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Healthy hosts rule within: ecological forces shaping the gut microbiota
Open accessAbstract
A balanced gut microbiota is important for human health, but the mechanisms that maintain homeostasis are incompletely understood. Recent insights suggest the host plays a key role in shaping its gut microbiota to be beneficial. While host control in the small intestine curbs bacterial numbers to avoid competition for simple sugars and amino acids, the host limits oxygen availability in the large intestine to obtain microbial fermentation products from fiber. Epithelial cells are major players in imposing ecological control mechanisms, which involves the release of antimicrobial peptides by small-intestinal Paneth cells and maintenance of luminal anaerobiosis by epithelial hypoxia in the colon. Harnessing these epithelial control mechanisms for therapeutic means could provide a novel lynchpin for strategies to remediate dysbiosis.
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“For example, the availability of oxygen during inflammation drives a disruption, or dysbiosis, of the microbiota by favoring Enterobacteriaceae expansion through respiration (Byndloss et al., 2018).”
From The Impact of Dietary Transition Metals on Host-Bacterial Interactions (2018) · cites this paper as Byndloss et al., 2018
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Pfister, C. A., Light, S. H., Bohannan, B. J. M., Schmidt, T. M., Martiny, A. C., Hynson, N. A., Devkota, S., David, L. A., & Whiteson, K. (2022) · mSystems · doi:10.1128/msystems.01374-21 · Cited by 6
“Although studies of human gut health indicate the importance of classifying aerobic and anaerobic bacteria and their interactions (83), an understanding of the redox environment across different human tissue types will likely enhance our understanding of pathogenesis and dysbiosis.”
BackgroundThe concept of balance in microbiome research
O’Malley, M. A. (2024) · BioEssays · doi:10.1002/bies.202400050 · Cited by 5
The role of probiotics in adolescents’ obesity
Chen, X., Li, Y., & Jia, Y. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1546627 · Cited by 7
“Their primary function is to regulate gut microbiota and maintain intestinal ecological balance, thereby promoting digestion, enhancing immunity, and preventing various diseases (Byndloss et al., 2018; Ezzaidi et al., 2019).”
Wu, Q., Liu, B., Yu, R., Sun, X., Wang, Z., Zhou, J., Lu, C., Wan, H., Zhang, J., Han, J., et al. (2023) · Food Bioscience · doi:10.1016/j.fbio.2023.102661 · Cited by 5
Huo, F., Liu, Q., Zhang, S., Liu, X., Lv, S., Zhao, M., Liu, Y., Zhu, X., Huang, C., Feng, S., et al. (2025) · Neuroscience Bulletin · doi:10.1007/s12264-025-01552-8 · Cited by 4
Liu, Y., Kou, C., Chen, J., Li, Y., & Li, J. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137425 · Cited by 4
“These physiological changes may be considered as feedback from the significant increase in the abundance of intestinal pathogens [42].”
BackgroundOrganic Acids: Key Products of Fermented Foods and Sources of Anti-Inflammatory Potential
Li, W., Ghamry, M., Xu, X., Zhang, L., & Li, J. (2025) · Food Reviews International · doi:10.1080/87559129.2025.2529546 · Cited by 3
“[207,210] Additionally, short-chain fatty acids can promote T-cell production of IL-10 through GPR43, thereby alleviating colitis, [211] and regulate glucose, lipid, and cholesterol metabolism in the liver and muscles via the AMPK pathway, thereby indirectly influencing gut homeostasis.”
Rodakova, K. S., Gancarčíková, S., Demečková, V., Lauko, S., Rynikova, M., Andrejčáková, Z., Spišáková, D., Fusek, M., Vlčková, R., Strompfová, V., et al. (2026) · Applied Sciences · doi:10.3390/app16115529 · Cited by 3
Tanca, A., & Uzzau, S. (2025) · Expert Review of Proteomics · doi:10.1080/14789450.2025.2580644 · Cited by 3
Host control and species interactions jointly determine microbiome community structure
Abbasi, E., & Akçay, E. (2024) · Theoretical Population Biology · doi:10.1016/j.tpb.2024.06.006 · Cited by 3
Wiles, T. J., Schlomann, B. H., Wall, E. S., Betancourt, R., Parthasarathy, R., & Guillemin, K. J. (2019) · SSRN Electronic Journal · doi:10.2139/ssrn.3467155 · Cited by 3
Ishiguro, E. E., Haskey, N., & Campbell, K. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-91387-4.00001-6 · Cited by 3
Vasa, S. R., Gardiner, G. E., Cormican, P., O’Driscoll, K., Bee, G., & Lawlor, P. G. (2024) · Journal of Animal Science · doi:10.1093/jas/skae380 · Cited by 2
Li, M., Liang, H., Xia, R., Zhang, J., Chen, J., Zhou, W., Ding, Q., Yang, Y., Zhang, Z., Yao, Y., et al. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102604 · Cited by 2
Houghton, C. A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820593-8.00014-8 · Cited by 3
Genetic Modification and Sequence Analysis of Probiotic Microorganisms
Akçelik, M., Akçelik, N., Şanlıbaba, P., & TEZEL, B. U. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822909-5.00006-x · Cited by 2
Tjaden, N. E. B., Liou, M. J., Sax, S. E., Lassoued, N., Lou, M., Schneider, S., Beigel, K., Eisenberg, J. D., Loeffler, E., Anderson, S. E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.10.637436 · Cited by 2
The gut microbiome in personalized precision medicine
Buschmann, M. M., & Gilbert, J. A. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-98808-7.00012-6 · Cited by 1
Bian, X., Xu, H., Li, J., Kuang, J., Shi, F., Li, X., & Li, J. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1668148 · Cited by 1
McDermott, K. (2018) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York) · Cited by 1
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) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.01.429213 · Cited by 1
“…with previous work showing loss of intestinal hypoxia due to high-fat low-fiber diet consumption, we found decreased expression of the hypoxia-inducible factor 1-alpha in the colon of HFt-LFb relative to LFt-HFb females (Figure 3E) (Byndloss et al., 2018; Faber and Bäumler, 2014; Lee et al., 2020).”
MethodDevelopment and dynamics of the normal gut microbiota
Olsson, L. M. (2020) · Gothenburg University Publications Electronic Archive (Gothenburg University)
The microbiome in preterm infants and implications in health
Wang, A. Z., & Claud, E. C. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820602-7.00004-0
The Role of High Sugar Diets in Colitis
Rajaruban, S. (2020) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3-tthe-t208
van der Meer, J. R., & Carraro, N. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737594052.793576386
Keskey, R. C., Nicholson, S. E., & Alverdy, J. C. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-69787-3.00111-8
Liu, Y., Kou, C., Chen, J., Li, Y., Zhu, L., & Li, J. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4777228
Huo, F., Liu, Q., Lv, S., Liu, Y., Zhu, X., Huang, C., Feng, S., Wang, H., Xu, S., Shen, J., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4388330/v1
Metadata
- Authors
- Byndloss, M. X., Pernitzsch, S. R., & Bäumler, A. J.
- Affiliations
- University of California, Davis (US)
- Corresponding author
- Bäumler, Andreas J.
- Venue
- Mucosal Immunology
- Publisher
- Elsevier BV
- Published
- 2018-09
- Volume
- 11
- Issue
- 5
- Pages
- 1299-1305
- ISSN
- 1933-0219 (ISSN-L)
- OpenAlex
- W2800529903
- Cited by
- 109
- References
- 106
- Citations by year
- 2026: 4 · 2025: 11 · 2024: 17 · 2023: 13 · 2022: 8 · 2021: 20 · 2020: 16 · 2019: 16 · 2018: 4
- FWCI
- 1.37
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Mucosal Immunology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- gut microbiota, host-microbe interactions, microbial homeostasis, Paneth cells, antimicrobial peptides, dietary fiber fermentation, small intestine, large intestine, dysbiosis
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Animals, Ecology, Epithelial Cells, Homeostasis, Humans, Intestinal Mucosa, Intestines, Microbiota
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