A comparative study and phage typing of silage-making Lactobacillus bacteriophages

Doi, Kunio; Zhang, Ye; Nishizaki, Yousuke; Umeda, Akira; Ohmomo, Sadahiro; Ogata, Seiya

doi:10.1016/s1389-1723(03)80054-3

Cited by 15 publications

(10 citation statements)

References 36 publications

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“…Pediococcus and L. plantarum strains are often found in the same ecological niches (cucumber fermentation, silage inoculants) (34,73); thus, these comparative analyses support the notion that coexistence in the same environment can lead to the exchange of genetic elements (45). Others have shown that phages of L. plantarum were able to infect strains of other bacterial species isolated from the same habitat (10,20,45), although this was not tested here. L. plantarum myophage LP65 unexpectedly infected Carnobacterium strains associated with fermented meat (10), and some L. plantarum phages isolated from silage and sauerkraut were able to infect Lactobacillus pentosus and Lactobacillus brevis strains (20,45).…”

Section: Methodssupporting

confidence: 57%

“…Others have shown that phages of L. plantarum were able to infect strains of other bacterial species isolated from the same habitat (10,20,45), although this was not tested here. L. plantarum myophage LP65 unexpectedly infected Carnobacterium strains associated with fermented meat (10), and some L. plantarum phages isolated from silage and sauerkraut were able to infect Lactobacillus pentosus and Lactobacillus brevis strains (20,45). On the other hand, Table 3.…”

Section: Methodsmentioning

confidence: 96%

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Characterization of Two Virulent Phages of Lactobacillus plantarum

Marcó

Garneau

Tremblay

et al. 2012

Appl Environ Microbiol

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We characterized two Lactobacillus plantarum virulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eight L. plantarum strains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least two L. plantarum strains, LMG9211 and WCSF1. The linear double-stranded DNA genome of the pac-type phage B1 had 38,002 bp, a G؉C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that of Pediococcus damnosus phage clP1 and 77% identity with that of L. plantarum phage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of the cos-type phage B2 had 80,618 bp, a G؉C content of 36.9%, and 127 ORFs with similarities to those of Bacillus and Lactobacillus strains as well as phages. Some phage B2 genes were similar to ORFs from L. plantarum phage LP65 of the Myoviridae family. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

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Section: Methodssupporting

confidence: 57%

Section: Methodsmentioning

confidence: 96%

Characterization of Two Virulent Phages of Lactobacillus plantarum

Marcó

Garneau

Tremblay

et al. 2012

Appl Environ Microbiol

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“…S7). Moreover, although the quantitative value of nestedness did decrease in one case, that particular study (39) was, in fact, still highly nested and marginally significant at a P = 0.067 level. We also recalculated modularity for the modified matrices and found that 9 of 38 are modular compared with 6 of 38 in the original analysis (SI Appendix, Fig.…”

Section: Addressing Sample Composition Biases As Potential Drivers Ofmentioning

confidence: 77%

Statistical structure of host–phage interactions

Flores

Meyer

Valverde

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

297

356

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Interactions between bacteria and the viruses that infect them (i.e., phages) have profound effects on biological processes, but despite their importance, little is known on the general structure of infection and resistance between most phages and bacteria. For example, are bacteria-phage communities characterized by complex patterns of overlapping exploitation networks, do they conform to a more ordered general pattern across all communities, or are they idiosyncratic and hard to predict from one ecosystem to the next? To answer these questions, we collect and present a detailed metaanalysis of 38 laboratory-verified studies of hostphage interactions representing almost 12,000 distinct experimental infection assays across a broad spectrum of taxa, habitat, and mode of selection. In so doing, we present evidence that currently available host-phage infection networks are statistically different from random networks and that they possess a characteristic nested structure. This nested structure is typified by the finding that hard to infect bacteria are infected by generalist phages (and not specialist phages) and that easy to infect bacteria are infected by generalist and specialist phages. Moreover, we find that currently available host-phage infection networks do not typically possess a modular structure. We explore possible underlying mechanisms and significance of the observed nested host-phage interaction structure. In addition, given that most of the available hostphage infection networks examined here are composed of taxa separated by short phylogenetic distances, we propose that the lack of modularity is a scale-dependent effect, and then, we describe experimental studies to test whether modular patterns exist at macroevolutionary scales.bacteriophage | complex networks | ecology | evolution | nestedness

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“…It was difficult to distinguish between L. plantarum and its related species, L. pentosus , and between L. casei and L. rhamonsus. Although we applied phage typing to these closely related LAB strains (Doi et al 2003), we were unable to do a complete identification. We therefore attempted to identify the isolated LABs by comparing the sequences of the 16S-23S rRNA ITS and the 16S rRNA V2-V3 region.…”

Section: Discussionmentioning

confidence: 99%

Identification of thermo tolerant lactic acid bacteria isolated from silage prepared in the hot and humid climate of Southwestern Japan

et al. 2013

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To develop high-quality silage starters adapted to hot and humid weather, 12 LAB isolates from silage produced in Kyushu and Okinawa, Japan were characterized based on their morphological features, growth curves and sugar utilization. In addition, the nucleotide sequences of the V2-V3 region of their 16S rRNA genes and the 16S-23S rRNA intergenic spacer (ITS) regions were determined. The isolates were also subjected to RAPD-PCR analysis, DNA-DNA hybridization, G+C content analysis and immuno-identification using species-specific monoclonal antibodies and SDS-PAGE profiling. Nearly all of the isolates exhibited high thermotolerance and rapid growth. Combining ITS sequence analysis, RAPD-PCR and immuno-identification enabled rapid and accurate identification of closely related LAB strains that other methods failed to appropriately differentiate; for example, L. plantarum was distinguished from L. pentosus, and L. casei was distinguished from L. rhamonsus. Using the aforementioned techniques, the isolated strains were identified as L. plantarum, L. rhamonsus, L. rapi, Pediococcus pentosaceus and P. lolii. Our findings also showed that there is greater diversity among thermophilic LABs in silage prepared in a hot and humid environment.

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A comparative study and phage typing of silage-making Lactobacillus bacteriophages

Cited by 15 publications

References 36 publications

Characterization of Two Virulent Phages of Lactobacillus plantarum

Characterization of Two Virulent Phages of Lactobacillus plantarum

Statistical structure of host–phage interactions

Identification of thermo tolerant lactic acid bacteria isolated from silage prepared in the hot and humid climate of Southwestern Japan

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