Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics

Abstract

Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography–mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.

Effects of continuous intravenous infusion with propofol on intestinal metabolites in rats

“…Only 6,810 metabolites were identified in the feces of the human metabolome database. This may be an order of magnitude lower compared with the true chemical diversity of the metabolites in the human gastrointestinal flora ( 38 ). Resolution of these issues relies on the development and improvement of metabolomics software tools related to metabolite identification and diverse data types.…”

Liquid Biopsy Proteomics in Ophthalmology

“…Quantitative proteomics allows the global evaluation, identification, and quantification of proteins in cells or tissues and helps to understand their composition, structure, interactions, and functions. , Thus, it can be a great exploratory technique that identifies candidate proteins for disease diagnosis and drug development, leading to unbiased data-driven hypotheses. − Most current proteomics techniques can be categorized in affinity-based or mass spectrometry-based identification (Figure ). Affinity-based identification involves the specific binding between a target protein and an affinity agent such as antibodies, proteins, or small molecules.…”

Integrating the analysis of human biopsies using post‐translational modifications proteomics

“…Dysbiotic microbial communities have been implicated in numerous adverse health outcomes, including cardiovascular disease, neurodevelopmental disorders, and inflammatory bowel disease (Chopra et al, 2021 ; Pettersen, Antunes, et al, 2022 ; Pettersen, Dufour, & Arrieta, 2022 ; Shreiner et al, 2015 ; Vijay & Valdes, 2022 ). Given the minimal invasiveness of obtaining fecal samples, microbial contributions to disease pathogenesis (diversity, metabolic activity, etc.)…”