Ribotyping of lactobacilli isolated from spoiled beer

Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates

In Japan, during a screening of lactic acid bacteria in spent mushroom substrates, an unknown bacterium was isolated and could not be assigned to any known species. Strain YK48G^T is Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative. The isolate grew in 0-4 % (w/v) NaCl, at 15-37 °C (optimum, 30 °C) and at pH 4.0-8.0 (optimum, pH 6.0). The genomic DNA G+C content of strain YK48G^T was 42.5 mol%. Based on its 16S rRNA gene sequence, strain YK48G^T represented a member of the genus Lentilactobacillus and showed the highest pairwise similarity to Lentilactobacillus rapi DSM 19907^T (97.86 %). Phylogenetic analyses based on amino acid sequences of 466 shared protein-encoding genes also revealed that the strain was phylogenetically positioned in the genus Lentilactobacillus but did not suggest an affiliation with previously described species. The average nucleotide identity and digital DNA-DNA hybridization values between strain YK48G^T and the type strains of phylogenetically related species were 72.2-76.6% and 19.0-21.2 %, respectively, indicating that strain YK48G^T represents a novel species within the genus Lentilactobacillus. Phenotypic data further confirmed the differentiation of strain YK48G^T from other members of the genus Lentilactobacillus. According to the results of the polyphasic characterization presented in this study, strain YK48G^T represents a novel species of the genus Lentilactobacillus, for which the name Lentilactobacillus fungorum sp. nov. is proposed. The type strain is YK48G^T (=JCM 32598^T=DSM 107968^T).

Lactobacillus buchneri subsp. silagei subsp. nov., isolated from rice grain silage

Two Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacteria, designated strains SG162^T and NK01, were isolated from Japanese rice grain silage and total mixed ration silage, respectively. They were initially identified as Lactobacillus buchneri based on the 16S rRNA gene sequence similarities. However, the two strains were separated into a distinct clade from L. buchneri DSM 20057^T (=JCM 1115^T) through whole-genome sequence-based characterization, forming an infraspecific subgroup together with strains CD034 and S42, whose genomic sequences were available in the public sequence database. Strains within the subgroup shared 99.4-99.7 % average nucleotide identity (ANI) and 97.5-99.0 % digital DNA-DNA hybridization (dDDH) with each other, albeit 96.9-97.0 % ANI and 76.0-76.6 % dDDH against DSM 20057^T. Strains SG162^T and NK01 could utilize more substrates as sole carbon sources than DSM 20057^T, potentially owing to the abundance of genes involved in carbon metabolism, especially the Entner-Doudoroff pathway. The inability of γ-aminobutyric acid (GABA) production was evidenced by the lack of glutamate decarboxylase and glutamate/GABA antiporter genes in the new subgroup strains. Strain SG162^T grew at 10-45 °C (optimum, 30 °C), pH 3.5-8.0, and 0-8 % (w/v) NaCl. Its genomic DNA G+C content was 44.1 mol%. The predominant fatty acids were C_16 : 0, C_19 : 0 cyclo ω8c, and summed feature 8. On the basis of the polyphasic characterization findings, strains SG162^T and NK01 represent a novel subspecies of L. buchneri, for which the name Lactobacillus buchneri subsp. silagei subsp. nov. is proposed. The type strain is SG162^T (=JCM 32599^T=DSM 107969^T), and strains CD034 and S42 are also transferred to L. buchneri subsp. silagei.

Genotypic and phenotypic characterization of Lactobacillus plantarum strains isolated from Thai fermented fruits and vegetables

Ten Lactobacillus strains originally isolated from Thai fruits and vegetables fermentation were characterized by various phenotypic and genotypic methods. The phenotypic analysis using the method of carbohydrate fermentation patterns (API50CHL) revealed that the isolates belonged to the L. plantarum species. This was further confirmed by 16S rRNA gene sequencing. Multilocus sequence typing (MLST) revealed a strongly clonal population structure and a low genotypic diversity in this collection. However, the analyzed L. plantarum population demonstrated a higher level of diversification after API50CHL that reflects the role of available carbohydrate sources in bacterial evolution. Our results support the postulate that a combination of conventional biochemical and genotyping methods allows a thorough characterization and identification of isolates. We propose that genotypic characterization could be complemented by biochemical characterization to discriminate L. plantarum strains.

Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

AIMS

The design and evaluation of an oligonucleotide microarray in order to detect and identify viable bacterial species that play a significant role in beer spoilage. These belong to the species of the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus.

METHODS AND RESULTS

Oligonucleotide probes specific to beer spoilage bacteria were designed. In order to detect viable bacteria, the probes were designed to target the intergenic spacer regions (ISR) between 16S and 23S rRNA. Prior to hybridization the ISR were amplified by combining reverse transcriptase and polymerase chain reactions using a designed consenus primer. The developed oligonucleotide microarrays allows the detection of viable beer spoilage bacteria.

CONCLUSIONS

This method allows the detection and discrimination of single bacterial species in a sample containing complex microbial community. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non growing bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage micro-organisms within a mixed population.

Identification of lactobacilli by pheS and rpoA gene sequence analyses

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.

RNA-based sandwich hybridisation method for detection of lactic acid bacteria in brewery samples

Recently we showed the applicability and sensitivity of the RNA-based sandwich hybridisation assay (SHA) for detection of gram-negative cells in environmental samples [Leskelä, T., Tilsala-Timisjärvi, A., Kusnetsov, J., Neubauer, P., Breitenstein, A., 2005. Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. J. Microbiol. Met. 62, 167-179.]. In this study the aim was to test and optimise this method for the detection of gram-positive cells from brewery yeast slurries that contain up to 10(9) yeast cells/ml. Eleven new oligonucleotide probes were designed for group-specific detection of different beer-spoiling lactic acid bacteria of the genera Lactobacillus and Pediococcus. Functionality of the designed probes was shown by testing individual and paired probes using in vitro transcribed 16S rRNA and crude cell extracts as samples. Various simple and fast cell disruption methods were evaluated for the efficient disruption of lactobacilli and pediococci. The applicability of the designed oligonucleotide probes and the SHA for detection of brewery contaminants was demonstrated using both artificial and actual yeast slurry samples from brewery fermentation tanks with either fluorimetric readout or an electric biochip analyser.

Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains

Lactobacillus plantarum is a species of considerable industrial and medical interest. To date, the lack of reliable molecular methods for definite identification at strain level has hindered studies of the population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in six housekeeping loci to determine the genetic relationship among isolates. The MLST system was established using 16 L. plantarum strains that were also characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rDNA intergenic spacer region (ISR). Ribotyping grouped the strains into four groups; however, RFLP analysis of the ISRs showed no differences in the strains analysed. In contrast, MLST had a good discriminatory ability. The sequence analysis of the six genes showed 14 different allelic combinations, with 12 of them represented by only one strain. By using this MLST approach we were able to confirm the identity of two strains deposited in the Spanish Type Culture Collection as different strains. Phylogenetic analysis indicated a panmictic population structure of L. plantarum and split decomposition analysis indicated that recombination plays a role in creating genetic heterogeneity in L. plantarum. As MLST allows precise identification, and easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be useful for the identification of valuable L. plantarum strains.

Detection of resistance of lactic acid bacteria to a mixture of the hop analogue compounds tetrahydroiso-alpha-acids by noninvasive measurement of intracellular pH

AIMS

To examine the resistance of beer isolates of lactic acid bacteria (LAB) towards a mixture of tetrahydroiso-alpha-acids (Tetra) by growth experiments as well as by measurement of intracellular pH.

METHODS AND RESULTS

Beer LAB isolates were identified to species level by SDS-PAGE of whole-cell proteins. Beer isolates of Lactobacillus brevis showed better ability for growth in the presence of Tetra than nonbeer isolates of the L. brevis or other species of LAB including beer and nonbeer isolates. The antimicrobial effect of Tetra was also examined by noninvasive measurement of intracellular pH by fluorescence ratio imaging microscopy for selected beer isolates of L. brevis and Pediococcus inopinatus. Strains of L. brevis showing limited decrease of intracellular pH during exposure to Tetra also showed better ability for growth in the presence of these compounds as well as in commercial beer products.

CONCLUSIONS

It was possible to apply a method for noninvasive measurement of intracellular pH to predict the resistance of beer spoilage LAB towards the Tetra hop analogue compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated the usability of a new rapid method for detecting hop-resistant variants of known beer spoilage LAB species.