Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics
Abstract Cross‐feeding is fundamental to the diversity and function of microbial communities. However, identification of cross‐fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use 13C isotope tracing in peptides to elucidate cross‐fed...
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| Format: | Article |
| Language: | English |
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Springer Nature
2023-02-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.202211501 |
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| author | Natalia Gabrielli Christoniki Maga‐Nteve Eleni Kafkia Mandy Rettel Jakob Loeffler Stephan Kamrad Athanasios Typas Kiran Raosaheb Patil |
| author_facet | Natalia Gabrielli Christoniki Maga‐Nteve Eleni Kafkia Mandy Rettel Jakob Loeffler Stephan Kamrad Athanasios Typas Kiran Raosaheb Patil |
| author_sort | Natalia Gabrielli |
| collection | DOAJ |
| description | Abstract Cross‐feeding is fundamental to the diversity and function of microbial communities. However, identification of cross‐fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use 13C isotope tracing in peptides to elucidate cross‐fed metabolites in co‐cultures of Saccharomyces cerevisiae and Lactococcus lactis. The community was grown on lactose as the main carbon source with either glucose or galactose fraction of the molecule labelled with 13C. Data analysis allowing for the possible mass‐shifts yielded hundreds of peptides for which we could assign both species identity and labelling degree. The labelling pattern showed that the yeast utilized galactose and, to a lesser extent, lactic acid shared by L. lactis as carbon sources. While the yeast provided essential amino acids to the bacterium as expected, the data also uncovered a complex pattern of amino acid exchange. The identity of the cross‐fed metabolites was further supported by metabolite labelling in the co‐culture supernatant, and by diminished fitness of a galactose‐negative yeast mutant in the community. Together, our results demonstrate the utility of 13C‐based proteomics for uncovering microbial interactions. |
| format | Article |
| id | doaj-art-3c565358b43c4edaaac68e3c97920bb7 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2023-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-3c565358b43c4edaaac68e3c97920bb72025-08-20T03:46:41ZengSpringer NatureMolecular Systems Biology1744-42922023-02-0119411310.15252/msb.202211501Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomicsNatalia Gabrielli0Christoniki Maga‐Nteve1Eleni Kafkia2Mandy Rettel3Jakob Loeffler4Stephan Kamrad5Athanasios Typas6Kiran Raosaheb Patil7European Molecular Biology LaboratoryEuropean Molecular Biology LaboratoryEuropean Molecular Biology LaboratoryEuropean Molecular Biology LaboratoryEuropean Molecular Biology LaboratoryMedical Research Council Toxicology Unit, University of CambridgeEuropean Molecular Biology LaboratoryEuropean Molecular Biology LaboratoryAbstract Cross‐feeding is fundamental to the diversity and function of microbial communities. However, identification of cross‐fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use 13C isotope tracing in peptides to elucidate cross‐fed metabolites in co‐cultures of Saccharomyces cerevisiae and Lactococcus lactis. The community was grown on lactose as the main carbon source with either glucose or galactose fraction of the molecule labelled with 13C. Data analysis allowing for the possible mass‐shifts yielded hundreds of peptides for which we could assign both species identity and labelling degree. The labelling pattern showed that the yeast utilized galactose and, to a lesser extent, lactic acid shared by L. lactis as carbon sources. While the yeast provided essential amino acids to the bacterium as expected, the data also uncovered a complex pattern of amino acid exchange. The identity of the cross‐fed metabolites was further supported by metabolite labelling in the co‐culture supernatant, and by diminished fitness of a galactose‐negative yeast mutant in the community. Together, our results demonstrate the utility of 13C‐based proteomics for uncovering microbial interactions.https://doi.org/10.15252/msb.202211501metabolic flux analysismicrobial interactionsprotein stable‐isotope labellingsynthetic microbial community |
| spellingShingle | Natalia Gabrielli Christoniki Maga‐Nteve Eleni Kafkia Mandy Rettel Jakob Loeffler Stephan Kamrad Athanasios Typas Kiran Raosaheb Patil Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics Molecular Systems Biology metabolic flux analysis microbial interactions protein stable‐isotope labelling synthetic microbial community |
| title | Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics |
| title_full | Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics |
| title_fullStr | Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics |
| title_full_unstemmed | Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics |
| title_short | Unravelling metabolic cross‐feeding in a yeast–bacteria community using 13C‐based proteomics |
| title_sort | unravelling metabolic cross feeding in a yeast bacteria community using 13c based proteomics |
| topic | metabolic flux analysis microbial interactions protein stable‐isotope labelling synthetic microbial community |
| url | https://doi.org/10.15252/msb.202211501 |
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