The Human Microbiome Study
The human body is a complex ecosystem, teeming with trillions of microorganisms that play a crucial role in our health and well-being. The study of the human microbiome, the vast community of bacteria, viruses, fungi, and other microbes residing in and on our bodies, has become a focal point in scientific research.
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Fig. 1 Definitions of microbiome, microbiota, metagenome, and 16S rDNA. (A) The concept of microbiome covers not only the microorganisms but also the surrounding environmental conditions. Microbiota only means the microorganisms. (B) Metagenome means all genomes of the microorganisms, while 16S rDNA only covers a segment of the genomes. (C) α-diversity measures the diversity within a sample, while β-diversity compares the difference between samples. (Qian XB, et al., 2020)
The human microbiome comprises microorganisms that inhabit different niches within the body, including the skin, mouth, gut, and other mucosal surfaces. The study of the human microbiome involves the collection and analysis of microbial DNA to gain a comprehensive understanding of the diverse microbial communities present in various body sites.
DNA Extraction from Different Samples
The success of any microbiome study relies on the efficient extraction of high-quality DNA from diverse sample types. Each body site poses unique challenges due to variations in microbial density, the presence of inhibitors, and the complexity of the sample matrix. Therefore, researchers employ tailored DNA extraction methods to ensure accurate and representative results.
Gut Microbiome
The gut microbiome is of particular interest due to its significant impact on human health. Studying the microbial communities in the gastrointestinal tract requires specialized DNA extraction protocols. Fecal samples, commonly used in gut microbiome studies, contain a rich source of microbial DNA. Researchers employ techniques such as bead-beating, enzymatic digestion, and chemical lysis to break open microbial cells and release their genetic material for subsequent analysis.
Oral Microbiome
The oral cavity hosts a diverse array of microorganisms, contributing to both oral and systemic health. Saliva and dental plaque are common sample types for oral microbiome studies. DNA extraction from these samples involves the use of mechanical disruption methods, such as bead-beating, to break down the tough cell walls of certain oral bacteria. Enzymatic treatments may also be employed to improve DNA yield and purity.
Skin Microbiome
The skin, our body's largest organ, harbors a complex microbial ecosystem. Swabbing is a common method for collecting skin samples. DNA extraction from skin samples often involves the use of detergents and surfactants to disrupt the cell membranes of microbial cells. Additionally, researchers may employ specialized kits designed to extract DNA from challenging sample types like skin, optimizing the process for maximum yield and purity.
Vaginal Microbiome
The vaginal microbiome plays a crucial role in women's health, influencing reproductive outcomes and protecting against infections. Swabs or lavage samples are commonly used for studying the vaginal microbiome. DNA extraction methods for these samples involve the use of enzymatic and mechanical disruption to release microbial DNA while minimizing contamination from host DNA.
The human microbiome study, coupled with advancements in DNA extraction techniques, has opened new frontiers in our understanding of microbial communities and their impact on human health. The ability to extract high-quality DNA from diverse sample types enables researchers to explore the intricate relationships between the microbiome and various physiological processes. As technology continues to evolve, the field of microbiome research holds great promise for uncovering novel therapeutic interventions and personalized approaches to health based on an individual's unique microbial profile. The journey to unlock the secrets within the human microbiome continues, paving the way for a deeper comprehension of the symbiotic relationship between humans and their microbial companions.
Reference
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Qian XB, Chen T, Xu YP, Chen L, Sun FX, Lu MP, Liu YX. A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. Chin Med J (Engl). 2020, 133(15):1844-1855.
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