Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Effects of pH and sugar supplements on bacteriocin-like inhibitory substance production by Pediococcus pentosaceus

To improve bacteriocin-like inhibitory substance (BLIS) production by Pediococcus pentosaceus ATCC 43200, the influence of pH as well as the addition of sugars-either prebiotic (inulin) or not (sucrose)-on its metabolism were investigated. This strain was grown at pH 5.0 or 6.0 either in glucose-based MRS medium (control) or after addition of 0.5, 1.0 or 1.5% (w/w) sucrose and inulin (GSI-MRS) in the same percentages. In the control medium at pH 5.0, cell mass concentration after 48 h of fermentation (X_max = 2.26 g/L), maximum specific growth rate (µ_max = 0.180 h^-1) and generation time (T_g = 3.84 h) were statistically coincident with those obtained in supplemented media. At pH 6.0 some variations occurred in these parameters between the control medium (X_max = 2.68 g/L; µ_max = 0.32 h^-1; T_g = 2.17 h) and the above supplemented media (X_max = 1.90, 2.52 and 1.86 g/L; µ_max = 0.26, 0.33 and 0.32 h^-1; T_g = 2.62, 2.06 and 2.11 h, respectively). Lactate production was remarkable at both pH values (13 and 16 g/L) and improved in all supplemented media, being 34 and 54% higher than in their respective control media, regardless of the concentration of these ingredients. Cell-free supernatant of the fermented control medium at pH 5.0 displayed an antimicrobial activity against Enterococcus 101 5.3% higher than that at pH 6.0 and even 20% higher than those of all supplemented media, regardless of the concentration of supplements. BLIS production was favored either at pH 5.0 or in the absence of any additional supplements, which were able, instead, to stimulate growth and lactate production by P. pentosaceus.

The Interior Surfaces of Wooden Barrels Are an Additional Microbial Inoculation Source for Lambic Beer Production

Traditional lambic beer production takes place through wort inoculation with environmental air and fermentation and maturation in wooden barrels. These wooden casks or foeders are possible additional inoculation sources of microorganisms for lambic worts. To date, however, these lambic barrels have been examined only with culture-dependent techniques, thereby missing a portion of the microorganisms present. Moreover, the effects of the cleaning procedures (involving high-pressure water and/or fumigation) and the barrel type on the microbial community structures of the interior surfaces of wooden lambic barrels were unclear. The culture-dependent plating and culture-independent amplicon sequencing of swab samples obtained from the interior surfaces of different wooden casks and foeders used for traditional lambic beer production in Belgium revealed that the microbial compositions of these surfaces differed statistically throughout the barrel-cleaning procedures applied. At the end of the cleaning procedures, amplicon sequencing still detected fermentation- and maturation-related microorganisms, although only a few colonies were still detectable using culture-dependent methods. It is possible that some of the surviving microorganisms were missed due to the presence of many of these cells in a viable but not culturable state and/or engrained deeper in the wood. These surviving microorganisms could act as an additional inoculation source, besides brewery air and brewery equipment, thereby helping to establish a stable microbial community in the wort to diminish batch-to-batch variations in fermentation profiles. Furthermore, the microbial compositions of the interior barrel surfaces differed statistically based on the barrel type, possibly reflecting different characteristics of the lambic barrels in terms of age, wood thickness, and wood porosity.IMPORTANCE Although the coolship step is generally regarded as the main contributor to the spontaneous inoculation by environmental air of fresh worts for lambic beer production, it is known that microorganisms often associate with specific surfaces present in a brewery. However, knowledge about the association of microorganisms with the interior surfaces of wooden lambic barrels is limited. To clarify the role of casks and foeders as additional microbial inoculation sources, it was important to determine the influence of the barrel characteristics and the cleaning procedures on the microbial communities of the interior barrel surfaces. Moreover, this helped to elucidate the complex spontaneous lambic beer fermentation and maturation process. It will allow further optimization of the lambic beer production process, as well as the wooden-barrel-cleaning procedures applied.

Antimicrobial activity of bacteriocin-like inhibitory substance produced by Pediococcus pentosaceus: from shake flasks to bioreactor

Bacteriocins are peptides produced by various species of bacteria, especially lactic acid bacteria (LAB), which have a large spectrum of action against spoilage bacteria and foodborne pathogens. However, when not entirely characterized, they are alternatively called bacteriocin-like inhibitory substances (BLIS). Pediococcus pentosaceus ATCC 43200 grew and produced BLIS optimally when cultivated anaerobically in bioreactor for 24 h at 30 °C and 200 rpm in De Man, Rogosa and Sharp (MRS) medium supplemented with 1.5% peptone. Under such optimal conditions, the cell mass concentration (3.41 g/L) was 66% higher, the generation time (1.28 h) 38% shorter and the BLIS activity against different indicator strains significantly higher than in MRS medium without any supplement taken as a control, and the exponential phase started 4 h before. The agar diffusion method showed BLIS inhibition halos against LAB strains with diameter in the range 11.0-19.5 mm and specific areas between 377.1 and 2654.6 mm²/mL, while BLIS activity against Listeria strains was better quantified by the liquid medium assay that showed, for the fermented broth without any dilution, 100 and 50% inhibition of Listeria innocua and Listeria seeligeri growth, respectively. These results highlight the potential of P. pentosaceus BLIS as a natural antimicrobial for application in the food industry.

Stimulating Effects of Sucrose and Inulin on Growth, Lactate, and Bacteriocin Productions by Pediococcus pentosaceus

Sucrose and inulin, when combined with glucose, behaved as stimulating agents of bacteriocin production by Pediococcus pentosaceus ATCC 43200. When such microbial strain was grown in glucose-based Man, Rogosa, and Sharpe (MRS) medium, without any additional supplement, it showed higher maximum cell concentration (2.68 ± 1.10 g/L) and longer generation time (2.17 ± 0.02 h), but lower specific growth rate (0.32 ± 0.01 h^-1) than in the same medium supplemented with 1.0% of both ingredients (2.53 ± 1.10 g/L, 1.60 ± 0.05 h and 0.43 ± 0.02 h^-1, respectively). Glucose replacement by sucrose or inulin almost completely suppressed growth, hence confirming that it is the preferred carbon source for this strain. Qualitatively, similar results were observed for lactate production, which was 59.8% higher in glucose-based medium. Enterococcus and Listeria strains were sensitive to bacteriocin, whose antimicrobial effect after 8 h increased from 120.25 ± 0.35 to 144.00 ± 1.41 or 171.00 ± 1.41 AU/mL when sucrose or inulin was added to the glucose-based MRS medium. Sucrose and inulin were also able to speed up P. pentosaceus growth in the exponential phase.

A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology

Lactobacilli are used widely in food, feed, and health applications. The taxonomy of the genus Lactobacillus, however, is confounded by the apparent lack of physiological markers for phylogenetic groups of lactobacilli and the unclear relationships between the diverse phylogenetic groups. This study used the core and pan-genomes of 174 type strains of Lactobacillus and Pediococcus to establish phylogenetic relationships and to identify metabolic properties differentiating phylogenetic groups. The core genome phylogenetic tree separated homofermentative lactobacilli and pediococci from heterofermentative lactobacilli. Aldolase and phosphofructokinase were generally present in homofermentative but not in heterofermentative lactobacilli; a two-domain alcohol dehydrogenase and mannitol dehydrogenase were present in most heterofermentative lactobacilli but absent in most homofermentative organisms. Other genes were predominantly present in homofermentative lactobacilli (pyruvate formate lyase) or heterofermentative lactobacilli (lactaldehyde dehydrogenase and glycerol dehydratase). Cluster analysis of the phylogenomic tree and the average nucleotide identity grouped the genus Lactobacillus sensu lato into 24 phylogenetic groups, including pediococci, with stable intra- and intergroup relationships. Individual groups may be differentiated by characteristic metabolic properties. The link between phylogeny and physiology that is proposed in this study facilitates future studies on the ecology, physiology, and industrial applications of lactobacilli.

Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis

A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999(T), was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999(T) (=CCUG 54535(T)=CRL 776(T)) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.

Identification of lactic acid bacteria from fermented tea leaves (miang) in Thailand and proposals of Lactobacillus thailandensis sp. nov., Lactobacillus camelliae sp. nov., and Pediococcus siamensis sp. nov

Eighteen rod-shaped homofermentatives, six heterofermentatives, and a coccal homofermentative lactic acid bacteria were isolated from fermented tea leaves (miang) produced in the northern part of Thailand. The isolates were placed in a monophyletic cluster consisting of Lactobacillus and Pediococcus species. They were divided into seven groups by phenotypic and chemotaxonomic characteristics, DNA-DNA similarity, and 16S rRNA gene sequences. Groups I to VI belonged to Lactobacillus and Group VII to Pediococcus. All of the strains tested produced DL-lactic acid but those in Group IV produced L-lactic acid. The strains tested in Groups I, II and V had meso-diaminopimelic acid in the cell wall. Six strains in Group I were identified as Lactobacillus pantheris; five strains in Group II as Lactobacillus pentosus; and four strains in Group V as Lactobacillus suebicus. Two strains in Group VI showed high DNA-DNA similarity for each other and MCH4-2 was closest to Lactobacillus fermentum CECT 562(T) with 99.5% of 16S rRNA gene sequence similarity. Five strains in Group III are proposed as Lactobacillus thailandensis sp. nov., and MCH5-2(T) (BCC 21235(T)=JCM 13996(T)=NRIC 0671(T)=PCU 272(T)) is the type strain which has 49 mol% G+C of DNA. Two strains in Group IV are proposed as Lactobacillus camelliae sp. nov., and the type strain is MCH3-1(T) (BCC 21233(T)=JCM 13995(T)=NRIC 0672(T)=PCU 273(T)) which has 51.9 mol% G+C of DNA. One strain in Group VII is proposed as Pediococcus siamensis sp. nov., and MCH3-2(T) (BCC 21234(T)=JCM 13997(T)=NRIC 0675(T)=PCU 274(T)) is the type strain which has 42 mol% G+C of DNA.

Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar

Two novel Pediococcus strains, Z-9T and Z-17, were isolated from a distilled-spirit-fermenting cellar in Hebei Province, China. The cells were Gram-positive, non-spore-forming, non-motile cocci and occurred in pairs or tetrads. The strains were facultatively anaerobic and produced only lactic acid [d(−) and l(+) isomers in the ratio 50 : 50] from glucose fermentation. Catalase activity was not present. Both strains were able to grow in 6.5 % ethanol and at pH 3.5, but not in 4 % NaCl. The mean genomic G+C content of the two strains was 39.5±0.5 mol% (39 mol% for the type strain, Z-9T). The levels of 16S rRNA gene sequence similarity between the two novel strains and related species of the genus Pediococcus ranged from 98.3 to 98.7 %. The levels of DNA–DNA relatedness between strain Z-9T and the phylogenetically closely related pediococci Pediococcus damnosus LMG 11484T, Pediococcus inopinatus LMG 11409T, Pediococcus parvulus LMG 11486T and Pediococcus cellicola LMG 22956T were 14.6, 33, 28.7 and 16.8 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analyses, a novel species, Pediococcus ethanolidurans sp. nov., is proposed, with strain Z-9T (=AS 1.3889T=LMG 23354T) as the type strain.