Exploring Human Microbiome: The Potential Future Role of Next-Generation Sequencing
The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract.
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Types of human microbiota include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.
Path to genome sequencing has changed human microbiome research from focusing on identity characterizations to metagenomics strategies that reveal not only microbial species but also how microbial metabolic activities correlate with human health and disease.
The interaction between the human microbiome and the immune system has an effect on several human metabolic activity. Research studies are going on to identify the relation between composition between the microbiome and infectious disease.
Metagenome assembly
The de novo approach is exploited; however, it presents some difficulties to be overcome. The coverage depends on each genome abundance in its specific community; low-abundance genomes may undergo fragmentation if the sequencing depth is not sufficient enough to avoid the formation of gaps. Luckily, there are metagenome-specific assemblers to help, since, if hundreds of strains are present, the sequencing depth needs to be increased to its maximum.
Marker gene analysis
It is a technique that exploits primers to target a specific genetic region and enables to determine the microbial phylogenies. The genetic region is characterized by a highly variable region which can confer detailed identification; it is delimited by conserved regions, which function as binding sites for primers used in PCR.
The main gene used to characterize bacteria and archaea is 16S rRNA gene, while fungi identification is based on Internal Transcribed Spacer (ITS). The technique is fast and not so expensive and enables to obtain a low-resolution classification of a microbial sample; it is optimal for samples that may be contaminated by host DNA.
Shotgun Sequencing
It is frequently difficult to culture in laboratory communities of bacteria, archaea and viruses, therefore sequencing technologies can be exploited in metagenomics, too. Indeed, the complete knowledge of the functions and the characterization of specific microbial strains offer a great potentiality in therapeutic discovery and human health.