Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies

Frontiers in Cellular and Infection Microbiology
Zheng WangRobert D Burk

Abstract

Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the "gold standard" immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene...Continue Reading

References

Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Mar 14, 2009·Journal of Proteome Research·Francois-Pierre J MartinJeremy K Nicholson
Aug 15, 2009·Journal of Proteome Research·Yunping QiuWei Jia
Nov 11, 2009·Current Opinion in Gastroenterology·Ruth E Ley
Nov 17, 2009·Bioinformatics·J Gregory CaporasoRob Knight
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Sep 30, 2010·Critical Reviews in Microbiology·Marco CandelaCarla Fiorentini
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
Mar 6, 2012·European Journal of Clinical Investigation·Roberto FloresJames J Goedert
Mar 23, 2012·Nature Reviews. Molecular Cell Biology·Gary J PattiGary Siuzdak
Aug 1, 2012·BMC Microbiology·Silvia CardonaChaysavanh Manichanh
Sep 3, 2013·Metabolomics : Official Journal of the Metabolomic Society·Xiaojiao ZhengWei Jia
Feb 25, 2014·Gastroenterology·Aleksandar D KosticDirk Gevers
Apr 25, 2014·BMC Microbiology·Christine DominianniJiyoung Ahn
May 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Apr 19, 2015·Genome Biology·Anita Y VoigtPeer Bork
Oct 31, 2015·Nature Communications·Geicho NakatsuJoseph J Y Sung
Nov 18, 2015·Scientific Reports·Jocelyn M ChooGeraint B Rogers
Nov 26, 2015·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Rashmi SinhaNicholas Chia
Dec 15, 2015·Genome Biology·Rashmi SinhaCurtis Huttenhower
Jan 6, 2016·British Journal of Cancer·Emily Vogtmann, James J Goedert
Nov 3, 2016·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Erikka LoftfieldRashmi Sinha
Dec 18, 2016·American Journal of Epidemiology·Emily VogtmannRashmi Sinha
Mar 5, 2017·Applied and Environmental Microbiology·Emily VogtmannRashmi Sinha
Aug 24, 2017·FEMS Microbiology Reviews·Doris VandeputteJeroen Raes

❮ Previous
Next ❯

Citations

Jul 3, 2019·Future Virology·Zheng Wang, Qibin Qi
Sep 10, 2019·Journal of Parkinson's Disease·Jeffrey M BoertienFilip Scheperjans
Dec 27, 2019·Cardiovascular Research·Theda U P Bartolomaeus, Sofia K Forslund
Jan 31, 2020·Expert Review of Proteomics·Esei T TeclemariamStephanie M Cologna
May 7, 2020·Cardiovascular Research·Theda U P BartolomaeusSofia K Forslund
Nov 22, 2019·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Zheng WangQibin Qi
Jul 1, 2020·Frontiers in Nutrition·Abigail J JohnsonAngela M Zivkovic
Apr 5, 2020·Metabolomics : Official Journal of the Metabolomic Society·Ken ChengRikard Landberg
Aug 8, 2020·Animals : an Open Access Journal From MDPI·Luca BorrelliAlessandro Fioretti
Apr 25, 2020·Frontiers in Cellular and Infection Microbiology·Qiang TangHailong Cao
Jun 18, 2020·Bioinformatics and Biology Insights·Zonghui PengKarsten Kristiansen
Nov 10, 2020·Metabolomics : Official Journal of the Metabolomic Society·Rupasri MandalDavid S Wishart
Oct 16, 2019·Journal of Pharmaceutical and Biomedical Analysis·Jessica FioriRoberto Gotti
Feb 24, 2021·Scientific Reports·Kailee J ReedStephen J Coleman
Apr 2, 2021·Circulation Research·Ellen G AveryDominik N Müller
Mar 30, 2021·JBMR Plus·Elizabeth A RettedalMarlena C Kruger
Apr 14, 2021·Scientific Reports·Lorie Neuberger-CastilloFay Betsou
Jan 14, 2021·Menopause : the Journal of the North American Menopause Society·Brandilyn A PetersQibin Qi
Aug 17, 2020·Journal of the Academy of Nutrition and Dietetics·Ana Maldonado-ContrerasKelsey M Mangano
Jun 25, 2021·Metabolomics : Official Journal of the Metabolomic Society·Nicole H TobinGrace M Aldrovandi
Jan 19, 2020·Schizophrenia Research·Nina VindegaardMichael Eriksen Benros
Aug 18, 2021·Analytica Chimica Acta·Sara Ramírez-AcostaTamara García Barrera
Oct 19, 2019·Analytical Chemistry·Carolina González-RianoCoral Barbas

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP153121

Methods Mentioned

BETA
metabolomics profiling
PCR
Assay
amplicon sequencing

Software Mentioned

R phyloseq / vegan
vegan
UCLUST
OMNIgene
QIIME
PyNAST
Genedata Expressionist
Quantitative Insights Into Microbial Ecology ( QIIME )
phyloseq
DESeq2

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
Emily VogtmannRashmi Sinha
Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
Erikka LoftfieldRashmi Sinha
Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
Rashmi SinhaN Chia
© 2022 Meta ULC. All rights reserved