Metaproteomics-An Advantageous Option in Studies of Host-Microbiota Interaction.

Oleg Karaduta,Zeljko Dvanajscak,Boris Zybailov

doi:10.3390/microorganisms9050980

Oleg Karaduta, Zeljko Dvanajscak + Show 1 more

Open Access

https://doi.org/10.3390/microorganisms9050980

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Abstract

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. Manipulating gut microbiota is being recognized as a therapeutic target to manage various chronic diseases. The therapeutic manipulation of the intestinal microbiome is achieved through diet modification, the administration of prebiotics, probiotics, or antibiotics, and more recently, fecal microbiome transplantation (FMT). In this opinion paper, we give a perspective on the current status of application of multi-omics technologies in the analysis of host-microbiota interactions. The aim of this paper was to highlight the strengths of metaproteomics, which integrates with and often relies on other approaches.

Highlights

The role of the gut microbiome in human health and disease is becoming clearer thanks to high throughput sequencing technologies (HTS)
Technological advances have mostly occurred in the realm of liquid chromatography (LC) enabling the separation of highly complex peptide mixtures, and high-resolution mass spectrometry (MS) instrumentation enabling the acquisition of large numbers of accurate mass spectra, and computational tools for data processing and analyses
The taxon-specific classification of peptide sequences can be performed using UniPept which uses shotgun proteomics data from UniProt KB with identification noise filtering to provide enhanced biodiversity analysis [21,22]. Another option for the analysis of metaproteomics data is MetaPro-IQ, which is ideal for fecal samples since the gut microbiome gene catalog was curated from fecal studies which negates the need for matched metagenomics data but makes it less applicable for other types of microbiome samples [21]

Summary

Introduction

The role of the gut microbiome in human health and disease is becoming clearer thanks to high throughput sequencing technologies (HTS). Regardless of the approach taken, it is important to note that these sequencing technologies require detailed bioinformatic analyses to deal with the large volumes of data generated [4,5] These gene-centric approaches have provided much information regarding the content of the gut, we need to understand the activity of these genes and their impact on the metabolic networks within the gut. To further determine specific microbial activity, it is necessary to analyze gene expression (metatranscriptomics), protein products (metaproteomics) and metabolic profiles (metabolomics). These techniques are complex, and to different extents, are still somewhat in their infancy. Technological advances have mostly occurred in the realm of liquid chromatography (LC) enabling the separation of highly complex peptide mixtures, and high-resolution mass spectrometry (MS) instrumentation enabling the acquisition of large numbers of accurate mass spectra, and computational tools for data processing and analyses

Tasks That Can Be Solved through Metaproteomics

Novel Software Tools in Metaproteomics Analysis

Metaproteomics

Experimental

Technical Challenges and Future Perspectives

Conclusions