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The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome
Open accessAbstract
Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.
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Citations
Cites
Development of the Human Infant Intestinal Microbiota
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877
O’Mahony, L., McCarthy, J., Kelly, P., Hurley, G., Luo, F., Chen, K., O’Sullivan, G. C., Kiely, B., Collins, J. K., Shanahan, F., et al. (2005) · Gastroenterology · doi:10.1053/j.gastro.2004.11.050 · Cited by 1,448
A Genomic View of the Human- Bacteroides thetaiotaomicron Symbiosis
Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C., Hooper, L. V., & Gordon, J. I. (2003) · Science · doi:10.1126/science.1080029 · Cited by 1,353
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869
Liévin, V, Peiffer, I., Hudault, S., Rochat, F., Brassart, D., Neeser, J.-R., & Servin, A. L. (2000) · Gut · doi:10.1136/gut.47.5.646 · Cited by 397
LoCascio, R. G., Ninonuevo, M. R., Freeman, S. L., Sela, D. A., Grimm, R., Lebrilla, C. B., Mills, D. A., & German, J. B. (2007) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf0710480 · Cited by 365
Self-citation
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Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540
Bifidobacteria can protect from enteropathogenic infection through production of acetate
Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., et al. (2011) · Nature · doi:10.1038/nature09646 · Cited by 2,387
Microbial degradation of complex carbohydrates in the gut
Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012) · Gut Microbes · doi:10.4161/gmic.19897 · Cited by 2,331
Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950
Human milk oligosaccharides: Every baby needs a sugar mama
Bode, L. (2012) · Glycobiology · doi:10.1093/glycob/cws074 · Cited by 1,809
Bacteria as vitamin suppliers to their host: A gut microbiota perspective
LeBlanc, J. G., Milani, C., de Giori, G. S., Sesma, F., van Sinderen, D., & Ventura, M. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.08.005 · Cited by 1,613
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
Vatanen, T., Kostic, A. D., d’Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A.-M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.007 · Cited by 1,289
Mechanisms and consequences of intestinal dysbiosis
Weiss, G. A., & Hennet, T. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2509-x · Cited by 775
Human milk glycobiome and its impact on the infant gastrointestinal microbiota
Zivkovic, A. M., German, J. B., Lebrilla, C. B., & Mills, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000083107 · Cited by 679
Self-citationInteractions of gut microbiota with functional food components and nutraceuticals
Laparra, J. M., & Sanz, Y. (2010) · Pharmacological Research · doi:10.1016/j.phrs.2009.11.001 · Cited by 684
Our gut microbiome: The evolving inner self
Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017) · Cell · doi:10.1016/j.cell.2017.11.024 · Cited by 633
Diversity of Bifidobacteria within the Infant Gut Microbiota
Turroni, F., Peano, C., Pass, D. A., Foroni, E., Severgnini, M., Claesson, M. J., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036957 · Cited by 647
“infantis) are genetically adapted to utilize hostproduced glycans like mucins and human milk oligosaccharides [50–53].”
BackgroundCharbonneau, M. R., O’Donnell, D., Blanton, L. V., Totten, S. M., Davis, J. C. C., Barratt, M. J., Cheng, J., Guruge, J., Talcott, M., Bain, J. R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.01.024 · Cited by 606
Self-citationBacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways
Marcobal, A., Barboza, M., Sonnenburg, E. D., Pudlo, N., Martens, E. C., Desai, P., Lebrilla, C. B., Weimer, B. C., Mills, D. A., German, J. B., et al. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.007 · Cited by 574
Consumption of human milk oligosaccharides by gut-related microbes
Marcobal, A., Barboza, M., Froehlich, J. W., Block, D. E., German, J. B., Lebrilla, C. B., & Mills, D. A. (2010) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf9044205 · Cited by 568
Self-citationFeeding the microbiota–gut–brain axis: Diet, microbiome, and neuropsychiatry
Sandhu, K. V., Sherwin, E., Schellekens, H., Stanton, C., Dinan, T. G., & Cryan, J. F. (2017) · Translational Research · doi:10.1016/j.trsl.2016.10.002 · Cited by 491
Bifidobacteria and Their Health-Promoting Effects
Hidalgo-Cantabrana, C., Delgado, S., Ruiz, L., Ruas-Madiedo, P., Sánchez, B., & Margolles, A. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.bad-0010-2016 · Cited by 490
Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides
Sela, D. A., & Mills, D. A. (2010) · Trends in Microbiology · doi:10.1016/j.tim.2010.03.008 · Cited by 468
Self-citationStrain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life
Yassour, M., Jason, E., Hogstrom, L. J., Arthur, T. D., Tripathi, S., Siljander, H., Selvenius, J., Oikarinen, S., Hyöty, H., Virtanen, S. M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.007 · Cited by 455
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
Self-citationEffects of microbiota-directed foods in gnotobiotic animals and undernourished children
Gehrig, J. L., Venkatesh, S., Chang, H.-W., Hibberd, M. C., Kung, V. L., Cheng, J., Chen, R. Y., Subramanian, S., Cowardin, C. A., Meier, M. F., et al. (2019) · Science · doi:10.1126/science.aau4732 · Cited by 431
Role of priority effects in the early-life assembly of the gut microbiota
Sprockett, D., Fukami, T., & Relman, D. A. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.173 · Cited by 419
Breast milk oligosaccharides: structure-function relationships in the neonate
Smilowitz, J. T., Lebrilla, C. B., Mills, D. A., German, J. B., & Freeman, S. L. (2014) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-071813-105721 · Cited by 410
Gut microbiota as the key controllers of 'healthy' aging of elderly people
Ragonnaud, E., & Biragyn, A. (2021) · Immunity & Ageing · doi:10.1186/s12979-020-00213-w · Cited by 383
Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.-H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011100107 · Cited by 364
Self-citationTurroni, F., Ventura, M., Buttó, L. F., Duranti, S., O’Toole, P. W., Motherway, M. O., & van Sinderen, D. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1318-0 · Cited by 336
Duranti, S., Lugli, G. A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferretti, P., Gorfer, V., Ferrario, C., Milani, C., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0282-6 · Cited by 327
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Milani, C., Lugli, G. A., Duranti, S., Turroni, F., Mancabelli, L., Ferrario, C., Mangifesta, M., Hevia, A., Viappiani, A., Scholz, M., et al. (2015) · Scientific Reports · doi:10.1038/srep15782 · Cited by 284
Walker, A. W., Martin, J. C., Scott, P., Parkhill, J., Flint, H. J., & Scott, K. P. (2015) · Microbiome · doi:10.1186/s40168-015-0087-4 · Cited by 273
Chichlowski, M., De Lartigue, G., German, J. B., Raybould, H. E., & Mills, D. A. (2012) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0b013e31824fb899 · Cited by 276
Self-citationGlycan Utilization and Cross-Feeding Activities by Bifidobacteria
Turroni, F., Milani, C., Duranti, S., Mahony, J., van Sinderen, D., & Ventura, M. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2017.10.001 · Cited by 263
LoCascio, R. G., Desai, P., Sela, D. A., Weimer, B., & Mills, D. A. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00675-10 · Cited by 229
Garrido, D., Dallas, D. C., & Mills, D. A. (2013) · Microbiology · doi:10.1099/mic.0.064113-0 · Cited by 228
An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides
Sela, D. A., Li, Y., Lerno, L., Wu, S., Marcobal, A. M., German, J. B., Chen, X., Lebrilla, C. B., & Mills, D. A. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.193359 · Cited by 192
Salazar, N., Gueimonde, M., de los Reyes-Gavilán, C. G., & Ruas-Madiedo, P. (2016) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2013.770728 · Cited by 188
Feeding the microbiota: Transducer of nutrient signals for the host
Shanahan, F., van Sinderen, D., O’Toole, P. W., & Stanton, C. (2017) · Gut · doi:10.1136/gutjnl-2017-313872 · Cited by 157
Validating bifidobacterial species and subspecies identity in commercial probiotic products
Lewis, Z. T., Shani, G., Masarweh, C. F., Popovic, M., Frese, S. A., Sela, D. A., Underwood, M. A., & Mills, D. A. (2016) · Pediatric Research · doi:10.1038/pr.2015.244 · Cited by 154
Self-citationBarrangou, R., Briczinski, E. P., Traeger, L. L., Loquasto, J. R., Richards, M., Horvath, P., Coûté-Monvoisin, A.-C., Leyer, G., Rendulic, S., Steele, J. L., et al. (2009) · Journal of Bacteriology · doi:10.1128/jb.00155-09 · Cited by 150
A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract
Garrido, D., Barile, D., & Mills, D. A. (2012) · Advances in Nutrition · doi:10.3945/an.111.001586 · Cited by 149
Self-citationFactors influencing the gut microbiome in children: from infancy to childhood
Kumbhare, S. V., Patangia, D. V., Patil, R. H., Shouche, Y. S., & Patil, N. P. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9860-z · Cited by 143
Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates
Tao, N., Wu, S., Kim, J., An, H. J., Hinde, K., Power, M. L., Gagneux, P., German, J. B., & Lebrilla, C. B. (2011) · Journal of Proteome Research · doi:10.1021/pr1009367 · Cited by 132
Self-citationGuglielmetti, S., Fracassetti, D., Taverniti, V., Del Bo’, C., Vendrame, S., Klimis-Zacas, D., Arioli, S., Riso, P., & Porrini, M. (2013) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf402495k · Cited by 123
Xiao, M., Zhang, C., Duan, H., Narbad, A., Zhao, J., Chen, W., Zhai, Q., Yu, L., & Tian, F. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00524-6 · Cited by 120
Song, Y., Malmuthuge, N., Steele, M. A., & Guan, L. L. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix179 · Cited by 115
Healthy hosts rule within: ecological forces shaping the gut microbiota
Byndloss, M. X., Pernitzsch, S. R., & Bäumler, A. J. (2018) · Mucosal Immunology · doi:10.1038/s41385-018-0010-y · Cited by 109
Avershina, E., Storrø, O., Øien, T., Johnsen, R., Wilson, R., Egeland, T., & Rudi, K. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.02359-12 · Cited by 101
Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria
Casaburi, G., Duar, R. M., Vance, D. P., Mitchell, R., Contreras, L., Frese, S. A., Smilowitz, J. T., & Underwood, M. A. (2019) · Antimicrobial Resistance & Infection Control · doi:10.1186/s13756-019-0583-6 · Cited by 101
Wickramasinghe, S., Pacheco, A. R., Lemay, D. G., & Mills, D. A. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0508-3 · Cited by 86
Self-citationKatoh, T., Ojima, M. N., Sakanaka, M., Ashida, H., Gotoh, A., & Katayama, T. (2020) · Microorganisms · doi:10.3390/microorganisms8040481 · Cited by 80
Obesogens: How They Are Identified and Molecular Mechanisms Underlying Their Action
Mohajer, N., Du, C. Y., Checkcinco, C., & Blumberg, B. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.780888 · Cited by 72
Duar, R. M., Kyle, D., & Casaburi, G. (2020) · High-Throughput · doi:10.3390/ht9020007 · Cited by 70
Odamaki, T., Horigome, A., Sugahara, H., Hashikura, N., Minami, J., Xiao, J.-Z., & Abe, F. (2015) · International Journal of Genomics · doi:10.1155/2015/567809 · Cited by 50
Differding, M. K., Doyon, M., Bouchard, L., Perron, P., Guérin, R., Asselin, C., Massé, E., Hivert, M., & Mueller, N. T. (2020) · Pediatric Obesity · doi:10.1111/ijpo.12642 · Cited by 49
Arboleya, S., Stanton, C., Ryan, C. A., Dempsey, E., & Ross, P. R. (2016) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-041715-033151 · Cited by 41
Casaburi, G., & Frese, S. A. (2018) · Human Microbiome Journal · doi:10.1016/j.humic.2018.05.001 · Cited by 38
Derrien, M., Mikulic, N., Uyoga, M. A., Chenoll, E., Climent, E., Howard-Varona, A., Nyilima, S., Stoffel, N. U., Karanja, S., Kottler, R., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2178793 · Cited by 36
O’Connell Motherway, M., O’Brien, F., O’Driscoll, T., Casey, P. G., Shanahan, F., & van Sinderen, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-29034-0 · Cited by 29
Kijner, S., Ennis, D., Shmorak, S., Florentin, A., & Yassour, M. (2024) · Nature Communications · doi:10.1038/s41467-023-44437-y · Cited by 25
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Van Rossum, T., Costea, P. I., Paoli, L., Alves, R., Thielemann, R., Sunagawa, S., & Bork, P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btab789 · Cited by 23
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Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.007 · Cited by 17
Wei, X., Yu, L., Zhang, C., Ni, Y., Zhang, H., Zhai, Q., & Tian, F. (2023) · Foods · doi:10.3390/foods12050922 · Cited by 17
Gao, W., Xiao, M., Gu, Z., Fu, X., Ren, X., Yu, Y., Liu, Z., Zhu, C., Kong, Q., & Mou, H. (2022) · Molecular Genetics and Genomics · doi:10.1007/s00438-022-01937-8 · Cited by 10
Freitas, A. C., Li, G., Shawon, J., Qamar, H., Pell, L. G., Kabir, M., Oduaran, O. H., Puebla-Barragan, S., Bassani, D. G., O'Callaghan, K. M., et al. (2025) · mSphere · doi:10.1128/msphere.00314-25 · Cited by 6
Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort
Mudhluli, T. E., Kujawska, M., Mueller, J., Felsl, A., Truppel, B.-A., Hall, L. J., Chitsike, I., Gomo, E., & Zhou, D. T. (2024) · BMC Genomics · doi:10.1186/s12864-024-10618-2 · Cited by 3
Metadata
- Authors
- Sela, D. A., Chapman, J., Adeuya, A., Kim, J. H., Chen, F., Whitehead, T. R., Lapidus, A., Rokhsar, D. S., Lebrilla, C. B., German, J. B., Price, N. P., Richardson, P. M., & Mills, D. A.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2008-12-02
- Volume
- 105
- Issue
- 48
- Pages
- 18964-18969
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1984600160
- Cited by
- 883
- References
- 6
- FWCI
- 27.43
- Type
- journal article
- Language
- en
- Open access
- green
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