Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation
Abstract Background Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and st...
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | Microbiome |
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| Online Access: | http://link.springer.com/article/10.1186/s40168-018-0458-8 |
| _version_ | 1819064175213674496 |
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| author | Kymberleigh A. Romano Kimberly A. Dill-McFarland Kazuyuki Kasahara Robert L. Kerby Eugenio I. Vivas Daniel Amador-Noguez Pamela Herd Federico E. Rey |
| author_facet | Kymberleigh A. Romano Kimberly A. Dill-McFarland Kazuyuki Kasahara Robert L. Kerby Eugenio I. Vivas Daniel Amador-Noguez Pamela Herd Federico E. Rey |
| author_sort | Kymberleigh A. Romano |
| collection | DOAJ |
| description | Abstract Background Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes. Results We describe the Fecal Aliquot Straw Technique (FAST) of fecal sample processing for storage and subsampling. This method uses a straw to collect fecal material from samples recently voided or preserved at low temperature but not frozen (i.e., 4 °C). Different straw aliquots collected from the same sample yielded highly reproducible communities as disclosed by 16S rRNA gene sequencing; operational taxonomic units that were lost, or gained, between the two aliquots represented very low-abundance taxa (i.e., < 0.3% of the community). FAST-processed samples inoculated into germ-free animals resulted in gut communities that retained on average ~ 80% of the donor’s bacterial community. Assessment of choline metabolism and trimethylamine-N-oxide accumulation in transplanted mice suggests large interpersonal variation. Conclusions Overall, FAST allows for repetitive subsampling without thawing of the specimens and requires minimal supplies and storage space, making it convenient to utilize both in the lab and in the field. FAST has the potential to advance microbiome research through easy, reproducible sample processing. |
| first_indexed | 2024-12-21T15:26:23Z |
| format | Article |
| id | doaj.art-6f6c70f6ce4b4c6e9c658d74302da446 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-21T15:26:23Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-6f6c70f6ce4b4c6e9c658d74302da4462022-12-21T18:58:53ZengBMCMicrobiome2049-26182018-05-01611810.1186/s40168-018-0458-8Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulationKymberleigh A. Romano0Kimberly A. Dill-McFarland1Kazuyuki Kasahara2Robert L. Kerby3Eugenio I. Vivas4Daniel Amador-Noguez5Pamela Herd6Federico E. Rey7Department of Bacteriology, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonCenter for the Demography of Health and Aging, University of Wisconsin-MadisonDepartment of Bacteriology, University of Wisconsin-MadisonAbstract Background Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes. Results We describe the Fecal Aliquot Straw Technique (FAST) of fecal sample processing for storage and subsampling. This method uses a straw to collect fecal material from samples recently voided or preserved at low temperature but not frozen (i.e., 4 °C). Different straw aliquots collected from the same sample yielded highly reproducible communities as disclosed by 16S rRNA gene sequencing; operational taxonomic units that were lost, or gained, between the two aliquots represented very low-abundance taxa (i.e., < 0.3% of the community). FAST-processed samples inoculated into germ-free animals resulted in gut communities that retained on average ~ 80% of the donor’s bacterial community. Assessment of choline metabolism and trimethylamine-N-oxide accumulation in transplanted mice suggests large interpersonal variation. Conclusions Overall, FAST allows for repetitive subsampling without thawing of the specimens and requires minimal supplies and storage space, making it convenient to utilize both in the lab and in the field. FAST has the potential to advance microbiome research through easy, reproducible sample processing.http://link.springer.com/article/10.1186/s40168-018-0458-8MicrobiomeFecal Aliquot Straw TechniqueFASTTMAOCholine |
| spellingShingle | Kymberleigh A. Romano Kimberly A. Dill-McFarland Kazuyuki Kasahara Robert L. Kerby Eugenio I. Vivas Daniel Amador-Noguez Pamela Herd Federico E. Rey Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation Microbiome Microbiome Fecal Aliquot Straw Technique FAST TMAO Choline |
| title | Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation |
| title_full | Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation |
| title_fullStr | Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation |
| title_full_unstemmed | Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation |
| title_short | Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation |
| title_sort | fecal aliquot straw technique fast allows for easy and reproducible subsampling assessing interpersonal variation in trimethylamine n oxide tmao accumulation |
| topic | Microbiome Fecal Aliquot Straw Technique FAST TMAO Choline |
| url | http://link.springer.com/article/10.1186/s40168-018-0458-8 |
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