Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS

Abstract

Our digestive tract hosts more than a billion microorganisms comprising non-pathogenic bacteria, viruses, fungi and parasites. Understanding and characterizing the human gut microbiota has become a fundamental common theme to establish a link between its dysbiosis and certain pathologies, especially autoimmune and inflammatory diseases. Meta-Omics studies have, so far, provided great progress in this field. Genomics is conventionally used to determine the composition of the microbiota and, subsequently, metatranscriptomics lists the transcribed genes. However, to better understand the relationship between microbiota and health, protein-based studies are being applied. Proteomics enables the functional study of proteins as they are expressed by microbial communities. Metaproteomics exploits the power of mass spectrometry to identify broad protein profiles in complex samples, such as gut microbiota. The lastest technological advances in the field of mass spectrometry have opened the field of large-scale characterization of microbial proteins. Despite these hardware improvements, bioinformatics analysis remains a primary challenge. Herein, we describe the state-of-the-art concerning specific sample preparation and powerful shotgun analysis techniques. We also review several scientific studies of the human gut microbiota. Moreover, we discuss the advantages and limitations encountered in this research area, concerning new methods of sample preparation and innovative bioinformatic tools. Finally, prospects are addressed regarding the application of metaproteomic in the field of clinical microbiology and its integration with other meta-Omics.

Keywords: (U)HPLC, (Ultra) High Performance Liquid Chromatography; BLAST, Basic Local Alignment Search Tool; CD, Crohn's disease; DDA/DIA, Data Dependent Acquisition / Data Independent Acquisition; FASP, Filter Aided Sample Preparation; FDR, False Discovery Rate; Human gut microbiota; IBD, Inflammatory Bowel Disease; IMS/MS, Ion-Mobility Spectrometry–Mass Spectrometry; LCA, Lowest Common Ancestor; Liquid chromatography; MALDI/ESI, Matrix-Assisted Laser Desorption Ionisation/Electrospray Ionization; Mass spectrometry; Metaproteomics; NGS, Next Generation Sequencing; OMICS; RP/SCX, Reverse Phase /Strong Cation Exchange; SDS-PAGE, Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis; TOF, Time-Of-Flight; Unipept.