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.