The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Viable bacterial colonization is highly limited in the human intestine in utero
Open accessAbstract
Mucosal immunity develops in the human fetal intestine by 11–14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune system is unknown. Bacteria-like morphology was identified in pockets of human fetal meconium at mid-gestation by scanning electron microscopy (n = 4), and a sparse bacterial signal was detected by 16S rRNA sequencing (n = 40 of 50) compared to environmental controls (n = 87). Eighteen taxa were enriched in fetal meconium, with Micrococcaceae (n = 9) and Lactobacillus (n = 6) the most abundant. Fetal intestines dominated by Micrococcaceae exhibited distinct patterns of T cell composition and epithelial transcription. Fetal Micrococcus luteus, isolated only in the presence of monocytes, grew on placental hormones, remained viable within antigen presenting cells, limited inflammation ex vivo and possessed genomic features linked with survival in the fetus. Thus, viable bacteria are highly limited in the fetal intestine at mid-gestation, although strains with immunomodulatory capacity are detected in subsets of specimens. Microscopy and 16S rRNA sequencing suggest that there is a limited bacterial presence in the human fetal intestine, with one enriched Micrococcus species exhibiting immunomodulatory activity ex vivo.
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.
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
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,987
lmerTest Package: Tests in Linear Mixed Effects Models
Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. (2017) · Journal of Statistical Software · doi:10.18637/jss.v082.i13 · Cited by 24,346
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., et al. (2001) · CRAN: Contributed Packages · doi:10.32614/cran.package.vegan · Cited by 22,615
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Cited by
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755
Self-citationQuestioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy, K. M., de Goffau, M. C., Perez-Muñoz, M. E., Arrieta, M.-C., Bäckhed, F., Bork, P., Braun, T., Bushman, F. D., Dore, J., de Vos, W. M., et al. (2023) · Nature · doi:10.1038/s41586-022-05546-8 · Cited by 371
Development of gut microbiota during the first 2 years of life
Wernroth, M.-L., Peura, S., Hedman, A. M., Hetty, S., Vicenzi, S., Kennedy, B., Fall, K., Svennblad, B., Andolf, E., Pershagen, G., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-13009-3 · Cited by 143
Metadata
- Authors
- Rackaityte, E., Halkias, J., Fukui, E. M., Mendoza, V. F., Hayzelden, C., Crawford, E. D., Fujimura, K. E., Burt, T. D., & Lynch, S. V.
- Venue
- Nature Medicine
- Published
- 2020-02-24
- Volume
- 26
- Issue
- 4
- Pages
- 599-607
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W3006904068
- Cited by
- 300
- References
- 66
- FWCI
- 13.07
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Viable bacterial colonization is highly limited in the human intestine in utero. https://app.cochat.ai/papers/10.1038/s41591-020-0761-3
- The paper
- Rackaityte, E., Halkias, J., Fukui, E. M., Mendoza, V. F., Hayzelden, C., Crawford, E. D., Fujimura, K. E., Burt, T. D., & Lynch, S. V. (2020). Viable bacterial colonization is highly limited in the human intestine in utero. Nature Medicine. https://doi.org/10.1038/s41591-020-0761-3
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
