Comparative evaluation of plasmid profiling and ribotyping in the analysis ofLactobacillus plantarumstrain heterogeneity in silage

The Potential Effects on Microbiota and Silage Fermentation of Alfalfa Under Salt Stress

This study investigated the fermentation quality of alfalfa grown in different salt stress regions in China. Following the production of silage from the natural fermentation of alfalfa, the interplay between the chemical composition, fermentation characteristics, and microbiome was examined to understand the influence of these factors on the fermentation quality of silage. The alfalfa was cultivated under salt stress with the following: (a) soil content of <1%0 (CK); (b) 1–2%0 (LS); (c) 2–3%0 (MS); (d) 3–4%0 (HS). The pH of the silage was high (4.9–5.3), and lactic acid content was high (26.3–51.0 g/kg DM). As the salt stress increases, the NA⁺ of the silages was higher (2.2–5.4 g/kg DM). The bacterial alpha diversities of the alfalfa silages were distinct. There was a predominance of desirable genera including Lactococcus and Lactobacillus in silage produced from alfalfa under salt stress, and this led to better fermentation quality. The chemical composition and fermentation characteristics of the silage were closely correlated with the composition of the bacterial community. Furthermore, NA⁺ was found to significantly influence the microbiome of the silage. The results confirmed that salt stress has a great impact on the quality and bacterial community of fresh alfalfa and silage. The salt stress and plant ions were thus most responsible for their different fermentation modes in alfalfa silage. The results of the study indicate that exogenous epiphytic microbiota of alfalfa under salt stress could be used as a potential bioresource to improve the fermentation quality.

Criteria for lactic acid bacteria screening to enhance silage quality

The main challenge of ensiling is conserving the feed through a fermentative process that results in high nutritional and microbiological quality while minimizing fermentative losses. This challenge is of growing interest to farmers, industry and research and involves the use of additives to improve the fermentation process and preserve the ensiled material. Most studies involved microbial additives; lactic acid bacteria (LAB) have been the focus of much research and have been widely used. Currently, LABs are used in modern and sustainable agriculture because of their considerable potential for enhancing human and animal health. Although the number of studies evaluating LABs in silages has increased, the potential use of these micro-organisms in association with silage has not been adequately studied. Fermentation processes using the same strain produce very different results depending on the unique characteristics of the substrate, so the choice of silage inoculant for different starting substrates is of extreme importance to maximize the nutritional quality of the final product. This review describes the current scenario of the bioprospecting and selection process for choosing the best LAB strain as an inoculant for ensiling. In addition, we analyse developments in the fermentation process and strategies and methods that will assist future studies on the selection of new strains of LAB as a starter culture or inoculant.

Discrimination of probiotic Lactobacillus strains for poultry by repetitive sequenced-based PCR fingerprinting

BACKGROUND

Four repetitive element sequence-based polymerase chain reaction (rep-PCR) methods, namely repetitive extragenic palindromic PCR (REP-PCR), enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), polytrinucleotide (GTG)₅ -PCR and BOX-PCR, were evaluated for the molecular differentiation of 12 probiotic Lactobacillus strains previously isolated from the gastrointestinal tract of chickens and used as a multistrain probiotic. This study represents the first analysis of the comparative efficacy of these four rep-PCR methods and their combination (composite rep-PCR) in the molecular typing of Lactobacillus strains based on a discriminatory index (D).

RESULTS

Species-specific and strain-specific profiles were observed from rep-PCR. From the numerical analysis of composite rep-PCR, BOX-PCR, (GTG)₅ -PCR, REP-PCR and ERIC-PCR, D values of 0.9118, 0.9044, 0.8897, 0.8750 and 0.8529 respectively were obtained. Composite rep-PCR analysis was the most discriminative method, with eight Lactobacillus strains, namely L. brevis ATCC 14869(T) , L. reuteri C 10, L. reuteri ATCC 23272(T) , L. gallinarum ATCC 33199(T) , L. salivarius ATCC 11741(T) , L. salivarius I 24, L. panis JCM 11053(T) and L. panis C 17, being differentiated at the strain level.

CONCLUSION

Composite rep-PCR analysis is potentially a useful fingerprinting method to discriminate probiotic Lactobacillus strains isolated from the gastrointestinal tract of chickens.

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".

Use of RAPD-PCR as a method to follow the progress of starter cultures in sauerkraut fermentation

DNA fingerprinting methods were used to follow the progress of unmarked starter cultures in laboratory sauerkraut fermentations (1.2 and 13 l). Random prime PCR (RAPD-PCR) was used for strain-specific identification of Leuconostoc mesenteroides cultures. A comparative analysis of RAPD banding patterns for fermentation isolates and starter cultures was carried out using both genetically marked and unmarked cultures. While some variation in the RAPD patterns was observed, the results showed that the starter cultures dominated the fermentation during early heterofermentative stage for up to 5 days after the start of fermentation. Results from marked and unmarked starter cultures were confirmed by intergenic transcribed spacer (ITS)-PCR, and strain identify was confirmed by pulse field gel electrophoresis (PFGE) patterns. The results demonstrate the utility of RAPD to follow the progression of unmarked starter cultures of L. mesenteroides in sauerkraut fermentations.

Characterization and differentiation of Lactobacillus manihotivorans strains isolated from cassava sour starch

Lactobacillus manihotivorans has been reported as one of the dominant species in cassava sour starch production process. Seven isolates that have previously been identified as belonging to this species were studied in the present work. Their molecular and phenotypic characteristics showed higher strain diversity than previously described. Differences were found in their fermentation profiles, whereas no major differences were observed in properties related to processing conditions (salt concentration, pH, temperature), or in potential functional properties (bile salt and pH 2.0 tolerance). Among the main characteristics of interest for the fermentation of cereals or cassava, blended or not with legumes, six out of seven strains were amylolytic and raffinose was fermented by all strains. Strains OND 32T and OLB 7 fermented the broadest range of carbohydrates. Most of the strains contained plasmids. Plasmid curing changed their phenotypic characteristics, particularly those of strain OND 32T, which, in addition, lost its starch and raffinose fermentation ability.

Taxonomy and important features of probiotic microorganisms in food and nutrition

Lactic acid bacteria are among the most important probiotic microorganisms typically associated with the human gastrointestinal tract. Traditionally, lactic acid bacteria have been classified on the basis of phenotypic properties, eg, morphology, mode of glucose fermentation, growth at different temperatures, lactic acid configuration, and fermentation of various carbohydrates. Studies based on comparative 16S ribosomal RNA sequencing analysis, however, showed that some taxa generated on the basis of phenotypic features do not correspond with the suggested phylogenetic relations. Thus, some species are not readily distinguishable by phenotypic characteristics. This is especially true for the so-called Lactobacillus acidophilus group, the Lactobacillus casei and Lactobacillus paracasei group, and some bifidobacteria, strains of which have been introduced in many probiotic foods, eg, the novel yogurt-like commodities. Consequently, modern molecular techniques, including polymerase chain reaction-based and other genotyping methods, have become increasingly important for species identification or for the differentiation of probiotic strains. Probiotic strains are selected for potential application on the basis of particular physiologic and functional properties, some of which may be determined in vitro. The classification and identification of a probiotic strain may give a strong indication of its typical habitat and origin. The species, or even genus name, may also indicate the strain's safety and technical applicability for use in probiotic products. Molecular typing methods such as pulsed-field gel electrophoresis, repetitive polymerase chain reaction, and restriction fragment length polymorphism are extremely valuable for specific characterization and detection of such strains selected for application as probiotics.

Identification of lactic acid bacteria constituting the predominating microflora in an acid-fermented condiment (tempoyak) popular in Malaysia

Tempoyak is a traditional Malaysian fermented condiment made from the pulp of the durian fruit (Durio zibethinus). Salt is sometime added to proceed fermentation at ambient temperature. In various samples obtained from night markets, lactic acid bacteria (LAB) were the predominant microorganisms, ranging from log 8.4 to log 9.2 cfu g(-1). No other microorganisms were present to such a level. These samples contained reduced amount of saccharose, glucose and fructose but increased amount of D- and L-lactic acid and acetic acid compared with samples of non-fermented durian fruit. Sixty-four isolates of LAB were divided into five groups by use of a few phenotypic tests. A total of 38 strains of LAB were selected for comparison by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of their whole cell protein patterns with a SDS-PAGE database of LAB. These strains were also examined for their carbohydrate fermentation patterns by use of API 50 CH. Isolates belonging to the Lactobacillus plantarum group were shown to be the predominant members of the LAB flora. In addition, isolates belonging to the Lactobacillus brevis group, Leuconostoc mesenteroides, Lactobacillus mali, Lactobacilus fermentum and an unidentified Lactobacillus sp. were also observed. A high degree of diversity among isolates belonging to the Lb. plantarum group was demonstrated by analysis of their plasmid profiles.

Genetics of lactobacilli in food fermentations

Lactobacilli play a substantial role in food biotechnology and influence our quality of life by their fermentative and probiotic properties. Despite their obvious importance in fermentation ecology and biotechnology only recent years have brought some insight into the genetics of lactobacilli. These genetic investigations allow the elucidation of traits determinative for competitiveness and ecology and thus product safety and quality. They have concentrated only on a small selection of lactobacilli whereas others are hardly touched or remained recalcitrant to genetic analysis and manipulation. The knowledge gained on the biochemistry, physiology, ecology and especially genetics is a prerequisite for the deliberate application and improved handling of lactobacilli in traditional and novel applications. In this review, the achievements in the genetics of lactobacilli are described including detection systems, genetic elements, host vector systems, gene cloning and expression and risk assessment of genetically engineered lactobacilli.

Plasmids in Lactobacillus

This review describes Lactobacillus plasmids on distribution, structure, function, vector construction, vector stability, application, and prospective. About 38% of species of the genus Lactobacillus were found to contain plasmids with different sizes (from 1.2 to 150 kb) and varied numbers (1 or more). Some Lactobacillus plasmids with small sizes were highly similar to those of single strand plasmids from other Gram-positive bacteria. The extensive sequence homologies of plus origins, replication initiation proteins, minus origins, cointegration sites, and the presence of single strand intermediates supported the fact that these small Lactobacillus plasmids replicate with a rolling-circle replication mechanism. Some Lactobacillus plasmid replicons were of broad host range that could function in other Gram-positive bacteria, and even in Escherichia coli, while replicons of other Gram-positive bacteria also function in Lactobacillus. Although most Lactobacillus plasmids are cryptic, some plasmid-encoded functions have been discovered and applied to vector construction and Lactobacillus identification, detection, and modification.

Strain-specific differentiation of lactococci in mixed starter culture populations using randomly amplified polymorphic DNA-derived probes

A hydrophobic grid membrane filtration (HGMF) colony hybridization assay was developed that allows strain-specific differentiation of defined bacterial populations. The randomly amplified polymorphic DNA (RAPD) fingerprinting technique was used to identify potential signature nucleic acid sequences unique to each member of a commercial cheese starter culture blend. The blend consisted of two closely related Lactococcus lactis subsp. cremoris strains, 160 and 331, and one L. lactis subsp. lactis strain, 210. Three RAPD primers (OPX 1, OPX 12, and OPX 15) generated a total of 32 products from these isolates, 20 of which were potential strain-specific markers. Southern hybridization analyses revealed, that the RAPD-generated signature sequences OPX15-0.95 and a 0.36-kb HaeIII fragment of OPX1-1.0b were specific for strains 331 and 210, respectively, within the context of the test starter culture blend. These strain-specific probes were used in a HGMF colony hybridization assay. Colony lysis, hybridization, and nonradioactive detection parameters were optimized to allow specific differentiation and quantitation of the target strains in the mixed starter culture population. When the 210 and 331 probes were tested at their optimal hybridization temperatures against single cultures, they detected 100% of the target strain CFUs, without cross-reactivity to the other strains. The probes for strains 210 and 331 also successfully detected their targets in blended cultures even with a high background of the other two strains.

Selective detection, enumeration and identification of potentially probiotic Lactobacillus and Bifidobacterium species in mixed bacterial populations

Lactobacillus and Bifidobacterium species constitute a significant proportion of probiotic cultures used in developed countries in 'microbial adjunct nutrition'. A number of differential plating methodologies have been developed which seek to selectively detect and enumerate these bacterial groups in bioproducts. Differences in oxygen tolerance, nutritional requirements, antibiotic susceptibility, and colony morphology and colour constitute the bases of differentiation in these methods. The choice of methodology depends on the nature of the bioproduct to be examined (wet or dry) and the presence of other bacteria such as starter cultures. In addition, a number of nucleic acid methods have been developed in recent years which enable the specific detection of these bacterial groups at species, subspecies and strain level in mixed populations. The methods use synthetic 16S and 23S rRNA-targeted hybridisation probes, the specificity of which can be adjusted to fit any taxonomic ranking from genus to genotype, for detection, enumeration and identification in situ or after differential plating. The combined use of differential plating and molecular strain typing methodologies provides food and medical microbiologists with a powerful and targeted approach to the detection, enumeration and identification of these bacterial groups and their members in a wide range of food and biological materials. An overview of these methods is presented in this review.