Is it who you are or what you do that is important in the human gut?
In: Beneficial MicrobesSearch for other papers by E. Avershina in
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Search for other papers by K. Rudi in
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The current leading view is that functionality and not phylotype is the most important determinant for the services provided by the gut microbiota. Here we present an alternative opinion, advocating the importance of phylotype in addition to function. We believe the literature is misled by technical artifacts in defining operational taxonomic units (OTUs), which are binned groups of bacteria based on sequence homology. Furthermore, the current metagenomic approaches where the total DNA in a sample is mixed prior to sequencing and subsequently resolved by a bioinformatics approach, are highly error prone with respect to both functional and phylotype assignments. We argue that the directions of the OTU and metagenome errors are such that stable phylotypes are overlooked, while functional stability is overestimated. Taking these errors into account, we propose that phylotype represents an interface for functionality, and is for this reason an important determinant for the services provided by the gut microbiota to the host.
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Avershina, E., Frisli, T. and Rudi, K., 2013. De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data. Microbes and Environments, in press. DOI: http://dx.doi.org/10.1264/jsme2.ME12157.
-
Chung, H., Pamp, S.J., Hill, J.A., Surana, N.K., Edelman, S.M., Troy, E.B., Reading, N.C., Villablanca, E.J., Wang, S., Mora, J.R., Umesaki, Y., Mathis, D., Benoist, C., Relman, D.A. and Kasper, D.L., 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149: 1578-1593.
'Gut immune maturation depends on colonization with a host-specific microbiota ' () 149 Cell : 1578 -1593.
-
Dale, C. and Moran, N.A., 2006. Molecular interactions between bacterial symbionts and their hosts. Cell 126: 453-465.
'Molecular interactions between bacterial symbionts and their hosts ' () 126 Cell : 453 -465.
-
Gomez-Alvarez, V., Teal, T.K. and Schmidt, T.M., 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME Journal 3: 1314-1317.
'Systematic artifacts in metagenomes from complex microbial communities ' () 3 ISME Journal : 1314 -1317.
-
Hamady, M. and Knight, R., 2009. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Research 19: 1141-1152.
'Microbial community profiling for human microbiome projects: Tools, techniques, and challenges ' () 19 Genome Research : 1141 -1152.
-
Holder, M. and Lewis, P.O., 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics 4: 275-284.
'Phylogeny estimation: traditional and Bayesian approaches ' () 4 Nature Reviews Genetics : 275 -284.
-
Ley, R.E., Turnbaugh, P.J., Klein, S. and Gordon, J.I., 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
'Microbial ecology: human gut microbes associated with obesity ' () 444 Nature : 1022 -1023.
-
Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K. and Knight, R., 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489: 220-230.
'Diversity, stability and resilience of the human gut microbiota ' () 489 Nature : 220 -230.
-
Moran, N.A., 2006. Symbiosis. Current Biology 16: R866-R871.
'Symbiosis ' () 16 Current Biology : R866 -R871.
-
Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J.O., Deppenmeier, U. and Martin, W.F., 2012. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proceedings of the National Academy of Sciences of the USA 109: 20537-20542.
'Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea ' () 109 Proceedings of the National Academy of Sciences of the USA : 20537 -20542.
-
Prakash, T. and Taylor, T.D., 2012. Functional assignment of metagenomic data: challenges and applications. Briefings in Bioinformatics 13: 711-727.
'Functional assignment of metagenomic data: challenges and applications ' () 13 Briefings in Bioinformatics : 711 -727.
-
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., Peng, Y., Zhang, D., Jie, Z., Wu, W., Qin, Y., Xue, W., Li, J., Han, L., Lu, D., Wu, P., Dai, Y., Sun, X., Li, Z., Tang, A., Zhong, S., Li, X., Chen, W., Xu, R., Wang, M., Feng, Q., Gong, M., Yu, J., Zhang, Y., Zhang, M., Hansen, T., Sanchez, G., Raes, J., Falony, G., Okuda, S., Almeida, M., LeChatelier, E., Renault, P., Pons, N., Batto, J.M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Yang, H., Wang, J., Ehrlich, S.D., Nielsen, R., Pedersen, O. and Kristiansen, K., 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: 55-60.
'A metagenome-wide association study of gut microbiota in type 2 diabetes ' () 490 Nature : 55 -60.
-
Rudi, K. and Sekelja, M., 2013. High or low correlation between co-occuring gene clusters and 16S rRNA phylogeny. FEMS Microbiology Letters 339: 23-29.
'High or low correlation between co-occuring gene clusters and 16S rRNA phylogeny ' () 339 FEMS Microbiology Letters : 23 -29.
-
Sekelja, M., Berget, I., Naes, T. and Rudi, K., 2011. Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach. ISME Journal 5: 519-531.
'Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach ' () 5 ISME Journal : 519 -531.
-
Smillie, C.S., Smith, M.B., Friedman, J., Cordero, O.X., David, L.A. and Alm, E.J., 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241-244.
'Ecology drives a global network of gene exchange connecting the human microbiome ' () 480 Nature : 241 -244.
-
Tremaroli, V. and Backhed, F., 2012. Functional interactions between the gut microbiota and host metabolism. Nature 489: 242-249.
'Functional interactions between the gut microbiota and host metabolism ' () 489 Nature : 242 -249.
-
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., Egholm, M., Henrissat, B., Heath, A.C., Knight, R. and Gordon, J.I., 2009. A core gut microbiome in obese and lean twins. Nature 457: 480-484.
'A core gut microbiome in obese and lean twins ' () 457 Nature : 480 -484.
-
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., Heath, A.C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J.G., Lozupone, C.A., Lauber, C., Clemente, J.C., Knights, D., Knight, R. and Gordon, J.I., 2012. Human gut microbiome viewed across age and geography. Nature 486: 222-227.
'Human gut microbiome viewed across age and geography ' () 486 Nature : 222 -227.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 189 | 113 | 18 |
| Full Text Views | 15 | 13 | 1 |
| PDF Views & Downloads | 9 | 5 | 0 |
Is it who you are or what you do that is important in the human gut?
In: Beneficial MicrobesSearch for other papers by E. Avershina in
Current site
Google Scholar
PubMed
Search for other papers by K. Rudi in
Current site
Google Scholar
PubMed
The current leading view is that functionality and not phylotype is the most important determinant for the services provided by the gut microbiota. Here we present an alternative opinion, advocating the importance of phylotype in addition to function. We believe the literature is misled by technical artifacts in defining operational taxonomic units (OTUs), which are binned groups of bacteria based on sequence homology. Furthermore, the current metagenomic approaches where the total DNA in a sample is mixed prior to sequencing and subsequently resolved by a bioinformatics approach, are highly error prone with respect to both functional and phylotype assignments. We argue that the directions of the OTU and metagenome errors are such that stable phylotypes are overlooked, while functional stability is overestimated. Taking these errors into account, we propose that phylotype represents an interface for functionality, and is for this reason an important determinant for the services provided by the gut microbiota to the host.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 189 | 113 | 18 |
| Full Text Views | 15 | 13 | 1 |
| PDF Views & Downloads | 9 | 5 | 0 |
