BACTIBASE: a new web-accessible database for bacteriocin characterization

<p>Abstract</p> <p>Background</p> <p>Bacteriocins are very diverse group of antimicrobial peptides produced by a wide range of bacteria and known for their inhibitory activity against various human and animal pathogens. Although many bacteriocins are now well characterized, much information is still missing or is unavailable to potential users. The assembly of such information in one central resource such as a database would therefore be of great benefit to the exploitation of these bioactive molecules in the present context of increasing antibiotic resistance and natural bio-preservation need.</p> <p>Description</p> <p>In the present paper, we present the development of a new and original database BACTIBASE that contains calculated or predicted physicochemical properties of 123 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.</p> <p>Conclusion</p> <p>The BACTIBASE database is freely available at <url>http://bactibase.pfba-lab.org</url>, web-based platform enabling easy retrieval, via various filters, of sets of bacteriocins that will enable detailed analysis of a number of microbiological and physicochemical data.</p

BACTIBASE second release: a database and tool platform for bacteriocin characterization

<p>Abstract</p> <p>Background</p> <p>BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.</p> <p>Description</p> <p>For its second release, BACTIBASE has been expanded and equipped with additional functions aimed at both casual and power users. The number of entries has been increased by 44% and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. Improvements brought to BACTIBASE include incorporation of various tools for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser.</p> <p>Conclusion</p> <p>The provided features should make BACTIBASE a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE is available at <url>http://bactibase.pfba-lab-tun.org</url>.</p

Detection and Extraction of Anti-Listerial Compounds from Calligonum Comosum, A Medicinal Plant from Arid Regions of Tunisia

Calligonum comosum, a Tunisian plant from arid regions, is traditionally used in folk medicine to treat rural population microbial infections. The plant was investigated in vitro for its ability to inhibit the growth of Listeria ivanovii. Various aqueous and organic extracts were prepared from different plant tissues. Results indicated that ethanolic, methanolic and acetonic extracts from whole plant tissues except seeds, exhibited significant antibacterial activity with growth inhibition zones (9 – 18mm) as shown by the agar-well diffusion method. Minimum Inhibitory Concentration (MIC) of 0.65mg/ml was obtained in acetonic extract generated from C. comosum roots. Preliminary phytochemical analysis based on heat and protease treatments showed that bioactive extracts were stable up to 10m in heating at 100°C and that they resist protease digestion. Based on these latter results, the activity of organic extracts may be related to the presence of sterols, terpenoids, and/or phenolics. Overall, these results indicate that C. comosum organic extracts are probably useful in the control of food contamination by listerial species

Histogram of the distribution of peptide length in the BACTIBASE database

<p><b>Copyright information:</b></p><p>Taken from "BACTIBASE: a new web-accessible database for bacteriocin characterization"</p><p>http://www.biomedcentral.com/1471-2180/7/89</p><p>BMC Microbiology 2007;7():89-89.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2211298.</p><p></p

Bar graph of the distribution of acidic and basic amino acids among peptides in the BACTIBASE database

<p><b>Copyright information:</b></p><p>Taken from "BACTIBASE: a new web-accessible database for bacteriocin characterization"</p><p>http://www.biomedcentral.com/1471-2180/7/89</p><p>BMC Microbiology 2007;7():89-89.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2211298.</p><p></p

Histogram of the distribution of the net charge among peptides in the BACTIBASE database

<p><b>Copyright information:</b></p><p>Taken from "BACTIBASE: a new web-accessible database for bacteriocin characterization"</p><p>http://www.biomedcentral.com/1471-2180/7/89</p><p>BMC Microbiology 2007;7():89-89.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2211298.</p><p></p