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Mammals have developed in environments dominated by microbes (29). The term microbiome primarily refers to the genomic repertoire of the microbiota, although it is often used interchangeably with microbiota (1). The current evidence suggests that the ratio of microorganisms to human cells is approximately 1:1, with about 3.8 × 10^13 microorganisms compared to 3 × 10^13 human cells (2, 28). This relation is noticeably higher when analyzing the genomes, microbial genetic content being 100 to 200 times superior to the content of our cells (3, 27). The microbiome refers to the complete collection of genomes from the microbes that reside within our bodies. This includes bacteria, bacteriophages, fungi, viruses, protozoa, and helminths.(6) A healthy microbiome lacks a clear definition due to the wide variation in dietary habits and geocultural practices across human societies (6). The human microbiome is a complex ecosystem that encompasses not only bacteria but also bacteriophages, fungi, viruses, and archaea. In regions of the developing world, this microbiome extends to include protozoa and helminths, which are parasitic worms. These diverse microbes inhabit various sites within the body, with the majority residing in the anaerobic environment of the lower gut. Remarkably, the number of these microbial inhabitants is at least equal to that of the host's somatic cells (20, 21, 22, 23).
The human microbiome of the 21st century are quite different from those of our ancestors. This difference is evident through sequence analyses of ancient paleofeces or samples from living indigenous populations (17, 18). In the last two decades, microbiome research has experienced rapid growth, evidenced by nearly 200,000 peer-reviewed articles featuring the term "microbiome." This surge in research has led to significant discoveries in microbial lineages, reshaping our understanding of the evolutionary tree of life (4).
The diversity in both genetic and phenotypic aspects of human microbiomes shows considerable variation among different populations. Studies conducted in Europe and North America might not be relevant or applicable to other parts of the world. Consequently, treatments that are developed in wealthier countries may not work effectively for people living in less affluent regions, even though these individuals might greatly benefit from such medical interventions (5).
The realization that trillions of symbiotic microbes inhabit various parts of the human body and play crucial roles in maintaining the health of these areas has emerged as one of the most important breakthroughs in biomedicine since the germ theory transformed the field in the 19th century (16).
Diet and lifestyle are well-known factors that modulate the composition of the human microbiome (7, 8, 9). However, since very few members of the microbiome can thrive outside the human body, most microorganisms must be acquired from other individuals (10, 11). The lifestyle changes that come with industrialisation, such as better hygiene, the use of antibiotics, eating processed foods, and living in urban areas, have led to a decrease in microbial diversity and have changed the structure and function of microbial communities (19).
The mucosal surfaces of the body are defined by intricate and specialized microbial communities, which are commonly referred to as the microbiome (15). The epithelial surfaces of our body, along with the gastrointestinal tract, respiratory system, and urogenital systems, are colonized by bacteria, archaea, fungi, protozoans, and viruses (12, 13, 14). The skin and mucosal surfaces, also known as mucous membranes, of vertebrates are inhabited by a vast array of microorganisms. These include bacteria, fungi, Parasites / Parasitism, and viruses, which are collectively known as the microbiota (24).
Actinomycetota, such as Propionibacterium, along with Firmicutes and Proteobacteria, are the primary colonizers of the skin. In the vaginal environment, Lactobacillus species, which belong to the phylum Firmicutes, are predominant. In the oral cavity, or mouth, the phylum Bacteroidetes, Streptococcus (also from the phylum Firmicutes), as well as the phyla Fusobacteriota and Proteobacteria, are the dominant groups. Furthermore, the diversity of the human microbiome or microbiota is influenced by the specific site from which samples are taken, as demonstrated in studies of the mouth (25). The great diversity in the microbial composition between individuals (beta-diversity) is also shown. Differences in bacterial concentration (genera and phyla) of the Skin microbiota, Vaginal microbiota, Gut microbiota, and mouth occur between individuals (25).
Microbes that live in and on the human body play a significant role in influencing human physiology. They particularly affect the metabolism of xenobiotic compounds, which include therapeutic drugs, antibiotics, and bioactive compounds derived from the diet (26).
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(7) Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016)
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see also:
Analytic Microbiome / Methodology
Food / Diets / Nutrients & Gut microbiota
Genome
Gut microbiota & Lifestyle / Lifestyle Changes
Gut microbiota & Physical well-being / Health
Manipulation / Modulation of Gut microbiota
Microbial Genes
Microbials / Microorganism