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

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.

Targeting the Gut Microbiota and Host Immunity with a Bacilli-Species Probiotic during Antibiotic Exposure in Mice

“…Our study has limitations; in particular, we did not perform whole metagenomic shotgun sequencing of fecal and cecal samples. Further studies incorporating technologies such as metagenomic shotgun sequencing that are able to take a deeper dive into microbial strain diversity as well as genetic content and function are warranted to delineate key mechanisms of each Bacillus-species in the probiotic blend, whether they work in concert or individually, as well as optimizing treatment doses and timing of delivery with antibiotic therapy [31]. Additionally, incorporation of transcriptomics as with RNA-Seq analysis of tissue samples could assist with determining causal effects of microbial changes on host responses [32].…”

Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence

“…Aside from the possibility to obtain genomes, transcriptomes and proteomes from individual species in cultures or single cells (Dam et al 2020 , Kaster and Sobol 2020 , Wiegand et al 2021 ) shotgun sequencing approaches such as metagenomics and metatranscriptomics have now become the methods of choice for studying microbes from various habitats and researching phylogenetic groups that currently lack cultured representatives (Aguiar-Pulido et al 2016 ). Shotgun proteomics can also be applied to whole microbial communities for metaproteomics (Karaduta et al 2021 ), and the translated portion of RNA has begun to be examined via metatranslatomics (Fremin et al 2020 ). All this data could in theory be used to improve gene annotation, but it has been argued that the application of methods designed for smaller datasets to this new wealth of data has in fact reduced the quality of annotations (Salzberg 2019 ).…”

The Role of the Gut Microbiome in Cancer Immunotherapy: Current Knowledge and Future Directions

“…Large-scale analysis of the gene expression and biosynthetic capacity of the gut microbial community can be performed using metatranscriptomics, metaproteomics, and metabolomics ( Figure 1 ). Although technological limitations still apply for these platforms [ 98 , 99 ], their integration into human microbiome studies offers clear advantages, providing better insights into dysbiosis and host-microbiome signaling [ 100 ]. In this frame, ongoing studies incorporate metabolomics into their design to determine the functional changes accompanying differential responses to ICI therapy (NCT03643289, NCT05251389, NCT03772899, NCT05199649) ( Table 2 and Table 3 ).…”