AccScience Publishing / JBM / Online First / DOI: 10.14440/jbm.2024.0050
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MINI-REVIEW

Advancements in analytical methods for studying the human gut microbiome

Gijsbert J. Jansen1 ,  Gerard P. Schouten1 ,  Marit Wiersma1*
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1 NL-Lab, Biotrack, Leeuwarden, Friesland, 8912 AP, Netherlands
JBM, e99010038 https://doi.org/10.14440/jbm.2024.0050
Submitted: 31 July 2024 | Revised: 20 September 2024 | Accepted: 10 October 2024 | Published: 18 November 2024
© 2024 by the Journal of Biological Methods published by POL Scientific. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
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Abstract

Background: The human gut microbiome, a complex ecosystem of microorganisms, plays a crucial role in maintaining human health. Perturbations in its composition are linked to a wide range of health conditions. Analytical techniques: Researchers employ various techniques to study the gut microbiome, each having its own strengths and limitations. Polymerase chain reaction (PCR) is highly sensitive but dependent on the quality of DNA extraction. Next-generation sequencing (NGS) is powerful but can be costly and requires extensive data analysis. Furthermore, the accuracy of NGS results also depends heavily on the quality of the DNA extraction process. Culture methods, while useful, are biased and time-consuming. Fluorescence in situ hybridization (FISH) excels in visualizing specific microbial populations and is the only method capable of providing in situ information. However, until recently, FISH was heavily reliant on human interpretation of digital photomicrographs, limiting its application in high-throughput strategies. Additionally, the sensitivity of FISH is restricted by the number of cells visualized. Conclusion: Understanding the strengths and weaknesses of these methods is essential for drawing robust conclusions in microbiome research.

Keywords
Culturing
Fluorescence in situ hybridization
Gut microbiome
Next-generation sequencing
Polymerase chain reaction
Funding
None.
Conflict of interest
Authors Gijsbert J. Jansen, Gerard P. Schouten, and Marit Wiersma are employed by the commercial company Biotrack, NL-Lab, and utilize the FISH technique. They hold patents issued (WO 2010/040371 A1, EP 08874964.3). This does not influence the authors’ adherence to the journal’s policies.
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Journal of Biological Methods, Electronic ISSN: 2326-9901 Print ISSN: TBA, Published by POL Scientific
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