A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus

R Kant, J Rintahaka, X Yu, P Sigvart-Mattila, L Paulin, J-P Mecklin, Maria Saarela, A Palva, I von Ossowski

Research output: Contribution to journalArticleScientificpeer-review

22 Citations (Scopus)

Abstract

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
Original languageEnglish
Article numbere102762
JournalPLoS ONE
Volume9
Issue number7
DOIs
Publication statusPublished - 2014
MoE publication typeA1 Journal article-refereed

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Lactobacillus rhamnosus
surface proteins
Membrane Proteins
niches
Genes
Genome
Phenotype
phenotype
genome
cells
Dietary supplements
digestive system
Cheeses
genomics
Orifices
fimbriae
Benchmarking
Yogurt
Functional Food
operon

Cite this

Kant, R., Rintahaka, J., Yu, X., Sigvart-Mattila, P., Paulin, L., Mecklin, J-P., ... von Ossowski, I. (2014). A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. PLoS ONE, 9(7), [e102762]. https://doi.org/10.1371/journal.pone.0102762
Kant, R ; Rintahaka, J ; Yu, X ; Sigvart-Mattila, P ; Paulin, L ; Mecklin, J-P ; Saarela, Maria ; Palva, A ; von Ossowski, I. / A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. In: PLoS ONE. 2014 ; Vol. 9, No. 7.
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abstract = "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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Kant, R, Rintahaka, J, Yu, X, Sigvart-Mattila, P, Paulin, L, Mecklin, J-P, Saarela, M, Palva, A & von Ossowski, I 2014, 'A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus', PLoS ONE, vol. 9, no. 7, e102762. https://doi.org/10.1371/journal.pone.0102762

A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. / Kant, R; Rintahaka, J; Yu, X; Sigvart-Mattila, P; Paulin, L; Mecklin, J-P; Saarela, Maria; Palva, A; von Ossowski, I.

In: PLoS ONE, Vol. 9, No. 7, e102762, 2014.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Kant, R

AU - Rintahaka, J

AU - Yu, X

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AU - Paulin, L

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AU - Saarela, Maria

AU - Palva, A

AU - von Ossowski, I

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