Gut microbiota drives structural variation of exogenous probiotics to enhance colonization
Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whe...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-12-01
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| Series: | Gut Microbes |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2025.2503371 |
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| author | Shuaiming Jiang Shi Huang Zeng Zhang Wenyao Ma Zhe Han Yuan Song Dongxue Huo Weipeng Cui Jiachao Zhang |
| author_facet | Shuaiming Jiang Shi Huang Zeng Zhang Wenyao Ma Zhe Han Yuan Song Dongxue Huo Weipeng Cui Jiachao Zhang |
| author_sort | Shuaiming Jiang |
| collection | DOAJ |
| description | Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy. |
| format | Article |
| id | doaj-art-3bacb5adbf8f4f4e837bd1f1bc0f4259 |
| institution | Kabale University |
| issn | 1949-0976 1949-0984 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj-art-3bacb5adbf8f4f4e837bd1f1bc0f42592025-08-20T03:53:21ZengTaylor & Francis GroupGut Microbes1949-09761949-09842025-12-0117110.1080/19490976.2025.2503371Gut microbiota drives structural variation of exogenous probiotics to enhance colonizationShuaiming Jiang0Shi Huang1Zeng Zhang2Wenyao Ma3Zhe Han4Yuan Song5Dongxue Huo6Weipeng Cui7Jiachao Zhang8School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaFaculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaSchool of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, ChinaProbiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.https://www.tandfonline.com/doi/10.1080/19490976.2025.2503371Gut-adapted strainsprobiotic bacteriaLactiplantibacillus plantarum HNU082divergent evolutionstructural variationscolonization |
| spellingShingle | Shuaiming Jiang Shi Huang Zeng Zhang Wenyao Ma Zhe Han Yuan Song Dongxue Huo Weipeng Cui Jiachao Zhang Gut microbiota drives structural variation of exogenous probiotics to enhance colonization Gut Microbes Gut-adapted strains probiotic bacteria Lactiplantibacillus plantarum HNU082 divergent evolution structural variations colonization |
| title | Gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| title_full | Gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| title_fullStr | Gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| title_full_unstemmed | Gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| title_short | Gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| title_sort | gut microbiota drives structural variation of exogenous probiotics to enhance colonization |
| topic | Gut-adapted strains probiotic bacteria Lactiplantibacillus plantarum HNU082 divergent evolution structural variations colonization |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2025.2503371 |
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