Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus)
The common marmoset (Callithrix jacchus) is increasingly used as an animal model for biomedical research; however, gastrointestinal diseases causing significant morbidity are endemic in many captive marmoset colonies. Establishing gut microbiome patterns in a marmoset colony may aid in clinical deci...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020
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| Online Access: | https://hdl.handle.net/1721.1/124795 |
| _version_ | 1826214022490357760 |
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| author | Artim, Stephen C. Sheh, Alexander Burns, Monika A. Fox, James G. |
| author2 | Massachusetts Institute of Technology. Division of Comparative Medicine |
| author_facet | Massachusetts Institute of Technology. Division of Comparative Medicine Artim, Stephen C. Sheh, Alexander Burns, Monika A. Fox, James G. |
| author_sort | Artim, Stephen C. |
| collection | MIT |
| description | The common marmoset (Callithrix jacchus) is increasingly used as an animal model for biomedical research; however, gastrointestinal diseases causing significant morbidity are endemic in many captive marmoset colonies. Establishing gut microbiome patterns in a marmoset colony may aid in clinical decision-making and model reproducibility. A standardized method of sample collection and storage is essential for proper interpretation of microbiome data. While microbiome studies commonly utilize fecal samples, the goal of this study was to determine whether the microbiome profile from a rectal swab performed on a sedated animal was comparable to the microbiome profile from a fecal sample. During routine physical exams, paired fecal and rectal swab samples were collected from each of 23 marmosets. DNA was extracted from all fecal and rectal swab samples and 16S ribosomal RNA gene sequences were amplified and analyzed. Initial comparison of the relative abundance of bacterial phyla between paired samples had a r2 value of 0.70 with S of 0.08 with no significant differences in α and β diversity metrics between fecal and rectal samples. Initial analysis however, revealed 5 discordant fecal-rectal pairs which corresponded only with the 5 rectal swabs that were classified as free of visible fecal matter during collection. Exclusion of these 5 pairs resulted in an optimized fit of the data as evidenced by a r2 value of 0.91 with S of 0.05. These results demonstrate that rectal swabs are a reliable method for profiling the fecal microbiome in the marmoset since the bacterial composition from a rectal swab with visible fecal contents correlated well with the bacterial composition from a fecal sample from the same marmoset. This study highlights the importance of standardized sample collection methods and exclusion of inappropriate samples. |
| first_indexed | 2024-09-23T15:58:33Z |
| format | Article |
| id | mit-1721.1/124795 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:58:33Z |
| publishDate | 2020 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1247952022-09-29T17:25:10Z Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) Artim, Stephen C. Sheh, Alexander Burns, Monika A. Fox, James G. Massachusetts Institute of Technology. Division of Comparative Medicine General Biochemistry, Genetics and Molecular Biology General Agricultural and Biological Sciences General Medicine The common marmoset (Callithrix jacchus) is increasingly used as an animal model for biomedical research; however, gastrointestinal diseases causing significant morbidity are endemic in many captive marmoset colonies. Establishing gut microbiome patterns in a marmoset colony may aid in clinical decision-making and model reproducibility. A standardized method of sample collection and storage is essential for proper interpretation of microbiome data. While microbiome studies commonly utilize fecal samples, the goal of this study was to determine whether the microbiome profile from a rectal swab performed on a sedated animal was comparable to the microbiome profile from a fecal sample. During routine physical exams, paired fecal and rectal swab samples were collected from each of 23 marmosets. DNA was extracted from all fecal and rectal swab samples and 16S ribosomal RNA gene sequences were amplified and analyzed. Initial comparison of the relative abundance of bacterial phyla between paired samples had a r2 value of 0.70 with S of 0.08 with no significant differences in α and β diversity metrics between fecal and rectal samples. Initial analysis however, revealed 5 discordant fecal-rectal pairs which corresponded only with the 5 rectal swabs that were classified as free of visible fecal matter during collection. Exclusion of these 5 pairs resulted in an optimized fit of the data as evidenced by a r2 value of 0.91 with S of 0.05. These results demonstrate that rectal swabs are a reliable method for profiling the fecal microbiome in the marmoset since the bacterial composition from a rectal swab with visible fecal contents correlated well with the bacterial composition from a fecal sample from the same marmoset. This study highlights the importance of standardized sample collection methods and exclusion of inappropriate samples. National Institutes of Health (U.S.) (Grant T32 OD010978) National Institute of Environmental Health Sciences (Award P30-ES002109) 2020-04-22T16:24:29Z 2020-04-22T16:24:29Z 2019-11-07 2020-03-06T14:21:14Z Article http://purl.org/eprint/type/JournalArticle 1932-6203 https://hdl.handle.net/1721.1/124795 Artim, Stephen C. et al. “Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus).” PLoS ONE 14 (2019): e0224950 © 2019 The Author(s) en 10.1371/journal.pone.0224950 PLoS ONE Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | General Biochemistry, Genetics and Molecular Biology General Agricultural and Biological Sciences General Medicine Artim, Stephen C. Sheh, Alexander Burns, Monika A. Fox, James G. Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title | Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title_full | Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title_fullStr | Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title_full_unstemmed | Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title_short | Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus) |
| title_sort | evaluating rectal swab collection method for gut microbiome analysis in the common marmoset callithrix jacchus |
| topic | General Biochemistry, Genetics and Molecular Biology General Agricultural and Biological Sciences General Medicine |
| url | https://hdl.handle.net/1721.1/124795 |
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