The DOI matches its Crossref record; 261 of the 261 references it cites were found in a registry or an index.
The Microbiome in Infectious Disease and Inflammation
Open accessAbstract
The mammalian alimentary tract harbors hundreds of species of commensal microorganisms (microbiota) that intimately interact with the host and provide it with genetic, metabolic, and immunological attributes. Recent reports have indicated that the microbiota composition and its collective genomes (microbiome) are major factors in predetermining the type and robustness of mucosal immune responses. In this review, we discuss the recent advances in our understanding of host-microbiota interactions and their effect on the health and disease susceptibility of the host.
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“The gastrointestinal microbiota is dominated by Firmicutes (e.g., Lactobacillus, Bacillus, and Clostridium) and Bacteroidetes (e.g., Bacteroides), with lower abundances of Proteobacteria (e.g., Escherichia) and Actinobacteria (e.g., Bifidobacterium)”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [19]
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“Increased nitrate concentrations13 and an altered mucosal oxygen gradient29 favour the growth of microbes in the Proteobacteria phylum”
From The microbiome and critical illness (2016) · cites this paper as [15]
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1 retracted
Kim, J. S., Smith‐Garvin, J. E., Koretzky, G. A., & Jordan, M. S. (2011) · The Journal of Experimental Medicine · doi:10.1084/jem.20110680 · Cited by 43
RetractedRepertoires of Autophagy in the Pathogenesis of Ocular Diseases
Li, Y., Jiang, Q. L., Cao, G.-F., Yao, J., & Yan, B. (2015) · Cellular Physiology and Biochemistry · doi:10.1159/000373980 · Cited by 16,351
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
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
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Enterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548
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
Autophagy fights disease through cellular self-digestion
Mizushima, N., Levine, B., Cuervo, A. M., & Klionsky, D. J. (2008) · Nature · doi:10.1038/nature06639 · Cited by 6,452
Research works printed but not linked: 2
- Cummings JH, 2003, Curr. Issues Intest. Microbiol., 4, 9
- Vijay-Kumar M, 2007, J. Clin. Investig., 117, 3909
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Self-citationSingh, N., Gurav, A., Sivaprakasam, S., Brady, E., Padia, R., Shi, H., Thangaraju, M., Prasad, P. D., Manicassamy, S., Munn, D. H., et al. (2014) · Immunity · doi:10.1016/j.immuni.2013.12.007 · Cited by 2,368
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Chang, P. V., Hao, L., Offermanns, S., & Medzhitov, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322269111 · Cited by 2,175
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Lopetuso, L. R., Scaldaferri, F., Petito, V., & Gasbarrini, A. (2013) · Gut Pathogens · doi:10.1186/1757-4749-5-23 · Cited by 753
An, D., Oh, S. F., Olszak, T., Neves, J. F., Avci, F. Y., Erturk-Hasdemir, D., Lu, X., Zeissig, S., Blumberg, R. S., & Kasper, D. L. (2014) · Cell · doi:10.1016/j.cell.2013.11.042 · Cited by 643
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Huda, M. N., Lewis, Z., Kalanetra, K. M., Rashid, M., Ahmad, S. M., Raqib, R., Qadri, F., Underwood, M. A., Mills, D. A., & Stephensen, C. B. (2014) · PEDIATRICS · doi:10.1542/peds.2013-3937 · Cited by 392
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Faith, J. J., Ahern, P. P., Ridaura, V. K., Cheng, J., & Gordon, J. I. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008051 · Cited by 373
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Jing, X., Zulfiqar, F., Park, S. Y., Núñez, G., Dziarski, R., & Gupta, D. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1301548 · Cited by 37
Metadata
- Authors
- Honda, K., & Littman, D. R.
- Affiliations
- The University of Tokyo (JP)
- Howard Hughes Medical Institute (US)
- Venue
- Annual Review of Immunology
- Publisher
- Annual Reviews
- Published
- 2012-04-23
- Volume
- 30
- Issue
- 1
- Pages
- 759-795
- ISSN
- 0732-0582 (ISSN-L)
- 1545-3278
- PMC
- PMC4426968
- OpenAlex
- W2120495574
- Cited by
- 791
- References
- 261
- Citations by year
- 2026: 22 · 2025: 27 · 2024: 61 · 2023: 58 · 2022: 55 · 2021: 61 · 2020: 64 · 2019: 59 · 2018: 63 · 2017: 57 · 2016: 62 · 2015: 52 · 2014: 73 · 2013: 55 · 2012: 20
- FWCI
- 5.84
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Annual Review of Immunology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5rc2ar058986-02)
- National Institute of Allergy and Infectious Diseases (R01AI080885)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (RC2-AR-058986)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Immunology › Immune Response and Inflammation
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, microbiota, host-microbiota interactions, mucosal immunity, commensal microorganisms, infection susceptibility, inflammation, disease susceptibility
- MeSH terms
- Animals, Communicable Diseases, Humans, Immunity, Innate, Inflammation, Intestinal Mucosa, Lymphocytes, Signal Transduction, Immunity, Mucosal, Host-Pathogen Interactions, Metagenome, Adaptive Immunity
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