Phage AR1 is similar to phage T4 in several essential genes but differs in host range. AR1 infects various isolates of Escherichia coli O157:H7 but does not infect K-12 strains that are commonly infected by T4. We report here the determinants that confer this infection specificity. In T-even phages, gp37 and gp38 are components of the tail fiber that are critical for phage-host interaction. The counterparts in AR1 may be similarly important and, therefore, were characterized. The AR1 gp37 has a sequence that differs totally from those of T2 and T4, except for a short stretch at the N terminus. The gp38 sequence, however, has some conservation between AR1 and T2 but not between AR1 and T4. The sequences that are most closely related to the AR1 gp37 and gp38 are those of phage Ac3 in the T2 family. To identify the AR1-specific receptor, E. coli O157:H7 was mutated by Tn10 insertion and selected for an AR1-resistant phenotype. A mutant so obtained has an insertion occurring at ompC that encodes an outer membrane porin. To confirm the role of OmpC in the AR1 infection, homologous replacement was used to create an ompC disruption mutant (RM). When RM was complemented with OmpC originated from an O157:H7 strain, but not from K-12, its AR1 susceptibility was fully restored. Our results suggest that the host specificity of AR1 is mediated at least in part through the OmpC molecule.
A total of 102 lactic acid bacteria (LAB) were isolated from three different coffee farms in Taiwan. These isolates were classified and identified by the restriction fragment length polymorphism analysis and sequencing of 16S ribosomal DNA. Heterofermentative Leuconostoc, and Weissella species were the most common LAB found in two farms located at an approximate altitude of 800 m. Lactococcus lactis subsp. lactis was the most common LAB found in the remaining farm was located at an approximate altitude of 1,200 m. It is therefore suggested that the altitude and climate may affect the distribution of LAB. On the basis of phylogenetic analysis, two strains included in the genera Enterococcus were considered as two potential novel species or subspecies. In addition, a total of 34 isolates showed the antifungal activity against Aspergillus flavus. Moreover, seven Lactococcus lactis subsp. lactis strains and one Enterococcus faecalis strain were found to have bacteriocin-like inhibitory substance-producing capability. These results suggest that various LAB are associated with fresh coffee cherries in Taiwan. Some of the isolates found in this study showed potential as antifungal agents.
Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at .
Lactococcus formosensis sp. nov., a lactic acid bacterium isolated from yan-tsai-shin (fermented broccoli stems) The Institute of Enology and Viticulture, University of Yamanashi, 1-13-1, Kitashin, Kofu, Yamanashi 400-0005, Japan A coccal-shaped organism, designated 516 T , was isolated from yan-tsai-shin (fermented broccoli stems), a traditional fermented food in Taiwan. 16S rRNA gene sequencing results showed that strain 516 T had 98.9 % sequence similarity to that of the type strain Lactococcus garvieae NBRC 100934 T . Comparison of three housekeeping genes, rpoA, rpoB and pheS, revealed that strain 516 T was well separated from Lactococcus garvieae NBRC 100934 T . DNA-DNA hybridization studies indicated that strain 516 T had low DNA relatedness with Lactococcus garvieae NBRC 100934 T (46.1 %). The DNA G+C content of strain 516 T was 38.1 mol% and the major fatty acids were C 16 : 0 (22.7 %), C 19 : 0 cyclo v8c (17.9 %) and summed feature 7 (29.0 %). Based on the evidence, strain 516 T represents a novel species of the genus Lactococcus, for which the name Lactococcus formosensis sp. nov. is proposed. The type strain is 516 T (5NBRC 109475 T 5BCRC 80576 T ).
One coccal strain, designated 0905C15 T , was isolated from fresh cummingcordia, which is the main ingredient of pobuzihi (fermented cummingcordia), a traditional fermented food in Taiwan. 16S rRNA gene sequencing results showed that strain 0905C15 T had 98.22-98.82 % sequence similarity to that of the type strains of four Lactococcus lactis subspecies (L. lactis subsp. lactis BCRC 12312 T , L. lactis subsp. cremoris BCRC 12586 T , L. lactis subsp. hordniae BCRC 80474 T and L. lactis subsp. tructae BCRC 80475 T ). Comparison of two housekeeping genes, recA and rpoB, revealed that strain 0905C15 T was well separated from the reference strains of the genus Lactococcus. DNA-DNA hybridization studies indicated that strain 0905C15 T had low DNA relatedness to the four Lactococcus lactis subspecies (9.7-15.24 %). The DNA G+C content of strain 0905C15 T was 39.6 mol %. Based on the evidence, strain 0905C15 T represents a novel species of the genus Lactococcus, for which the name Lactococcus taiwanensis sp. nov. is proposed. The type strain is 0905C15 T (5NBRC 109049 T 5BCRC 80460 T ).Lactic acid bacteria (LAB) are widely distributed in traditional fermented foods in Taiwan. In our previous study, we isolated a novel species of the genus Lactobacillus named Lactobacillus pobuzihii sp. nov. from pobuzihi (fermented cummingcordia) (Chen et al., 2010). In order to obtain more information on LAB diversity in pobuzihi and fresh cummingcordia, isolation of LAB was performed and a total of 196 LAB strains were isolated (Chen et al., 2013). All isolates were identified based on their phenotypic and phylogenetic characteristics. Phylogenetic analyses, based on 16S rRNA gene sequences, initially placed strain 0905C15 T within the species Lactococcus lactis.
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