Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods
Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the pr...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-06-01
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| Series: | Journal of Clinical Medicine |
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| Online Access: | https://www.mdpi.com/2077-0383/9/7/2036 |
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| author | Jaroslaw Bilinski Mikolaj Dziurzynski Pawel Grzesiowski Edyta Podsiadly Anna Stelmaszczyk-Emmel Tomasz Dzieciatkowski Lukasz Dziewit Grzegorz W. Basak |
| author_facet | Jaroslaw Bilinski Mikolaj Dziurzynski Pawel Grzesiowski Edyta Podsiadly Anna Stelmaszczyk-Emmel Tomasz Dzieciatkowski Lukasz Dziewit Grzegorz W. Basak |
| author_sort | Jaroslaw Bilinski |
| collection | DOAJ |
| description | Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and <i>Anaeroplasma</i> found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately. |
| first_indexed | 2024-03-10T18:49:19Z |
| format | Article |
| id | doaj.art-50cf965778b544e0b455127b4697adb0 |
| institution | Directory Open Access Journal |
| issn | 2077-0383 |
| language | English |
| last_indexed | 2024-03-10T18:49:19Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Clinical Medicine |
| spelling | doaj.art-50cf965778b544e0b455127b4697adb02023-11-20T05:17:06ZengMDPI AGJournal of Clinical Medicine2077-03832020-06-0197203610.3390/jcm9072036Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary MethodsJaroslaw Bilinski0Mikolaj Dziurzynski1Pawel Grzesiowski2Edyta Podsiadly3Anna Stelmaszczyk-Emmel4Tomasz Dzieciatkowski5Lukasz Dziewit6Grzegorz W. Basak7Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, PolandDepartment of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandFoundation for the Infection Prevention Institute, 02-991 Warsaw, PolandDepartment of Microbiology, Institute of Medical Sciences, University of Rzeszów, 35-310 Rzeszów, PolandDepartment of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 02-091 Warsaw, PolandDepartment of Medical Microbiology, Medical University of Warsaw, 02-091 Warsaw, PolandDepartment of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandDepartment of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, PolandMethods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and <i>Anaeroplasma</i> found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.https://www.mdpi.com/2077-0383/9/7/2036fecal microbiota transplantationfeces donorfecal microbiotaflow cytometryviability of bacterianext-generation sequencing |
| spellingShingle | Jaroslaw Bilinski Mikolaj Dziurzynski Pawel Grzesiowski Edyta Podsiadly Anna Stelmaszczyk-Emmel Tomasz Dzieciatkowski Lukasz Dziewit Grzegorz W. Basak Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods Journal of Clinical Medicine fecal microbiota transplantation feces donor fecal microbiota flow cytometry viability of bacteria next-generation sequencing |
| title | Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods |
| title_full | Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods |
| title_fullStr | Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods |
| title_full_unstemmed | Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods |
| title_short | Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods |
| title_sort | multimodal approach to assessment of fecal microbiota donors based on three complementary methods |
| topic | fecal microbiota transplantation feces donor fecal microbiota flow cytometry viability of bacteria next-generation sequencing |
| url | https://www.mdpi.com/2077-0383/9/7/2036 |
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