Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution
<i>Limosilactobacillus fermentum</i> is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of <i&...
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| Format: | Article |
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MDPI AG
2022-10-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/11/19/3135 |
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| author | Yan Zhao Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Yuzheng Xue Qixiao Zhai |
| author_facet | Yan Zhao Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Yuzheng Xue Qixiao Zhai |
| author_sort | Yan Zhao |
| collection | DOAJ |
| description | <i>Limosilactobacillus fermentum</i> is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of <i>L. fermentum</i> from the human gut and food remain unknown. In this study, comparative genomic analysis of 224 <i>L. fermentum</i> strains isolated from food and human gut (164 <i>L. fermentum</i> strains isolated from human gut was sequenced in our lab) was performed to access genetic diversity and explore genomic features associated with environment. A total of 20,505 gene families were contained by 224 <i>L. fermentum</i> strains and these strains separated mainly into six clades in phylogenetic tree connected with their origin. Food source <i>L. fermentum</i> strains carried more carbohydrate active enzyme genes (belonging to glycosyltransferase family 2, glycoside hydrolase family 43_11, and glycoside hydrolase family 68) compared with that of human gut and <i>L. fermentum</i> derived from food showed higher ability to degrade xylulose and ribose. Moreover, the number of genes encoding otr(A), tetA(46), lmrB, poxtA, and efrB were more abundant in food source <i>L. fermentum</i>, which was consistent with the number of CRISPR spacers and prophages in <i>L. fermentum</i> of food source. This study provides new insight into the adaption of <i>L. fermentum</i> to the food and intestinal tract of humans, suggesting that the genomic evolution of <i>L. fermentum</i> was to some extent driven by environmental stress. |
| first_indexed | 2024-03-09T21:44:17Z |
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| id | doaj.art-afacef09e125482a8fafd2689ca6db9b |
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| language | English |
| last_indexed | 2024-03-09T21:44:17Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
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| series | Foods |
| spelling | doaj.art-afacef09e125482a8fafd2689ca6db9b2023-11-23T20:22:42ZengMDPI AGFoods2304-81582022-10-011119313510.3390/foods11193135Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption EvolutionYan Zhao0Leilei Yu1Fengwei Tian2Jianxin Zhao3Hao Zhang4Wei Chen5Yuzheng Xue6Qixiao Zhai7Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, ChinaDepartment of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi 214122, ChinaState Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China<i>Limosilactobacillus fermentum</i> is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of <i>L. fermentum</i> from the human gut and food remain unknown. In this study, comparative genomic analysis of 224 <i>L. fermentum</i> strains isolated from food and human gut (164 <i>L. fermentum</i> strains isolated from human gut was sequenced in our lab) was performed to access genetic diversity and explore genomic features associated with environment. A total of 20,505 gene families were contained by 224 <i>L. fermentum</i> strains and these strains separated mainly into six clades in phylogenetic tree connected with their origin. Food source <i>L. fermentum</i> strains carried more carbohydrate active enzyme genes (belonging to glycosyltransferase family 2, glycoside hydrolase family 43_11, and glycoside hydrolase family 68) compared with that of human gut and <i>L. fermentum</i> derived from food showed higher ability to degrade xylulose and ribose. Moreover, the number of genes encoding otr(A), tetA(46), lmrB, poxtA, and efrB were more abundant in food source <i>L. fermentum</i>, which was consistent with the number of CRISPR spacers and prophages in <i>L. fermentum</i> of food source. This study provides new insight into the adaption of <i>L. fermentum</i> to the food and intestinal tract of humans, suggesting that the genomic evolution of <i>L. fermentum</i> was to some extent driven by environmental stress.https://www.mdpi.com/2304-8158/11/19/3135genomic analysis<i>Limosilactobacillus fermentum</i>sourceadaptationcarbohydrate metabolism |
| spellingShingle | Yan Zhao Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Yuzheng Xue Qixiao Zhai Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution Foods genomic analysis <i>Limosilactobacillus fermentum</i> source adaptation carbohydrate metabolism |
| title | Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution |
| title_full | Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution |
| title_fullStr | Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution |
| title_full_unstemmed | Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution |
| title_short | Environment-Related Genes Analysis of <i>Limosilactobacillus fermentum</i> Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution |
| title_sort | environment related genes analysis of i limosilactobacillus fermentum i isolated from food and human gut genetic diversity and adaption evolution |
| topic | genomic analysis <i>Limosilactobacillus fermentum</i> source adaptation carbohydrate metabolism |
| url | https://www.mdpi.com/2304-8158/11/19/3135 |
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