Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways
Summary: A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-10-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223020813 |
| _version_ | 1797647834506330112 |
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| author | Liam H. Walsh Mairéad Coakley Aaron M. Walsh Fiona Crispie Paul W. O’Toole Paul D. Cotter |
| author_facet | Liam H. Walsh Mairéad Coakley Aaron M. Walsh Fiona Crispie Paul W. O’Toole Paul D. Cotter |
| author_sort | Liam H. Walsh |
| collection | DOAJ |
| description | Summary: A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow’s milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage. |
| first_indexed | 2024-03-11T15:22:15Z |
| format | Article |
| id | doaj.art-9a1044c99cbe4dbc84c8915ff0475dc6 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-11T15:22:15Z |
| publishDate | 2023-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-9a1044c99cbe4dbc84c8915ff0475dc62023-10-28T05:09:16ZengElsevieriScience2589-00422023-10-012610108004Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathwaysLiam H. Walsh0Mairéad Coakley1Aaron M. Walsh2Fiona Crispie3Paul W. O’Toole4Paul D. Cotter5Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; School of Microbiology, University College Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandSchool of Microbiology, University College Cork, Ireland; APC Microbiome Ireland SFI Research Centre, University College Cork, IrelandTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland SFI Research Centre, University College Cork, Ireland; VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland; Corresponding authorSummary: A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow’s milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage.http://www.sciencedirect.com/science/article/pii/S2589004223020813Geographic areasMicrobial genomicsMicrobial metabolismGenomics |
| spellingShingle | Liam H. Walsh Mairéad Coakley Aaron M. Walsh Fiona Crispie Paul W. O’Toole Paul D. Cotter Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways iScience Geographic areas Microbial genomics Microbial metabolism Genomics |
| title | Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways |
| title_full | Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways |
| title_fullStr | Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways |
| title_full_unstemmed | Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways |
| title_short | Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways |
| title_sort | analysis of the milk kefir pan metagenome reveals four community types core species and associated metabolic pathways |
| topic | Geographic areas Microbial genomics Microbial metabolism Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223020813 |
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