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

Abstract

BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.
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.
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 http://bactibase.pfba-lab-tun.org.

Full text

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DATABASEOpen Access
BACTIBASE second release: a database and tool
platform for bacteriocin characterization
Riadh Hammami1,2, Abdelmajid Zouhir2, Christophe Le Lay1, Jeannette Ben Hamida2, Ismail Fliss1*
Abstract
Background: BACTIBASE is an integrated open-access database designed for the characterization of bacterial
antimicrobial peptides, commonly known as bacteriocins.
Description: 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.
Conclusion: 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 http://bactibase.pfba-lab-tun.org.
Background
The dramatic rise in antibiotic-resistant pathogens has
renewed efforts to identify, develop and redesign anti-
biotics. Bacteriocins are non-toxic inhibitors of bacteria
and thus represent potential alternatives or comple-
ments to conventional antibiotics in the treatment of
infections and in livestock production.
Bacteriocins were first identified almost 100 years ago.
A heat-labile substance in Escherichia coli V culture
supernatant was found toxic to E. coli S and given the
name “colicin”. It was thus decided that bacteriocins
would be named after the producing species [1]. Freder-
icq demonstrated that colicins were proteins and that
the inhibitory activity depended on the presence of spe-
cific receptors on the surface of sensitive cells and was
therefore limited to specific species or strains [2]. Since
then, bacteriocins have been found among most families
of bacteria and many actinomycetes and described as
universally produced, including by some members of the
Archaea [3,4]. Klaenhammer estimates that 99% of all
bacteria probably produce at least one bacteriocin and
the only reason we have not isolated more is that few
researchers are looking for them [5].
Two main features distinguish the majority of bacter-
iocins from conventional antibiotics: bacteriocins are
ribosomally synthesized and have a relatively narrow
killing spectrum (3). They make up a highly diverse
family of proteins in terms of size, microbial target,
mode of action and release and mechanism of immunity
and can be divided into two broad groups: those pro-
duced by Gram-negative bacteria and those produced by
Gram-positive bacteria [6,7].
We have previously developed and described a data-
base (BACTIBASE) that contains calculated or predicted
physicochemical properties of bacteriocins produced by
both Gram-positive and Gram-negative bacteria [8].
BACTIBASE is a relational database that uses the
MySQL server with a web interface composed of several
PHP, JavaScript, Perl and Python scripts. The relational
design of the database (i.e. the tables and the relations
between them) has since been updated. In this paper,
we describe this and other modifications, in particular
the expansion of the biological information and the
improvement of the query and navigation interfaces. We
have also integrated several applications and utilities for
bacteriocin sequences analysis and characterization. The
* Correspondence: ismail.fliss@fsaa.ulaval.ca
1STELA Dairy Research Center, Nutraceuticals and Functional Foods Institute,
Université Laval, G1K 7P4 Québec, QC, Canada
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new features should make BACTIBASE an even more
useful tool in food preservation or food safety applica-
tions and could have implications for the development
of new drugs for medical use.
Construction and content
The content and format of BACTIBASE have been
described previously [8]. While the general format has
remained essentially unchanged, data retrieval and pre-
sentation have been improved. Data collection and
annotation was done essentially the same way as for ver-
sion 1 and the dataset is currently limited to natural
sources. All microbiological information was collected
from the literature by PubMed search. A physicochem-
ical dataset was designed using SciDBMaker [9] and
then provided with empirical formula, mass, length, iso-
electric point, net charge, the number of basic, acidic,
hydrophobic and polar residues, hydropathy index, bind-
ing potential index, instability index, aliphatic index,
half-life in mammalian cells, yeast and E. coli, cysteine
and glycine content, extinction coefficient, absorbance at
280 nm, absent and most prevalent amino acids, sec-
ondary (a-helix or b-strand) and tertiary structure
(when available), physical method used for structural
determination (e.g. NMR spectroscopy or X-ray diffrac-
tion) and critical residues for activity, whenever infor-
mation was available. The Jmol applet http://www.jmol.
org was included for tertiary structure visualization. The
statistical interface provides data on peptide sequence,
function and structure. Data were analyzed using SPSS
software (version 17, SPSS Inc.) and medians and stan-
dard deviations were calculated. The following is a brief
description of the database content.
The current release of the BACTIBASE dataset (ver-
sion 2, July 2009) contains 177 (44% more) bacteriocin
sequences, of which 156 are the products of Gram-posi-
tive organisms and 18 of Gram-negative organisms. We
also note the presence of three bacteriocins from the
Archaea domain. The database now comprises 31 gen-
era, as shown in Table S1 (additional file 1). Without
surprise, the lactic acid bacteria (order Lactobacillales)
make up the predominant group of producers, with 113
bacteriocins. Figure 1 illustrates the distribution of pep-
tide length among the bacteriocins of Gram-positive
organisms, which varies from 20 to 60 amino acids in
84% of cases. In contrast, Gram-negative bacteriocins
come in a very broad range of lengths, the longest
(BAC127) being 688 amino acid residues (data not
shown). Amino acid percentages are close to those cal-
culated for the previous version of BACTIBASE. Table
S1 lists averages for the net charge and amino acid con-
tents of the bacteriocins produced by each of the 31
genera. These characteristics may serve as a physico-
chemical fingerprint for each group. Investigation of the
PDB database revealed only 22 bacteriocins having a
resolved 3D structure (by NMR spectroscopy or crystal-
lography). Some of these are represented by more than
one structure in the PDB database, bringing the total
number of known 3D structures to 40. BACTIBASE
provides detailed statistics on the bacteriocins. The
improved database should be useful for discovering and
characterizing potent bacteriocins or designing novel
peptides with greater antimicrobial activity against
pathogens.
Utility
Taxonomy explorer
An integrated phylogenetic tree view was designed (Fig-
ure 2) to facilitate data retrieval via bacterial species
name. The tree is displayed on the left and the corre-
sponding bacteriocins are listed in tabled form on the
right. In the default setting, the tree is collapsed and dis-
plays only the phyla assigned to the Bacteria and
Archaea domains along with a brief definition of these
in the table. A click on the ‘Expand All’ hyperlink at the
top displays the entire tree and the user may then select
and expand the branches by clicking on nodes (family/
genus). All bacteriocins associated with the selected
genus are summarized in the table and a report can be
generated in PDF format for further analysis. Clicking
on the provided link displays the detailed entry for each
bacteriocin.
References sub-database
The entire database is linked to the Bibliography section,
which lists all published scientific articles consulted on
the subject of each bacteriocin. The ‘news’ link points to
the latest hundred published review articles in PubMed.
Bacteriocin structural analysis tool set
Several useful tools for protein analysis have been inte-
grated into the platform. Users may search bacteriocin
homologies using not only the BLAST program [10] but
also FASTA [11] and SSEARCH [11]. Multiple sequence
alignment may be done using CLUSTALW [12], MUS-
CLE [13] and T-COFFEE [14] and displayed graphically
using the embedded JalView applet [15]. We used hid-
den Markov modeling (HMM) to produce bacteriocin
profiles for each known family. The HMMER program
was used to provide statistical descriptions of family
consensus sequences [16] in order to allow users to
identify the bacterial family that produces the bacterio-
cins most similar to their sequences.
Understanding of the molecular function of bacterio-
cins has been enhanced greatly by insight gained from
three-dimensional structure. During the past decade, the
use of homology modeling to study protein structure
has become widespread. This technique generates a
model of a protein using an experimental structure of a
related protein as a template. We thus incorporated the
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Figure 1 Peptide length distribution among the bacteriocins produced by the Gram-positive organisms in the BACTIBASE database.
Figure 2 The user interface displaying the taxonomic browser.
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program MODELLER [17] into the platform, which
implements comparative protein structure modeling by
satisfaction of spatial restraint. A sub-database of bacter-
iocins for which experimental structures have been
developed was built. Users should note that only bacter-
iocins are used as templates in the homology modeling
process. A modeling pipeline has been developed for
automatic homology modeling from an initial bacterio-
cin sequence. This feature should be very useful for the
in silico design of novel bacteriocins. The ability to
develop novel bacteriocin-based-drugs that target pro-
karyotic as well as eukaryotic cells may open new possi-
bilities for the design of improved antibiotics possessing
refined characteristics.
Linking to the BACTIBASE database
It remains very easy to link directly to a specific BACTI-
BASE entry. With our new domain name, users may
link directly to records using their BACTIBASE ID in
the format http://bactibase.pfba-lab-tun.org/bacteriocins-
view.php?id=BAC059, which will allow links to be main-
tained even if the bacteriocin data changes.
Forum
The forum section is provided to allow anyone to
exchange information or ask questions regarding
bacteriocins.
Discussion
Comparison with other databases
In the last decade, several databases dealing with AMPs
were developed http://bactibase.pfba-lab-tun.org/links.
php. The AMSDb (see: http://www.bbcm.univ.trieste.it/
~tossi/amsdb.html), ANTIMIC [18], APD2 [19], and
CAMP [20] databases cover all AMPs sequences from
diverse origins. Alternatively, some databases focus on
AMPs produced by bacteria (BACTIBASE [8]), plants
(PhytAMP [21]) and shrimp (PenBase [22]). While
AMSdb database covers only AMPs of eukaryotic origin,
ANTIMIC database contains about 1700 AMPs from
diverse origins (eukaryotes, prokaryotes). Regrettably, this
resource was discontinued. The Antimicrobial Peptide
Database (APD2) is the most popular of the currently
available public collections (containing 944 antibacterial
peptides of eukaryotic and prokaryotic origin) [19].
Recently, a new database containing a large Collection of
Anti-Microbial Peptides (CAMP) was developed and
holds 3782 antimicrobial sequences [20]. While lantibio-
tics are the class I of bacteriocins, the CAMP database
lists them as a distinct family from bacteriocins. This
may confuse novice users. Although APD2 and CAMP
databases contain very general information about pep-
tides of all types having antibacterial, antifungal or anti-
viral activities and originating from either eukaryotic or
prokaryotic cells, bacteriocins are not described with a
useful amount of detail in either of these databases. Not
only does BACTIBASE (version 2, July 2009) contain sig-
nificantly more antimicrobial peptides of bacterial origin,
than the APD2 and CAMP databases (177 in BACTI-
BASE versus ~120 in APD2 and ~68 in CAMP), but also
every entry in BACTIBASE is much more detailed. BAC-
TIBASE features, for example, physicochemical and
structural information, detailed lists of target organisms
and a description of the mode of action for each bacterio-
cin – data not available in APD2 or any other online
resource (to the best of our knowledge). Also, BACTI-
BASE hosts a rich and highly usable collection of refer-
ences, where (i) each entry has been supplied with a
short annotation summarizing its topic in ~10 words or
less, (ii) is cross-linked to PubMed, and (iii) can be con-
veniently exported to Citation Manager Software of
user’s choice. The database provides several tools for bac-
teriocin sequence analysis (unavailable in APD2; unavail-
able or static in CAMP), such as homology search,
multiple sequence alignments, Hidden Markov Models
and molecular modeling. All this makes BACTIBASE a
truly unique resource for bacteriocins.
Future directions
We are currently developing a system for automatic
updating of the database. New types of data will be
added in the near future. Subsequent development will
include integrating a system that automates the predic-
tion of bacteriocin functional amino acids as well as
enriching the platform with useful tools for bacteriocin
characterization. We also hope to develop new meth-
ods/techniques for structural and functional classifica-
tion of bacteriocins.
Conclusion
The purpose of the database is to serve the research
community by organizing information relevant to all
types of bacteriocins from all groups of Bacteria. With
the inclusion of most known bacteriocin sequences,
BACTIBASE 2 has grown into an integrated knowledge
base for bacteriocin investigators. It is our hope that the
implementation of ‘Molecule Authorities’ will transform
BACTIBASE into a community-driven database (via
notes) and that this trend will continue so that the indi-
vidual investigators will verify or contribute to verifying
every entry. We thank all investigators who have pro-
vided or will provide valuable feedback regarding the
individual entries in this database. As more information
about bacteriocins becomes available, the database will
be expanded and improved accordingly. While database
updating and developments continue, we welcome your
comments, suggestions, or corrections.
Availability and requirements
BACTIBASE can be accessed freely at http://bactibase.
pfba-lab-tun.org.
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Additional file 1: Table S1. Distribution, average net charge and amino
acid contents of bacteriocins by organism grouping in the BACTIBASE
database.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2180-10-
22-S1.DOC]
Acknowledgements
Authors thank Dr. Stephen Davids for his critical reading of the manuscript.
Author details
1STELA Dairy Research Center, Nutraceuticals and Functional Foods Institute,
Université Laval, G1K 7P4 Québec, QC, Canada.2Unité de Protéomie
Fonctionnelle & Biopréservation Alimentaire, Institut Supérieur des Sciences
Biologiques Appliquées de Tunis, Université El Manar, Tunisie.
Authors’ contributions
RH conceived the study, developed the database and web interface and
performed the statistical analysis. AZ participated in the design of the study.
CLL helped RH annotate sequences and compile the microbiological and
physicochemical data. JBH and IF jointly coordinated the project and IF
refined the manuscript drafted by RH. All authors read and approved the
final manuscript.
Received: 4 August 2009
Accepted: 27 January 2010 Published: 27 January 2010
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doi:10.1186/1471-2180-10-22
Cite this article as: Hammami et al.: BACTIBASE second release: a
database and tool platform for bacteriocin characterization. BMC
Microbiology 2010 10:22.
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