*4.1.2 Metaproteomics*

The proteome is the complete protein complement expressed by a cell or tissue at a particular moment, and the study of the proteome is known as "proteomics." The metaproteomics or community proteomics is the variant of proteomics in the sense that it is the protein complement expressed by a metagenome from a microbial community. Currently, a small number of reports are available on gut community meta-proteomics that is attributed to the small amount of proteins available in the sample, and its detection makes it further a less applied method in comparison to metagenomics and metatranscriptome. There are still lacking standardized protocols related to protein extraction and its downstream processing. The detection of low abundant proteins in the sample is still a challenge. Moreover, its high cost, time-consuming, and labor-intensive nature further restricted its applications. But many labs have applied metaproteomics in the study of functional analysis of hostmicrobiome interactions and proteins expressed by gut metagenome. There are two types of proteomics methods, i.e., gel-dependent and gel-independent methods. First, the category of protocols includes the combination of 2D gel electrophoresis, mass spectroscopy, and various bioinformatics tools. Second, categories, namely, shotgun proteomics, mainly depend on most expensive and more sophisticated instruments like two-dimensional liquid chromatography (LC) coupled with nanospray tandem mass spectrometry (nano 2D LC–MS/MS) and powerful bioinformatics data analysis pipeline. Both types of technologies have provided large-scale protein analysis data in the case of the human gut proteome [57]. Currently,

**15**

*Genomic Techniques Used to Investigate the Human Gut Microbiota*

metaproteomics methods are applied to analyze the effect of dietary components, e.g., resistant starch on protein expression, enzymes, and composition of microbes involved in starch metabolism inside the gut. This technique is useful to investigate the ratio of two important bacterial species *Firmicutes* to *Bacteroidetes* inside gut

Metabolites are the final outcome of the gene expression process; they are highly

In the last two decades, bioinformatics has provided much needed help to annotate the complex genome sequences and metagenomic data. The microbial bioinformatics offers help to understand microbial agents of the microbial ecosystem and their mutual and host-microbes interactions. Recently, community-based bioinformatics platforms and pipelines are developed like Mothur and QIIME which help in downstreaming of high-throughput genome sequencing data of variable regions of bacterial 16S ribosomal genes or amplicons. These platforms also help in data analysis and visualization of gut microbiome composition. The high-throughput method like shotgun sequencing and WGS metagenomics produced a huge amount of data, and its annotation is a great challenge in the field of microbiome analysis [60]. In order to know the functions of a particular microbial community, it requires

integrating data from other studies such as metatranscriptomics sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and other techniques. The integration of data provides holistic knowledge of a gut community in terms of its structure and functions [61]. For example, any perturbation such as antibiotics or heavy metal toxicities leads to the change in gut microbial community that can be studied at the level of metabolite production and protein expression. Multi-omics data integration is the uphill task and requires a highly advanced level of computational skill, but current few tools have been developed, e.g., XCMS is a new web-based tool that integrates transcriptome, proteome, and metabolome data [62]. The new systems-level integration can also provide valuable insights, especially when they are combined with community surveys and metagenomics (**Table 1**).

unique in the case of the gut microbiota. Large numbers of metabolites are produced by gut microbiota, which can act as pharmaceutical agents or bioactive products. The metabolomics is a high-throughput omics-based method that mainly deals with the identification and quantification of total metabolites produced in a cell, tissue, and organ which are also called the metabolome. The "meta-metabolome" is the whole complement of metabolites and is produced by a specific microbial community. The analysis of meta-metabolomics requires a set of very sophisticated tools and techniques like matrix-assisted laser desorption/ionization time-of-flight, secondary ion mass spectrometry (SIMS), and Fourier transform ion cyclotron resonance MS that are used for metabolome analysis [59]. The complete annotation of the metabolome produced by a metagenome will help us to understand the physiology and functionality of a microbial community. Inside the human gut, fermentation of short-chain fatty acid is carried out by specific bacteria and produced many types of metabolites that participate in host metabolism and influence the physiology of both host-microbial communities inside the gut. The metabolome analysis offered the investigation of functional gene products in a sample that is helpful in functional analysis of microbes present a microbial niche. Currently, many unique

metabolites are identified that are produced by gut microbiota.

*4.1.4 Bioinformatics and multi-omics data integration*

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

microbiota [58].

*4.1.3 Metabolomics*

metaproteomics methods are applied to analyze the effect of dietary components, e.g., resistant starch on protein expression, enzymes, and composition of microbes involved in starch metabolism inside the gut. This technique is useful to investigate the ratio of two important bacterial species *Firmicutes* to *Bacteroidetes* inside gut microbiota [58].
