Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota
Open accessAbstract
Background & aims The gut microbiota is a complex and densely populated community in a dynamic environment determined by host physiology. We investigated how intestinal oxygen levels affect the composition of the fecal and mucosally adherent microbiota.Methods We used the phosphorescence quenching method and a specially designed intraluminal oxygen probe to dynamically quantify gut luminal oxygen levels in mice. 16S ribosomal RNA gene sequencing was used to characterize the microbiota in intestines of mice exposed to hyperbaric oxygen, human rectal biopsy and mucosal swab samples, and paired human stool samples.Results Average Po2 values in the lumen of the cecum were extremely low (<1 mm Hg). In altering oxygenation of mouse intestines, we observed that oxygen diffused from intestinal tissue and established a radial gradient that extended from the tissue interface into the lumen. Increasing tissue oxygenation with hyperbaric oxygen altered the composition of the gut microbiota in mice. In human beings, 16S ribosomal RNA gene analyses showed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with rectal mucosa, compared with feces. A consortium of asaccharolytic bacteria of the Firmicute and Bacteroidetes phyla, which primarily metabolize peptones and amino acids, was associated primarily with mucus. This could be owing to the presence of proteinaceous substrates provided by mucus and the shedding of the intestinal epithelium.Conclusions In an analysis of intestinal microbiota of mice and human beings, we observed a radial gradient of microbes linked to the distribution of oxygen and nutrients provided by host tissue.
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Spatial niche partitioning of microbial populations can result from mucus from goblet cells and differential oxygen tolerance.
“Spatial niche partitioning of microbial populations can also be a result of mucus from goblet cells 46 and differential oxygen tolerance47.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [47]
Increased nitrate concentrations and an altered mucosal oxygen gradient favour the growth of microbes in the Proteobacteria phylum and some members of the Firmicutes phylum.
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The influx of oedema into alveoli creates steep oxygen gradients, which shape bacterial community structure.
“The influx of oedema creates steep oxygen gradients, which shape bacterial community structure.”
From The microbiome and critical illness (2016) · cites this paper as [29]
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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 · see citing works
Self-citationBergey's Manual of Systematic Bacteriology
(1990) · Annals of Internal Medicine · doi:10.7326/0003-4819-112-5-391_3 · Cited by 15,633 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · see citing works
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Self-citationFrank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3145 · Cited by 4,386 · see citing works
Self-citationBergey's manual of systematic bacteriology
(1987) · Gene · doi:10.1016/0378-1119(87)90414-8 · Cited by 3,971 · see citing works
Development of the Human Infant Intestinal Microbiota
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877 · see citing works
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., Reyes, J. A., Shah, S. A., LeLeiko, N., Snapper, S. B., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-r79 · Cited by 2,713 · see citing works
Cellular Defenses against Superoxide and Hydrogen Peroxide
Imlay, J. A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.061606.161055 · Cited by 1,563 · see citing works
Johansson, M., Larsson, J. M. H., & Hansson, G. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006451107 · Cited by 1,459 · see citing works
How glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works
Glycan foraging in vivo by an intestine-adapted bacterial symbiont
Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works
Tibbles, P. M., & Edelsberg, J. (1996) · New England Journal of Medicine · doi:10.1056/nejm199606203342506 · Cited by 1,026 · see citing works
Molecular Monitoring of Succession of Bacterial Communities in Human Neonates
Favier, C. F., Vaughan, E. E., de Vos, W. M., & Akkermans, A. D. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.1.219-226.2002 · Cited by 859 · see citing works
Bacterial coaggregation: an integral process in the development of multi-species biofilms
Rickard, A. H., Gilbert, P., High, N. J., Kolenbrander, P. E., & Handley, P. S. (2003) · Trends in Microbiology · doi:10.1016/s0966-842x(02)00034-3 · Cited by 765 · see citing works
Intestinal microflora in early infancy: composition and development
Fanaro, S., Chierici, R., Guerrini, P., & Vigi, V. (2003) · Acta Paediatrica · doi:10.1111/j.1651-2227.2003.tb00646.x · Cited by 738 · see citing works
Microbes inside—from diversity to function: the case of Akkermansia
Belzer, C., & de Vos, W. M. (2012) · The ISME Journal · doi:10.1038/ismej.2012.6 · Cited by 715 · see citing works
Hyperbaric Oxygen: Its Mechanisms and Efficacy
Thom, S. R. (2011) · Plastic & Reconstructive Surgery · doi:10.1097/prs.0b013e3181fbe2bf · Cited by 591 · see citing works
Self-citationImaging of Phosphorescence: A Novel Method for Measuring Oxygen Distribution in Perfused Tissue
Rumsey, W. L., Vanderkooi, J. M., & Wilson, D. F. (1988) · Science · doi:10.1126/science.3420417 · Cited by 537 · see citing works
Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut
Fischbach, M. A., & Sonnenburg, J. L. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.002 · Cited by 494 · see citing works
Biology of asaccharolytic black-pigmented Bacteroides species
Mayrand, D., & Holt, S. C. (1988) · Microbiological Reviews · doi:10.1128/mr.52.1.134-152.1988 · Cited by 457 · see citing works
Espey, M. G. (2013) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2012.10.554 · Cited by 396 · see citing works
He, G., Shankar, R. A., Chzhan, M., Samouilov, A., Kuppusamy, P., & Zweier, J. L. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4586 · Cited by 383 · see citing works
Brune, A., Emerson, D., & Breznak, J. A. (1995) · Applied and Environmental Microbiology · doi:10.1128/aem.61.7.2681-2687.1995 · Cited by 330 · see citing works
The dynamics of gut‐associated microbial communities during inflammation
Winter, S., Lopez, C. A., & Bäumler, A. J. (2013) · EMBO Reports · doi:10.1038/embor.2013.27 · Cited by 328 · see citing works
Modulation of Shigella virulence in response to available oxygen in vivo
Marteyn, B., West, N. P., Browning, D. F., Cole, J. A., Shaw, J. G., Palm, F., Mounier, J., Prévost, M., Sansonetti, P. J., & Tang, C. M. (2010) · Nature · doi:10.1038/nature08970 · Cited by 323 · see citing works
McHardy, I. H., Goudarzi, M., Tong, M., Ruegger, P. M., Schwager, E., Weger, J. R., Graeber, T. G., Sonnenburg, J. L., Horvath, S., Huttenhower, C., et al. (2013) · Microbiome · doi:10.1186/2049-2618-1-17 · Cited by 316 · see citing works
Role of the microbiota in inflammatory bowel diseases
Nagalingam, N. A., & Lynch, S. V. (2012) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21866 · Cited by 315 · see citing works
Aerotaxis and Other Energy-Sensing Behavior in Bacteria
Taylor, B. L., Zhulin, I. B., & Johnson, M. S. (1999) · Annual Review of Microbiology · doi:10.1146/annurev.micro.53.1.103 · Cited by 290 · see citing works
Ezaki, T., Kawamura, Y., Li, N., et al. (2001) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-51-4-1521 · Cited by 279 · see citing works
Two New “Protected” Oxyphors for Biological Oximetry: Properties and Application in Tumor Imaging
Esipova, T. V., Karagodov, A. I., Miller, J. M., Wilson, D. F., Busch, T. M., & Vinogradov, S. A. (2011) · Analytical Chemistry · doi:10.1021/ac2022234 · Cited by 248 · see citing works
Self-citationShallow breathing: bacterial life at low O2
Morris, R. L., & Schmidt, T. M. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2970 · Cited by 240 · see citing works
Dendritic Phosphorescent Probes for Oxygen Imaging in Biological Systems
Lebedev, A. Y., Cheprakov, A. V., Sakadžić, S., Boas, D. A., Wilson, D. F., & Vinogradov, S. A. (2009) · ACS Applied Materials & Interfaces · doi:10.1021/am9001698 · Cited by 233 · see citing works
Self-citationThe measurement of oxygenin vivousing EPR techniques
Swartz, H. M., & Clarkson, R. B. (1998) · Physics in Medicine and Biology · doi:10.1088/0031-9155/43/7/017 · Cited by 219 · see citing works
Biostructure of Fecal Microbiota in Healthy Subjects and Patients With Chronic Idiopathic Diarrhea
Swidsinski, A., Loening–Baucke, V., Verstraelen, H., Osowska, S., & Doerffel, Y. (2008) · Gastroenterology · doi:10.1053/j.gastro.2008.04.017 · Cited by 178 · see citing works
Noninvasive imaging of the distribution in oxygen in tissue in vivo using near-infrared phosphors
Vinogradov, S. A., Lo, L., Jenkins, W. T., et al. (1996) · Biophysical Journal · doi:10.1016/s0006-3495(96)79764-3 · Cited by 176 · see citing works
Self-citationAntagonism of carbon monoxide-mediated brain lipid peroxidation by hyperbaric oxygen
Thom, S. R. (1990) · Toxicology and Applied Pharmacology · doi:10.1016/0041-008x(90)90195-z · Cited by 161 · see citing works
Self-citationTsushima, M., Tokuda, K., & Ohsaka, T. (1994) · Analytical Chemistry · doi:10.1021/ac00096a024 · Cited by 144 · see citing works
Insights into human colonic physiology obtained from the study of flatus composition
Suarez, F. L., Furne, J. K., Springfield, J. R., & Levitt, M. D. (1997) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.1997.272.5.g1028 · Cited by 141 · see citing works
Nutrient Acquisition and Metabolism by Campylobacter jejuni
Stahl, M., Butcher, J., & Stintzi, A. P. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00005 · Cited by 139 · see citing works
Wilson, D. F., Lee, W. M. F., Makonnen, S., Finikova, O. S., Apreleva, S. V., & Vinogradov, S. A. (2006) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00394.2006 · Cited by 116 · see citing works
Self-citationIntraoperative tissue oximetry in the human gastrointestinal tract
Sheridan, W. G., Lowndes, R. H., & Young, H. L. (1990) · The American Journal of Surgery · doi:10.1016/s0002-9610(05)81226-7 · Cited by 103 · see citing works
Rozhkov, V. V., Wilson, D. F., & Vinogradov, S. A. (2002) · Macromolecules · doi:10.1021/ma0121161 · Cited by 94 · see citing works
Self-citationChronic intestinal inflammation induces stress-response genes in commensal Escherichia coli
Patwa, L. G., Fan, T., Tchaptchet, S., Liu, Y., Lussier, Y. A., Sartor, R. B., & Hansen, J. J. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.06.064 · Cited by 85 · see citing works
Small Bowel Tonometry : Assessment of Small Gut Mucosal Oxygen Tension in Dog and Man
Dawson, A. M., Trenchard, D. W., & Guz, A. (1965) · Nature · doi:10.1038/206943b0 · Cited by 84 · see citing works
Wexler, H. M., Reeves, D., Summanen, P., Molitoris, E., Mcteague, M., Duncan, J., Wilson, K. H., & Finegold, S. (1996) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-46-1-252 · Cited by 80 · see citing works
Tomographic imaging of oxygen by phosphorescence lifetime
Apreleva, S. V., Wilson, D. F., & Vinogradov, S. A. (2006) · Applied Optics · doi:10.1364/ao.45.008547 · Cited by 70 · see citing works
Self-citationQuantifying the role of oxygen pressure in tissue function
Wilson, D. F. (2007) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.01293.2007 · Cited by 65 · see citing works
Collins, M. D., Hoyles, L., Törnqvist, E., von Essen, R., & Falsen, E. (2001) · Systematic and Applied Microbiology · doi:10.1078/0723-2020-00047 · Cited by 61 · see citing works
Oxygen diffusion and consumption in active aerobic granules of heterogeneous structure
Chiu, Z. C., Chen, M. Y., Lee, D., et al. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-007-0847-6 · Cited by 56 · see citing works
Measurements of the Oxygen Tension in the Lumen of the Small Intestine of the Domestic Duck
Crompton, D. W. T., Shrimpton, D. H., & Silver, I. A. (1965) · Journal of Experimental Biology · doi:10.1242/jeb.43.3.473 · Cited by 54 · see citing works
Ohara‐Nemoto, Y., Shimoyama, Y., Kimura, S., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.278572 · Cited by 44 · see citing works
Oxygen Diffusion in Glassy Polymer Films: Effects of Other Gases and Changes in Pressure
Poulsen, L., & Ogilby, P. R. (2000) · The Journal of Physical Chemistry A · doi:10.1021/jp993449r · Cited by 42 · see citing works
Toprak, N. Ü., Liu, C., Summanen, P. H., et al. (2009) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.015909-0 · Cited by 42 · see citing works
Ceroni, P., Lebedev, A. Y., Marchi, E. B., et al. (2011) · Photochemical & Photobiological Sciences · doi:10.1039/c0pp00356e · Cited by 41 · see citing works
Mani, T., Niedzwiedzki, D. M., & Vinogradov, S. A. (2012) · The Journal of Physical Chemistry A · doi:10.1021/jp301345h · Cited by 40 · see citing works
Self-citation(2011) · SpringerReference · doi:10.1007/springerreference_3647 · Cited by 32 · see citing works
Extremely low oxygen tension in the rectal lumen of human subjects.
Due, V. L., Bonde, J., Kann, T., & Perner, A. (2003) · Acta Anaesthesiologica Scandinavica · doi:10.1034/j.1399-6576.2003.00542.x · Cited by 31 · see citing works
Hyperbaric Oxygen Ameliorates Bacterial Translocation in Rats with Mechanical Intestinal Obstruction
Akin, M. L., Uluutku, H., Erenoğlu, C., et al. (2002) · Diseases of the Colon & Rectum · doi:10.1007/s10350-004-6337-3 · Cited by 26 · see citing works
Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase
Khajehpour, M., Rietveld, I. B., Vinogradov, S. A., et al. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10475 · Cited by 24 · see citing works
Self-citation
Flagged first, then by citations
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- [25]Vinogradov SA Wilson DF Porphyrin-dendrimers as biological oxygen sensors Capagna S Ceroni P Designing Dendrimers New York Wiley 2012
Cited by
Sorted by citations
Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400 · see citing works
Gut biogeography of the bacterial microbiota
Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro3552 · Cited by 2,535 · see citing works
Kelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., Wilson, K. E., Glover, L. E., Kominsky, D. J., Magnuson, A., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.005 · Cited by 1,716 · see citing works
A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip
Jalili-Firoozinezhad, S., Gazzaniga, F. S., Calamari, E. L., Camacho, D. M., Fadel, C. W., Bein, A., Swenor, B., Nestor, B., Cronce, M. J., Tovaglieri, A., et al. (2019) · Nature Biomedical Engineering · doi:10.1038/s41551-019-0397-0 · Cited by 855 · see citing works
Lewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works
Self-citationA novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
Hall, A. B., Yassour, M., Sauk, J., Garner, A., Jiang, X., Arthur, T., Lagoudas, G. K., Vatanen, T., Fornelos, N., Wilson, R., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0490-5 · Cited by 777 · see citing works
Sartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808 · see citing works
Self-citationThe gut microbiome: connecting spatial organization to function
Tropini, C., Earle, K. A., Huang, K. C., & Sonnenburg, J. L. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.03.010 · Cited by 685 · see citing works
Regulation of Immunity and Inflammation by Hypoxia in Immunological Niches
Taylor, C. T., & Colgan, S. P. (2017) · Nature reviews. Immunology · doi:10.1038/nri.2017.103 · Cited by 713 · see citing works
Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction
Litvak, Y., Byndloss, M. X., Tsolis, R. M., & Bäumler, A. J. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.07.003 · Cited by 658 · see citing works
A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
Shah, P., Fritz, J. V., Glaab, E., Desai, M. S., Greenhalgh, K., Frachet, A., Niegowska, M., Estes, M., Jäger, C., Seguin-Devaux, C., et al. (2016) · Nature Communications · doi:10.1038/ncomms11535 · Cited by 660 · see citing works
De la Cuesta-Zuluaga, J., Mueller, N., Álvarez-Quintero, R., Velásquez-Mejía, E., Sierra, J., Corrales-Agudelo, V., Carmona, J., Abad, J., & Escobar, J. (2018) · Nutrients · doi:10.3390/nu11010051 · Cited by 533 · see citing works
The outer mucus layer hosts a distinct intestinal microbial niche
Li, H., Limenitakis, J. P., Fuhrer, T., Geuking, M. B., Lawson, M. A., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J. A., Rupp, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9292 · Cited by 511 · see citing works
Self-citationThe microbiome and critical illness
Dickson, R. P. (2016) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(15)00427-0 · Cited by 460 · see citing works
The human microbiome in evolution
Davenport, E. R., Sanders, J. G., Song, S. J., Amato, K. R., Clark, A. G., & Knight, R. (2017) · BMC Biology · doi:10.1186/s12915-017-0454-7 · Cited by 393 · see citing works
Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis
Das, N. K., Schwartz, A. J., Barthel, G., Inohara, N., Liu, Q., Sankar, A., Hill, D. R., Ma, X., Lamberg, O., Schnizlein, M. K., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2019.10.005 · Cited by 331 · see citing works
Keeley, T. P., & Mann, G. E. (2019) · Physiological Reviews · doi:10.1152/physrev.00041.2017 · Cited by 329 · see citing works
Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?
Pais, P., Almeida, V., Yılmaz, M., & Teixeira, M. C. (2020) · Journal of Fungi · doi:10.3390/jof6020078 · Cited by 327 · see citing works
Gut reactions: Breaking down xenobiotic–microbiome interactions
Clarke, G., Sandhu, K. V., Griffin, B. T., Dinan, T. G., Cryan, J. F., & Hyland, N. P. (2019) · Pharmacological Reviews · doi:10.1124/pr.118.015768 · Cited by 319 · see citing works
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque
Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., Miller, A. D., Westmoreland, S. V., Mansfield, K. G., Vallender, E. J., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.01.015 · Cited by 298 · see citing works
An integrative view of microbiome-host interactions in inflammatory bowel diseases
Wlodarska, M., Kostic, A. D., & Xavier, R. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.008 · Cited by 287 · see citing works
Gut microbiota, inflammation and colorectal cancer
Sun, J., & Kato, I. (2016) · Genes & Diseases · doi:10.1016/j.gendis.2016.03.004 · Cited by 257 · see citing works
“But it is now clear that bacterial populations in feces and mucosa are distinct.(6,7) As summarized in Table 1, the majority of these studies have demonstrated beta diversity by principal coordinate or component analysis illustrating structural difference of gut microbiome, where samples belonging to different disease…”
BackgroundSpatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
Mark Welch, J. L., Hasegawa, Y., McNulty, N. P., Gordon, J. I., & Borisy, G. G. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711596114 · Cited by 236 · see citing works
Virulence factors enhance <i>Citrobacter rodentium</i> expansion through aerobic respiration
Lopez, C. A., Miller, B. M., Rivera-Chávez, F., Velazquez, E. M., Byndloss, M. X., Chávez-Arroyo, A., Lokken, K. L., Tsolis, R. M., Winter, S. E., & Bäumler, A. J. (2016) · Science · doi:10.1126/science.aag3042 · Cited by 201 · see citing works
The gut Microbiome in adult and pediatric functional gastrointestinal disorders
Shin, A., Preidis, G. A., Shulman, R., & Kashyap, P. C. (2019) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.08.054 · Cited by 163 · see citing works
van der Lugt, B., Rusli, F., Lute, C., Lamprakis, A., Salazar, E., Boekschoten, M. V., Hooiveld, G. J., Müller, M., Vervoort, J., Kersten, S., et al. (2018) · Aging · doi:10.18632/aging.101439 · Cited by 72 · see citing works
Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis
Ammer-Herrmenau, C., Antweiler, K. L., Asendorf, T., Beyer, G., Buchholz, S. M., Cameron, S., Capurso, G., Damm, M., Dang, L., Frost, F., et al. (2024) · Gut · doi:10.1136/gutjnl-2023-330987 · Cited by 67 · see citing works
Rivera, K. R., Yokus, M. A., Erb, P. D., Pozdin, V. A., & Daniele, M. (2019) · The Analyst · doi:10.1039/c8an02201a · Cited by 57 · see citing works
Mashaqi, S., & Gozal, D. (2020) · Sleep Medicine · doi:10.1016/j.sleep.2020.03.020 · Cited by 40 · see citing works
Selective serotonin reuptake inhibitors and inflammatory bowel disease; Beneficial or malpractice
Hatamnejad, M. R., Baradaran Ghavami, S., Shirvani, M., Asghari Ahmadabad, M., Shahrokh, S., Farmani, M., Sherkat, G., Asadzadeh Aghdaei, H., & Zali, M. R. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.980189 · Cited by 28 · see citing works
- Authors
- Albenberg, L., Esipova, T. V., Judge, C. P., Bittinger, K., Chen, J., Laughlin, A., Grunberg, S., Baldassano, R. N., Lewis, J. D., Li, H., Thom, S. R., Bushman, F. D., Vinogradov, S. A., & Wu, G. D.
- Affiliations
- Children's Hospital of Philadelphia (US)
- University of Pennsylvania (US)
- University of Maryland, Baltimore (US)
- Corresponding author
- Vinogradov, Sergei A.
- Wu, Gary D.
- ORCID
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2014-11
- Volume
- 147
- Issue
- 5
- Pages
- 1055-1063.e8
- ISSN
- 0016-5085 (ISSN-L)
- PMC
- PMC4252572
- OpenAlex
- W2162133321
- Cited by
- 886
- References
- 63
- Citations by year
- 2026: 68 · 2025: 78 · 2024: 76 · 2023: 85 · 2022: 74 · 2021: 116 · 2020: 78 · 2019: 76 · 2018: 82 · 2017: 60 · 2016: 53 · 2015: 34 · 2014: 5 · 2012: 1
- FWCI
- 20.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Gastroenterology (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM103591)
- National Institute of Allergy and Infectious Diseases (P30AI045008)
- National Institute of Diabetes and Digestive and Kidney Diseases (UH2/3 DK083981, UH3DK083981, UH2DK083981, P30DK050306)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, oxygen gradients, fecal microbiota, hyperbaric oxygen therapy, tissue oxygenation, Proteobacteria, actinobacteria, Firmicutes, Bacteroidetes, phosphorescence quenching, mouse model
- MeSH terms
- Animals, Bacteria, Child, Child, Preschool, Diffusion, Feces, Female, Humans, Hyperbaric Oxygenation, Intestinal Mucosa, Intestines, Mice, Inbred C57BL, Oximetry, Oxygen, RNA, Bacterial, RNA, Ribosomal, 16S, Gene Expression Regulation, Bacterial, Ribotyping, Carbohydrate Metabolism, Host-Pathogen Interactions, Microbiota
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