title: A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus.
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.
authors.affiliation: Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Ravi
authors.initials: R
authors.lastname: Kant
authors.affiliation: Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Rintahaka
authors.affiliation: Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Xia
authors.initials: X
authors.lastname: Yu
authors.affiliation: MTT Agrifood Research Finland, Jokioinen, Finland.
authors.forename: Pia
authors.initials: P
authors.lastname: Sigvart-Mattila
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Lars
authors.initials: L
authors.lastname: Paulin
authors.affiliation: Department of Surgery, Jyväskylä Central Hospital and Institute of Clinical Medicine, University of Eastern Finland, Jyväskylä, Finland.
authors.forename: Jukka-Pekka
authors.initials: JP
authors.lastname: Mecklin
authors.affiliation: VTT Technical Research Center of Finland, Espoo, Finland.
authors.forename: Maria
authors.initials: M
authors.lastname: Saarela
authors.affiliation: Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Airi
authors.initials: A
authors.lastname: Palva
authors.affiliation: Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Ingemar
authors.initials: I
authors.lastname: von Ossowski
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D001422:Bacterial Adhesion / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D056726:Genetic Association Studies / Q000379:methods; D014644:Genetic Variation / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D052201:Lacticaseibacillus rhamnosus / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics*; D009876:Operon / Q000235:genetics; D010641:Phenotype
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins