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Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics

1
Evolve BioSystems, Inc., Davis, CA 95618, USA
2
Foods for Health Institute, University of California at Davis, Davis, CA 95616, USA
3
Department of Food Science and Technology, University of California at Davis, Davis, CA 95616, USA
4
Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
*
Author to whom correspondence should be addressed.
Nutrients 2020, 12(11), 3247; https://doi.org/10.3390/nu12113247
Received: 3 September 2020 / Revised: 16 October 2020 / Accepted: 19 October 2020 / Published: 23 October 2020
(This article belongs to the Special Issue Nutritional Interventions of Necrotizing Enterocolitis in Newborns)
Dysbiosis is associated with acute and long-term consequences for neonates. Probiotics can be effective in limiting the growth of bacteria associated with dysbiosis and promoting the healthy development of the infant microbiome. Given its adaptation to the infant gut, and promising data from animal and in vitro models, Bifidobacterium longum subsp. infantis is an attractive candidate for use in infant probiotics. However, strain-level differences in the ability of commercialized strains to utilize human milk oligosaccharides (HMOs) may have implications in the performance of strains in the infant gut. In this study, we characterized twelve B. infantis probiotic strains and identified two main variants in one of the HMO utilization gene clusters. Some strains possessed the full repertoire of HMO utilization genes (H5-positive strains), while H5-negative strains lack an ABC-type transporter known to bind core HMO structures. H5-positive strains achieved significantly superior growth on lacto-N-tetraose and lacto-N-neotetraose. In vitro, H5-positive strains had a significant fitness advantage over H5-negative strains, which was also observed in vivo in breastfed infants. This work provides evidence of the functional implications of genetic differences among B. infantis strains and highlights that genotype and HMO utilization phenotype should be considered when selecting a strain for probiotic use in infants. View Full-Text
Keywords: gut microbiome; dysbiosis; probiotics; HMO; NEC gut microbiome; dysbiosis; probiotics; HMO; NEC
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MDPI and ACS Style

Duar, R.M.; Casaburi, G.; Mitchell, R.D.; Scofield, L.N.C.; Ortega Ramirez, C.A.; Barile, D.; Henrick, B.M.; Frese, S.A. Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. Nutrients 2020, 12, 3247. https://doi.org/10.3390/nu12113247

AMA Style

Duar RM, Casaburi G, Mitchell RD, Scofield LNC, Ortega Ramirez CA, Barile D, Henrick BM, Frese SA. Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. Nutrients. 2020; 12(11):3247. https://doi.org/10.3390/nu12113247

Chicago/Turabian Style

Duar, Rebbeca M., Giorgio Casaburi, Ryan D. Mitchell, Lindsey N.C. Scofield, Camila A. Ortega Ramirez, Daniela Barile, Bethany M. Henrick, and Steven A. Frese 2020. "Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics" Nutrients 12, no. 11: 3247. https://doi.org/10.3390/nu12113247

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