Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jan 10:2017:baw157.
doi: 10.1093/database/baw157. Print 2017.

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

Aitor Blanco-Míguez  1   2 , Alberto Gutiérrez-Jácome  1 , Florentino Fdez-Riverola  1 , Anália Lourenço  3   4 , Borja Sánchez  5
Affiliations

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

Aitor Blanco-Míguez et al. Database (Oxford). .

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/.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Data sections and curation workflow. The curation workflow is divided into two processes: manual curation and automatic annotation.
Figure 2.
Figure 2.
Snapshot of the advanced search. The query sequence is ‘LASDPIVLSKPDYGWANNHTFV’ and both data sections are searched, with the following custom BLAST options: threshold set to 3, window size set to 3, word size set to 2, gap extend set to 2, gap open set to 9 and ungapped search selected.
Figure 3.
Figure 3.
Snapshot of the hit distribution of results for a query search. The query sequence is ‘LASDPIVLSKPDYGWANNHTFV’ and both data sections are searched, with the following custom BLAST options: threshold set to 3, window size set to 3, word size set to 2, gap extend set to 2, gap open set to 9 and ungapped search selected. Returned hits are presented in the same order as they appear in the BLAST file. Also, hits are coloured based on the assigned bit score.
Figure 4.
Figure 4.
Snapshot of the table detailing the hits of a query search. This table gathers together all BLAST hits and their attributes (bit score, expected value, identities, positives and gaps). Clicking on one hit, it redirects the user to the alignment information of this hit.
Figure 5.
Figure 5.
Snapshot of the hit alignment information. Properties table includes the high-scoring pair attributes of the hit, bioactivity (potential bioactivity, in the case of in silico predictions), molecular weight and isoelectric point. Source proteins are cross-linked to UniProt and Metahit metagenome entries. The alignment figure compares in more depth (amino acid by amino acid) the alignment of the proposed hit with the query sequence.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Hooper L.V., Gordon J.I. (2001) Commensal host-bacterial relationships in the gut. Science, 292, 1115–1118. - PubMed
    1. Eckburg P.B., Bik E.M., Bernstein C.N. et al. (2005) Diversity of the human intestinal microbial flora. Science, 308, 1635–1638. - PMC - PubMed
    1. Gevers D., Kugathasan S., Denson L.A. et al. (2014) The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe, 15, 382–392. - PMC - PubMed
    1. Sommer F., Bäckhed F. (2013) The gut microbiota—masters of host development and physiology. Nat. Rev. Microbiol., 11, 227–238. - PubMed
    1. Sánchez B., Urdaci M.C., Margolles A. (2010) Extracellular proteins secreted by probiotic bacteria as mediators of effects that promote mucosa-bacteria interactions. Microbiology, 156, 3232–3242. - PubMed

Publication types

MeSH terms

LinkOut - more resources