The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
The function of our microbiota: who is out there and what do they do?
Open accessAbstract
Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome further revealed unique functions carried out in the intestinal environment and provided the basis for newly discovered mechanisms for signaling, vitamin production and glycan, amino-acid and xenobiotic metabolism. The activity and composition of the microbiota is affected by genetic background, age, diet, and health status of the host. In its turn the microbiota composition and activity influence host metabolism and disease development. Exemplified by the differences in microbiota composition and activity between breast- as compared to formula-fed babies, healthy and malnourished infants, elderly and centenarians as compared to youngsters, humans that are either lean or obese and healthy or suffering of inflammatory bowel diseases (IBD). In this review we will focus on our current understanding of the functionality of the human intestinal microbiota based on all available metagenome, metatranscriptome, and metaproteome results.
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Cites
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
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · cited 3×
“…either fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice revealed a stable and heritable colonization which enabled a diet intervention, where the mice were switched from a low-fat, plant polysaccharide to a high-fat, high-sugar diet (Turnbaugh et al., 2009b).”
BackgroundDevelopment 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
The gut flora as a forgotten organ
O'Hara, A. M., & Shanahan, F. (2006) · The EMBO Reports · doi:10.1038/sj.embor.7400731 · Cited by 2,791
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Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J. P., Druart, C., Bindels, L. B., Guiot, Y., Derrien, M., Muccioli, G. G., Delzenne, N. M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219451110 · Cited by 4,511
Self-citationMilani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950
Self-citationEmerging Pathogenic Links Between Microbiota and the Gut-Lung Axis
Budden, K. F., Gellatly, S. L., Wood, D. L. A., Cooper, M. A., Morrison, M., Hugenholtz, P., & Hansbro, P. M. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.142 · Cited by 1,606
Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J.-Z., Abe, F., & Osawa, R. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0708-5 · Cited by 1,521
Gut Microbiota and Obesity: A Role for Probiotics
Abenavoli, L., Scarpellini, E., Colica, C., Boccuto, L., Salehi, B., Sharifi-Rad, J., Aiello, V., Romano, B., De Lorenzo, A., Izzo, A. A., et al. (2019) · Nutrients · doi:10.3390/nu11112690 · Cited by 615
Li, W., Wu, X., Hu, X., Wang, T., Liang, S., Duan, Y., Jin, F., & Qin, B. (2017) · Science China Life Sciences · doi:10.1007/s11427-016-9001-4 · Cited by 406
Age-Related Changes in the Composition of Gut Bifidobacterium Species
Kato, K., Odamaki, T., Mitsuyama, E., Sugahara, H., Xiao, J.-Z., & Osawa, R. (2017) · Current Microbiology · doi:10.1007/s00284-017-1272-4 · Cited by 180
Kim, D.-H., Kim, H., Jeong, D., Kang, I.-B., Chon, J.-W., Kim, H.-S., Song, K.-Y., & Seo, K.-H. (2017) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2017.02.014 · Cited by 179
Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases
Opazo, M. C., Ortega-Rocha, E. M., Coronado-Arrázola, I., Bonifaz, L. C., Boudin, H., Neunlist, M., Bueno, S. M., Kalergis, A. M., & Riedel, C. A. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00432 · Cited by 179
Aging and the human gut microbiota—from correlation to causality
Saraswati, S., & Sitaraman, R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00764 · Cited by 153
Diet can impact microbiota composition in children with autism spectrum disorder
Berding, K., & Donovan, S. M. (2018) · Frontiers in Neuroscience · doi:10.3389/fnins.2018.00515 · Cited by 144
Factors influencing the gut microbiome in children: from infancy to childhood
Kumbhare, S. V., Patangia, D. V., Patil, R. H., Shouche, Y. S., & Patil, N. P. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9860-z · Cited by 143
Baars, A., Oosting, A., Knol, J., Garssen, J., & Van Bergenhenegouwen, J. (2015) · Microorganisms · doi:10.3390/microorganisms3040641 · Cited by 135
Influence of fermented milk products, prebiotics and probiotics on microbiota composition and health
Ceapa, C., Wopereis, H., Rezaïki, L., Kleerebezem, M., Knol, J., & Oozeer, R. (2013) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2013.04.004 · Cited by 98
Next generation probiotics for human health: An emerging perspective
Jan, T., Negi, R., Sharma, B., Kumar, S., Singh, S., Rai, A. K., Shreaz, S., Rustagi, S., Chaudhary, N., Kaur, T., et al. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e35980 · Cited by 95
Iron in micronutrient Powder promotes an Unfavorable gut microbiota in Kenyan infants
Tang, M., Frank, D., Hendricks, A., Ir, D., Esamai, F., Liechty, E., Hambidge, K., & Krebs, N. (2017) · Nutrients · doi:10.3390/nu9070776 · Cited by 94
New hope for Parkinson’s disease treatment: Targeting gut microbiota
Fan, H., Sheng, S., & Zhang, F. (2022) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.13916 · Cited by 66
Modulation of intestinal microbiota in mice by kefir administration
Kim, D.-H., Chon, J.-W., Kim, H., & Seo, K.-H. (2015) · Food Science and Biotechnology · doi:10.1007/s10068-015-0179-8 · Cited by 48
Oduro-Donkor, D., Turner, M. C., Farnaud, S., Renshaw, D., Kyrou, I., Hanson, P., Hattersley, J., Weickert, M. O., Menon, V., Randeva, H. S., et al. (2020) · Expert Review of Endocrinology & Metabolism · doi:10.1080/17446651.2020.1801412 · Cited by 33
Murtaza, N., Ó Cuív, P., & Morrison, M. (2017) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2016.09.005 · Cited by 32
The Microbiome, Metabolism, and Networks in Precision Nutrition
Mensah, G. E., Maseng, M. G., Allard, S., & Gilbert, J. A. (2024) · Precision Nutrition · doi:10.1016/b978-0-443-15315-0.00011-0 · Cited by 2
Metadata
- Authors
- Ottman, N., Smidt, H., de Vos, W. M., & Belzer, C.
- Venue
- Frontiers in Cellular and Infection Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2012
- Volume
- 2
- Pages
- 104-104
- ISSN
- 2235-2988 (ISSN-L)
- OpenAlex
- W2138276746
- Cited by
- 488
- References
- 23
- FWCI
- 8.36
- Type
- journal article
- Language
- en
- Open access
- gold
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