The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
The Comprehensive Antibiotic Resistance Database
McArthur, A. G., Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A. J., Bhullar, K., Canova, M. J., Pascale, G. D., Ejim, L. J., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00419-13 · Cited by 2,287
Factors influencing the composition of the intestinal microbiota in early infancy
Penders, J., Thijs, C., Vink, C., Stelma, F. F., Snijders, B., Kummeling, I., van den Brandt, P. A., & Stobberingh, E. E. (2006) · PEDIATRICS · doi:10.1542/peds.2005-2824 · Cited by 2,232
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
Self-citationThe Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776
Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function
Olszak, T., An, D., Zeissig, S., Vera, M. P., Richter, J., Franke, A., Glickman, J. N., Siebert, R., Baron, R. M., Kasper, D. L., et al. (2012) · Science · doi:10.1126/science.1219328 · Cited by 1,661
Perez-Muñoz, M. E., Arrieta, M.-C., Ramer-Tait, A. E., & Walter, J. (2017) · Microbiome · doi:10.1186/s40168-017-0268-4 · Cited by 1,096
Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043
Jakobsson, H. E., Abrahamsson, T. R., Jenmalm, M. C., Harris, K., Quince, C., Jernberg, C., Björkstén, B., Engstrand, L., & Andersson, A. F. (2014) · Gut · doi:10.1136/gutjnl-2012-303249 · Cited by 1,011
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 895
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839
Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm
Martens, E. C., Koropatkin, N. M., Smith, T. J., & Gordon, J. I. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.r109.022848 · Cited by 657
Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels
Cahenzli, J., Köller, Y., Wyss, M., Geuking, M. B., & McCoy, K. D. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.10.004 · Cited by 611
Bacteroides 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
Mode of delivery affects the bacterial community in the newborn gut
Biasucci, G., Rubini, M., Riboni, S., Morelli, L., Bessi, E., & Retetangos, C. (2010) · Early Human Development · doi:10.1016/j.earlhumdev.2010.01.004 · Cited by 507
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470
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
Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., et al. (2017) · mSystems · doi:10.1128/msystems.00164-16 · Cited by 445
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 389
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
Kaminski, J., Gibson, M. K., Franzosa, E. A., Segata, N., Dantas, G. A., & Huttenhower, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004557 · Cited by 332
ConStrains identifies microbial strains in metagenomic datasets
Luo, C., Knight, R. D., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D. (2015) · Nature Biotechnology · doi:10.1038/nbt.3319 · Cited by 263
Exploring Vertical Transmission of Bifidobacteria from Mother to Child
Milani, C., Mancabelli, L., Lugli, G. A., Duranti, S., Turroni, F., Ferrario, C., Mangifesta, M., Viappiani, A., Ferretti, P., Gorfer, V., et al. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02037-15 · Cited by 259
Ilonen, J., Kiviniemi, M., Lempainen, J., Simell, O., Toppari, J., Veijola, R., Knip, M., & Register, T. F. P. D. (2016) · Pediatric Diabetes · doi:10.1111/pedi.12327 · Cited by 134
Gut resistome development in healthy twin pairs in the first year of life
Moore, A. M., Ahmadi, S., Patel, S., Gibson, M. K., Wang, B., Ndao, I. M., Deych, E., Shannon, W., Tarr, P. I., Warner, B. B., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0090-9 · Cited by 109
Flagged first, then by citations
Cited by
Sorted by citations
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
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
Prevotella Diversity, Niches and Interactions with the Human Host
Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748
Self-citation
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
