Cited by 693Gut microbiota and healthMicrobial Community Ecology and PhysiologyGastrointestinal motility and disorders

The DOI matches its Crossref record; 107 of the 107 references it cites were found in a registry or an index.

The Gut Microbiome: Connecting Spatial Organization to Function

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Tropini, Carolina, Earle, Kristen A., Huang, Kerwyn Casey, Sonnenburg, Justin L.·2017·Cell Host & Microbe

DOI 10.1016/j.chom.2017.03.010PMC PMC5576359

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Abstract

The first rudimentary evidence that the human body harbors a microbiota hinted at the complexity of host-associated microbial ecosystems. Now, almost 400 years later, a renaissance in the study of microbiota spatial organization, driven by coincident revolutions in imaging and sequencing technologies, is revealing functional relationships between biogeography and health, particularly in the vertebrate gut. In this Review, we present our current understanding of principles governing the localization of intestinal bacteria, and spatial relationships between bacteria and their hosts. We further discuss important emerging directions that will enable progressing from the inherently descriptive nature of localization and -omics technologies to provide functional, quantitative, and mechanistic insight into this complex ecosystem.

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Additional file 4 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157625
Additional file 2 of Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle
LI, Z., Cui, R., Wang, Y.-B., Luo, Y., Xue, P., Tang, Q.-G., & Fang, M.-Y. (2024) · Figshare · doi:10.6084/m9.figshare.24522891
Additional file 3 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579492
Additional file 1 of Bacterial accumulation in intestinal folds induced by physical and biological factors
Yang, J., Isaka, T., Kikuchi, K., Numayama‐Tsuruta, K., & Ishikawa, T. (2024) · Figshare · doi:10.6084/m9.figshare.25556605
Additional file 7 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157634
Additional file 1 of A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice
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Additional file 2 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157616
Additional file 3 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618630
Additional file 1 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618624
Additional file 6 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157631
Additional file 2 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618627
Additional file 2 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779882
Additional file 2 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579489
Additional file 3 of A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice
Bleich, R. M., Li, C., Sun, S., Ahn, J.-H., Dogan, B., Barlogio, C. J., Broberg, C. A., Franks, A., Bulik‐Sullivan, E. C., Carroll, I. M., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26656783
Additional file 3 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779885
Additional file 5 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
Claassen-Weitz, S., Gardner‐Lubbe, S., Mwaikono, K. S., du Toit, E., Zar, H. J., & Nicol, M. P. (2020) · Figshare · doi:10.6084/m9.figshare.12292046
Additional file 1 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779879
Additional file 5 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779891
Additional file 4 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579495
Additional file 6 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579501
Additional file 4 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lu, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779888
Additional file 6 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
Claassen-Weitz, S., Gardner‐Lubbe, S., Mwaikono, K. S., du Toit, E., Zar, H. J., & Nicol, M. P. (2020) · Figshare · doi:10.6084/m9.figshare.12292049
Additional file 6 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618639
Additional file 7 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618642
Additional file 3 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157622
Additional file 8 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618645
Additional file 2 of Bacterial accumulation in intestinal folds induced by physical and biological factors
Yang, J., Isaka, T., Kikuchi, K., Numayama‐Tsuruta, K., & Ishikawa, T. (2024) · Figshare · doi:10.6084/m9.figshare.25556672
Additional file 2 of A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice
Bleich, R. M., Li, C., Sun, S., Ahn, J.-H., Dogan, B., Barlogio, C. J., Broberg, C. A., Franks, A., Bulik‐Sullivan, E. C., Carroll, I. M., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26656780
Additional file 1 of A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts
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Additional file 3 of Bacterial accumulation in intestinal folds induced by physical and biological factors
Yang, J., Isaka, T., Kikuchi, K., Numayama‐Tsuruta, K., & Ishikawa, T. (2024) · Figshare · doi:10.6084/m9.figshare.26702782
Additional file 4 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618633
Additional file 9 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618648
Additional file 5 of Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Lind, A., & Pollard, K. S. (2021) · Figshare · doi:10.6084/m9.figshare.14157628
Additional file 1 of Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation
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Additional file 2 of The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet
Lin, L., Lai, Z., Zhang, J., Zhu, W., & Mao, S. (2023) · Figshare · doi:10.6084/m9.figshare.22611512
Additional file 5 of Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Burckhardt, J. C., Chong, D., Pett, N., & Tropini, C. (2023) · Figshare · doi:10.6084/m9.figshare.22618636
Additional file 5 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579498
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Authors: Tropini, C., Earle, K. A., Huang, K. C., & Sonnenburg, J. L.
Affiliations: Stanford Medicine (US)
Stanford University (US)
Corresponding author: Huang, Kerwyn Casey
Sonnenburg, Justin L.
ORCID: Tropini, Carolina
Earle, Kristen A.
Huang, Kerwyn Casey
Sonnenburg, Justin L.
Venue: Cell Host & Microbe
Publisher: Elsevier BV
Published: 2017-04
Volume: 21
Issue: 4
Pages: 433-442
ISSN: 1931-3128 (ISSN-L)
DOI: 10.1016/j.chom.2017.03.010
PMC: PMC5576359
OpenAlex: W2606802599
Cited by: 685
References: 107
Citations by year: 2026: 71 · 2025: 86 · 2024: 79 · 2023: 80 · 2022: 84 · 2021: 99 · 2020: 84 · 2019: 54 · 2018: 36 · 2017: 11
FWCI: 4.76
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 376 d)
Locations: Cell Host & Microbe (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: NSF CAREER Award (MCB-1149328)
James S. McDonnell Studying Complex Systems Postdoctoral Fellowship (R01-DK101674, R01-DK085025)
National Institutes of Health NIDDK
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
Keywords: gut microbiota, host-microbe interactions
MeSH terms: Gastrointestinal Microbiome, Animals, Bacteria, Humans, Ecosystem, Bacterial Physiological Phenomena, Gastrointestinal Tract, Microbiota

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The Gut Microbiome: Connecting Spatial Organization to Function

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