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Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation

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 me...

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Autores principales: Romano, Kymberleigh A., Dill-McFarland, Kimberly A., Kasahara, Kazuyuki, Kerby, Robert L., Vivas, Eugenio I., Amador-Noguez, Daniel, Herd, Pamela, Rey, Federico E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960144/
https://www.ncbi.nlm.nih.gov/pubmed/29776435
http://dx.doi.org/10.1186/s40168-018-0458-8
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author Romano, Kymberleigh A.
Dill-McFarland, Kimberly A.
Kasahara, Kazuyuki
Kerby, Robert L.
Vivas, Eugenio I.
Amador-Noguez, Daniel
Herd, Pamela
Rey, Federico E.
author_facet Romano, Kymberleigh A.
Dill-McFarland, Kimberly A.
Kasahara, Kazuyuki
Kerby, Robert L.
Vivas, Eugenio I.
Amador-Noguez, Daniel
Herd, Pamela
Rey, Federico E.
author_sort Romano, Kymberleigh A.
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0458-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-59601442018-05-24 Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation Romano, Kymberleigh A. Dill-McFarland, Kimberly A. Kasahara, Kazuyuki Kerby, Robert L. Vivas, Eugenio I. Amador-Noguez, Daniel Herd, Pamela Rey, Federico E. Microbiome Methodology 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0458-8) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-18 /pmc/articles/PMC5960144/ /pubmed/29776435 http://dx.doi.org/10.1186/s40168-018-0458-8 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology
Romano, Kymberleigh A.
Dill-McFarland, Kimberly A.
Kasahara, Kazuyuki
Kerby, Robert L.
Vivas, Eugenio I.
Amador-Noguez, Daniel
Herd, Pamela
Rey, Federico E.
Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation
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 Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960144/
https://www.ncbi.nlm.nih.gov/pubmed/29776435
http://dx.doi.org/10.1186/s40168-018-0458-8
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