Draft Genome Sequence of Probiotic Strain Lactobacillus rhamnosus R0011

Tompkins, Thomas A.; Barreau, Guillaume; Carvalho, Vanessa G. de

doi:10.1128/jb.06584-11

Cited by 9 publications

(6 citation statements)

References 6 publications

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“…To undertake our in silico scrutinization of the “regulatory DNA” for the fimbrial spaFED operon, we compiled a multiple sequence alignment encompassing an arbitrarily chosen ∼600-nucleotide (nt) length immediately upstream of the spaF locus ( Figure S1 ). For this, we used the corresponding sequence data from the genomes ( n = 13) of several different L. rhamnosus strains that had become available in public databases (either published [20] – [23] or not published) or through our own earlier nucleotide sequencing [11] . Immediately evident from a cursory inspection of this sequence alignment is the minimal variability within the first ∼140-nt segment directly upstream the coding region of the spaF gene within the spaFED operon.…”

Section: Resultsmentioning

confidence: 99%

Phenotypical Analysis of the Lactobacillus rhamnosus GG Fimbrial spaFED Operon: Surface Expression and Functional Characterization of Recombinant SpaFED Pili in Lactococcus lactis

et al. 2014

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A noticeable genomic feature of many piliated Gram-positive bacterial species is the presence of more than one pilus-encoding operon. Paradigmatically, the gut-adapted Lactobacillus rhamnosus GG strain contains two different fimbrial operons in its genome. However, whereas one of these operons (called spaCBA) is encoding for the functionally mucus-/collagen-binding SpaCBA pilus, for the other operon (called spaFED) any native expression of the SpaFED-called pili is still the subject of some uncertainty. Irrespective of such considerations, we decided it would be of relevance or interest to decipher the gross structure of this pilus type, and as well assess its functional capabilities for cellular adhesion and immunostimulation. For this, and by following the approach we had used previously to explicate the immuno-properties of SpaCBA pili, we constructed nisin-inducible expression clones producing either wild-type or SpaF pilin-deleted surface-assembled L. rhamnosus GG SpaFED pili on Lactococcus lactis cells. Using these piliated lactococcal constructs, we found that the pilin-polymerized architecture of a recombinant-produced SpaFED pilus coincides with sequence-based functional predictions of the related pilins, and in fact is prototypical of those other sortase-dependent pilus-like structures thus far characterized for piliated Gram-positive bacteria. Moreover, we confirmed that among the different pilin subunits encompassing spaFED operon-encoded pili, the SpaF pilin is a main adhesion determinant, and when present in the assembled structure can mediate pilus binding to mucus, certain extracellular matrix proteins, and different gut epithelial cell lines. However, somewhat unexpectedly, when recombinant SpaFED pili are surface-attached, we found that they could not potentiate the existing lactococcal cell-induced immune responses so elicited from intestinal- and immune-related cells, but rather instead, they could dampen them. Accordingly, we have now provided the first phenotypical description of a spaFED pilus operon, and with that furthered the functional understanding of surface piliation for a particular gut-commensalic genre of piliated Gram-positive bacteria.

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Section: Resultsmentioning

confidence: 99%

Phenotypical Analysis of the Lactobacillus rhamnosus GG Fimbrial spaFED Operon: Surface Expression and Functional Characterization of Recombinant SpaFED Pili in Lactococcus lactis

et al. 2014

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“…In our predicted pan-genome of L. rhamnosus , the strains involved come from natural habitats and origins, with these being the human gut and airways, dental infections and intestinal biopsies, and those that are milk-based ( Table 1 ). However, because we calculated our pan-genome using a mix of both completed and draft L. rhamnosus genome sequences [20] , [38] – [41] , a cautionary caveat needs to be considered when interpreting the corresponding reconstructed phylogenomic tree ( Figure 1 ). Still, even despite such limitations, but what might be expected, it would seem that among a few of the genomes there is an apparent clustering into clades based on the similar origins of the strains.…”

Section: Resultsmentioning

confidence: 99%

A Comparative Pan-Genome Perspective of Niche-Adaptable Cell-Surface Protein Phenotypes in Lactobacillus rhamnosus

et al. 2014

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Lactobacillus rhamnosus is a ubiquitously adaptable Gram-positive bacterium and as a typical commensal can be recovered from various microbe-accessible bodily orifices and cavities. Then again, other isolates are food-borne, with some of these having been long associated with naturally fermented cheeses and yogurts. Additionally, because of perceived health benefits to humans and animals, numerous L. rhamnosus strains have been selected for use as so-called probiotics and are often taken in the form of dietary supplements and functional foods. At the genome level, it is anticipated that certain genetic variances will have provided the niche-related phenotypes that augment the flexible adaptiveness of this species, thus enabling its strains to grow and survive in their respective host environments. For this present study, we considered it functionally informative to examine and catalogue the genotype-phenotype variation existing at the cell surface between different L. rhamnosus strains, with the presumption that this might be relatable to habitat preferences and ecological adaptability. Here, we conducted a pan-genomic study involving 13 genomes from L. rhamnosus isolates with various origins. In using a benchmark strain (gut-adapted L. rhamnosus GG) for our pan-genome comparison, we had focused our efforts on a detailed examination and description of gene products for certain functionally relevant surface-exposed proteins, each of which in effect might also play a part in niche adaptability among the other strains. Perhaps most significantly of the surface protein loci we had analyzed, it would appear that the spaCBA operon (known to encode SpaCBA-called pili having a mucoadhesive phenotype) is a genomic rarity and an uncommon occurrence in L. rhamnosus. However, for any of the so-piliated L. rhamnosus strains, they will likely possess an increased niche-specific fitness, which functionally might presumably be manifested by a protracted transient colonization of the gut mucosa or some similar microhabitat.

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“…However, the lack of effect on other neutrophil parameters, such as phagocytosis, suggests only a partial overlap in underlying mechanisms of action. Accordingly, although both L. rhamnosus strains secrete soluble proteins that promote intestinal epithelial homeostasis, R0011 lacks the functional pili that are present on LGG (41).…”

Section: Discussionmentioning

confidence: 99%

Probiotic Lactobacillus rhamnosus Inhibits the Formation of Neutrophil Extracellular Traps

Vong

Lorentz

Assa

et al. 2014

The Journal of Immunology

107

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Alterations in the gut microbiota, referred to as dysbiosis, are strongly associated with chronic inflammatory bowel diseases. Neutrophils are one of the earliest cells to respond to an inflammatory stimulus and, in the inflamed intestine, constitute a significant proportion of cells that are recruited. Whereas probiotics have been shown to exert beneficial effects on gut homeostasis, their effect on neutrophil extracellular trap (NET) formation remains undefined. Therefore, the aim of this study was to determine the effects of the probiotic Lactobacillus rhamnosus GG (LGG) on the dynamics of NET formation. Bone marrow‐derived neutrophils (BMDN) were isolated from C57BL6 mice and co‐incubated with LGG (1 h, 37°C, 5% CO2) prior to stimulation with phorbol 12‐myristate 13‐acetate (PMA, 100 nM), which is an inducer of NET formation. Measurements of extracellular DNA (Sytox Green, 5 nM) and immunofluorescence microscopy staining for DNA, elastase and histones demonstrated that LGG mediated a concentration‐dependent reduction in NET‐osis. Given the proximity of recruited neutrophils to the lumen of the inflamed gut and the resident intestinal microbiota, it is important to define how neutrophil‐microbe interactions affect the local microenvironment. This work was funded by CIHR (operating grant MOP‐89894).

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Draft Genome Sequence of Probiotic Strain Lactobacillus rhamnosus R0011

Abstract: Lactobacillus rhamnosus R0011 is a commercially available probiotic that is widely used in human dietary supplements and pharmaceutical products. We prepared a draft genome sequence consisting of 10 contigs totaling 2,900,620 bases and a G؉C content of 46.7% for this strain.

Cited by 9 publications

References 6 publications

Phenotypical Analysis of the Lactobacillus rhamnosus GG Fimbrial spaFED Operon: Surface Expression and Functional Characterization of Recombinant SpaFED Pili in Lactococcus lactis

Phenotypical Analysis of the Lactobacillus rhamnosus GG Fimbrial spaFED Operon: Surface Expression and Functional Characterization of Recombinant SpaFED Pili in Lactococcus lactis

A Comparative Pan-Genome Perspective of Niche-Adaptable Cell-Surface Protein Phenotypes in Lactobacillus rhamnosus

Probiotic Lactobacillus rhamnosus Inhibits the Formation of Neutrophil Extracellular Traps

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