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1.  Antimicrobial and Probiotic Properties of Yeasts: From Fundamental to Novel Applications 
The yeasts constitute a large and heterogeneous group of microorganisms that are currently attracting increased attention from scientists and industry. Numerous and diverse biological activities make them promising candidates for a wide range of applications not limited to the food sector. In addition to their major contribution to flavor development in fermented foods, their antagonistic activities toward undesirable bacteria, and fungi are now widely known. These activities are associated with their competitiveness for nutrients, acidification of their growth medium, their tolerance of high concentrations of ethanol, and release of antimicrobial compounds such as antifungal killer toxins or “mycocins” and antibacterial compounds. While the design of foods containing probiotics (microorganisms that confer health benefits) has focused primarily on Lactobacillus and Bifidobacterium, the yeast Saccharomyces cerevisiae var. boulardii has long been known effective for treating gastroenteritis. In this review, the antimicrobial activities of yeasts are examined. Mechanisms underlying this antagonistic activity as well as recent applications of these biologically active yeasts in both the medical and veterinary sectors are described.
doi:10.3389/fmicb.2012.00421
PMCID: PMC3525881  PMID: 23267352
yeasts; antagonistic activities; probiotic; killer toxin; mycocin; veterinary; medical
2.  BACTIBASE second release: a database and tool platform for bacteriocin characterization 
BMC Microbiology  2010;10:22.
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.
doi:10.1186/1471-2180-10-22
PMCID: PMC2824694  PMID: 20105292
3.  Evaluation of the Persistence of Infectious Human Noroviruses on Food Surfaces by Using Real-Time Nucleic Acid Sequence-Based Amplification▿  
Applied and Environmental Microbiology  2008;74(11):3349-3355.
Noroviruses (NoV) are the major cause of nonbacterial gastroenteritis. However, there is no published study to ascertain their survival on foodstuffs which are directly related to human health risk. In the present study, we developed a rapid, simple, and sensitive real-time nucleic acid sequence-based amplification (NASBA) combined with an enzymatic treatment for distinguishing infectious from noninfectious human NoV. The developed method was validated using spiked ready-to-eat food samples. When feline calicivirus (FCV) was used as a NoV surrogate in the preliminary assays, it appeared more sensitive to heat inactivation and enzymatic pretreatment than the human NoV. This suggests that FCV may not be an ideal model for studying NoV. Our results reveal clearly that the developed enzymatic pretreatment/real-time NASBA combination successfully distinguished the infectious from heat-inactivated NoV. Moreover, we demonstrate that NoV survived for at least 10 days on refrigerated ready-to-eat foods, such as lettuce and turkey. However, the survival rate was higher on turkey than on lettuce, probably because of their different surface natures. The approach developed in this study may be suitable for more in-depth studies of the persistence and inactivation of human NoV and may be applied to other nonculturable RNA viruses. Moreover, the evaluation of infectious NoV survival provided valuable information concerning its persistence on ready-to-eat food.
doi:10.1128/AEM.02878-07
PMCID: PMC2423024  PMID: 18378643
4.  PhytAMP: a database dedicated to antimicrobial plant peptides 
Nucleic Acids Research  2008;37(Database issue):D963-D968.
Plants produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. Based on amino acid sequence homology, these peptides were classified mostly as α-defensins, thionins, lipid transfer proteins, cyclotides, snakins and hevein-like. Although many antimicrobial plant peptides are now well characterized, much information is still missing or is unavailable to potential users. The compilation of such information in one centralized resource, such as a database would therefore facilitate the study of the potential these peptide structures represent, for example, as alternatives in response to increasing antibiotic resistance or for increasing plant resistance to pathogens by genetic engineering. To achieve this goal, we developed a new database, PhytAMP, which contains valuable information on antimicrobial plant peptides, including taxonomic, microbiological and physicochemical data. Information is very easy to extract from this database and allows rapid prediction of structure/function relationships and target organisms and hence better exploitation of plant peptide biological activities in both the pharmaceutical and agricultural sectors. PhytAMP may be accessed free of charge at http://phytamp.pfba-lab.org.
doi:10.1093/nar/gkn655
PMCID: PMC2686510  PMID: 18836196
5.  SciDBMaker: new software for computer-aided design of specialized biological databases 
BMC Bioinformatics  2008;9:121.
Background
The exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive for completeness, the range of user interests is often beyond their scope. Large databases covering a broad range of domains tend to offer less detailed information than smaller, more specialized resources, often creating a need to combine data from many sources in order to obtain a complete picture. Scientific researchers are continually developing new specific databases to enhance their understanding of biological processes.
Description
In this article, we present the implementation of a new tool for protein data analysis. With its easy-to-use user interface, this software provides the opportunity to build more specialized protein databases from a universal protein sequence database such as Swiss-Prot. A family of proteins known as bacteriocins is analyzed as 'proof of concept'.
Conclusion
SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results.
doi:10.1186/1471-2105-9-121
PMCID: PMC2267701  PMID: 18298861
6.  BACTIBASE: a new web-accessible database for bacteriocin characterization 
BMC Microbiology  2007;7:89.
Background
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.
Description
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.
Conclusion
The BACTIBASE database is freely available at , 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.
doi:10.1186/1471-2180-7-89
PMCID: PMC2211298  PMID: 17941971
7.  Induction of a Humoral Immune Response following an Escherichia coli O157:H7 Infection with an Immunomodulatory Peptidic Fraction Derived from Lactobacillus helveticus-Fermented Milk 
Numerous beneficial effects have been attributed to probiotic lactic acid bacteria (LAB), such as the stimulation of the immune system, the prevention of enteric infections by enteropathogens, and the regression of immunodependent tumors. It has been shown that biologically active metabolites released during fermentation, in particular biopeptides, could act as immunomodulatory agents. However, no studies have been conducted to evaluate the implication of these bioactive peptides in the induction of a protective immune response against enteric infections. The present study aimed to evaluate the possible immunomodulatory and anti-infectious effects of a peptidic fraction released in milk fermented by Lactobacillus helveticus. The immune response in the mucosa-associated lymphoid tissue was monitored following an administration of the potentially bioactive peptidic fraction. The total immunoglobulin A (IgA) immune response was evaluated after an Escherichia coli O157:H7 infection in a BALB/c murine model. Immunohistochemical and enzyme-linked immunosorbent assays revealed an increase in the number of IgA-secreting B lymphocytes in the intestinal lamina propria and an enhanced total secretory and systemic IgA response. Cytokine profiling also revealed stimulation of a Th2 response in mice fed the peptidic fraction, whereas infected controls demonstrated a proinflammatory Th1 response. These results indicate that bioactive peptides released during fermentation by LAB could contribute to the known immunomodulatory effects of probiotic bacteria.
doi:10.1128/CDLI.11.6.1171-1181.2004
PMCID: PMC524790  PMID: 15539524
8.  Stimulation of Interleukin-10 Production by Acidic β-Lactoglobulin-Derived Peptides Hydrolyzed with Lactobacillus paracasei NCC2461 Peptidases 
We have previously demonstrated that Lactobacillus paracasei NCC2461 may help to prevent cow's milk allergy in mice by inducing oral tolerance to β-lactoglobulin (BLG). To investigate the mechanisms involved in this beneficial effect, we examined the possibility that L. paracasei induces tolerance by hydrolyzing BLG-derived peptides and liberating peptides that stimulate interleukin-10 (IL-10) production. L. paracasei peptidases have been shown to hydrolyze tryptic-chymotryptic peptides from BLG, releasing numerous small peptides with immunomodulating properties. We have now shown that acidic tryptic-chymotryptic peptides stimulate splenocyte proliferation and gamma interferon (IFN-γ) production in vitro. Hydrolysis of these peptides with L. paracasei peptidases repressed the lymphocyte stimulation, up-regulated IL-10 production, and down-regulated IFN-γ and IL-4 secretion. L. paracasei NCC2461 may therefore induce oral tolerance to BLG in vivo by degrading acidic peptides and releasing immunomodulatory peptides stimulating regulatory T cells, which function as major immunosuppressive agents by secreting IL-10.
doi:10.1128/CDLI.11.2.266-271.2004
PMCID: PMC371205  PMID: 15013974
9.  Effect of Probiotic Bacteria on Induction and Maintenance of Oral Tolerance to β-Lactoglobulin in Gnotobiotic Mice 
In this study, the effect of Lactobacillus paracasei (NCC 2461), Lactobacillus johnsonii (NCC 533) and Bifidobacterium lactis Bb12 (NCC 362) on the induction and maintenance of oral tolerance to bovine β-lactoglobulin (BLG) was investigated in mice. Germfree mice were monocolonized with one of the three strains before oral administration of whey protein to induce tolerance. Mice were then injected with BLG and sacrificed 28 or 50 days after whey protein feeding for humoral and cellular response measurement. Conventional and germfree mice were used as controls. Both humoral and cellular responses were better suppressed in conventional mice than in germfree and monoassociated mice throughout the experiment and better suppressed in L. paracasei-associated mice than in mice colonized with B. lactis or L. johnsonii. The latter two mono-associations suppressed humoral responses only partially and cellular responses not at all. This study provides evidence that probiotics modulate the oral tolerance response to BLG in mice. The mono-colonization effect is strain-dependant, the best result having been obtained with L. paracasei.
doi:10.1128/CDLI.10.5.787-792.2003
PMCID: PMC193892  PMID: 12965905

Results 1-9 (9)