The lactobin A and amylovorin L471 encoding genes are identical, and their distribution seems to be restricted to the species Lactobacillus amylovorus that is of interest for cereal fermentations

Identification of Structural and Immunity Genes of a Class IIb Bacteriocin Encoded in the Enterocin A Operon of Enterococcus faecium Strain MXVK29

The Enterococcus faecium strain MXVK29, isolated from fermented sausages, produces a bacteriocin with a molecular mass of 3.5 kDa that belongs to the class of enterocins II.1, according to the terminal amino acid sequence, and has been identified as enterocin A. This bacteriocin is active against selected strains of Listeria, Staphylococcus, Pediococcus, and Enterococcus. In this study, we identified the genes adjacent to the structural gene for this bacteriocin, such as the immunity gene (entI) and the inducer gene (entF). Accessory genes for this bacteriocin, such as entK, entR, and entT, were identified as well, in addition to the orf2 and orf3, showing a high identity with class IIb peptides bacteriocins. The orf2 shows the consensus motif GxxxG, similar to those shown by bacteriocins such as PlnNC8α, EntCα, and Ent1071A, whereas orf3 shows a consensus motif SxxxS similar to that present in PlnNC8β (AxxxA). PlnNC8 is expressed only in bacterial cocultures, so there is the possibility that the expression of this two-peptide bacteriocin can be induced by a similar mechanism. So far, only the expression of enterocin A has been found in this strain; however, the presence of the genes ent29α and ent29β opens the possibility for further research on its induction, functionality, and origin. Although there are reports on this type of bacteriocin (EntX, EntC, and Ent1071) in other strains of E. faecium, no report exists yet on an Enterococcus strain producing two different classes of bacteriocin.

Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

BACKGROUND

Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species.

RESULTS

We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales.

CONCLUSIONS

Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.

Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters

We identified the lactic acid bacteria within rye sourdoughs and starters from four bakeries with different propagation parameters and tracked their dynamics for between 5–28 months after renewal. Evaluation of bacterial communities was performed using plating, denaturing gradient gel electrophoresis, and pyrosequencing of 16S rRNA gene amplicons. Lactobacillus amylovorus and Lactobacillus frumenti or Lactobacillus helveticus, Lactobacillus pontis and Lactobacillus panis prevailed in sourdoughs propagated at higher temperature, while ambient temperature combined with a short fermentation cycle selected for Lactobacillus sanfranciscensis, Lactobacillus pontis, and Lactobacillus zymae or Lactobacillus helveticus, Lactobacillus pontis and Lactobacillus zymae. The ratio of species in bakeries employing room-temperature propagation displayed a seasonal dependence. Introduction of different and controlled propagation parameters at one bakery (higher fermentation temperature, reduced inoculum size, and extended fermentation time) resulted in stabilization of the microbial community with an increased proportion of L. helveticus and L. pontis. Despite these new propagation parameters no new species were detected.

Wide-Inhibitory Spectra Bacteriocins Produced by Lactobacillus gasseri K7

The aim of our study was to determine the genetic characterization and classification of Lb. gasseri K7 bacteriocins, comparison with bacteriocins of the Lb. gasseri LF221 strain and other related strains. Bacteriocin-encoding genes were amplified by PCR, subjected to DNA sequencing, and BLAST sequence analysis was performed to search the database for homologous peptides. Lb. gasseri K7 produces two two-peptide bacteriocins, named gassericin K7 A and gassericin K7 B. Their nucleotide sequences were deposited at GenBank, under accession numbers EF392861 for the gassericin K7 A and AY307382 for the gassericin K7 B. Analysis of gene clusters of bacteriocins in Lb. gasseri K7 strain revealed a 100 percent sequence identity with bacteriocins in LF221 strain. An active peptide of gassericin K7 B is homologous to the complementary peptide of gassericin T, and a complementary peptide of gassericin K7 B is homologous to the active peptide of gassericin T. Another surprising finding was that the sakacin T-beta peptide is partly homologous to the active peptide of gassericin K7 A, while the other sakacin T peptide (alfa) is partly homologous to the complementary peptide of gassericin K7 B. Gassericins of Lb. gasseri K7 strain were both classified as two-peptide bacteriocins. Human probiotic strains Lb. gasseri K7 and LF221 are different isolates but with identical bacteriocin genes. They produce wide-inhibitory spectra bacteriocins that are new members of two-peptide bacteriocins with some homologies to other bacteriocins in this group. Described bacteriocins offer a great potential in applications in food industry, pharmacy and biomedicine.

Characterization of bacterial antimicrobial peptides active against Campylobacter jejuni

Campylobacter jejuni is one of the major causes of food poisoning, often resulting from the consumption of improperly cooked poultry products. The emergence of C. jejuni strains resistant to conventional antibiotics necessitates the evaluation of other possible treatments or preventative measures to minimize the impact and prevalence of infections. Antimicrobial peptides produced by bacteria have begun to emerge as a potential means of decreasing the levels of C. jejuni in poultry, thereby limiting Campylobacter contamination in associated food products. A number of bacteriocins produced by Gram-positive bacteria have unexpectedly been described as having antimicrobial activity against the Gram-negative C. jejuni. Additionally, some nonribosomal lipopeptides produced by Bacillus and Paenibacillus spp. show efficacy against this pathogen. This review will describe the bacterial antimicrobial peptides reported to be active against C. jejuni, with an emphasis on the characterization of their primary structures. However, for many of these peptides, little is known about their amino acid sequences and structures. Furthermore, there are unusual inconsistencies associated with the reported amino acid sequences for several of the more well-studied bacteriocins. Clarifying the chemical nature of these promising antimicrobial peptides is necessary before their potential utility for livestock protection from C. jejuni can be fully explored. Once these peptides are better characterized, they may prove to be strong candidates for minimizing the impact of Campylobacter on human health.

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.rpbs.univ-paris-diderot.fr, is a database that aims at providing an exhaustive re-annotation of all complete prokaryotic genomes—chromosomal and plasmid DNA—available in RefSeq for coding sequences ranging between 10 and 80 amino acids. The identified peptides are classified as (i) previously identified in RefSeq, (ii) entity-overlapping (intragenic) or intergenic, and (iii) potential pseudogenes—intergenic sequences corresponding to a portion of a previously annotated larger gene. Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.

Database URL:http://www.yeastgenome.org/

Bacteriocins from lactic acid bacteria: production, purification, and food applications

In fermented foods, lactic acid bacteria (LAB) display numerous antimicrobial activities. This is mainly due to the production of organic acids, but also of other compounds, such as bacteriocins and antifungal peptides. Several bacteriocins with industrial potential have been purified and characterized. The kinetics of bacteriocin production by LAB in relation to process factors have been studied in detail through mathematical modeling and positive predictive microbiology. Application of bacteriocin-producing starter cultures in sourdough (to increase competitiveness), in fermented sausage (anti-listerial effect), and in cheese (anti-listerial and anti-clostridial effects), have been studied during in vitro laboratory fermentations as well as on pilot-scale level. The highly promising results of these studies underline the important role that functional, bacteriocinogenic LAB strains may play in the food industry as starter cultures, co-cultures, or bioprotective cultures, to improve food quality and safety. In addition, antimicrobial production by probiotic LAB might play a role during in vivo interactions occurring in the human gastrointestinal tract, hence contributing to gut health.

The S-layer proteins of Lactobacillus crispatus strain ZJ001 is responsible for competitive exclusion against Escherichia coli O157:H7 and Salmonella typhimurium

Lactobacillus crispatus ZJ001, isolated from pig intestines and identified by sequencing analysis based on partial 16S rRNA gene, was examined in vitro for probiotic activity exerted by the surface layer proteins (S-layer). The characteristics of L. crispatus ZJ001 were compared to Lactobacillus acidophilus ATCC 4356 from the same genus which also produces the S-layer proteins. The strain ZJ001 was resistant to acidic condition and bile salt. Its antagonistic properties such as adhesion, inhibition of the pathogen growth and competitive exclusion against Escherichia coli O157:H7 and Salmonella typhimurium were apparently advantageous over L. acidophilus ATCC 4356. SDS-PAGE analysis of cell surface proteins revealed the presence of S-layer proteins, approximately at 42 kDa in L. crispatus ZJ001. Removal of the S-layer proteins reduced autoaggregation and adhesion to HeLa cells. The functional role of the S-layer proteins in adhesion was also confirmed by the antibody-mediated inhibition assay using the polyclonal antibody against the S-layer protein. The S-layer proteins from L. crispatus ZJ001 inhibited adhesion of S. typhimurium and E. coli O157:H7 to HeLa cells. These results suggest that L. crispatus ZJ001 possesses probiotic properties and the S-layer proteins are involved in the adhesion and competitive exclusion of pathogens to HeLa cells.

Sugars relevant for sourdough fermentation stimulate growth of and bacteriocin production by Lactobacillus amylovorus DCE 471

The effects of sugars relevant for sourdough fermentation (i.e. glucose, fructose, maltose, and sucrose) on the kinetics of the bacteriocin-producing Lactobacillus amylovorus DCE 471 strain were assessed. The sugars were applied solely or in combination in a sourdough simulation medium during batch fermentations at temperature and pH conditions encountered during the production of type II sourdoughs. When growing on a single energy source, glucose was preferentially consumed by L. amylovorus DCE 471, followed by maltose and fructose. The strain was unable to grow on sucrose. In glucose-containing mixtures, glucose was always consumed most rapidly by L. amylovorus DCE 471 and seemed to steer its growth during the early growth phase, mainly because of the delaying effect on maltose consumption. Maltose consumption started only when low glucose levels were reached. In all cases, fructose was used as an energy source and not as a terminal electron acceptor, since no acetic acid or mannitol were produced. Increased bacteriocin titres were observed with binary or ternary sugar combinations compared to single energy sources. Thus, the diversity of the energy source seemed to stimulate the production of amylovorin L. Cell growth of and production of amylovorin L by L. amylovorus DCE 471 paralleled for all sugar combinations tested.

Effects of spent culture supernatant of Lactobacillus acidophilus on intestinal flora in mice with antibiotic-associated diarrhoea

AIM: To study the effects of the spent culture supernatant (SCS) of Lactobacillus acidophilus strain LA14 on the intestinal flora in mice with antibiotic-associated diarrhoea.

METHODS: Sixty mice were randomly and averagely divided into 6 groups: normal control group, model group, SCS group, living bacteria group, SCS plus living bacteria group, and spontaneous recovery group. The animal model of the intestinal flora imbalance was made by intraperitoneal administration of ampicillin 2000 mg/(kg•d) for 3 d. Then the mice in normal control group and model group were killed, while the mice in the other groups were administered (ig) with the corresponding drugs or normal saline (30 mL/kg per day, the adopted concentration of living bacteria was 3×10⁹ CFU/kg per day) for another 3 d. At the end of the 3^rd day, all the mice were killed and the floras in the contents of the caecum were analyzed.

RESULTS: Intestinal flora imbalance occurred in the mice administered with ampicillin and the numbers (lgCFU/L) of four main intestinal floras changed obviously. In comparison with those in normal control group, the numbers of Escherichia coli andEnterococcus were significantly increased (10.13 ± 0.10 vs 9.03 ± 0.11, P < 0.01; 10.52 ± 0.11 vs 9.11 ± 0.09, P < 0.01), while the numbers of Lactobacillus and Bifidobacterium were remarkably decreased (10.51 ± 0.07 vs 11.88 ± 0.10, P < 0.01; 10.38 ± 0.31 vs 11.61 ± 0.13, P < 0.05). After the mice were administered with SCS, living bacteria and SCS plus living bacteria, the numbers (compared with those in spontaneous recovery group) of Lactobacillus and Bifidobacterium were remarkably increased (Lactobacillus: 11.53 ± 0.17 vs 9.74 ± 0.37, P < 0.01; 11.54 ± 0.05, 11.45 ± 0.07 vs 9.74 ± 0.37, P < 0.05; Bifidobacterium: 11.54 ± 0.22, 11.30 ± 0.99 vs 9.51 ± 0.52, P < 0.05; 11.13 ± 0.16 vs 9.51 ± 0.52, P < 0.01), while the numbers of Escherichia coli and Enterococcus were significantly decreased again (Escherichia coli: 9.42 ± 0.22, 9.50 ± 0.06, 9.22 ± 0.39 vs 9.97 ± 0.61, P< 0.05; Enterococcus: 9.48 ± 0.20, 9.45 ± 0.16, 9.37 ± 0.21 vs 9.89 ± 0.43, P < 0.05).

CONCLUSION: Both living bacteria and SCS of Lactobacillus acidophilus can regulate the intestinal flora imbalance in mice with antibiotic-associated diarrhoea, and help to recover the numbers of Lactobacillus and Bifidobacterium in the intestinal tract.

Enterocin A production by Enterococcus faecium FAIR-E 406 is characterised by a temperature- and pH-dependent switch-off mechanism when growth is limited due to nutrient depletion

The biokinetics of cell growth and bacteriocin production of Enterococcus faecium FAIR-E 406 was studied as a function of temperature (20-45 degrees C) and pH (5.5-8.5) using de Man-Rogosa-Sharpe medium. Growth of E. faecium FAIR-E 406 was characterized by three successive growth phases and was modelled with the mechanistic nutrient depletion model. Bacteriocin production showed primary metabolite kinetics but was limited to the early growth phase. The critical biomass for switching off bacteriocin production was dependent on medium pH and incubation temperature, and was inversely correlated with the specific bacteriocin production. Doubling the concentration of the nitrogen source as well as a step-wise pH increase shifted the bacteriocin production towards a higher switch-off cell density.