Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides
Open accessAbstract
The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants (n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis (B. infantis) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum. Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III (Se+, Le-) (22%) than in most previously studied populations, with an enrichment in 2′-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis, and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.
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The HMO composition in the milk of African mothers appears to differ from that of mothers from Westernized cohorts, with a lower content of fucosylated HMO.
“The HMO composition in the milk of African mothers appears to differ from that of mothers from Westernized cohorts, with a lower content of fucosylated HMO [98,99] , altering the availability of a useful substrate for B. bifidum , hypothetically favoring strains harboring the specific fucosidase gene variants.”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [99]
The Introduction says HMO profiles vary by geographic location, and the Discussion reports that a Lewis-defined milk group was more prevalent in the rural Kenyan cohort than in most other populations studied. But neither passage establishes that African mothers generally have less fucosylated HMO than mothers in Westernized cohorts; the Results compare HMO abundance chiefly between maternal milk phenotypes, not those populations. Page numbers are unavailable in our copy. (LLM, conf=0.82)
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Cites
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · see citing works
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Estimation of Average Concentration in the Presence of Nondetectable Values
Hornung, R. W., & Reed, L. D. (1990) · Applied Occupational and Environmental Hygiene · doi:10.1080/1047322x.1990.10389587 · Cited by 3,495 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Multivariable association discovery in population-scale meta-omics studies
Mallick, H., Rahnavard, A., McIver, L. J., Ma, S., Zhang, Y., Nguyen, L. H., Tickle, T. L., Weingart, G., Ren, B., Schwager, E. H., et al. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009442 · Cited by 2,596 · see citing works
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., & Yin, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky418 · Cited by 2,224 · see citing works
Temporal development of the gut microbiome in early childhood from the TEDDY study
Stewart, C. J., Ajami, N. J., O’Brien, J. L., Hutchinson, D. S., Smith, D. P., Wong, M. C., Ross, M. C., Lloyd, R. E., Doddapaneni, H., Metcalf, G., et al. (2018) · Nature · doi:10.1038/s41586-018-0617-x · Cited by 1,996 · see citing works
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 · see citing works
BBMerge – Accurate paired shotgun read merging via overlap
Bushnell, B., Rood, J., & Singer, E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185056 · Cited by 1,495 · see citing works
The composition of the gut microbiota throughout life, with an emphasis on early life
Rodríguez, J. M., Murphy, K., Stanton, C., Ross, R. P., Kober, O. I., Juge, N., Avershina, E., Rudi, K., Narbad, A., Jenmalm, M. C., et al. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26050 · Cited by 1,320 · 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 878 · see citing works
Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics
Holmes, I. H., Harris, K. J., & Quince, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030126 · Cited by 834 · see citing works
Bifidobacteria-mediated immune system imprinting early in life
Henrick, B. M., Rodriguez, L., Lakshmikanth, T., Pou, C., Henckel, E., Arzoomand, A., Olin, A., Wang, J., Mikeš, J., Tan, Z., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.030 · Cited by 808 · see citing works
The Human Microbiome and Child Growth – First 1000 Days and Beyond
Robertson, R. C., Manges, A. R., Finlay, B. B., & Prendergast, A. J. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.09.008 · Cited by 793 · see citing works
Dynamics and stabilization of the human gut microbiome during the first year of life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.05.012 · Cited by 738 · see citing works
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 · see citing works
Jaeggi, T., Kortman, G. A. M., Moretti, D., Chassard, C., Holding, P., Dostal, A., Boekhorst, J., Timmerman, H. M., Swinkels, D. W., Tjalsma, H., et al. (2015) · Gut · doi:10.1136/gutjnl-2014-307720 · Cited by 622 · see citing works
Self-citationQin, Y., Havulinna, A. S., Liu, Y., Jousilahti, P., Ritchie, S. C., Tokolyi, A., Sanders, J. G., Valsta, L., Brożyńska, M., Zhu, Q., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00991-z · Cited by 586 · see citing works
Lewis, Z. T., Totten, S. M., Smilowitz, J. T., Popović, M., Parker, E. A., Lemay, D. G., Tassell, M. L. V., Miller, M. J., Jin, Y., German, J. B., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0071-z · Cited by 413 · see citing works
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 · see citing works
Systematic review of the concentrations of oligosaccharides in human milk
Thurl, S., Munzert, M., Boehm, G., Matthews, C., & Stahl, B. (2017) · Nutrition Reviews · doi:10.1093/nutrit/nux044 · Cited by 407 · see citing works
Self-citationMcGuire, M. K., Meehan, C. L., McGuire, M. A., Williams, J. E., Foster, J., Sellen, D., Kamau‐Mbuthia, E. W., Kamundia, E. W., Mbugua, S., Moore, S. E., et al. (2017) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.116.139980 · Cited by 397 · see citing works
A key genetic factor for fucosyllactose utilization affects infant gut microbiota development
Matsuki, T., Yahagi, K., Mori, H., Matsumoto, H., Hara, T., Tajima, S., Ogawa, E., Kodama, H., Yamamoto, K., Yamada, T., et al. (2016) · Nature Communications · doi:10.1038/ncomms11939 · Cited by 376 · see citing works
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 374 · see citing works
Lawson, M. A., O’Neill, I. J., Kujawska, M., Javvadi, S. G., Wijeyesekera, A., Flegg, Z., Chalklen, L., & Hall, L. J. (2019) · The ISME Journal · doi:10.1038/s41396-019-0553-2 · Cited by 369 · see citing works
Human milk oligosaccharides: Shaping the infant gut microbiota and supporting health
Walsh, C., Lane, J. A., van Sinderen, D., & Hickey, R. M. (2020) · Journal of Functional Foods · doi:10.1016/j.jff.2020.104074 · Cited by 355 · see citing works
Tsukuda, N., Yahagi, K., Hara, T., Watanabe, Y., Matsumoto, H., Mori, H., Higashi, K., Tsuji, H., Matsumoto, S., Kurokawa, K., et al. (2021) · The ISME Journal · doi:10.1038/s41396-021-00937-7 · Cited by 324 · see citing works
Newburg, D. S., Ruiz-Palacios, G. M., Altaye, M., Chaturvedi, P., Meinzen‐Derr, J. K., Guerrero, M. D. L., & Morrow, A. L. (2003) · Glycobiology · doi:10.1093/glycob/cwh020 · Cited by 252 · see citing works
Ruiz‐Moyano, S., Totten, S. M., Garrido, D. A., Smilowitz, J. T., German, J. B., Lebrilla, C. B., & Mills, D. A. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01843-13 · Cited by 236 · see citing works
Wang, M., Li, M., Wu, S., Lebrilla, C. B., Chapkin, R. S., Ivanov, I. V., & Donovan, S. M. (2015) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000000752 · Cited by 232 · see citing works
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 · see citing works
Vatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0321-5 · Cited by 216 · see citing works
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles
Olm, M. R., Dahan, D., Carter, M. M., Merrill, B. D., Yu, F. B., Jain, S., Meng, X., Tripathi, S. M., Wastyk, H. C., Neff, N. F., et al. (2022) · Science · doi:10.1126/science.abj2972 · Cited by 210 · see citing works
Davis, J. C. C., Lewis, Z. T., Krishnan, S., Bernstein, R. M., Moore, S. E., Prentice, A. M., Mills, D. A., Lebrilla, C. B., & Zivkovic, A. M. (2017) · Scientific Reports · doi:10.1038/srep40466 · Cited by 187 · see citing works
de Nies, L., Lopes, S., Busi, S. B., Galata, V., Heintz‐Buschart, A., Laczny, C. C., May, P., & Wilmes, P. (2021) · Microbiome · doi:10.1186/s40168-020-00993-9 · Cited by 186 · see citing works
Young, S. L., Simon, M. A., Baird, M. A., Tannock, G. W., Bibiloni, R., Spencely, K., Lane, J. M., Fitzharris, P., Crane, J., Town, I., et al. (2004) · Clinical and Vaccine Immunology · doi:10.1128/cdli.11.4.686-690.2004 · Cited by 175 · see citing works
Bunešová, V., Lacroix, C., & Schwab, C. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0867-4 · Cited by 173 · see citing works
Paganini, D., Uyoga, M. A., Kortman, G. A. M., Cercamondi, C. I., Moretti, D., Barth-Jaeggi, T., Schwab, C., Boekhorst, J., Timmerman, H. M., Lacroix, C., et al. (2017) · Gut · doi:10.1136/gutjnl-2017-314418 · Cited by 172 · see citing works
Self-citationBarratt, M. J., Nuzhat, S., Ahsan, K., Frese, S. A., Arzamasov, A. A., Sarker, S. A., Islam, M. M., Palit, P., Islam, M. R., Hibberd, M. C., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abk1107 · Cited by 169 · see citing works
Gotoh, A., Katoh, T., Sakanaka, M., Ling, Y., Yamada, C., Asakuma, S., Urashima, T., Tomabechi, Y., Katayama-Ikegami, A., Kurihara, S., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-32080-3 · Cited by 167 · see citing works
Distinct Gut Microbiota in Southeastern African and Northern European Infants
Grześkowiak, Ł., Collado, M. C., Mangani, C., Maleta, K. M., Laitinen, K., Ashorn, P., Isolauri, E., & Salminen, S. (2012) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0b013e318249039c · Cited by 163 · see citing works
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
Bifidobacterium Abundance in Early Infancy and Vaccine Response at 2 Years of Age
Huda, M. N., Ahmad, S. M., Alam, J., Khanam, A., Kalanetra, K. M., Taft, D. H., Raqib, R., Underwood, M. A., Mills, D. A., & Stephensen, C. B. (2019) · PEDIATRICS · doi:10.1542/peds.2018-1489 · Cited by 157 · see citing works
Successional Stages in Infant Gut Microbiota Maturation
Beller, L., Deboutte, W., Falony, G., Vieira‐Silva, S., Tito, R. Y., Valles‐Colomer, M., Rymenans, L., Jansen, D., Espen, L. V., Papadaki, M. I., et al. (2021) · mBio · doi:10.1128/mbio.01857-21 · Cited by 137 · see citing works
Korpela, K., Salonen, A., Hickman, B., Kunz, C., Sprenger, N., Kukkonen, A. K., Savilahti, E., Kuitunen, M., & de Vos, W. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-32037-6 · Cited by 118 · see citing works
Mucosal glycan degradation of the host by the gut microbiota
Bell, A., & Juge, N. (2020) · Glycobiology · doi:10.1093/glycob/cwaa097 · Cited by 111 · see citing works
Bai, Y., Tao, J., Zhou, J., Fan, Q., Liu, M., Hu, Y., Yao, X., Zhang, L., Yuan, J., Li, W., et al. (2018) · mSystems · doi:10.1128/msystems.00206-18 · Cited by 103 · see citing works
Zeng, S., Patangia, D. V., Almeida, A., Zhou, Z., Mu, D., Ross, R. P., Stanton, C., & Wang, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32805-z · Cited by 103 · see citing works
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 · see citing works
Borewicz, K., Gu, F., Saccenti, E., Hechler, C., Beijers, R., de Weerth, C., van Leeuwen, S. S., Schols, H. A., & Smidt, H. (2020) · Scientific Reports · doi:10.1038/s41598-020-61024-z · Cited by 93 · see citing works
Untangling human milk oligosaccharides and infant gut microbiome
Masi, A. C., & Stewart, C. J. (2021) · iScience · doi:10.1016/j.isci.2021.103542 · Cited by 93 · see citing works
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Coelho, L. P., Alves, R., Monteiro, P., Huerta‐Cepas, J., Freitas, A. T., & Bork, P. (2019) · Microbiome · doi:10.1186/s40168-019-0684-8 · Cited by 86 · see citing works
de Goffau, M. C., Jallow, A. T., Sanyang, C., Prentice, A. M., Meagher, N., Price, D. J., Revill, P. A., Parkhill, J., Pereira, D. I. A., & Wagner, J. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01023-6 · Cited by 82 · see citing works
Urine profiling using capillary electrophoresis-mass spectrometry and multivariate data analysis
Ullsten, S., Danielsson, R., Bäckström, D., Sjöberg, P. J. R., & Bergquist, J. (2006) · Journal of Chromatography A · doi:10.1016/j.chroma.2006.03.048 · Cited by 80 · see citing works
Kumar, H., Collado, M. C., Wopereis, H., Salminen, S., Knol, J., & Roeselers, G. (2020) · Microorganisms · doi:10.3390/microorganisms8121855 · Cited by 80 · see citing works
Seppo, A., Bu, K., Jumabaeva, M., Thakar, J., Choudhury, R. A., Yonemitsu, C., Bode, L., Martina, C. A., Allen, M., Tamburini, S., et al. (2021) · Allergy · doi:10.1111/all.14877 · Cited by 78 · see citing works
Extensive polymorphism of the FUT2 gene in an African (Xhosa) population of South Africa
Liu, Y., Koda, Y., Soejima, M., Pang, H., Schlaphoff, T., du Toit, E. D., & Kimurâ, H. (1998) · Human Genetics · doi:10.1007/s004390050808 · Cited by 77 · see citing works
Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal
James, K., Bottacini, F., Serrano-Contreras, J. I., Vigoureux, M., Egan, M., Motherway, M. O., Holmes, E. C., & van Sinderen, D. (2019) · Scientific Reports · doi:10.1038/s41598-019-51901-7 · Cited by 76 · see citing works
Casaburi, G., Duar, R. M., Brown, H. K., Mitchell, R. D., Kazi, S., Chew, S., Cagney, O., Flannery, R. L., Sylvester, K. G., Frese, S. A., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-80583-9 · Cited by 75 · see citing works
Human milk: From complex tailored nutrition to bioactive impact on child cognition and behavior
de Weerth, C., Aatsinki, A., Azad, M. B., Bartol, F. F., Bode, L., Collado, M. C., Dettmer, A. M., Field, C. J., Guilfoyle, M. M., Hinde, K., et al. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2022.2053058 · Cited by 71 · see citing works
Duar, R. M., Kyle, D., & Casaburi, G. (2020) · High-Throughput · doi:10.3390/ht9020007 · Cited by 70 · see citing works
The human gut microbiota during the initial stages of life: insights from bifidobacteria
Turroni, F., Milani, C., Ventura, M., & van Sinderen, D. (2021) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2021.07.012 · Cited by 70 · see citing works
Walsh, C., Lane, J. A., van Sinderen, D., & Hickey, R. M. (2020) · Journal of Functional Foods · doi:10.1016/j.jff.2020.104052 · Cited by 66 · see citing works
Human Milk Oligosaccharide Compositions Illustrate Global Variations in Early Nutrition
Vinjamuri, A., Davis, J. C. C., Totten, S. M., Wu, L. D., Klein, L. D., Martin, M., Quinn, E. A., Scelza, B., Breakey, A., Gurven, M., et al. (2022) · The Journal of Nutrition · doi:10.1093/jn/nxac027 · Cited by 53 · see citing works
Paganini, D., Uyoga, M. A., Kortman, G. A. M., Boekhorst, J., Schneeberger, S., Karanja, S. M., Hennet, T., & Zimmermann, M. B. (2019) · Nutrients · doi:10.3390/nu11112596 · Cited by 49 · see citing works
Self-citationKottler, R., Mank, M., Hennig, R., Müller‐Werner, B., Stahl, B., Reichl, U., & Rapp, E. (2013) · Electrophoresis · doi:10.1002/elps.201300016 · Cited by 48 · see citing works
Self-citationHuman Milk Oligosaccharide Profiles over 12 Months of Lactation: The Ulm SPATZ Health Study
Siziba, L. P., Mank, M., Stahl, B., Gonsalves, J., Blijenberg, B., Rothenbacher, D., & Genuneit, J. (2021) · Nutrients · doi:10.3390/nu13061973 · Cited by 45 · see citing works
Self-citationGut microbiota in Malawian infants in a nutritional supplementation trial
Cheung, Y. B., Xu, Y., Mangani, C., Fan, Y., Dewey, K. G., Salminen, S., Maleta, K. M., & Ashorn, P. (2015) · Tropical Medicine & International Health · doi:10.1111/tmi.12650 · Cited by 29 · see citing works
Lawley, B., Otal, A., Moloney‐Geany, K., Diana, A., Houghton, L. A., Heath, A. M., Taylor, R. W., & Tannock, G. W. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.01105-19 · Cited by 29 · see citing works
Fonvig, C. E., Amundsen, I. D., Vigsnæs, L. K., Sørensen, N., Frithioff‐Bøjsøe, C., Michael, C., Hedley, P. L., Holm, L. A., McConnell, B., & Holm, J. (2021) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000003205 · Cited by 28 · see citing works
Hundshammer, C., & Minge, O. (2020) · Nutrients · doi:10.3390/nu12113568 · Cited by 25 · see citing works
Eussen, S. R. B. M., Mank, M., Kottler, R., Hoffmann, X., Behne, A., Rapp, E., Stahl, B., Mearin, M. L., & Koletzko, B. V. (2021) · Nutrients · doi:10.3390/nu13072324 · Cited by 25 · see citing works
Self-citationVigsnæs, L. K., Ghyselinck, J., den Abbeele, P. V., McConnell, B., Moens, F., Marzorati, M., & Bajic, D. (2021) · Pathogens · doi:10.3390/pathogens10080927 · Cited by 22 · see citing works
Tso, L., Bonham, K. S., Fishbein, A., Rowland, S., & Klepac‐Ceraj, V. (2021) · Nutrients · doi:10.3390/nu13082833 · Cited by 20 · see citing works
Human milk nutritional composition across lactational stages in Central Africa
Moya‐Alvarez, V., Eussen, S. R. B. M., Mank, M., Koyembi, J.-C. J., Nyasenu, Y. T., Ngaya, G., Mad‐Bondo, D., Kongoma, J., Stahl, B., Sansonetti, P. J., et al. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.1033005 · Cited by 13 · see citing works
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Lordan, C., Roche, A. K., Delsing, D. J. M., Nauta, A., Groeneveld, A., MacSharry, J. A., Cotter, P. D., & van Sinderen, D. (2024) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00094-23 · Cited by 113 · see citing works
Gut microbiota development across the lifespan: Disease links and health‐promoting interventions
Schoultz, I., Claesson, M. J., Domínguez-Bello, M. G., Hållenius, F. F., Konturek, P. C., Korpela, K., Laursen, M. F., Penders, J., Roager, H. M., Vatanen, T., et al. (2025) · Journal of Internal Medicine · doi:10.1111/joim.20089 · Cited by 93 · see citing works
Ennis, D., Shmorak, S., Jantscher‐Krenn, E., & Yassour, M. (2024) · Nature Communications · doi:10.1038/s41467-024-45209-y · Cited by 60 · see citing works
Paternal and induced gut microbiota seeding complement mother-to-infant transmission
Dubois, L., Valles‐Colomer, M., Ponsero, A. J., Helve, O., Andersson, S., Kolho, K.-L., Asnicar, F., Korpela, K., Salonen, A., Segata, N., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.004 · Cited by 61 · see citing works
Arzamasov, A. A., Rodionov, D. A., Hibberd, M. C., Guruge, J. L., Kent, J. E., Kazanov, M. D., Leyn, S. A., Elane, M. L., Sejane, K., Fürst, A., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02056-x · Cited by 53 · see citing works
Early-life exposures and the microbiome: implications for IBD prevention
Zhang, L., Agrawal, M., Ng, S. C., & Jess, T. (2023) · Gut · doi:10.1136/gutjnl-2023-330002 · Cited by 49 · see citing works
The gut core microbial species Bifidobacterium longum: Colonization, mechanisms, and health benefits
Xiao, Y., Huang, L., Zhao, J., Chen, W., & Lu, W. (2024) · Microbiological Research · doi:10.1016/j.micres.2024.127966 · Cited by 31 · see citing works
Matharu, D., Ponsero, A. J., Lengyel, M., Meszaros-Matwiejuk, A., Kolho, K., de Vos, W. M., Molnár-Gábor, D., & Salonen, A. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105182 · Cited by 29 · see citing works
Ayeni, K. I., Seki, D., Pjevac, P., Hausmann, B., Krausová, M., Braun, D., Wisgrill, L., Berry, D., Warth, B., & Ezekiel, C. N. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.3c07786 · Cited by 23 · see citing works
Human milk oligosaccharides and polyphenols: Mechanisms, effects, and applications in allergies
den Elzen, C. C. M., Carvalho, A., Bazan‐Socha, S., Jeurink, P. V., Wygrecka, M., Kool, M., Garssen, J., Potaczek, D. P., Garn, H., & van Esch, B. C. A. M. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.09.029 · Cited by 21 · see citing works
Ladeira, R., Tap, J., & Derrien, M. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2023.01 · Cited by 19 · see citing works
Self-citationNeonatal microbiome in the multiomics era: development and its impact on long-term health
Neu, J., & Stewart, C. J. (2025) · Pediatric Research · doi:10.1038/s41390-025-03953-x · Cited by 17 · see citing works
A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa
Pheeha, S. M., Tamuzi, J. L., Chale-Matsau, B., Manda, S., & Nyasulu, P. S. (2023) · Microorganisms · doi:10.3390/microorganisms11082118 · Cited by 13 · see citing works
Cabrera, P. M., Rachmühl, C., Derrien, M., Bourdet‐Sicard, R., Lacroix, C., & Geirnaert, A. (2024) · ISME Communications · doi:10.1093/ismeco/ycae033 · Cited by 13 · see citing works
Self-citationAl‐Beltagi, M. (2025) · World Journal of Clinical Pediatrics · doi:10.5409/wjcp.v14.i2.104797 · Cited by 14 · see citing works
Houngbédji, M., Jespersen, J. S., Padonou, S. W., & Jespersen, L. (2024) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2024.2365342 · Cited by 10 · see citing works
FXR protects against neonatal sepsis by enhancing the immunosuppressive function of MDSCs
He, J., Zhang, Y., Jing, Y., Dong, R., Li, T., Zheng, X., Zhou, P., Shi, K., Zhong, W., Liu, Q., et al. (2025) · Cellular and Molecular Immunology · doi:10.1038/s41423-025-01289-4 · Cited by 10 · see citing works
A Systematic Review of Isotopically Measured Iron Absorption in Infants and Children Under 2 Years
Gallahan, S., Brower, S., Wapshott‐Stehli, H. L., dos Santos, J. B., & Ho, T. T. B. (2024) · Nutrients · doi:10.3390/nu16223834 · Cited by 9 · see citing works
Zou, X., Zhou, X., Wang, C., Zheng, Y., Li, Y., & Suo, H. (2025) · Food & Function · doi:10.1039/d5fo02271a · Cited by 8 · see citing works
Kaktcham, P. M., Kujawska, M., Kouam, E. M. F., Piame, L. T., Tientcheu, M. L. T., Mueller, J., Felsl, A., Truppel, B.-A., Ngoufack, F. Z., & Hall, L. J. (2025) · Microbial Genomics · doi:10.1099/mgen.0.001354 · Cited by 6 · see citing works
Rachmühl, C., Lacroix, C., Cabrera, P. M., & Geirnaert, A. (2023) · Scientific Reports · doi:10.1038/s41598-023-47131-7 · Cited by 6 · see citing works
Fan, W., Mu, C., Li, X., Zhang, Y., Yu, K., Su, Y., & Zhu, W. (2025) · Animal nutrition · doi:10.1016/j.aninu.2025.04.015 · Cited by 4 · see citing works
Hellinga, A. H., Cajic, S., Linde, H. F., van Stigt, A. H., de Vries, J. H. M., Brouwer-Brolsma, E. M., Hennig, R., Rapp, E., Mank, M., Stahl, B., et al. (2025) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.70165 · Cited by 2 · see citing works
Self-citationJiang, J., Poulsen, C. S., Boulund, U., Shah, S. A., Trivedi, U., Bhattacharyya, M., Neumann, A. U., Dai, D. L. Y., Petersen, C., Hoskinson, C., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71185-6 · Cited by 1 · see citing works
Ovaska, M., Tamminen, M. V., Lahdenperä, M., Rautava, S., Jeevannavar, A., Isokääntä, H., Bode, L., & Lagström, H. (2026) · American Journal of Clinical Nutrition · doi:10.1016/j.ajcnut.2026.101318 · Cited by 1 · see citing works
Modular microgel flow reactors for automated glycan synthesis with immobilized enzymes
Hussnaetter, K. P., Pieper, M. I., Thiele, U., Palm, P., Burock, R., Hennig, R., Bleher, K., Pich, A., Franzreb, M., Rapp, E., et al. (2026) · Chemical Engineering Journal · doi:10.1016/j.cej.2026.178229 · Cited by 1 · see citing works
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
Ennis, D., Shmorak, S., Jantscher‐Krenn, E., & Yassour, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.17.549354
Fan, W., Mu, C., Li, X., Zhang, Y., & Zhu, W. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.5064871
HARINI, P., Dinesh, S., & PALANISWAMY, R. (2025) · Innovare Journal of Medical Sciences · doi:10.22159/ijms.2025v13i3.54218
Duan, R., Wang, K., & Duan, L. P. (2026) · Medical Review · doi:10.1515/mr-2026-0008
Parizadeh, M., Laforest‐Lapointe, I., Serrano-Vázquez, A., Morán-Silva, P., Rojas-Velázquez, L., Torres, J., Ximénez-García, C., & Arrieta, M. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag124
Guo, W., Zhang, W., Yang, L., Zachariasen, T., Li, X., Stokholm, J., Dai, M., Thorsen, J., Sørensen, S. J., & Trivedi, U. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.13.737801
Babu, P., Prakash, V., Subhash, S., Vanuopadath, M., Haripriyan, J., Rajan, K., Anu, A. G., Padmakumar, S., Kumar, G. B., Nair, B. G., et al. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1905445 · Cited by 1 · see citing works
Global biogeography of Bifidobacterium infantis : stratification and precision probiotic design
Deng, X., & Yang, J. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2732532
Ringlander, J., Andersson, M., Ndagijimana, A., Dusingizimana, T., Lind, T., & Elfving, K. (2026) · Scientific Reports · doi:10.1038/s41598-026-72042-8
- Authors
- Derrien, M., Mikulic, N., Uyoga, M. A., Chenoll, E., Climent, E., Howard-Varona, A., Nyilima, S., Stoffel, N. U., Karanja, S., Kottler, R., Stahl, B., Zimmermann, M. B., & Bourdet-Sicard, R.
- Affiliations
- Danone (France) (FR)
- ETH Zurich (CH)
- Universitat de València (ES)
- Jomo Kenyatta University of Agriculture and Technology (KE)
- glyXera GmbH, Magdeburg, Germany
- Utrecht University (NL)
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
- Corresponding author
- Derrien, Muriel
- ORCID
- Venue
- Gut Microbes
- Publisher
- Informa UK Limited
- Published
- 2023-02-16
- Volume
- 15
- Issue
- 1
- Pages
- 2178793-2178793
- ISSN
- 1949-0976 (ISSN-L)
- 1949-0984
- PMC
- PMC9980514
- OpenAlex
- W4321003201
- Cited by
- 36
- References
- 78
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 10 · 2023: 5
- FWCI
- 3.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Gut Microbes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lirias (KU Leuven) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Funders
- Danone
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- infant gut microbiota, human milk oligosaccharides, Bifidobacterium infantis, Bifidobacterium longum, Bifidobacterium breve, 2'-fucosyllactose, breast milk, rural infants, pan-genome, pathogenic genes
- MeSH terms
- Gastrointestinal Microbiome, Bifidobacterium, Humans, Infant, Kenya, Milk, Human, Oligosaccharides
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