Cargando…

Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction

Analysis of enteric microbiota function indirectly through the fecal metabolome has the potential to be an informative diagnostic tool. However, metabolomic analysis of feces is hampered by high concentrations of macromolecules such as proteins, fats, and fiber in samples. Three methods—ultrafiltrat...

Descripción completa

Detalles Bibliográficos
Autores principales: Brown, Catherine L. J., Scott, Hannah, Mulik, Crystal, Freund, Amy S., Opyr, Michael P., Metz, Gerlinde A. S., Inglis, G. Douglas, Montina, Tony
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875708/
https://www.ncbi.nlm.nih.gov/pubmed/35208222
http://dx.doi.org/10.3390/metabo12020148
_version_ 1784657997701578752
author Brown, Catherine L. J.
Scott, Hannah
Mulik, Crystal
Freund, Amy S.
Opyr, Michael P.
Metz, Gerlinde A. S.
Inglis, G. Douglas
Montina, Tony
author_facet Brown, Catherine L. J.
Scott, Hannah
Mulik, Crystal
Freund, Amy S.
Opyr, Michael P.
Metz, Gerlinde A. S.
Inglis, G. Douglas
Montina, Tony
author_sort Brown, Catherine L. J.
collection PubMed
description Analysis of enteric microbiota function indirectly through the fecal metabolome has the potential to be an informative diagnostic tool. However, metabolomic analysis of feces is hampered by high concentrations of macromolecules such as proteins, fats, and fiber in samples. Three methods—ultrafiltration (UF), Bligh–Dyer (BD), and no extraction (samples added directly to buffer, vortexed, and centrifuged)—were tested on multiple rat (n = 10) and chicken (n = 8) fecal samples to ascertain whether the methods worked equally well across species and individuals. An in silico baseline correction method was evaluated to determine if an algorithm could produce spectra similar to those obtained via UF. For both rat and chicken feces, UF removed all macromolecules and produced no baseline distortion among samples. By contrast, the BD and no extraction methods did not remove all the macromolecules and produced baseline distortions. The application of in silico baseline correction produced spectra comparable to UF spectra. In the case of no extraction, more intense peaks were produced. This suggests that baseline correction may be a cost-effective method for metabolomic analyses of fecal samples and an alternative to UF. UF was the most versatile and efficient extraction method; however, BD and no extraction followed by baseline correction can produce comparable results.
format Online
Article
Text
id pubmed-8875708
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-88757082022-02-26 Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction Brown, Catherine L. J. Scott, Hannah Mulik, Crystal Freund, Amy S. Opyr, Michael P. Metz, Gerlinde A. S. Inglis, G. Douglas Montina, Tony Metabolites Article Analysis of enteric microbiota function indirectly through the fecal metabolome has the potential to be an informative diagnostic tool. However, metabolomic analysis of feces is hampered by high concentrations of macromolecules such as proteins, fats, and fiber in samples. Three methods—ultrafiltration (UF), Bligh–Dyer (BD), and no extraction (samples added directly to buffer, vortexed, and centrifuged)—were tested on multiple rat (n = 10) and chicken (n = 8) fecal samples to ascertain whether the methods worked equally well across species and individuals. An in silico baseline correction method was evaluated to determine if an algorithm could produce spectra similar to those obtained via UF. For both rat and chicken feces, UF removed all macromolecules and produced no baseline distortion among samples. By contrast, the BD and no extraction methods did not remove all the macromolecules and produced baseline distortions. The application of in silico baseline correction produced spectra comparable to UF spectra. In the case of no extraction, more intense peaks were produced. This suggests that baseline correction may be a cost-effective method for metabolomic analyses of fecal samples and an alternative to UF. UF was the most versatile and efficient extraction method; however, BD and no extraction followed by baseline correction can produce comparable results. MDPI 2022-02-05 /pmc/articles/PMC8875708/ /pubmed/35208222 http://dx.doi.org/10.3390/metabo12020148 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Brown, Catherine L. J.
Scott, Hannah
Mulik, Crystal
Freund, Amy S.
Opyr, Michael P.
Metz, Gerlinde A. S.
Inglis, G. Douglas
Montina, Tony
Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title_full Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title_fullStr Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title_full_unstemmed Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title_short Fecal (1)H-NMR Metabolomics: A Comparison of Sample Preparation Methods for NMR and Novel in Silico Baseline Correction
title_sort fecal (1)h-nmr metabolomics: a comparison of sample preparation methods for nmr and novel in silico baseline correction
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875708/
https://www.ncbi.nlm.nih.gov/pubmed/35208222
http://dx.doi.org/10.3390/metabo12020148
work_keys_str_mv AT browncatherinelj fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT scotthannah fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT mulikcrystal fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT freundamys fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT opyrmichaelp fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT metzgerlindeas fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT inglisgdouglas fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection
AT montinatony fecal1hnmrmetabolomicsacomparisonofsamplepreparationmethodsfornmrandnovelinsilicobaselinecorrection