Phenotypic and genotypic identification of lactic acid bacteria isolated from a small-scale facility producing traditional dry sausages

Whole-genome analysis suggesting probiotic potential and safety properties of Pediococcus pentosaceus DSPZPP1, a promising LAB strain isolated from traditional fermented sausages of the Basilicata region (Southern Italy)

Introduction

Many lactic acid bacteria (LAB) strains are currently gaining attention in the food industry and various biological applications because of their harmless and functional properties. Given the growing consumer demand for safe food, further research into potential probiotic bacteria is beneficial. Therefore, we aimed to characterize Pediococcus pentosaceus DSPZPP1, a LAB strain isolated from traditional fermented sausages from the Basilicata region of Southern Italy.

Methods

In this study, we analyzed the whole genome of the P. pentosaceus DSPZPP1 strain and performed in silico characterization to evaluate its applicability for probiotics and use in the food industry.

Results and Discussion

The whole-genome assembly and functional annotations revealed many interesting characteristics of the DSPZPP1 strain. Sequencing raw reads were assembled into a draft genome of size 1,891,398 bp, with a G + C content of 37.3%. Functional annotation identified 1930 protein-encoding genes and 58 RNAs including tRNA, tmRNA, and 16S, 23S, and 5S rRNAs. The analysis shows the presence of genes that encode water-soluble B-group vitamins such as biotin, folate, coenzyme A, and riboflavin. Furthermore, the analysis revealed that the DSPZPP1 strain can synthesize class II bacteriocin, penocin A, adding importance to the food industry for bio-enriched food. The DSPZPP1 genome does not show the presence of plasmids, and no genes associated with antimicrobial resistance and virulence were found. In addition, two intact bacteriophages were identified. Importantly, the lowest probability value in pathogenicity analysis indicates that this strain is non-pathogenic to humans. 16 s rRNA-based phylogenetic analysis and comparative analysis based on ANI and Tetra reveal that the DSPZPP1 strain shares the closest evolutionary relationship with P. pentosaceus DSM 20336 and other Pediococcus strains. Analysis of carbohydrate active enzymes (CAZymes) identified glycosyl transferases (GT) as a main class of enzymes followed by glycoside hydrolases (GH). Our study shows several interesting characteristics of the isolated DSPZPP1 strain from fermented Italian sausages, suggesting its potential use as a promising probiotic candidate and making it more appropriate for selection as a future additive in biopreservation.

Lactic Acid Bacteria: Variability Due to Different Pork Breeds, Breeding Systems and Fermented Sausage Production Technology

Changes in the ecology of the various lactic acid bacteria (LAB) species, which are involved in traditional fermented sausages, were investigated in the light of the use of different breeds of pork, each of which was raised in two different environments and processed using two different technologies. The semi-quantitative molecular method was applied in order to understand how the different species alternate over time, as well as their concentration ratios. A significant increase in LAB over the first days of fermentation characterized the trials where the starter culture wasn't added (T), reaching values of 107-108 cfu g-1. On the other hand, in the trials in which sausages were produced with starter addition, LAB counts had a less significant incremental jump from about 106 cfu g-1 (concentration of the inoculum) to 108 cfu g-1. Lactobacillus sakei and Lb. curvatus were detected as the prevalent population in all the observed fermentations. Pediococcus pentosaceus, Lb. casei, Leuconostoc mesenteroides, Lactococcus garviae, and Lb. graminis also appeared, but their concentration ratios varied depending on the diverse experimental settings. The results of cluster analysis showed that a plant- and breed-specific LAB ecology exists. In addition, it was also observed that the breeding system can influence the presence of certain LAB species.

Molecular and in vitro assessment of some probiotic characteristics of amylolytic Lactobacillus plantarum strains from Bulgarian fermented products

In the recent years, consumers' interest in healthy diet opened a new field for functional food development through combining the valuable composition of cereals and the health-promoting properties of lactic acid bacteria (LAB). LAB with amylolytic properties can assimilate starch in a single-step process and could be successfully applied as starter cultures offering an efficient nutritional conversion of cereal matrices. The probiotic potential of amylolytic LAB has not been investigated so far, therefore the present study focused on the molecular screening and in vitro tests of five amylolytic Lactobacillus plantarum strains to assess their tolerance to high acid and bile salts concentrations and antibiotic resistance as basic characteristics required for probiotic strains selection. Results showed excellent correspondence between the genetic screening and the phenotypic tests performed. Survivability at high acidity and bile salts presence was strain specific, with significant positive effect observed for cultures in stationary phase compared to those in exponential phase. Effect of starch in the medium proved most important to ensure viability of the amylolytic strains, which reveals the excellent potential of amylolytic LAB for commercially relevant probiotic applications. The strains proved to be generally safe in terms of antibiotic resistance. Among the five tested strains, L. plantarum Bom2 showed the best probiotic potential.

Shelf-life Reduction as an Emerging Problem in Cooked Hams Underlines the Need for Improved Preservation Strategies

Cooked hams have gained an important position within the delicatessen market. Nowadays, consumers not only demand superior sensory properties but also request low levels of sodium and fat and the absence of conventional chemicals and preservatives used for the increase of the technological yield and shelf-life of the products. As a result, products that apply strict quality certificates or ''clean'' labels become increasingly important. However, such cooked hams suffer from a limited shelf-life. Besides some physicochemical effects, this is mainly due to microbial impact, despite the application of modified-atmosphere-packaging and chilling. Microbial spoilage is mostly due to the metabolic manifestation of lactic acid bacteria and Brochothrix thermosphacta, although Enterobacteriaceae and yeasts may occur too. Several preservation strategies have been developed to prolong the shelf-life of such vulnerable cooked meat products by targeting the microbial communities, with different rates of success. Whereas high-pressure treatments do not always pose a straightforward solution, a promising strategy relates to the use of bioprotective cultures containing lactic acid bacteria. The latter consist of strains that are deliberately added to the ham to outcompete undesirable microorganisms. Spoilage problems seem, however, to be specific for each product and processing line, underlining the importance of tailor-made solutions.

Draft Genome Sequence of Lactobacillus sakei Strain wikim 22, Isolated from Kimchi in Chungcheong Province, South Korea

We report the draft genome sequence of Lactobacillus sakei strain wikim 22, a Lactobacillus species isolated from kimchi in North Chungcheong Province, South Korea, having 155 contigs with 2,447 genes and an average G+C content of 40.61%.

Evaluation of anti-Listeria meat borne Lactobacillus for biofilm formation on selected abiotic surfaces

The ability of meat borne anti-Listeria Lactobacillus to form biofilms under different in vitro conditions and on abiotic surfaces was investigated. Biofilm formation by the adhesion to polystyrene microtiter plates was determined, this being higher for Lactobacillus curvatus CRL1532 and CRL705 and Lactobacillus sakei CRL1862. The physicochemical properties of the cell surface were relatively hydrophilic and acidic in character; L. sakei CRL1862 exhibiting the strongest autoaggregation. The adhesion of lactobacilli to stainless steel (SS) and polytetrafluoroethylene (PTFE) supports at 10°C was found to be maximal for L. sakei CRL1862 on SS after 6 days. When biofilm architecture was characterized by epifluorescence and SEM, L. sakei CRL1862 homogeneously covered the SS surface while cell clusters were observed on PTFE; the extracellular polymeric substance matrix adapted to the topography and hydrophilic/hydrophobic characteristics of each material. The feasibility of L. sakei CRL1862 to form biofilm on materials used in meat processing highlights its potential as a control strategy for Listeria monocytogenes biofilms.

Species diversity and metabolic impact of the microbiota are low in spontaneously acidified Belgian sausages with an added starter culture of Staphylococcus carnosus

Quality of fermented sausages is affected by acidifying lactic acid bacteria (LAB) and colour- and flavour-promoting coagulase-negative staphylococci (CNS), whether or not used as starter culture. Artisan fermented sausages are often perceived as superior to industrial variants, partially because of the specific microbiota due to spontaneous acidification, which may be considered as an artisan characteristic. Therefore, two kinds of spontaneously acidified Belgian sausages were prepared (Belgian-type salami and Boulogne sausage), but with addition of a Staphylococcus carnosus culture. The Belgian-type salami was made from pork and beef, whereas the Boulogne sausage contained pork and horse meat. In all cases, Lactobacillus sakei was the dominant LAB species present on the raw materials and during fermentation, whereas enterococci remained present in the background. Enterobacteriaceae vanished after fermentation. The CNS species diversity on the raw materials was large and differed between the pork, beef, and horse meat. Nevertheless, this species diversity was annihilated during fermentation by the added S. carnosus culture. The volatiles fraction was mainly composed of aldehydes that originated from lipid oxidation and spices-derived compounds. Aromatic compounds that are typically associated to CNS activity, such as end-products from the metabolism of branched-chain amino acids, were not present in the Belgian-type salami and only marginally present in the Boulogne sausage. In conclusion, spontaneous acidification of Belgian-type fermented sausages leads to dominance of L. sakei and is no guarantee for bacterial contribution to the aroma profile when S. carnosus is added as a starter culture.

Antimicrobial effect of ammonium hydroxide when used as an alkaline agent in the formulation of injection brine solutions

Paired U.S. Department of Agriculture Select strip loins were injected with either a conventional brine (4.5% potassium and sodium polyphosphate blend [Brifisol 750], 3.6% NaCl, 1% Herbalox seasoning HT-S, and 90.9% ice water) or an ammonium hydroxide (AH) brine (1% AH, 3.6% NaCl, 1% Herbalox seasoning HT-S, and 94.4% ice water). The steaks were sliced, high-oxygen modified atmosphere packaged, placed at 5°C in dark storage for 5 days, and then transferred to a retail display at 5°C for another 14 days. Steaks injected with AH brine appeared to have lower counts of psychrotrophic, mesophilic, and gram-negative bacteria. Immediately after injection, there was ∼1 log CFU/g difference between treatments in gram-negative bacterial counts. No differences in coliform and lactic acid bacterial counts were found.

Identification of lactic acid bacteria associated with the production of plaa-som, a traditional fermented fish product of Thailand

Plaa-som is a Thai fermented fish product for which whole fish or fish fillets are fermented with either cooked rice or steamed sticky rice, salt, and garlic. A total of 762 lactic acid bacteria (LAB) were isolated during plaa-som fermentation by culture on CaCO(3)-MRS agar plates. They were screened and grouped by amplified ribosomal DNA restriction analysis (ARDRA), giving six groups that were identified by ribosomal DNA sequencing as Lactococcus garvieae, Streptococcus bovis, Weissella cibaria, Pediococcus pentosaceus, Lactobacillus plantarum, and Lactobacillus fermentum. Freshly mixed ingredients contained low populations of LAB (less than 10 CFU/g) that subsequently grew during fermentation to final populations of approximately 10(7)CFU/g. Early stages of the process were dominated by the presence of Lc. garvieae, S. bovis, and W. cibaria. At 48 h into fermentation, W. cibaria, P. pentosaceus, and Lb. plantarum were prevalent, and gave way to a dominance of Lb. plantarum that completed the fermentation. A mixture of these LAB species could be considered as species for development of a starter culture for plaa-som fermentation.

Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice

A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10(9) CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.

Occurrence, population structure, and antimicrobial resistance of enterococci in marginal and apical periodontitis

Subgingival plaque samples and root canal samples were collected from 2,839 marginal periodontitis (MP) patients and 21 apical periodontitis (AP) patients. Enterococcus species were identified by a series of phenotypic and genotypic tests. Antimicrobial susceptibility assays were performed by an agar disk diffusion test. Multilocus sequence typing (MLST), eBURST, and minimum spanning tree were used for enterococcal genetic clustering and population analysis. Enterococcus faecalis was recovered from 3.7% MP patients and 9.5% AP patients, and Enterococcus faecium was recovered from 0.04% MP patients. Enterococci were detected more often in older male patients. E. faecalis isolates of MP were found resistant to tetracycline (49.1%), erythromycin (8.5%), trimethoprim (2.8%), and gentamicin (1.9%), while one AP isolate was resistant to tetracycline. A total of 40 sequence types (STs) were resolved in 108 E. faecalis isolates. Comparison with E. faecalis international MLST database revealed that 27 STs were previously found, 13 STs were novel, and several major clonal complexes in the database were also found in MP isolates. The tetracycline-resistant isolates distributed mainly in the major clonal complexes and singletons, whereas the erythromycin-resistant isolates were more dispersed. Although the rate of occurrence of enterococci recovered in the MP and AP samples was low, 50% of these isolates are resistant to at least one antimicrobial agent, which is most often tetracycline. This implies that subgingival E. faecalis might represent a reservoir of resistance to tetracycline and erythromycin. The subgingival E. faecalis isolates show high genetic diversity but are grouped, in general, with the known isolates from the international database.

Phenotypic and genetic heterogeneity of lactic acid bacteria isolated from "Alheira", a traditional fermented sausage produced in Portugal

The aim of this study was to evaluate the phenotypic and genetic heterogeneity of lactic acid bacteria (LAB) isolated from "Alheira", a fermented sausage produced in Portugal. LAB were identified to genus and species level by phenotypic characteristics, using genus or species-specific primers and sequencing of the gene encoding 16S rRNA. Two-hundred and eighty-three isolates were grouped into 14 species. Lactobacillus plantarum was isolated from all sausages and Enterococcusfaecalis from most of the samples. Low numbers of Lactobacillus paraplantarum, Lactobacillus brevis, Lactobacillus rhamnosus, Lactobacillus sakei, Lactobacillus zeae, Lactobacillus paracasei, Leuconostoc mesenteroides, Pediococcus pentosaceus, Pediococcus acidilactici, Weissella cibaria, Weissella viridescens and Enterococcus faecium were recorded. The genetic heterogeneity of L. plantarum and E. faecalis strains were determined by numerical analysis of DNA banding patterns obtained by RAPD-PCR. Strains of L. plantarum and E. faecalis were different from different producers. This study forms the basis from which starter cultures could be selected for production of "Alheira".

Microbial ecosystems of traditional fermented meat products: The importance of indigenous starters

This paper reviews the diversity of microbiota, both in the environment and in traditional fermented European sausages. The environments of processing units were colonised at variable levels by resident spoilage and technological microbiota, with sporadic contamination by pathogenic microbiota. Several critical points were identified such as the machines, the tables and the knives - knowledge crucial for the improvement of cleaning and disinfecting practices. Traditionally fermented sausages generally did not present a sanitary risk. The great diversity of lactic acid bacteria and staphylococci was linked to manufacturing practices. Development of indigenous starters is very promising because it enables sausages to be produced with both high sanitary and sensory qualities. Our increasing knowledge of the genomes of technological bacteria will allow a better understanding of their physiology in sausages.

Selection criteria for lactic acid bacteria to be used as functional starter cultures in dry sausage production: An update

Lactic acid bacteria (LAB) have long been used as starter cultures in the production of fermented dry sausages and other meat-derived commodities. These cultures are generally designed to meet food safety, shelf-life, technological effectiveness and economic feasibility criteria. Besides all these traditional properties, novel starter cultures should take into account the risks posed by the formation of biogenic amines in food, and the development and spreading of bacterial resistance to antibiotics. Further, 'functional starters' could protect consumers from harmful bacteria either by a rapid acidification or by the production of antimicrobials (bacteriocins). Specially-selected cultures may also provide probiotic benefits, and, if properly modified, they may even be endorsed with nutraceutical traits. The present review discusses the technological and new selection criteria that should be taken into account when selecting LAB starter cultures for the production of fermented dry sausages.

Investigation of the physicochemical and sensory homogeneity of traditional French dry sausages

The aim of this study was to investigate the homogeneity of the traditional dry sausages manufactured in small scale facilities from the Massif Central region in France by taking into account the diversity of the production in this area. The homogeneity was estimated by analysis of the physicochemical parameters of 6 types of traditional dry sausages chosen as representatives of the production diversity. The homogeneity was evaluated (i) within the product, (ii) in the production batch and (iii) over 2 different seasons for each type of dry sausage. When heterogeneity was detected, sensory analysis was performed in order to check if the physicochemical differences found were perceived by a sensory panel. The physicochemical results showed that there was no significant heterogeneity within the product nor there was in the production batch. Over the 2 seasons studied, 3 out of the 6 dry sausages were heterogeneous in composition and this feature was perceived by the sensory panel. The possible causes of this heterogeneity (amounts of ingredients added, type and composition of the raw materials used, length of drying) are discussed.