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Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life
Open accessAbstract
Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child's life. We identified mother-to-child bacterial transmission events and describe the incidence of family-specific antibiotic resistance genes. We observed two inheritance patterns across multiple species, where often the mother's dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant gut. In families where the secondary strain of B. uniformis was inherited, a starch utilization gene cluster that was absent in the mother's dominant strain was identified in the child, suggesting the selective advantage of a mother's secondary strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high resolution and give insights into early colonization of the infant gut.
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“Although it is unlikely that infants acquire many of such species directly from food consumption since maternal transmission is the most probable route of acquisition, 103-105”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [103]
Experimental — accuracy not yet measuredIn the citing paper
“that have been found to be highly transmitted from mother to child in several studies10,15,16,17,41 and that are also present but not shared in pairs from non-westernized populations (Figure 2C).”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [17]
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“While Escherichia coli and Bifidobacterium spp. are the most shared within the European pairs, as previously described,10,15,16,17,41”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [17]
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
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
The carbohydrate-active enzymes database (CAZy) in 2013
Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,452
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis
Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413
Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774
Host-gut microbiota metabolic interactions
Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012) · Science · doi:10.1126/science.1223813 · Cited by 4,760
Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria
Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554
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
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
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Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
Self-citationStunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Shao, Y., Forster, S. C., Tsaliki, E., Vervier, K., Strang, A., Simpson, N., Kumar, N., Stares, M. D., Rodger, A., Brocklehurst, P., et al. (2019) · Nature · doi:10.1038/s41586-019-1560-1 · Cited by 1,088
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
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Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748
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Barcik, W., Boutin, R. C. T., Sokołowska, M., & Finlay, B. B. (2020) · Immunity · doi:10.1016/j.immuni.2020.01.007 · Cited by 636
Intergenerational and transgenerational epigenetic inheritance in animals
Perez, M. F., & Lehner, B. (2019) · Nature Cell Biology · doi:10.1038/s41556-018-0242-9 · Cited by 528
Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00797-0 · Cited by 537
The person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449
Gut Bacteria and Neurotransmitters
Dicks, L. M. T. (2022) · Microorganisms · doi:10.3390/microorganisms10091838 · Cited by 482
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy, K. M., de Goffau, M. C., Pérez-Muñoz, M. E., Arrieta, M., Bäckhed, F., Bork, P., Braun, T., Bushman, F. D., Dore, J. M., de Vos, W. M., et al. (2023) · Nature · doi:10.1038/s41586-022-05546-8 · Cited by 415
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 386
The Long-Term Genetic Stability and Individual Specificity of the Human Gut Microbiome
Chen, L., Wang, D., Garmaeva, S., Kurilshikov, A., Vila, A. V., Gaćeša, R., Sinha, T., Study, L. C., Segal, E., Weersma, R. K., et al. (2020) · Cell · doi:10.1016/j.cell.2021.03.024 · Cited by 344
The microbiome extends host evolutionary potential
Henry, L. P., Bruijning, M., Forsberg, S. K. G., & Ayroles, J. F. (2021) · Nature Communications · doi:10.1038/s41467-021-25315-x · Cited by 373
Understanding the impact of antibiotic perturbation on the human microbiome
Schwartz, D. J., Langdon, A. E., & Dantas, G. A. (2020) · Genome Medicine · doi:10.1186/s13073-020-00782-x · Cited by 348
Wampach, L., Heintz-Buschart, A., Fritz, J. V., Ramiro-Garcia, J., Habier, J., Herold, M., Narayanasamy, S., Kaysen, A., Hogan, A. H., Bindl, L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07631-x · Cited by 292
Li, X. O., Li, X. O., Xia, B., Jin, X., Zou, Q., Zeng, Z., Zhao, W., Yan, S., Li, L., Yuan, S., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.02.002 · Cited by 316
Viable bacterial colonization is highly limited in the human intestine in utero
Rackaityte, E., Halkias, J., Fukui, E., Mendoza, V. F., Hayzelden, C., Crawford, E. D., Fujimura, K. E., Burt, T. D., & Lynch, S. V. (2020) · Nature Medicine · doi:10.1038/s41591-020-0761-3 · Cited by 310
Evolutionary and Ecological Consequences of Gut Microbial Communities
Moran, N. A., Ochman, H., & Hammer, T. J. (2019) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062453 · Cited by 290
Co-evolution and Co-speciation of Host-Gut Bacteria Systems
Groussin, M., Mazel, F., & Alm, E. J. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.013 · Cited by 292
Factors affecting early-life intestinal microbiota development
Vandenplas, Y., Carnielli, V. P., Ksiazyk, J., Luna, M. S., Migacheva, N., Mosselmans, J. M., Picaud, J. C., Possner, M., Singhal, A., & Wabitsch, M. (2020) · Nutrition · doi:10.1016/j.nut.2020.110812 · Cited by 247
Transmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 248
Maternal vertical transmission affecting early-life microbiota development
Wang, S., Ryan, C. A., Boyaval, P., Dempsey, E. M., Ross, R. P., & Stanton, C. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2019.07.010 · Cited by 243
Delivery Mode Affects Stability of Early Infant Gut Microbiota
Mitchell, C. M., Mazzoni, C., Hogstrom, L. J., Bryant, A., Bergerat, A., Cher, A., Pochan, S., Herman, P., Carrigan, M., Sharp, K., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2020.100156 · Cited by 252
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 222
Food allergy and the microbiome: Current understandings and future directions
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Preserving microbial diversity
Domínguez-Bello, M. G., Knight, R. D., Gilbert, J. A., & Blaser, M. J. (2018) · Science · doi:10.1126/science.aau8816 · Cited by 207
Pichler, M. J., Yamada, C., Shuoker, B., Silva, M. C. A., Gotoh, A., Leth, M. L., Schoof, E. M., Katoh, T., Sakanaka, M., Katayama, T., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17075-x · Cited by 187
Vatanen, T., Jabbar, K. S., Ruohtula, T., Honkanen, J. K., Ávila-Pacheco, J., Siljander, H., Stražar, M., Oikarinen, S., Hyöty, H., Ilonen, J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.11.023 · Cited by 182
An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint
Ramanan, D., Sefik, E., Galván-Peña, S., Wu, M., Yang, L., Yang, Z., Kostic, A. D., Golovkina, T. V., Kasper, D. L., Mathis, D. J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.030 · Cited by 179
Microbial transmission, colonisation and succession: from pregnancy to infancy
Xiao, L., & Zhao, F. (2023) · Gut · doi:10.1136/gutjnl-2022-328970 · Cited by 191
Malnutrition and Gut Microbiota in Children
Iddrisu, I., Monteagudo-Mera, A., Poveda, C. G., Pyle, S., Shahzad, M. A., Andrews, S. C., & Walton, G. (2021) · Nutrients · doi:10.3390/nu13082727 · Cited by 186
Zhou, W. L., Spoto, M., Hardy, R., Guan, C., Fleming, E. S., Larson, P. J., Brown, J. S., & Oh, J. (2020) · Cell · doi:10.1016/j.cell.2020.01.006 · Cited by 169
Role of gut microbiota in intestinal wound healing and barrier function
Alam, A., & Neish, A. (2018) · Tissue Barriers · doi:10.1080/21688370.2018.1539595 · Cited by 166
Pursuing Human-Relevant Gut Microbiota-Immune Interactions
Spencer, S. P., Fragiadakis, G. K., & Sonnenburg, J. L. (2019) · Immunity · doi:10.1016/j.immuni.2019.08.002 · Cited by 167
The gut microbiome in food allergy
Zhao, W., Ho, H.-E., & Bunyavanich, S. (2019) · Annals of Allergy, Asthma & Immunology · doi:10.1016/j.anai.2018.12.012 · Cited by 160
Strain-level epidemiology of microbial communities and the human microbiome
Yan, Y., Nguyen, L. H., Franzosa, E. A., & Huttenhower, C. (2020) · Genome Medicine · doi:10.1186/s13073-020-00765-y · Cited by 152
Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146
Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis
Singer, J. R., Blosser, E. G., Zindl, C. L., Silberger, D. J., Conlan, S., Laufer, V. A., Ditoro, D. F., Deming, C., Kumar, R., Morrow, C. D., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0640-y · Cited by 145
Population Genetics in the Human Microbiome
Garud, N. R., & Pollard, K. S. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.10.010 · Cited by 142
Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota
Turroni, F., Duranti, S., Milani, C., Lugli, G. A., van Sinderen, D., & Ventura, M. (2019) · Microorganisms · doi:10.3390/microorganisms7110544 · Cited by 140
Williams, J. E., Carrothers, J. M., Lackey, K. A., Beatty, N. F., Brooker, S. L., Peterson, H. K., Steinkamp, K. M., York, M. A., Shafii, B., Price, W. J., et al. (2018) · Journal of Nutrition · doi:10.1093/jn/nxy299 · Cited by 143
Genetic innovations in animal–microbe symbioses
Perreau, J. M., & Moran, N. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00395-z · Cited by 141
He, Q., Kwok, L., Xi, X., Zhong, Z., Ma, T., Xu, H., Meng, H., Zhao, F., & Zhang, H. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1794266 · Cited by 140
Li, X., Stokholm, J., Brejnrod, A., Vestergaard, G., Russel, J., Trivedi, U., Thorsen, J., Gupta, S., Hjelmsø, M. H., Shah, S. A., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.017 · Cited by 133
Enterosignatures define common bacterial guilds in the human gut microbiome
Frioux, C., Ansorge, R., Özkurt, E., Nedjad, C. G., Fritscher, J., Quince, C., Waszak, S. M., & Hildebrand, F. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.05.024 · Cited by 137
Dispersal strategies shape persistence and evolution of human gut bacteria
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Maqsood, R., Rodgers, R., Rodríguez, C., Handley, S. A., Ndao, I. M., Tarr, P. I., Warner, B. B., Lim, E. S., & Holtz, L. R. (2019) · Microbiome · doi:10.1186/s40168-019-0766-7 · Cited by 122
The developing infant gut microbiome: A strain-level view
Enav, H., Bäckhed, F., & Ley, R. E. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.009 · Cited by 120
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New, F. N., & Brito, I. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-012520-072314 · Cited by 124
Starter Culture Development and Innovation for Novel Fermented Foods
Gänzle, M. G., Monnin, L., Zheng, J., Zhang, L., Coton, M., Sicard, D., & Walter, J. (2023) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-072023-034207 · Cited by 121
The role of the gut microbiome in the development of schizophrenia
Kelly, J. R., Minuto, C., Cryan, J. F., Clarke, G. A., & Dinan, T. G. (2020) · Schizophrenia Research · doi:10.1016/j.schres.2020.02.010 · Cited by 121
The role of gut mycobiome in health and diseases
Zhang, L., Zhan, H., Xu, W., Yan, S., & Ng, S. C. (2021) · Therapeutic Advances in Gastroenterology · doi:10.1177/17562848211047130 · Cited by 118
Mother–infant transmission of human microbiota
Browne, H. P., Shao, Y., & Lawley, T. D. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102173 · Cited by 117
Determinants of Vaginal Microbiota Composition
Moosa, Y., Kwon, D. S., de Oliveira, T., & Wong, E. B. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00467 · Cited by 112
Vertical transfer of antibiotics and antibiotic resistant strains across the mother/baby axis
Patangia, D. V., Ryan, C. A., Dempsey, E. M., Stanton, C., & Ross, R. P. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2021.05.006 · Cited by 108
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 104
The Oral and Gut Bacterial Microbiomes: Similarities, Differences, and Connections
Maki, K. A., Kazmi, N., Barb, J. J., & Ames, N. J. (2020) · Biological Research For Nursing · doi:10.1177/1099800420941606 · Cited by 112
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
Roodgar, M., Good, B. H., Garud, N. R., Martis, S., Avula, M., Zhou, W., Lancaster, S. M., Lee, H., Babveyh, A., Nesamoney, S. N., et al. (2021) · Genome Research · doi:10.1101/gr.265058.120 · Cited by 93
Maternal prenatal gut microbiota composition predicts child behaviour
Dawson, S. L., O’Hely, M., Jacka, F. N., Ponsonby, A., Symeonides, C., Loughman, A., Collier, F., Moreno‐Betancur, M., Sly, P. D., Burgner, D. P., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103400 · Cited by 107
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Pinto, Y., & Bhatt, A. S. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00746-6 · Cited by 109
Lou, Y. C., Olm, M. R., Diamond, S., Crits‐Christoph, A., Firek, B., Baker, R. W., Morowitz, M. J., & Banfield, J. F. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100393 · Cited by 91
Li, W., Tapiainen, T., Brinkac, L. M., Lorenzi, H., Moncera, K. J., Tejesvi, M. V., Salo, J., & Nelson, K. E. (2020) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa155 · Cited by 98
Variation and transmission of the human gut microbiota across multiple familial generations
Valles‐Colomer, M., Bacigalupe, R., Vieira‐Silva, S., Suzuki, S., Darzi, Y., Tito, R. Y., Yamada, T., Segata, N., Raes, J., & Falony, G. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01021-8 · Cited by 91
Blanco‐Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.22.504593 · Cited by 89
The Role of Diet and Nutritional Interventions for the Infant Gut Microbiome
Catassi, G. N., Aloi, M., Giorgio, V., Gasbarrini, A., Cammarota, G., & Ianiro, G. (2024) · Nutrients · doi:10.3390/nu16030400 · Cited by 94
The microbiota composition of the offspring of patients with gestational diabetes mellitus (GDM)
Ponzo, V., Ferrocino, I., Zarovska, A., Amenta, M. B., Leone, F., Monzeglio, C., Rosato, R., Pellegrini, M., Gambino, R., Cassader, M., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226545 · Cited by 86
Utter, D. R., Borisy, G. G., Eren, A. M., Cavanaugh, C. M., & Welch, J. L. M. (2020) · Genome biology · doi:10.1186/s13059-020-02200-2 · Cited by 82
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Berry, A. S. F., Pierdon, M. K., Misic, A. M., Sullivan, M. C., O’Brien, K. M., Chen, Y., Murray, S. J., Ramharack, L. A., Baldassano, R. N., Parsons, T. D., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01089-8 · Cited by 85
Jašarević, E., Hill, E. M., Kane, P. J., Rutt, L., Gyles, T. M., Folts, L. M., Rock, K. D., Howard, C. D., Morrison, K. E., Ravel, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26634-9 · Cited by 86
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Nishida, A. H., & Ochman, H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0085-z · Cited by 84
Andreu-Sánchez, S., Blanco-Míguez, A., Wang, D., Golzato, D., Manghi, P., Heidrich, V., Fackelmann, G., Zhernakova, D. V., Kurilshikov, A., Valles-Colomer, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.014 · Cited by 81
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
Siranosian, B. A., Tamburini, F. B., Sherlock, G., & Bhatt, A. S. (2020) · Nature Communications · doi:10.1038/s41467-019-14103-3 · Cited by 74
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 81
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept
Sharon, I., Quijada, N. M., Pasolli, E., Fabbrini, M., Vitali, F., Agamennone, V., Dötsch, A., Selberherr, E., Grau, J. H., Meixner, M., et al. (2022) · Nutrients · doi:10.3390/nu14142872 · Cited by 83
Wang, S., Egan, M., Ryan, C. A., Boyaval, P., Dempsey, E. M., Ross, R. P., & Stanton, C. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa030 · Cited by 80
Shenhav, L., Fehr, K. B., Reyna, M. E., Petersen, C., Dai, D. L., Dai, R., Breton, V. L., Rossi, L., Smieja, M., Simons, E., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.022 · Cited by 87
The resistance within: antibiotic disruption of the gut microbiome and resistome dynamics in infancy
Thänert, R., Sawhney, S. S., Schwartz, D. J., & Dantas, G. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.013 · Cited by 76
The Sporobiota of the Human Gut
Egan, M., Dempsey, E. M., Ryan, C. A., Ross, R. P., & Stanton, C. (2021) · Gut Microbes · doi:10.1080/19490976.2020.1863134 · Cited by 79
Establishment of the early-life microbiome: a DOHaD perspective
Stinson, L. F. (2019) · Journal of Developmental Origins of Health and Disease · doi:10.1017/s2040174419000588 · Cited by 77
Selma‐Royo, M., Dubois, L., Manara, S., Armanini, F., Cabrera‐Rubio, R., Valles‐Colomer, M., González, S., Llorca, A. P., Escuriet, R., Bode, L., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.005 · Cited by 76
Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly
Shao, Y., García-Mauriño, C., Clare, S., Dawson, N. J. R., Mu, A., Adoum, A., Harcourt, K., Liu, J., Browne, H. P., Stares, M., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01804-9 · Cited by 79
The intersection of undernutrition, microbiome, and child development in the first years of life
Fontaine, F., Turjeman, S., Callens, K., & Koren, O. (2023) · Nature Communications · doi:10.1038/s41467-023-39285-9 · Cited by 84
Honey bee genetics shape the strain-level structure of gut microbiota in social transmission
Wu, J., Lang, H., Mu, X., Zhang, Z., Su, Q., Hu, X., & Zheng, H. (2021) · Microbiome · doi:10.1186/s40168-021-01174-y · Cited by 72
Natural selection for imprecise vertical transmission in host–microbiota systems
Bruijning, M., Henry, L. P., Forsberg, S. K. G., Metcalf, C. J. E., & Ayroles, J. F. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01593-y · Cited by 73
Podlesny, D., Arze, C., Dörner, E., Verma, S., Dutta, S., Walter, J., & Fricke, W. F. (2022) · Microbiome · doi:10.1186/s40168-022-01251-w · Cited by 73
Feehily, C., O’Neill, I. J., Walsh, C. J., Moore, R., Killeen, S. L., Geraghty, A. A., Lawton, E. M., Byrne, D. F., Sánchez-Gallardo, R., Nori, S. R. C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38694-0 · Cited by 74
Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age
Mallott, E. K., Sitarik, A. R., Leve, L. D., Cioffi, C. C., Camargo, C. A., Hasegawa, K., & Bordenstein, S. R. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002230 · Cited by 79
Human milk microbiome: From actual knowledge to future perspective
Selma‐Royo, M., Calvo‐Lerma, J., Cortés-Macías, E., & Collado, M. C. (2021) · Seminars in Perinatology · doi:10.1016/j.semperi.2021.151450 · Cited by 76
Li, X., Brejnrod, A., Thorsen, J., Zachariasen, T., Trivedi, U., Russel, J., Vestergaard, G., Stokholm, J., Rasmussen, M. A., & Sørensen, S. J. (2023) · Nature Communications · doi:10.1038/s41467-023-44289-6 · Cited by 73
Ungaro, F., Massimino, L., D’Alessio, S., & Danese, S. (2019) · United European Gastroenterology Journal · doi:10.1177/2050640619876787 · Cited by 71
The infant gut resistome is associated with E. coli and early-life exposures
Lebeaux, R. M., Coker, M. O., Dade, E. F., Palys, T. J., Morrison, H. G., Ross, B. D., Baker, E., Karagas, M. R., Madan, J. C., & Hoen, A. G. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02129-x · Cited by 69
Timescales of gut microbiome dynamics
Schlomann, B. H., & Parthasarathy, R. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.011 · Cited by 69
A cryptic plasmid is among the most numerous genetic elements in the human gut
Fogarty, E. C., Schechter, M. S., Lolans, K., Sheahan, M. L., Veseli, I., Moore, R. M., Kiefl, E., Moody, T. U., Rice, P. A., Yu, M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.01.039 · Cited by 70
Early life gut microbiome and its impact on childhood health and chronic conditions
Núñez, H., Nieto, P. A., Mars, R. A. T., Ghavami, M., Hoy, C. S., & Sukhum, K. V. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2463567 · Cited by 80
Ecological succession in the vaginal microbiota during pregnancy and birth
Rasmussen, M. A., Thorsen, J., Domínguez-Bello, M. G., Blaser, M. J., Mortensen, M. S., Brejnrod, A., Shah, S. A., Hjelmsø, M. H., Lehtimäki, J., Trivedi, U., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-0686-3 · Cited by 65
Gough, E. K., Edens, T. J., Geum, H. M., Baharmand, I., Gill, S. K., Robertson, R. C., Mutasa, K., Ntozini, R., Smith, L. E., Chasekwa, B., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103421 · Cited by 65
Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy
Cowardin, C. A., Syed, S., Iqbal, N. T., Jamil, Z., Sadiq, K., Iqbal, J., Ali, A., & Moore, S. R. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00714-7 · Cited by 71
Metadata
- Authors
- Yassour, M., Jason, E., Hogstrom, L. J., Arthur, T. D., Tripathi, S., Siljander, H., Selvenius, J., Oikarinen, S., Hyöty, H., Virtanen, S. M., Ilonen, J., Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Segata, N., Vlamakis, H., Lander, E. S., Huttenhower, C., Knip, M., & Xavier, R. J.
- Affiliations
- Broad Institute (US)
- Tampere University Hospital (FI)
- University of Helsinki (FI)
- Tampere University (FI)
- University of Turku (FI)
- University of Trento (IT)
- Corresponding author
- Yassour, Moran
- Xavier, Ramnik J.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 24
- Issue
- 1
- Pages
- 146-154.e4
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC6091882
- OpenAlex
- W2821623253
- Cited by
- 455
- References
- 35
- Citations by year
- 2026: 28 · 2025: 54 · 2024: 65 · 2023: 62 · 2022: 55 · 2021: 74 · 2020: 74 · 2019: 30 · 2018: 11
- FWCI
- 17.16
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- Iris (University of Trento) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- Funders
- National Institutes of Health (1DP3DK094338-01)
- Juvenile Diabetes Research Foundation in Israel (2-SRA-2016-247-S-B)
- National Institute of Diabetes and Digestive and Kidney Diseases
- 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, strain-level analysis, antibiotic resistance genes, Bacteroides uniformis
- MeSH terms
- Gastrointestinal Microbiome, Adult, Bacteroides, DNA, Bacterial, Feces, Female, Humans, Infant, Infant, Newborn, Longitudinal Studies, Male, Meconium, Mother-Child Relations, Prospective Studies, Cohort Studies, Drug Resistance, Bacterial, Metagenomics
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