Identification of Lactobacillus sakei and Lactobacillus curvatus by multiplex PCR-based restriction enzyme analysis

Smart-Plexer: a breakthrough workflow for hybrid development of multiplex PCR assays

Developing multiplex PCR assays requires extensive experimental testing, the number of which exponentially increases by the number of multiplexed targets. Dedicated efforts must be devoted to the design of optimal multiplex assays ensuring specific and sensitive identification of multiple analytes in a single well reaction. Inspired by data-driven approaches, we reinvent the process of developing and designing multiplex assays using a hybrid, simple workflow, named Smart-Plexer, which couples empirical testing of singleplex assays and computer simulation to develop optimised multiplex combinations. The Smart-Plexer analyses kinetic inter-target distances between amplification curves to generate optimal multiplex PCR primer sets for accurate multi-pathogen identification. In this study, the Smart-Plexer method is applied and evaluated for seven respiratory infection target detection using an optimised multiplexed PCR assay. Single-channel multiplex assays, together with the recently published data-driven methodology, Amplification Curve Analysis (ACA), were demonstrated to be capable of classifying the presence of desired targets in a single test for seven common respiratory infection pathogens.

Distribution, inducibility, and characteristics of Latilactobacillus curvatus temperate phages

Aim: Temperate phages are known to heavily impact the growth of their host, be it in a positive way, e.g., when beneficial genes are provided by the phage, or negatively when lysis occurs after prophage induction. This study provides an in-depth look into the distribution and variety of prophages in Latilactobacillus curvatus (L. curvatus). This species is found in a wide variety of ecological niches and is routinely used as a meat starter culture. Methods: Fourty five L. curvatus genomes were screened for prophages. The intact predicted prophages and their chromosomal integration loci were described. Six L. curvatus lysogens were analysed for phage-mediated lysis post induction via UV light and/or mitomycin C. Their lysates were analysed for phage particles via viral DNA sequencing and transmission electron microscopy. Results: Two hundred and six prophage sequences of any completeness were detected within L. curvatus genomes. The 50 as intact predicted prophages show high levels of genetic diversity on an intraspecies level with conserved regions mostly in the replication and head/tail gene clusters. Twelve chromosomal loci, mostly tRNA genes, were identified, where intact L. curvatus phages were integrated. The six analysed L. curvatus lysogens showed strain-dependent lysis in various degrees after induction, yet only four of their lysates appeared to contain fully assembled virions with the siphovirus morphotype. Conclusion: Our data demonstrate that L. curvatus is a (pro)phage-susceptible species, harbouring multiple intact prophages and remnant sequences thereof. This knowledge provides a basis to study phage-host interaction influencing microbial communities in food fermentations.

Application of 16S rRNA virtual RFLP for the discrimination of some closely taxonomic-related lactobacilli species

BACKGROUND

Several species in Lactobacillaceae family were recognized as potential probiotic bacteria. In this group of lactic acid bacteria, species are taxonomically closed and usually share similar 16S rRNA gene, thus, instead of so their identification and discrimination are too difficult.

METHOD

In the present study, virtual restriction fragment length polymorphism (RFLP) is instead of was used as a tool to discriminate between the closely related species Lactiplantibacillus plantarum (L plantarum), Lactiplantibacillus paraplantarum (L paraplantarum), and Lactiplantibacillus pentosus (L pentosus); Latilactobacillus sakei (L sakei), Latilactobacillus curvatus(L curvatus), and Latilactobacillus graminis (L graminis); Lacticaseibacillus casei (L casei), Lacticaseibacillus paracasei (L paracasei), Lacticaseibacillus zeae, and Lacticaseibacillus rhamnosus; Lactobacillus gasseri (L gasseri) and Lactobacillus johnsonii (L johnsonii). In silico comparative analysis of 16S rRNA sequences digested by 280 restriction enzymes was performed in order to search the key enzymes which gives different profiles.

RESULTS

Results revealed that L casei, L paracasei, L zeae, and Lb rhamnosus could be separated from each other on the basis of AlwI, BpuEI, BsgI, BsrDI, BstYI, EarI, MluCI, and NsPI RFLP. Results showed also that different RFLP patterns were obtained from L sakei, L graminis and L curvatus by using both AflI and NspI endonucleases (in separated restriction) and L plantarum, L paraplantarum, and L pentosus were distinguished each one from the other by MucI, NspI, and TspDTI PCR-RFLP. Lb gasseri and L johnsonii were also separated on the basis of Mse I, Taq I, and Dra I RFLP.

CONCLUSION

In this study, we proved that too closely related species could be separated in virtual analysis on basis of their 16S rRNA RFLP patterns using key restriction enzymes method.

Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish

Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.

In vitro and in vivo activity of Lactobacillus sakei L14 strain against Campylobacter jejuni DC3 strain

Introduction

Domestic poultry is a natural reservoir of Campylobacter, the host–pathogen interaction being predominantly asymptomatic. This study investigated whether chickens remain asymptomatic partly because of lactic acid bacteria (LAB).

Material and Methods

Campylobacter spp. and LAB were isolated from the gut of poultry chickens using enrichment and screening assays and were identified via rDNA sequencing. The C. jejuni DC3 isolate was grown in different cell-free supernatants (CFS) generated from a priority LAB isolate. An in vivo challenge involving the C. jejuni and LAB isolates using a chicken model was performed to confirm the in vitro findings.

Results

Twelve presumptive LAB isolates had anti-C. jejuni activity based on cross-streak and agar plug assays, with Lactobacillus sakei L14 isolate exhibiting the highest activity. Inhibition by L. sakei L14 CFS of the growth of C. jejuni occurred in a dose-dependent manner. Campylobacter jejuni DC3 inhibition was most evident in CFS harvested at 72 h and produced by co-culture with the pathogen. Neutralisation of the CFS abrogated the observed inhibition. Co-infection with C. jejuni DC3 and L. sakei L14 in vivo, however, failed to inhibit C. jejuni colonisation in chickens.

Conclusion

The results suggest that the anti-C. jejuni effect of L. sakei L14 in chickens may be due to mechanisms other than direct inhibition of growth.

Selenium bio-enrichment of Mediterranean fruit juices through lactic acid fermentation

This work was carried out to elaborate selenium (Se) bio-enriched fermented Mediterranean fruit juices. To this purpose, pomegranate and table red grape juices were added with sodium selenite (Na₂SeO₃) and fermented by Levilactobacillus brevis CRL 2051 and Fructobacillus tropaeoli CRL 2034 individually or combined. To better evaluate the effect of selenite addition and starter strain inoculums on the total bacterial community of the fruit juices, fermentation trials were performed with raw and pasteurized fruit juices. No statistical significant differences were observed for total mesophilic microorganisms (TMM) and rod-shaped lactic acid bacteria (LAB) levels among raw and pasteurized juices inoculated with the starter strains, while significant differences between those juices with and without selenite were registered. LAB cocci, Pseudomonadaceae and yeasts were detected only for the raw juice preparations. The dominance of L. brevis CRL 2051 and F. tropaeoli CRL 2034 was confirmed by randomly amplified polymorphic DNA (RAPD)-PCR analysis. After fermentation, pH dropped for all inoculated trials and control raw juices. The soluble solid content (SSC) levels of the raw juices were higher than the corresponding pasteurized trials. The thermal treatment affected consistently yellowness of grape juice trials and redness of pomegranate juices. No microbial Se accumulation was registered for pomegranate juices, while F. tropaeoli CRL 2034 accumulated the highest amount of Se (65.5 μg/L) in the grape juice. For this reason, only trials carried out with raw grape juices were investigated by metagenomics analysis by Illumina MiSeq technology. Non-inoculated grape juices were massively fermented by acetic acid bacteria while Fructobacillus and Lactobacillus (previous genus name of Levilactobacillus) represented the highest operational taxonomy units (OTUs) relative abundance % of the trials inoculated with the starter strains as confirmed by this technique.

Conjugated linoleic acid producing potential of lactobacilli isolated from goat (AXB) rumen fluid samples

OBJECTIVE

The present investigation was aimed to explore the potential of lactobacilli for conjugated linoleic acid (CLA) production, isolated from rumen fluid samples of lactating goats.

METHODS

A total of 64 isolates of lactobacilli were obtained using deMan-Rogosa-Sharpe (MRS) agar from rumen fluid of goats and further subjected to morphological and biochemical characterizations. Isolates found as gram-positive, catalase negative rods were presumptively identified as Lactobacillus species and further confirmed by genus specific polymerase chain reaction (PCR). The phylogenetic tree was constructed from the nucleotide sequences using MEGA6.

RESULTS

Out of the 64 isolates, 23 isolates were observed positive for CLA production by linoleate isomerase gene-based amplification and quantitatively by UV-spectrophotometric assay for the conversion of linoleic acid to CLA as well as gas chromatography-based assay. In all Lactobacillus species cis9, trans11 isomer was observed as the most predominant CLA isomer. These positive isolates were identified by 16S rRNA gene-based PCR sequencing and identified to be different species of L. ingluviei (2), L.salivarius (2), L. curvatus (15), and L. sakei (4).

CONCLUSION

The findings of the present study concluded that lactic acid bacteria isolated from ruminal fluid samples of goat have the potential to produce bioactive CLA and may be applied as a direct fed microbial to enhance the nutraceutical value of animal food products.

Characterization of Diversity and Probiotic Efficiency of the Autochthonous Lactic Acid Bacteria in the Fermentation of Selected Raw Fruit and Vegetable Juices

The diversity of indigenous lactic acid bacteria (LAB) in fermented broccoli, cherry, ginger, white radish, and white-fleshed pitaya juices was analyzed using culture-independent and -dependent approaches. The major properties of selected probiotic strains, including dynamic variations in pH, viable cell counts, antibiotic resistance, bacterial adhesion to hydrophobic compounds, and survivability during simulated gastrointestinal transit, were investigated using broccoli as the fermentation substrate. In broccoli and ginger juices, the genus Lactobacillus occupied the dominant position (abundances of 79.0 and 30.3%, respectively); in cherry and radish juices, Weissella occupied the dominant position (abundances of 78.3 and 83.2%, respectively); and in pitaya juice, Streptococcus and Lactococcus occupied the dominant positions (52.2 and 37.0%, respectively). Leuconostoc mesenteroides, Weissella cibaria/soli/confusa, Enterococcus gallinarum/durans/hirae, Pediococcus pentosaceus, Bacillus coagulans, and Lactococcus garvieae/lactis subspecies were identified by partial 16S rRNA gene sequencing. In general, the selected autochthonous LAB isolates displayed no significant differences in comparison with commercial strains with regard to growth rates or acidification in fermented broccoli juice. Among all the isolates, L. mesenteroides B4-25 exhibited the highest antibiotic resistance profile (equal to that of L. plantarum CICC20265), and suitable adhesion properties (adhesion of 13.4 ± 5.2% ∼ 36.4 ± 3.2% and 21.6 ± 1.4% ∼ 69.6 ± 2.3% to ethyl acetate and xylene, respectively). Furthermore, P. pentosaceus Ca-4 and L. mesenteroides B-25 featured the highest survival rates (22.4 ± 2.6 and 21.2 ± 1.4%, respectively), after simulated gastrointestinal transit. These results indicated a high level of diversity among the autochthonous bacterial community in fermented fruit and vegetable juices, and demonstrated the potential of these candidate probiotics for applications in fermentation.

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%.

Lactobacillus species identification by amplified ribosomal 16S-23S rRNA restriction fragment length polymorphism analysis

Lactic acid bacteria strains are commonly used for animal and human consumption due to their probiotic properties. One of the major genera used is Lactobacillus, a highly diverse genus comprised of several closely related species. The selection of new strains for probiotic use, especially strains of Lactobacillus, is the focus of several research groups. Accurate identification to species level is fundamental for research on new strains, as well as for safety assessment and quality assurance. The 16S-23S internal transcribed spacer (ITS-1) is a deeply homologous region among prokaryotes that is commonly used for identification to the species level because it is able to acquire and accumulate mutations without compromising general bacterial metabolism. In the present study, 16S-23S ITS regions of 45 Lactobacillus species (48 strains) were amplified and subjected to independent enzymatic digestions, using 12 restriction enzymes that recognise six-base sequences. Twenty-nine species showed unique restriction patterns, and could therefore be precisely identified solely by this assay (64%). This approach proved to be reproducible, allowing us to establish simplified restriction patterns for each evaluated species. The restriction patterns of each species were similar among homologous strains, and to a large extent reflected phylogenetic relationships based on 16S rRNA sequences, demonstrating the promising nature of this region for evolutionary studies.

Identification, technological and safety characterization of Lactobacillus sakei and Lactobacillus curvatus isolated from Argentinean anchovies (Engraulis anchoita)

In this study, the identification and characterization of Lactobacillus previously isolated from fresh anchovies (Engraulis anchoita) are investigated. 16S rDNA partial sequencing assigned all the isolates to belong to the Lactobacillus sakei/curvatus group. Fourteen out of 15 isolates were identified as L. sakei by phenotypic traits: they exhibited catalase activity and fermented melibiose, although only 10 of them hydrolyzed arginine. These results were confirmed by multiplex PCR-based restriction enzyme analysis with HindIII and by restriction fragment length polymorphic (RFLP) analysis of the 16S-23S rDNA intergenic spacer region with TaqI. Among identified isolates, four L. sakei strains and the sole L. curvatus strain showing sensitivity to chloramphenicol, erythromycin and tetracycline and exhibiting high tolerance to NaCl (10-18%) were unable to produce neither dextran nor biogenic amines. Based on technological and safety features, L. sakei SACB₇04 and L. curvatus SACB03a naturally present in fresh anchovies may be promising strains for the development of a starter culture to accelerate and control the fermentation of salt fermented anchovy-based products.

Species and strain identification of lactic acid bacteria using FTIR spectroscopy and artificial neural networks

Lactic acid bacteria (LAB) are a heterogeneous group of micro-organisms with high relevance for fermented food and beverages as well as human and animal health. Identification of LAB is complicated by species richness, a high degree of heterogeneity between species and the presence of very closely related species at the same time. In the present study we developed identification systems based on FTIR spectra and artificial neural networks (ANNs) for species identification of 92 LAB species out of nine genera and strain identification of probiotic and environmental Enterococcus faecium strains used as additives for animal feed. The reference databases established in this work permit reliable identification of LAB with accuracies of 93.2% at species and 97.1% at strain level for Ec. faecium, demonstrating the excellent suitability of FTIR spectroscopy as a technique applicable for simultaneous species and strain identification.

Rapid identification of Lactobacillus nantensis, Lactobacillus spicheri and Lactobacillus hammesii species using species-specific primers

Based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR), an identification tool for rapid differentiation of Lactobacillus nantensis, Lactobacillus spicheri and Lactobacillus hammesii, species isolated recently from French sourdough was developed. The DNA fragments containing ISRs were amplified with primers pairs 16S/p2 and 23S/p7. Clone libraries of the PCR-amplified rDNA with these primers were constructed using a pCR2.1 TA cloning kit and sequenced. The DNA sequences obtained were analyzed and species-specific primers were designed from these sequences. Two PCR amplicons, which were designated small ISR (S-ISR) and large ISR (L-ISR), were obtained for all Lactobacillus species studied. The L-ISR sequence reveale2d the presence of two tRNA genes, tRNAAla and tRNAIle. Species-specific primers designed allowed rapid identification of these species. The specificity of these primers was positively demonstrated as no response was obtained for more than 200 other species tested.

Characterization of new bacteriocinogenic lactic acid bacteria isolated using a medium designed to simulate inhibition of Listeria by Lactobacillus sakei 2512 on meat

Bacteriocinogenic bacteria have been proposed to protect food products from Listeria contamination as bioprotective cultures. Lactobacillus sakei 2512 was demonstrated to inhibit the growth of Listeria on sliced cooked ham by challenge test. A liquid medium simulating ham, BHI5L200, was designed in order to select bioprotective strains for meat protection. Two strains were selected, from the 201 lactic acid bacteria screened, that produced bacteriocins at pH 5.8 in BHI5L200. The first one, Leuconostoc pseudomesenteroides 2733, produced a new bacteriocin which was purified and partially characterized. The second, Lactobacillus curvatus 2711, produced sakacin X and was shown to contain sakacin T and sakacin P structural genes. Co-culture experiments in BHI5L200 demonstrated that growth of Listeria was inhibited by L. sakei 2512 as well as by L. curvatus 2711.

New developments in the study of the microbiota of naturally fermented sausages as determined by molecular methods: A review

The microflora of different types of fermented sausages has been defined by isolation and biochemical identification of the microorganisms commonly found in these products. It is generally agreed that the main microbial groups involved in such products are lactic acid bacteria and coagulase-negative cocci. In addition, and depending on the product, other groups may play a role, such as yeasts and enterococci. Since it appears that the types of microbial groups, or even the specific strains of a given microbial group, that dominate the fermentation, significantly affect the organoleptic profile of the final product, there is an increasing interest in the description of the microbiota that are found in different fermented sausages. More recently, new tools, based on molecular methods, allowing fast and unequivocal identification of strains, isolated from fermented sausages, became available. These methods have been successfully applied and, in general, biochemical and molecular identification compared well. However, new information comes to light when molecular methods are applied to DNA and/or RNA extracted directly from sausages. This approach eliminates problems related to traditional isolation. This review deals with the recent findings and results of the application of molecular methods, in a culture-dependent and culture-independent manner, on the study of the microflora of fermented sausages.

Microbial population dynamics of kimchi, a fermented cabbage product

Lactic acid bacteria are known to perform significant roles in the fermentation of kimchi, a fermented cabbage product. However, the microbial population dynamics inherent to kimchi fermentation remain to be clearly elucidated. In this study, we have characterized the microbial dynamics via the identification of a total of 970 bacterial isolates, representing 15 species of the genera Lactobacillus, Leuconostoc, and Weissella, all of which were primarily identified by PCR-based restriction enzyme analysis. These population dynamics appear to be influenced markedly by fermentation temperature. Distinct biphasic microbial growth was observed with preliminary 2-day incubation at 15 degrees C, conducted before main fermentation at -1 degrees C. Leuconostoc citreum, as well as Leuconostoc gasicomitatum, predominated during the first growth phase, whereas Weissella koreensis predominated during the second phase. By way of contrast, with preliminary 4-day incubation at 10 degrees C, only W. koreensis grew rapidly from the beginning of the process. Therefore, our findings suggest that a short incubation at 15 degrees C enhances the growth of the less psychrophilic Leuconostoc species, including Lc. citreum, thus delaying the growth of the predominant W. koreensis, which is a more adaptive species at -1 degrees C.