A genomic view of food-related and probiotic Enterococcus strains

Bonacina, Julieta; Suárez, Nadia E.; Hormigo, Ricardo; Fadda, Silvina; Lechner, Marcus; Saavedra, Lucila

doi:10.1093/dnares/dsw043

Cited by 37 publications

(42 citation statements)

References 67 publications

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“…We could not observe any correlation between higher G + C content with higher number of coding sequences as described in the earlier study [33]. On further annotation by RAST we identify enriched carbohydrates metabolism in all the strains and this is in agreement with the E. faecium ability to utilize a wide range of mono-, di-, oligo-saccharides [34, 35].…”

Section: Discussionsupporting

confidence: 79%

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

Ghattargi

Gaikwad

Meti³

et al. 2018

BMC Genomics

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BackgroundEnterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.ResultsE. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.ConclusionsBeyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5043-9) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 79%

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

Ghattargi

Gaikwad

Meti³

et al. 2018

BMC Genomics

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“…Genome sizes ranged from approximately 2.57–2.99 Mb with strain DO exhibiting the smallest and 6E6 the largest genome. Average GC content varied between 37.90 ± 0.65% and the strains with high G+C% do not have higher CDS, this contradicts with the results stated earlier (Bonacina et al 2017). The genomic features of the strains under study are provided in Table 1.…”

Section: Resultscontrasting

confidence: 87%

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property inEnterococcus faeciumstrains

Ghattargi

Gaikwad

Meti³

et al. 2018

Preprint

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Enterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will help to reveal the genomic differences responsible for the said properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. The core genome analysis revealed, 17OM39 was closely related with marketed probiotic strain T110. Strain 17OM39 was found to be devoid of known vancomycin, tetracycline resistance genes and functional virulence genes. Moreover, 17OM39 is „less open‟ due to absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Additional, genes associated with colonization within gastrointestinal tract were detected across all the strains. Beyond shared genetic features; this study particularly identified genes that are responsible to impart probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. The study also provides insights into the acquired and intrinsic drug resistance genes, which will be helpful for better understanding of the physiology of antibiotic resistance in E. faecium strains. In addition, we could identify genes contributing to the intrinsic ability of 17OM39 E. faecium isolate to be a potential probiotic.The study has comprehensively characterized genome sequence of each strain to find the genetic variation and understand effects of these on functionality, phenotypic complexity. Further the evolutionary relationship of species along with adaptation strategies have been including in this study.

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“…Three potassium‐transporting related proteins, one sensor protein, and a tagatose aldolase were located in GI‐8. There were 25 ribosomal proteins in GI‐1, a common feature among the genomic islands of foodborne enterococcal genomes previously sequenced (Bonacina et al., ).…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, the pathogenic potential of E. hirae may be underappreciated due to misidentification. Limited genetic information has been published to date describing E. hirae , particularly clinically relevant properties (Bonacina et al., ; Gaechter, Wunderlin, Schmidheini, & Solioz, ; Katyal, Chaban, & Hill, ; Porcellato, Ostlie, & Skeie, ).…”

Section: Introductionmentioning

confidence: 99%

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

Peng

Wang

et al. 2017

MicrobiologyOpen

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Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin‐resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC ™9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain‐specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug‐resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug‐resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.

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A genomic view of food-related and probiotic Enterococcus strains

Cited by 37 publications

References 67 publications

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property inEnterococcus faeciumstrains

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

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