**5. New advancements**

#### **5.1 Machine learning**

The advancements made in the area of NGS also coincide with machine learning in the last two decades. Machine learning, a branch of artificial intelligence, is based on computational and statistical principles and is recently applied to various fields of genomics including microbiome genomics. Machine learning deals with the development and testing of algorithms to identify, classify, and forecast patterns that emerged from a huge data set [63]. The gut microbial community is comprised of trillion of microbes which further affected various types of factors such as diet, drugs, age, environment, and even lifestyles. To extract the information from such an intricate system cannot be carried out by humans but rather require machine intervention. The machine learning methods such as deep learning and neural network are used to predict severity and susceptibility gingivitis on the basis of the oral microbiome. The two most important machine learning algorithms, random forest and SourceTracker, are applied to know the effect of antibiotics on the genomic and metagenomic studies [64]. In the near future, machine learning can be used to know the host-trait prediction.

### **5.2 Genome editing/synthetic biology of microbial community**

Genome sequencing data of thousands of bacteria are now available in various databases. Currently, many types of genome editing tools are available to manipulate the genome of animals and plants including microbial genomes. Many scientists have exploited these tools in the manipulation of gut microbiota so that desirable genetic changes can be brought into the metagenomes. The most widely used genome editing tool CRISPR-Cas systems also called clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins are present in the microbes which are mainly responsible for adaptive immunity for prokaryote cells. CRISPR-Cas systems comprise combinations of short DNA sequences called spacers that guide Cas proteins to cleave foreign DNA. So far, CRISPR-Cas systems are the most widely studied and applied method used for genetic manipulation. There are several types of a spacer or genome editing CRISPR-Cas systems, for example, Cas9, CasX, and CRISPR-CasY, that can be used to manipulate genomic content of gut microorganisms. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. Actually, components of Class 2 CRISPR-Cas systems are studied, and assembly from its components in vitro system has revolutionized the field of synthetic biology.

The gut microbiota also comprises a microorganism, for example, single-cell eukaryotes, bacteria, fungus, and bacteriophages. They live in the gut in a very harmonious manner with trillions of bacteria in a natural environment, hence, well adapted to the local environment. Therefore, researchers are embarking on the idea that gut symbionts can be potential agents or vectors for genetic manipulation of gut microbial communities. The new genome editing tools are used to genetically reprogram gut communities under synthetic biology [65]. CRISPR-Cas systems have been exploited to modification of gene expression, change of the production of metabolites, biocatalyst, and protein production that can act as better microbiome modulators. Moreover, genome editing tools will prove extremely helpful in the functional characterization of gut microbiota. Current genome editing tools have offered opportunities in the investigation of intricate relationships between members of the microbiome and host and have opened new avenues for the development of pharmaceutical agents that target the microbiome. But still many demerits are also linked with genome editing tools including their off-targets and inability to introduce exogenous DNA into the metagenome [66]. Moreover, many bacteria particularly unculturable are naturally ill-adapted to transformation methods such as electroporation, conjugation, or transduction in lab conditions.

#### **6. Summary and future prospectus**

The gut microbiome is an unexploited huge wealth of microbes that synthesized the valuable and unique metabolites to be used for pharmaceutical industries and the preparation of functional foods. Additionally, metabolites produced by the gut microbiome also contribute in maintaining the health and immunity of the host. In order to exploit microbiome's wealth, we need to apply appropriate and suitable analytical techniques in a highly systematic manner to dig out unique biomolecules. The gut microbial community contains trillions of microbes that make it highly complex. It carried out thousands of metabolic and biochemical reactions in the natural environment. Hence, investigating gut microbiota requires new culturomics methods because of a large number of microbes not able to grow in an artificial environment. Currently, data generated by high-throughput sequencing

**19**

**Author details**

Akhlash P. Singh

Panjab University, Chandigarh, India

provided the original work is properly cited.

The authors declare no conflict of interest.

composition of gut microbiota.

preparation of this manuscript.

**Acknowledgements**

**Conflict of interest**

Genomics and Proteomics Lab, Department of Biochemistry, GGDSD College,

© 2020 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

\*Address all correspondence to: akhlash@ggdsd.ac.in; akhlash@gmail.com

*Genomic Techniques Used to Investigate the Human Gut Microbiota*

techniques of bioinformatics and microbiology techniques.

contain a wealth of information and must be analyzed by using advanced tools and

Now the picture of the human gut microbiome is available but still hazy in terms of how microbes impact their host and other microbes living in the gut microbial community. The NGS has revolutionized every field of biological sciences including human microbiome research. It not only sequenced thousands of genome of microorganisms but also helped to emerge many supplementary technologies which are very significant in the functional investigation of the microbial community. Therefore, the advent of modern "omics-based" high-throughput methodologies will help in the identification and characterization of previously unknown microbial strains and modulation mechanisms of the gut ecosystem. But the huge data generation by the omics-based methodologies is a great challenge which needs to be dealt with the development of new bioinformatics tools and techniques. Simultaneously, methods of big data analysis also need to be designed like machine learning and deep learning that will certainly help us in the study of microbial communities.

The availability of cheap and sufficient raw data has opened new avenues. In the near future, gut microbiota can be used as biomarkers and can be personalized to microflora on the line of personalized diet and personalized genomics. Moreover, the recent development of genomic editing tools can manipulate the microbial community under the techniques of synthetic biology. Hence we can cure lifestylerelated diseases such as obesity, cancer, and diabetes by positive manipulation in the

I would like to thank to the Department of Biochemistry, GGDSD College (Panjab University), India, for providing me all the facilities and support for

*DOI: http://dx.doi.org/10.5772/intechopen.91808*

#### *Genomic Techniques Used to Investigate the Human Gut Microbiota DOI: http://dx.doi.org/10.5772/intechopen.91808*

contain a wealth of information and must be analyzed by using advanced tools and techniques of bioinformatics and microbiology techniques.

Now the picture of the human gut microbiome is available but still hazy in terms of how microbes impact their host and other microbes living in the gut microbial community. The NGS has revolutionized every field of biological sciences including human microbiome research. It not only sequenced thousands of genome of microorganisms but also helped to emerge many supplementary technologies which are very significant in the functional investigation of the microbial community. Therefore, the advent of modern "omics-based" high-throughput methodologies will help in the identification and characterization of previously unknown microbial strains and modulation mechanisms of the gut ecosystem. But the huge data generation by the omics-based methodologies is a great challenge which needs to be dealt with the development of new bioinformatics tools and techniques. Simultaneously, methods of big data analysis also need to be designed like machine learning and deep learning that will certainly help us in the study of microbial communities.

The availability of cheap and sufficient raw data has opened new avenues. In the near future, gut microbiota can be used as biomarkers and can be personalized to microflora on the line of personalized diet and personalized genomics. Moreover, the recent development of genomic editing tools can manipulate the microbial community under the techniques of synthetic biology. Hence we can cure lifestylerelated diseases such as obesity, cancer, and diabetes by positive manipulation in the composition of gut microbiota.
