four isolates were primarily associated with metabolism. Two antibiotic resistance genes were identified in AKK-HX001 and AKK-HX002, while three resistance genes were detected in AKK-HX003 and AKK-HX004. Additionally, each of the four isolates possessed two virulence genes and three pathogenicity genes, none of which were associated with pathogenicity. The prediction of mobile genetic elements indicated unequal distributions of GIs among the isolates, and a complete CRISPR system was identified in all isolates except AKK-HX003. Two annotated regions of secondary metabolite biosynthesis genes, both belonging to Terpene, were detected using the antiSMASH online tool.ConclusionThese findings indicate that the four Akkermansia isolates, which belong to a phylogroup distinct from the model strain DSM 22959, exhibit lower genetic risk and may serve as potential probiotic resources for future research. |
| format | Article |
| id | doaj-art-4fda4c3d1eec436c8ed361381d9b8f14 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-4fda4c3d1eec436c8ed361381d9b8f142024-12-16T12:00:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-12-011510.3389/fmicb.2024.15008861500886Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human fecesWenjing Lu0Biqing Zha1Jie Lyu2Chenxi LingHu3Jing Chen4Sisi Deng5Xiangling Zhang6Liang Li7Guoqing Wang8West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, ChinaJiujiang Center for Disease Control and Prevention, Jiujiang, ChinaMicrobiome Research and Application Center, BYHEALTH Institute of Nutrition and Health, Guangzhou, ChinaWest China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, ChinaChengdu East New District Public Health Center, Chengdu, ChinaHunan Provincial Center for Disease Control and Prevention, Changsha, ChinaWest China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, ChinaMicrobiome Research and Application Center, BYHEALTH Institute of Nutrition and Health, Guangzhou, ChinaWest China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, ChinaBackgroundNumerous studies have demonstrated that Akkermansia is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. Akkermansia spp. exhibit potential as probiotics under specific conditions. However, the gene accumulation curve derived from pan-genome analysis suggests that the genome of Akkermansia strains remains open. Consequently, current genome mining efforts are insufficient to fully capture the intraspecific and interspecific characteristics of Akkermansia, necessitating continuous exploration of the genomic and phenotypic diversity of new isolates.MethodsBased on this finding, we sequenced, assembled, and functionally annotated the whole genomes of four new human isolates from our laboratory: AKK-HX001, AKK-HX002, AKK-HX003, and AKK-HX004.ResultsPhylogenetic analysis revealed that all four isolates belonged to the AmII phylogroup, whereas the type strain DSM 22959 is classified within the AmI phylogroup. Moreover, 2,184 shared homologous genes were identified among the four isolates. Functional annotation using the COG, KEGG, and CAZy databases indicated that the functional genes of the four isolates were primarily associated with metabolism. Two antibiotic resistance genes were identified in AKK-HX001 and AKK-HX002, while three resistance genes were detected in AKK-HX003 and AKK-HX004. Additionally, each of the four isolates possessed two virulence genes and three pathogenicity genes, none of which were associated with pathogenicity. The prediction of mobile genetic elements indicated unequal distributions of GIs among the isolates, and a complete CRISPR system was identified in all isolates except AKK-HX003. Two annotated regions of secondary metabolite biosynthesis genes, both belonging to Terpene, were detected using the antiSMASH online tool.ConclusionThese findings indicate that the four Akkermansia isolates, which belong to a phylogroup distinct from the model strain DSM 22959, exhibit lower genetic risk and may serve as potential probiotic resources for future research.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1500886/fullAkkermansiawhole-genome sequencinggenomic analysisgenomic diversityprobiotics |
| spellingShingle | Wenjing Lu Biqing Zha Jie Lyu Chenxi LingHu Jing Chen Sisi Deng Xiangling Zhang Liang Li Guoqing Wang Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces Frontiers in Microbiology Akkermansia whole-genome sequencing genomic analysis genomic diversity probiotics |
| title | Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces |
| title_full | Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces |
| title_fullStr | Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces |
| title_full_unstemmed | Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces |
| title_short | Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces |
| title_sort | whole genome sequencing and genomic analysis of four akkermansia strains newly isolated from human feces |
| topic | Akkermansia whole-genome sequencing genomic analysis genomic diversity probiotics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1500886/full |
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