MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

Abstract

The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome. Bioactivity prediction is based on the global alignment of the automatically processed peptides with experimentally validated immunomodulatory and antiproliferative peptides, in the reference section. MAHMI provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated. Moreover, researchers are welcome to submit new experimental evidence on peptide bioactivity, namely, empiric and structural data, as a proactive, expert means to keep the database updated and improve the implemented bioactivity prediction method. Bioactive peptides identified by MAHMI have a huge biotechnological potential, including the manipulation of aberrant immune responses and the design of new functional ingredients/foods based on the genetic sequences of the human microbiome. Hopefully, the resources provided by MAHMI will be useful to those researching gastrointestinal disorders of autoimmune and inflammatory nature, such as Inflammatory Bowel Diseases. MAHMI database is routinely updated and is available free of charge.Database URL: http://mahmi.org/

Respiratory microbiota and lower respiratory tract disease

“…In 2008, the National Institutes of Health and the European Commission launched two multicentric mega projects: the Human Microbiome Project, where samples from up to 18 body sites of healthy individuals were collected, and MetaHIT, focused on the metagenomics of the intestinal tract. 1,2 The respiratory tract was left apart, partly because of problems in collecting lower respiratory tract samples, but also because lungs have traditionally been considered sterile. Recent studies have shown that the lower respiratory tract harbours a diverse bacterial community both in healthy and diseased individuals, which has boosted respiratory microbiota research that is currently growing rapidly.…”

Molecules Produced by Probiotics and Intestinal Microorganisms with Immunomodulatory Activity

“…As an example, the STp peptide, a serine and threonine rich peptide included in one of the main extracellular proteins from Lactobacillus plantarum, was the first to be described as inducing an anti-inflammatory response in dendritic cells from IBD patients [19,20]. More recently, the development of proteomic databases of the gut microbiome has enabled the prediction of immunomodulatory potential of peptides encrypted in the gut commensals metaproteome [21]. Such an approach has led to the identification and validation of the immunomodulatory potential of two encrypted peptides, FR-16 and LR-17, included in proteins from B. longum DJO10A and Bacteroides fragilis YCH46, which exhibited a capacity to differentiate Th17 and Th22 differentiation pathways using immune cells models [7].…”

Release of potential pro-inflammatory peptides from SARS-CoV-2 spike glycoproteins in neutrophil-extracellular traps

“…To this end, a computational approach was proposed based on our knowledge predicting the immunomodulatory potential of microbial extracellular peptides (Blanco-Míguez et al, 2016) . The proposed method combines an in silico digestion with machine learning and sequence alignment techniques ( Figure 1).…”