Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics

Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Tong Pan [verfasserIn] Zhangming Pei [verfasserIn] Zhifeng Fang [verfasserIn] Hongchao Wang [verfasserIn] Jinlin Zhu [verfasserIn] Hao Zhang [verfasserIn] Jianxin Zhao [verfasserIn] Wei Chen [verfasserIn] Wenwei Lu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	tryptophan metabolism lactic acid bacteria specificity predictability genomics

Übergeordnetes Werk:	In: Frontiers in Cellular and Infection Microbiology - Frontiers Media S.A., 2016, 13(2023)
Übergeordnetes Werk:	volume:13 ; year:2023

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fcimb.2023.1154346

Katalog-ID:	DOAJ087903059

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allfields	10.3389/fcimb.2023.1154346 doi (DE-627)DOAJ087903059 (DE-599)DOAJb777814fc4b04cd885b69e7c4d593022 DE-627 ger DE-627 rakwb eng QR1-502 Tong Pan verfasserin aut Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology Tong Pan verfasserin aut Zhangming Pei verfasserin aut Zhangming Pei verfasserin aut Zhifeng Fang verfasserin aut Hongchao Wang verfasserin aut Hongchao Wang verfasserin aut Jinlin Zhu verfasserin aut Jinlin Zhu verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 13(2023) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:13 year:2023 https://doi.org/10.3389/fcimb.2023.1154346 kostenfrei https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023
spelling	10.3389/fcimb.2023.1154346 doi (DE-627)DOAJ087903059 (DE-599)DOAJb777814fc4b04cd885b69e7c4d593022 DE-627 ger DE-627 rakwb eng QR1-502 Tong Pan verfasserin aut Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology Tong Pan verfasserin aut Zhangming Pei verfasserin aut Zhangming Pei verfasserin aut Zhifeng Fang verfasserin aut Hongchao Wang verfasserin aut Hongchao Wang verfasserin aut Jinlin Zhu verfasserin aut Jinlin Zhu verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 13(2023) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:13 year:2023 https://doi.org/10.3389/fcimb.2023.1154346 kostenfrei https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023
allfields_unstemmed	10.3389/fcimb.2023.1154346 doi (DE-627)DOAJ087903059 (DE-599)DOAJb777814fc4b04cd885b69e7c4d593022 DE-627 ger DE-627 rakwb eng QR1-502 Tong Pan verfasserin aut Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology Tong Pan verfasserin aut Zhangming Pei verfasserin aut Zhangming Pei verfasserin aut Zhifeng Fang verfasserin aut Hongchao Wang verfasserin aut Hongchao Wang verfasserin aut Jinlin Zhu verfasserin aut Jinlin Zhu verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 13(2023) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:13 year:2023 https://doi.org/10.3389/fcimb.2023.1154346 kostenfrei https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023
allfieldsGer	10.3389/fcimb.2023.1154346 doi (DE-627)DOAJ087903059 (DE-599)DOAJb777814fc4b04cd885b69e7c4d593022 DE-627 ger DE-627 rakwb eng QR1-502 Tong Pan verfasserin aut Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology Tong Pan verfasserin aut Zhangming Pei verfasserin aut Zhangming Pei verfasserin aut Zhifeng Fang verfasserin aut Hongchao Wang verfasserin aut Hongchao Wang verfasserin aut Jinlin Zhu verfasserin aut Jinlin Zhu verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 13(2023) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:13 year:2023 https://doi.org/10.3389/fcimb.2023.1154346 kostenfrei https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023
allfieldsSound	10.3389/fcimb.2023.1154346 doi (DE-627)DOAJ087903059 (DE-599)DOAJb777814fc4b04cd885b69e7c4d593022 DE-627 ger DE-627 rakwb eng QR1-502 Tong Pan verfasserin aut Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites. tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology Tong Pan verfasserin aut Zhangming Pei verfasserin aut Zhangming Pei verfasserin aut Zhifeng Fang verfasserin aut Hongchao Wang verfasserin aut Hongchao Wang verfasserin aut Jinlin Zhu verfasserin aut Jinlin Zhu verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Hao Zhang verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Jianxin Zhao verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wei Chen verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut Wenwei Lu verfasserin aut In Frontiers in Cellular and Infection Microbiology Frontiers Media S.A., 2016 13(2023) (DE-627)664968554 (DE-600)2619676-1 22352988 nnns volume:13 year:2023 https://doi.org/10.3389/fcimb.2023.1154346 kostenfrei https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 kostenfrei https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full kostenfrei https://doaj.org/toc/2235-2988 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023
language	English
source	In Frontiers in Cellular and Infection Microbiology 13(2023) volume:13 year:2023
sourceStr	In Frontiers in Cellular and Infection Microbiology 13(2023) volume:13 year:2023
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	tryptophan metabolism lactic acid bacteria specificity predictability genomics Microbiology
isfreeaccess_bool	true
container_title	Frontiers in Cellular and Infection Microbiology
authorswithroles_txt_mv	Tong Pan @@aut@@ Zhangming Pei @@aut@@ Zhifeng Fang @@aut@@ Hongchao Wang @@aut@@ Jinlin Zhu @@aut@@ Hao Zhang @@aut@@ Jianxin Zhao @@aut@@ Wei Chen @@aut@@ Wenwei Lu @@aut@@
publishDateDaySort_date	2023-01-01T00:00:00Z
hierarchy_top_id	664968554
id	DOAJ087903059
language_de	englisch
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Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. 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callnumber-first	Q - Science
author	Tong Pan
spellingShingle	Tong Pan misc QR1-502 misc tryptophan misc metabolism misc lactic acid bacteria misc specificity misc predictability misc genomics misc Microbiology Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
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topic_title	QR1-502 Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics tryptophan metabolism lactic acid bacteria specificity predictability genomics
topic	misc QR1-502 misc tryptophan misc metabolism misc lactic acid bacteria misc specificity misc predictability misc genomics misc Microbiology
topic_unstemmed	misc QR1-502 misc tryptophan misc metabolism misc lactic acid bacteria misc specificity misc predictability misc genomics misc Microbiology
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title	Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
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title_full	Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
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title_sort	uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
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title_auth	Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
abstract	Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites.
abstractGer	Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites.
abstract_unstemmed	Tryptophan is metabolized by microorganisms into various indole derivatives that have been proven to alleviate diseases and promote human health. Lactic acid bacteria (LAB) are a broad microbial concept, some of which have been developed as probiotics. However, the capacity of most LAB to metabolize tryptophan is unknown. In this study, the aim is to reveal the rule of tryptophan metabolism in LAB by multi-omics. The findings showed that LAB were rich in genes for tryptophan catabolism and that multiple genes were shared among LAB species. Although the number of their homologous sequences was different, they could still form the same metabolic enzyme system. The metabolomic analysis revealed that LAB were capable of producing a variety of metabolites. Strains belonging to the same species can produce the same metabolites and have similar yields. A few strains showed strain-specificity in the production of indole-3-lactic acid (ILA), indole-3-acetic acid, and 3-indolealdehyde (IAld). In the genotype-phenotype association analysis, the metabolites of LAB were found to be highly consistent with the outcomes of gene prediction, particularly ILA, indole-3-propionic acid, and indole-3-pyruvic acid. The overall prediction accuracy was more than 87% on average, which indicated the predictability of tryptophan metabolites of LAB. Additionally, genes influenced the concentration of metabolites. The levels of ILA and IAld were significantly correlated with the numbers of aromatic amino acid aminotransferase and amidase, respectively. The unique indolelactate dehydrogenase in Ligilactobacillus salivarius was the primary factor contributing to its large production of ILA. In summary, we demonstrated the gene distribution and production level of tryptophan metabolism in LAB and explored the correlation between genes and phenotypes. The predictability and specificity of the tryptophan metabolites in LAB were proven. These results provide a novel genomic method for the discovery of LAB with tryptophan metabolism potential and offer experimental data for probiotics that produce specific tryptophan metabolites.
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title_short	Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics
url	https://doi.org/10.3389/fcimb.2023.1154346 https://doaj.org/article/b777814fc4b04cd885b69e7c4d593022 https://www.frontiersin.org/articles/10.3389/fcimb.2023.1154346/full https://doaj.org/toc/2235-2988
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