Microbiome Research Technologies

**3**

**Chapter 1**

**Abstract**

Microbiota

*Akhlash P. Singh*

lifestyle-related diseases.

**1. Introduction**

Genomic Techniques Used to

The human gut is the complex microbial ecosystem comprises more than 100 trillion microbes also known as microbiota. The gut microbiota does not only include about 400–500 types of bacterial strains, but it also contains archaea, bacteriophage, fungi, and protozoa species. In order to complete the characterization of the gut microbial community, we need the help of many culture-dependent and cultureindependent genomic technologies. Recently, next-generation sequencing (NGS), mediated metagenomics that rely on 16S rRNA gene amplification, and wholegenome sequencing (WGS) have provided us deep knowledge related to important interactions such as host-microbiota and microbe-microbe interactions under various perturbation inside the gut. But, we still lack complete knowledge related to unique gene products encoded by gut meta-genome. Hence, it required the application of high-throughput "omics-based" methods to support metagenomics. Currently, a combination of high-throughput culturing and microfluidics assays is providing a new method to characterize non-amenable bacterial strains from the gut environment. The recent additions of artificial intelligence and deep learning to the area of microbiome studies have enhanced the capability of identification of thousand microbes simultaneously. Given above, it is necessary to apply new genome editing tools that can be used to design the personalized microflora which can be used to cure

**Keywords:** culturomics, gut microbiota, human microbiome, metagenomics, metaproteomics, metabolomics, microfluidics, "multi-omics", personalized diet

In the beginning of the twenty-first century, the human genome was sequenced. The main aim of this gigantic scientific effort was to identify all genes present in the human genome, also considered as the "blueprint of human life." Since then, most of the efforts are focused on the identification of all genes and annotate their functions which are responsible for genetic variation prevailed in human physiology and its association with diseases [1]. Currently, many experiments have proved that the gut microbes are more responsible than host genetics in the development of life stylerelated diseases. Hence, it becomes essential to investigate the crucial roles played by gut microbes in health and diseases. The human gut is a complex microbial ecosystem which is comprised of approximately 100 trillion microbes collectively known as "gut microbiota" [1]. It does not only include about 400–500 types of bacterial species but

Investigate the Human Gut
