Colonization of breastfed infants by Bifidobacterium longum subsp. infantis EVC001 reduces virulence gene abundance
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The infant gut microbiome is rapidly colonized by bacteria from the environment after birth, and this gut ecosystem can facilitate expansion of potential pathogens. Human milk shapes the infant gut microbiome and has evolved to foster the growth of specific bacteria. Breastfed infants fed the coevolved infant gut symbiont Bifidobacterium longum subsp . infantis EVC001 had significant modifications to their gut metagenome, including a decreased number of virulence factor genes.
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Administering SCFA-producing commensals such as Bifidobacterium longum subspecies infantis to infants reduces intestinal pH from 5.97 to 5.15 and decreased virulence factor gene abundance.
“For example, administering SCFA-producing commensals such as Bifidobacterium longum subspecies infantis to infants reduces intestinal pH from 5.97 to 5.15 and decreased virulence factor gene abundance [41–43].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [41]
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works
Nosocomial Bloodstream Infections in United States Hospitals: A Three‐Year Analysis
Edmond, M. B., Wallace, S. E., McClish, D. K., Pfaller, M. A., Jones, R. N., & Wenzel, R. P. (1999) · Clinical Infectious Diseases · doi:10.1086/520192 · Cited by 1,387 · see citing works
Host-Derived Nitrate Boosts Growth of <i>E. coli</i> in the Inflamed Gut
Winter, S. E., Winter, M. G., Xavier, M. N., Thiennimitr, P., Poon, V., Keestra, A. M., Laughlin, R. C., Gomez, G., Wu, J., Lawhon, S. D., et al. (2013) · Science · doi:10.1126/science.1232467 · Cited by 1,019 · see citing works
Sela, D. A., Chapman, J., Adeuya, A., Kim, J., Chen, F., Whitehead, T. R., Lapidus, A. L., Rokhsar, D. S., Lebrilla, C. B., German, J. B., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809584105 · Cited by 884 · see citing works
Hospital-acquired neonatal infections in developing countries
Zaidi, A. K., Huskins, W. C., Thaver, D., Bhutta, Z. A., Abbas, Z., & Goldmann, D. A. (2005) · The Lancet · doi:10.1016/s0140-6736(05)71881-x · Cited by 830 · see citing works
Regulated virulence controls the ability of a pathogen to compete with the gut microbiota
Kamada, N., Kim, Y.-G., Sham, H. P., Vallance, B. A., Puente, J. L., Martens, E. C., & Núñez, G. (2012) · Science · doi:10.1126/science.1222195 · Cited by 682 · see citing works
Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis
Ochman, H., & Moran, N. A. (2001) · Science · doi:10.1126/science.1058543 · Cited by 566 · see citing works
Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut
Underwood, M. A., German, J. B., Lebrilla, C. B., & Mills, D. A. (2015) · Pediatric Research · doi:10.1038/pr.2014.156 · Cited by 439 · see citing works
Oxygen as a driver of gut dysbiosis
Rivera-Chávez, F., Lopez, C. A., & Bäumler, A. J. (2016) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.09.022 · Cited by 311 · see citing works
Thaver, D., & Zaidi, A. K. M. (2009) · Pediatric Infectious Disease Journal · doi:10.1097/inf.0b013e3181958755 · Cited by 292 · see citing works
Housekeeping enzymes as virulence factors for pathogens
Pancholi, V., & Chhatwal, G. S. (2003) · International Journal of Medical Microbiology · doi:10.1078/1438-4221-00283 · Cited by 290 · see citing works
Review of Medical Microbiology and Immunology
Levinson, W. E. (2002) · Repository of the University of Ljubljana (University of Ljubljana) · Cited by 256 · see citing works
Frese, S. A., Hutton, A. A., Contreras, L. N., Shaw, C. A., Palumbo, M. C., Casaburi, G., Xu, G., Davis, J. C. C., Lebrilla, C. B., Henrick, B. M., et al. (2017) · mSphere · doi:10.1128/msphere.00501-17 · Cited by 231 · see citing works
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Dodds, D. R. (2016) · Biochemical Pharmacology · doi:10.1016/j.bcp.2016.12.005 · Cited by 189 · see citing works
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Henrick, B. M., Hutton, A. A., Palumbo, M., Casaburi, G., Mitchell, R. D., Underwood, M. A., Smilowitz, J. T., & Frese, S. A. (2018) · mSphere · doi:10.1128/msphere.00041-18 · Cited by 157 · see citing works
Self-citationRegulation of virulence: the rise and fall of gastrointestinal pathogens
Kitamoto, S., Nagao‐Kitamoto, H., Kuffa, P., & Kamada, N. (2015) · Journal of Gastroenterology · doi:10.1007/s00535-015-1141-5 · Cited by 81 · see citing works
Bench-to-bedside review: Bacterial virulence and subversion of host defences
Webb, S. A. R., & Kahler, C. M. (2008) · Critical Care · doi:10.1186/cc7091 · Cited by 56 · see citing works
Strategies for managing today's infections
Carmeli, Y. (2008) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2008.01957.x · Cited by 45 · see citing works
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- Authors
- Casaburi, G., & Frese, S. A.
- Affiliations
- Infinant Health Inc. (United States) (US)
- University of Nebraska–Lincoln (US)
- Corresponding author
- Frese, Steven A.
- Venue
- Human Microbiome Journal
- Publisher
- Elsevier BV
- Published
- 2018-08
- Volume
- 9
- Pages
- 7-10
- ISSN
- 2452-2317 (ISSN-L)
- OpenAlex
- W2805733557
- Cited by
- 38
- References
- 19
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 5 · 2023: 3 · 2022: 7 · 2021: 5 · 2020: 6 · 2019: 4 · 2018: 2
- FWCI
- 3.52
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Human Microbiome Journal (publishedVersion, cc-by-nc-nd)
- Lincoln (University of Nebraska) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (S10 OD018174)
- Topics
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- breastfeeding, infant gut microbiota, intestinal colonization, virulence genes, breast milk, gut metagenome, pathogen colonization, symbiotic bacteria
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