Antigenic and biochemical characterization of bovine rotavirus V1005, a new member of rotavirus serotype 10

Bovine rotavirus (BRV) V1005 is serologically distinct from rotavirus serotypes 1, 2, 3, 4, 5, 6, 8 and 9. BRV V1005 showed cross-reactions with BRV B223, the American prototype of serotype 10 rotavirus, and with BRV E4049, a British serotype 10 isolate. BRV V1005 was, however, not neutralized by four monoclonal antibodies directed against VP7 of BRV B223. Two-way cross-reactions were observed between BRV V1005 and a reassortant rotavirus containing the VP4 from BRV UK. In addition the major tryptic cleavage product of VP4, VP5*, from BRV V1005 is indistinguishable by peptide mapping and its isoelectric point from the homologous protein of BRV UK, but is clearly different from VP5* of BRV NCDV. The peptide map of VP7 from BRV V1005 differed from that obtained for VP7 of BRV U

Transcription Analysis of Streptococcus thermophilus Phages in the Lysogenic State

AbstractThe transcription of prophage genes was studied in two lysogenic Streptococcus thermophilus cells by Northern blot and primer-extension experiments. In the lysogen containing the cos-site phage Sfi21 only two gene regions of the prophage were transcribed. Within the lysogeny module an 1.6-kb-long mRNA started at the promoter of the phage repressor gene and covered also the next two genes, including a superinfection exclusion (sie) gene. A second, quantitatively more prominent 1-kb-long transcript was initiated at the promoter of the sie gene. Another prophage transcript of 1.6-kb length covered a group of genes without database matches that were located between the lysin gene and the right attachment site. The rest of the prophage genome was transcriptionally silent. A very similar transcription pattern was observed for a S. thermophilus lysogen containing the pac-site phage O1205 as a prophage. Prophages from pathogenic streptococci encode virulence genes downstream of the lysin gene. We speculate that temperate phages from lactic streptococci also encode nonessential phage genes (“lysogenic conversion genes”) in this region that increase the ecological fitness of the lysogen to further their own evolutionary success. A comparative genome analysis revealed that many temperate phages from low GC content Gram-positive bacteria encode a variable number of genes in that region and none was linked to known phage-related function. Prophages from pathogenic streptococci encode toxin genes in this region. In accordance with theoretical predictions on prophage–host genome interactions a prophage remnant was detected in S. thermophilus that had lost most of the prophage DNA while transcribed prophage genes were spared from the deletion process

Widespread distribution of a group I Intron and Its three deletion derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages.

Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysingene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variantform of the intron resulting from three distinct deletion events located in the intron-harbored open readingframe (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than thesurrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleasesfound in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genesrevealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere inthe phage or S. thermophilus bacterial genomes. Folding of the intron RNA revealed secondary structureelements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be foldedinto two stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, aconserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in theP8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequencesimilarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobacillus,and Bacillus phages

In vitro activity of commercial probiotic Lactobacillus strains against uropathogenic Escherichia coli

Urinary tract infection (UTI) is one of the most prevalent infections in humans. In ≥80% of cases, the etiologic agents are strains of uropathogenic Escherichia coli (UPEC), which commonly reside in the gastrointestinal tract. Lactobacilli have been shown to prevent UTI reoccurrence by restoring the urogenital microbiota when administered vaginally or orally. The goal of this study was to determine if commercial probiotic Lactobacillus spp. reduce or clear UPEC in vitro. Results show that it is likely that lactobacilli may, in addition to restoring a healthy urogenital microbiota through acidification of their environment, also displace adhering UPEC and cause a reduction of infectio

Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants

The species Bifidobacterium longum currently comprises four subspecies: B. longum subsp. longum, B. longum subsp. infantis, B. longum subsp. suis and B. longum subsp. suillum. Recently, several studies on B. longum suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to B. longum subsp. suis DSM 20210T and B. longum subsp. suillum JCM1995T [average nucleotide identity (ANI) of 98.1%) while showed an ANI of 96.5% with both B. longum subsp. infantis and B. longum subsp. longum. The current work describes five novel additional B. longum strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species B. longum with B. longum subsp. suis and B. longum subsp. suillum as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to B. longum subsp. infantis, show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies, B. longum subsp. suis and B. longum subsp. suillum. Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name Bifidobacterium longum subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T =CCOS 2034T ), is proposed

DNA-Binding Activity of the Streptococcus thermophilus Phage Sfi21 Repressor

The cloned Streptococcus thermophilus phage Sfi21 repressor open reading frame (orf) 127 gp protects a cell against superinfection with the homologous temperate, but not against virulent phages. As demonstrated by DNase protection assay and gel shift experiments, the repressor binds to a 25-bp operator site located upstream of the repressor gene. A second sequence-related operator was identified 265 bp apart at the 3?-end of orf 75, the topological equivalent of a cro repressor gene. The replacement of a bp at the middle or at the right side of the operator decreased substantially the affinity of the repressor for the operator. In gel shift assays, the 75 gp did not bind DNA from the genetic switch region. However, when increasing amounts of orf 75 gp containing cell extracts were added to orf 127 gp containing cell extracts, the repressor could no longer bind its operator site

The site-specific Integration system of the temperate Streptococcus thermophiles Bacteriophage φSfi21

The temperate bacteriophage fSfi21 integrates its DNA into the chromosome of Streptococcus thermophilus strains viasite-specific recombination. Nucleotide sequencing of the attachment sites identified a 40-bp identity region which surprisinglyoverlaps both the 18-terminal bp of the phage integrase gene and the 11-terminal bp of a host tRNAArg gene. A 2.4-kb phageDNA segment, covering attP, the phage integrase, and a likely immunity gene contained all the genetic information for faithfulintegration of a nonreplicative plasmid into the attB site. A deletion within the int gene led to the loss of integration proficiency.A number of spontaneous deletions were observed in plasmids containing the 2.4-kb phage DNA segment. The deletionsites were localized to the tRNA side of the identity region and to phage or vector DNA with 3- to 6-bp-long repeats fromthe border region. A similar type of deletion was previously observed in a spontaneous phage mutant

Comparative Genomics of the T4-Like Escherichia coli Phage JS98: Implications for the Evolution of T4 Phages

About 130 kb of sequence information was obtained from the coliphage JS98 isolated from the stool of a pediatric diarrhea patient in Bangladesh. The DNA shared up to 81% base pair identity with phage T4. The most conserved regions between JS98 and T4 were the structural genes, but their degree of conservation was not uniform. The head genes showed the highest sequence conservation, followed by the tail, baseplate, and tail fiber genes. Many tail fiber genes shared only protein sequence identity. Except for the insertion of endonuclease genes in T4 and gene 24 duplication in JS98, the structural gene maps of the two phages were colinear. The receptor-recognizing tail fiber proteins gp37 and gp38 were only distantly related to T4, but shared up to 83% amino acid identity to other T6-like phages, suggesting lateral gene transfer. A greater degree of variability was seen between JS98 and T4 over DNA replication and DNA transaction genes. While most of these genes came in the same order and shared up to 76% protein sequence identity, a few rearrangements, insertions, and replacements of genes were observed. Many putative gene insertions in the DNA replication module of T4 were flanked by intron-related endonuclease genes, suggesting mobile DNA elements. A hotspot of genome diversification was located downstream of the DNA polymerase gene 43 and the DNA binding gene 32. Comparative genomics of 100-kb genome sequence revealed that T4-like phages diversify more by the accumulation of point mutations and occasional gene duplication events than by modular exchanges