scholarly journals Comparative Genomic and Functional Analysis of Lactobacillus casei and Lactobacillus rhamnosus Strains Marketed as Probiotics

2013 ◽  
Vol 79 (6) ◽  
pp. 1923-1933 ◽  
Author(s):  
François P. Douillard ◽  
Angela Ribbera ◽  
Hanna M. Järvinen ◽  
Ravi Kant ◽  
Taija E. Pietilä ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Transcription Initiation ◽  
Lactobacillus Rhamnosus ◽  
Comparative Genomic ◽  
Phenotypic Analysis ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Host Signaling ◽  
Toll Like Receptor 2 ◽  
Genome Content

ABSTRACTFourLactobacillusstrains were isolated from marketed probiotic products, includingL. rhamnosusstrains from Vifit (Friesland Campina) and Idoform (Ferrosan) andL. caseistrains from Actimel (Danone) and Yakult (Yakult Honsa Co.). Their genomes and phenotypes were characterized and compared in detail withL. caseistrain BL23 andL. rhamnosusstrain GG. Phenotypic analysis of the new isolates indicated differences in carbohydrate utilization betweenL. caseiandL. rhamnosusstrains, which could be linked to their genotypes. The two isolatedL. rhamnosusstrains had genomes that were virtually identical to that ofL. rhamnosusGG, testifying to their genomic stability and integrity in food products. TheL. caseistrains showed much greater genomic heterogeneity. Remarkably, all strains contained an intactspaCBApilus gene cluster. However, only theL. rhamnosusstrains produced mucus-binding SpaCBA pili under the conditions tested. Transcription initiation mapping demonstrated that the insertion of aniso-IS30element upstream of the pilus gene cluster inL. rhamnosusstrains but absent inL. caseistrains had constituted a functional promoter driving pilus gene expression. AllL. rhamnosusstrains triggered an NF-κB response via Toll-like receptor 2 (TLR2) in a reporter cell line, whereas theL. caseistrains did not or did so to a much lesser extent. This study demonstrates that the twoL. rhamnosusstrains isolated from probiotic products are virtually identical toL. rhamnosusGG and further highlights the differences between these andL. caseistrains widely marketed as probiotics, in terms of genome content, mucus-binding and metabolic capacities, and host signaling capabilities.

scholarly journals Comparative Genomic and Phenotypic Analysis of the Vaginal Probiotic Lactobacillus rhamnosus GR-1

2018 ◽  
Vol 9 ◽  
Author(s):  
Mariya I. Petrova ◽  
Jean M. Macklaim ◽  
Sander Wuyts ◽  
Tine Verhoeven ◽  
Jos Vanderleyden ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Comparative Genomic ◽  
Phenotypic Analysis ◽  
Probiotic Lactobacillus

scholarly journals Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Haijian Du ◽  
Wenyan Zhang ◽  
Wensi Zhang ◽  
Weijia Zhang ◽  
Hongmiao Pan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Cluster ◽  
Geomagnetic Field ◽  
Evolutionary Biology ◽  
Genomic Analysis ◽  
Magnetotactic Bacteria ◽  
Duplication Event ◽  
Comparative Genomic ◽  
Content Type ◽  
Evolutionary Trajectories

ABSTRACT The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. IMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.

scholarly journals Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling

2015 ◽  
Vol 81 (16) ◽  
pp. 5458-5470 ◽  
Author(s):  
Corina Ceapa ◽  
Jolanda Lambert ◽  
Kees van Limpt ◽  
Michiel Wels ◽  
Tamara Smokvina ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Bacterial Species ◽  
Draft Genome ◽  
Carbon Sources ◽  
Lactobacillus Rhamnosus ◽  
Genotypic Diversity ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Healthy Humans ◽  
Niche Adaptation

ABSTRACTLactobacillus rhamnosusis a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains ofL. rhamnosusin relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65L. rhamnosusstrains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification ofL. rhamnosusstrains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes ofL. rhamnosusGG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters:l-rhamnose, cellobiose,l-sorbose, and α-methyl-d-glucoside. From the analysis, candidate genes were identified that correlate withl-sorbose and α-methyl-d-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the speciesL. rhamnosusand explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.

scholarly journals Functional Analysis of Lactobacillus rhamnosus GG Pili in Relation to Adhesion and Immunomodulatory Interactions with Intestinal Epithelial Cells

2011 ◽  
Vol 78 (1) ◽  
pp. 185-193 ◽  
Author(s):  
Sarah Lebeer ◽  
Ingmar Claes ◽  
Hanne L. P. Tytgat ◽  
Tine L. A. Verhoeven ◽  
Eyra Marien ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Lipoteichoic Acid ◽  
Good Survival ◽  
Intestinal Epithelial ◽  
Wild Type ◽  
Knockout Mutant ◽  
Phenotypic Analysis ◽  
Adhesion Properties ◽  
Content Type ◽  
Adhesive Interactions

ABSTRACTLactobacillus rhamnosusGG, a probiotic with good survival capacity in the human gut, has well-documented adhesion properties and health effects. Recently,spaCBA-encoded pili that bind to human intestinal mucus were identified on its cell surface. Here, we report on the phenotypic analysis of aspaCBApilus knockout mutant in comparison with the wild type and other adhesin mutants. The SpaCBA pilus ofL. rhamnosusGG showed to be key for efficient adherence to the Caco-2 intestinal epithelial cell (IEC) line and biofilm formation. Moreover, thespaCBAmutant induces an elevated level of interleukin-8 (IL-8) mRNA in Caco-2 cells compared to the wild type, possibly involving an interaction of lipoteichoic acid with Toll-like receptor 2. In contrast, anL. rhamnosusGG mutant without exopolysaccharides but with an increased exposure of pili leads to the reduced expression of IL-8. Using Transwells to partition bacteria from Caco-2 cells, IL-8 induction is blocked completely regardless of whether wild-type or mutantL. rhamnosusGG cells are used. Taken together, our data suggest thatL. rhamnosusGG SpaCBA pili, while promoting strong adhesive interactions with IECs, have a functional role in balancing IL-8 mRNA expression induced by surface molecules such as lipoteichoic acid.

scholarly journals Lactobacillus rhamnosus GG Genomic and Phenotypic Stability in an Industrial Production Process

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Marianne Stage ◽  
Anita Wichmann ◽  
Mette Jørgensen ◽  
Natalia Ivonne Vera-Jimenéz ◽  
Malue Wielje ◽  
...  
Keyword(s):  
Production Process ◽  
Gene Cluster ◽  
Industrial Production ◽  
Lactobacillus Rhamnosus ◽  
Probiotic Properties ◽  
Phenotypic Stability ◽  
Content Type ◽  
Freeze Dried ◽  
Probiotic Strains

ABSTRACT Lactobacillus rhamnosus GG is one of the most widely marketed and studied probiotic strains. In L. rhamnosus GG, the spaCBA-srtC1 gene cluster encodes pili, which are important for some of the probiotic properties of the strain. A previous study showed that the DNA sequence of the spaCBA-srtC1 gene cluster was not present in some L. rhamnosus GG variants isolated from liquid dairy products. To examine the stability of the L. rhamnosus GG genome in an industrial production process, we sequenced the genome of samples of L. rhamnosus GG (DSM 33156) collected at specific steps of the industrial production process, including the culture collection stock, intermediate fermentations, and final freeze-dried products. We found that the L. rhamnosus GG genome sequence was unchanged throughout the production process. Consequently, the spaCBA-srtC1 gene locus was intact and fully conserved in all 31 samples examined. In addition, different production batches of L. rhamnosus GG exhibited consistent phenotypes, including the presence of pili in final freeze-dried products, and consistent characteristics in in vitro assays of probiotic properties. Our data show that L. rhamnosus GG is highly stable in this industrial production process. IMPORTANCE Lactobacillus rhamnosus GG is one of the best-studied probiotic strains. One of the well-characterized features of the strain is the pili encoded by the spaCBA-srtC1 gene cluster. These pili are involved in persistence in the gastrointestinal tract and are important for the probiotic properties of L. rhamnosus GG. Previous studies demonstrated that the L. rhamnosus GG genome can be unstable under certain conditions and can lose the spaCBA-srtC1 gene cluster. Since in vitro studies have shown that the loss of the spaCBA-srtC1 gene cluster decreases certain L. rhamnosus GG probiotic properties, we assessed both the genomic stability and phenotypic properties of L. rhamnosus GG throughout an industrial production process. We found that neither genomic nor phenotypic changes occurred in the samples. Therefore, we demonstrate that L. rhamnosus GG retains the spaCBA-srtC1 cluster and exhibits excellent genomic and phenotypic stability in the specific industrial process examined here.

scholarly journals Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay

2017 ◽  
Vol 83 (18) ◽  
Author(s):  
Charles H. D. Williamson ◽  
Adam J. Vazquez ◽  
Karen Hill ◽  
Theresa J. Smith ◽  
Roxanne Nottingham ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Gene Cluster ◽  
Botulinum Neurotoxin ◽  
Comparative Genomic ◽  
Pcr Assay ◽  
Content Type ◽  
Multiplex Pcr Assay ◽  
Group I ◽  
Pcr Assays ◽  
Group Ii

ABSTRACT Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This report introduces a multiplex PCR assay for differentiating members of C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Coding region sequences unique to each of the four species/subgroups were identified by in silico analyses of thousands of genome assemblies, and PCR primers were designed to amplify each marker. The resulting multiplex PCR assay correctly assigned 41 tested isolates to the appropriate species or subgroup. A separate PCR assay to determine the presence of the ntnh gene (a gene associated with the botulinum neurotoxin gene cluster) was developed and validated. The ntnh gene PCR assay provides information about the presence or absence of the botulinum neurotoxin gene cluster and the type of gene cluster present (ha positive [ha +] or orfX +). The increased availability of whole-genome sequence data and comparative genomic tools enabled the design of these assays, which provide valuable information for characterizing BoNT-producing clostridia. The PCR assays are rapid, inexpensive tests that can be applied to a variety of sample types to assign isolates to species/subgroups and to detect clostridia with botulinum neurotoxin gene (bont) clusters. IMPORTANCE Diverse clostridia produce the botulinum neurotoxin, one of the most potent known neurotoxins. In this study, a multiplex PCR assay was developed to differentiate clostridia that are most commonly isolated in connection with human botulism cases: C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Since BoNT-producing and nontoxigenic isolates can be found in each species, a PCR assay to determine the presence of the ntnh gene, which is a universally present component of bont gene clusters, and to provide information about the type (ha + or orfX +) of bont gene cluster present in a sample was also developed. The PCR assays provide simple, rapid, and inexpensive tools for screening uncharacterized isolates from clinical or environmental samples. The information provided by these assays can inform epidemiological studies, aid with identifying mixtures of isolates and unknown isolates in culture collections, and confirm the presence of bacteria of interest.

scholarly journals Metabolism of Four α-Glycosidic Linkage-Containing Oligosaccharides by Bifidobacterium breve UCC2003

2013 ◽  
Vol 79 (20) ◽  
pp. 6280-6292 ◽  
Author(s):  
Kerry Joan O'Connell ◽  
Mary O'Connell Motherway ◽  
John O'Callaghan ◽  
Gerald F. Fitzgerald ◽  
R. Paul Ross ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Molecular Mechanisms ◽  
Functional Genomic ◽  
Adjacent Gene ◽  
Glycosidic Linkage ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Bifidobacterium Breve

ABSTRACTMembers of the genusBifidobacteriumare common inhabitants of the gastrointestinal tracts of humans and other mammals, where they ferment many diet-derived carbohydrates that cannot be digested by their hosts. To extend our understanding of bifidobacterial carbohydrate utilization, we investigated the molecular mechanisms by which 11 strains ofBifidobacterium brevemetabolize four distinct α-glucose- and/or α-galactose-containing oligosaccharides, namely, raffinose, stachyose, melibiose, and melezitose. Here we demonstrate that allB. brevestrains examined possess the ability to utilize raffinose, stachyose, and melibiose. However, the ability to metabolize melezitose was not common to allB. brevestrains tested. Transcriptomic and functional genomic approaches identified a gene cluster dedicated to the metabolism of α-galactose-containing carbohydrates, while an adjacent gene cluster, dedicated to the metabolism of α-glucose-containing melezitose, was identified in strains that are able to use this carbohydrate.

scholarly journals Genomic and Functional Portrait of a Highly Virulent, CTX-M-15-ProducingH30-Rx Subclone of Escherichia coli Sequence Type 131

2015 ◽  
Vol 59 (10) ◽  
pp. 6087-6095 ◽  
Author(s):  
Amit Ranjan ◽  
Sabiha Shaik ◽  
Arif Hussain ◽  
Nishant Nandanwar ◽  
Torsten Semmler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Analysis ◽  
Virulence Gene ◽  
Sequence Type ◽  
Fluoroquinolone Resistance ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Phenotypic Analysis ◽  
Content Type ◽  
E Coli

ABSTRACTEscherichia colisequence type 131 (ST131) is a pandemic clone associated with multidrug-resistant, extraintestinal infections, attributable to the presence of the CTX-M-15 extended-spectrum β-lactamase gene and mutations entailing fluoroquinolone resistance. Studies on subclones withinE. coliST131 are critically required for targeting and implementation of successful control efforts. Our study comprehensively analyzed the genomic and functional attributes of theH30-Rx subclonal strains NA097 and NA114, belonging to the ST131 lineage. We carried out whole-genome sequencing, comparative analysis, phenotypic virulence assays, and profiling of the antibacterial responses of THP1 cells infected with these subclones. Phylogenomic analysis suggested that the strains were clonal in nature and confined entirely to a single clade. Comparative genomic analysis revealed that the virulence and resistance repertoires were comparable among theH30-Rx ST131 strains except for the commensal ST131 strain SE15. Similarly, seven phage-specific regions were found to be strongly associated with theH30-Rx strains but were largely absent in the genome of SE15. Phenotypic analysis confirmed the virulence and resistance similarities between the two strains. However, NA097 was found to be more robust than NA114 in terms of virulence gene carriage (draoperon), invasion ability (P< 0.05), and antimicrobial resistance (streptomycin resistance). RT2gene expression profiling revealed generic upregulation of key proinflammatory responses in THP1 cells, irrespective of ST131 lineage status. In conclusion, our study provides comprehensive, genome-inferred insights into the biology and immunological properties of ST131 strains and suggests clonal diversification of genomic and phenotypic features within theH30-Rx subclone ofE. coliST131.

scholarly journals Lumen and mucosa-associated Lactobacillus rhamnosus from the intestinal tract of organ donors

2020 ◽  
Vol 1 ◽  
Author(s):  
Alan J. Marsh ◽  
Al-Mounawara A. Yaya ◽  
Sandy Ng ◽  
Kshipra Chandrashekhar ◽  
Jeff Roach ◽  
...  
Keyword(s):  
Small Intestine ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Load ◽  
Regional Distribution ◽  
Lactobacillus Rhamnosus ◽  
Microbial Interactions ◽  
Comparative Genomic ◽  
Organ Donors ◽  
Bacterial Strains ◽  
Carbohydrate Utilization

ABSTRACT Knowledge of the intra-individual spatial and regional distribution of intestinal microbial populations is essential to understand gut host–microbial interactions. In this study, we performed a compositional analysis of luminal and mucosal samples from the small and large intestine of four organ donors by 16S rRNA amplicon sequencing and high-throughput quantitative polymerase chain reaction. Since the human microbiota is subject to selection pressure at lower taxonomic levels, we isolated over 400 bacterial strains and investigated strain-level variation of 11 Lactobacillus rhamnosus from different intestinal regions. Results substantiate reported inter-individual variability as well as intra-individual differences along the gastrointestinal tract. Although the luminal and mucosal-associated communities were similar within individuals, relative abundance reflected the donors’ demographic and potential pathologies. The total bacterial load of all donors increased from small intestine to colon, while Bifidobacterium was in greater abundance in the small intestine. Comparative genomic analysis of L. rhamnosus showed the strains segregated into two distinct clusters and identified no features specific to location. Analysis revealed genetic differences for exopolysaccharide production, carbohydrate utilization, pilus formation and vitamin K biosynthesis between clusters. This study contributes to the understanding of niche-specific microbial communities, encouraging subsequent studies to better understand microbial signatures at lower taxonomic levels.

scholarly journals Genomic Characterization of Non-Mucus-Adherent Derivatives of Lactobacillus rhamnosus GG Reveals Genes Affecting Pilus Biogenesis

2014 ◽  
Vol 80 (22) ◽  
pp. 7001-7009 ◽  
Author(s):  
Pia Rasinkangas ◽  
Justus Reunanen ◽  
François P. Douillard ◽  
Jarmo Ritari ◽  
Virva Uotinen ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Lactobacillus Rhamnosus ◽  
Illumina Miseq ◽  
Class Iii ◽  
Dot Blot ◽  
Content Type ◽  
Intestinal Mucus ◽  
Pilus Biogenesis ◽  
Dot Blot Analysis ◽  
The Impact

ABSTRACTLactobacillus rhamnosusGG is one of the best-characterized lactic acid bacteria and can be considered a probiotic paradigm. Comparative and functional genome analysis showed thatL. rhamnosusGG harbors a genomic island including thespaCBA-srtC1gene cluster, encoding the cell surface-decorating host-interacting pili. Here, induced mutagenesis was used to study pilus biogenesis inL. rhamnosusGG. A combination of two powerful approaches, mutation selection and next-generation sequencing, was applied toL. rhamnosusGG for the selection of pilus-deficient mutants from an enriched population. The isolated mutants were first screened by immuno-dot blot analysis using antiserum against pilin proteins. Relevant mutants were selected, and the lack of pili was confirmed by immunoelectron microscopy. The pilosotype of 10 mutant strains was further characterized by analyzing pilin expression using Western blot, dot blot, and immunofluorescence methods. A mucus binding assay showed that the mutants did not adhere to porcine intestinal mucus. Comparative genome sequence analysis using the Illumina MiSeq platform allowed us to determine the nature of the mutations in the obtained pilus-deficient derivatives. Three major classes of mutants with unique genotypes were observed: class I, with mutations in thesrtC1gene; class II, with a deletion containing thespaCBA-srtC1gene cluster; and class III, with mutations in thespaAgene. Only a limited number of collateral mutations were observed, and one of the pilus-deficient derivatives with a deficientsrtC1gene contained 24 other mutations. This strain, PB12, can be considered a candidate for human trials addressing the impact of the absence of pili.

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