R. Macarthur and R. Levins, The Limiting Similarity, Convergence, and Divergence of Coexisting Species, The American Naturalist, vol.101, issue.921, pp.377-385, 1967.
DOI : 10.1086/282505

P. Chesson, Mechanisms of Maintenance of Species Diversity, Annual Review of Ecology and Systematics, vol.31, issue.1, pp.343-366, 2000.
DOI : 10.1146/annurev.ecolsys.31.1.343

P. Turnbaugh, R. Ley, M. Hamady, C. Fraser-liggett, R. Knight et al., The Human Microbiome Project, Nature, vol.112, issue.7164, pp.804-810, 2007.
DOI : 10.1038/nature06244

H. Consortium, A framework for human microbiome research, Nature, vol.486, issue.7402, pp.215-221, 2012.

H. Consortium, Structure, function and diversity of the healthy human microbiome, Nature, vol.486, issue.7402, pp.207-214, 2012.

F. Dewhirst, T. Chen, J. Izard, B. Paster, A. Tanner et al., The Human Oral Microbiome, Journal of Bacteriology, vol.192, issue.19, pp.5002-5017, 2010.
DOI : 10.1128/JB.00542-10

J. Wooley, A. Godzik, and I. Friedberg, A Primer on Metagenomics, PLoS Computational Biology, vol.14, issue.2, pp.1000667-20195499, 2010.
DOI : 10.1371/journal.pcbi.1000667.t002

URL : http://doi.org/10.1371/journal.pcbi.1000667

J. Caporaso, C. Lauber, E. Costello, D. Berg-lyons, A. Gonzalez et al., Moving pictures of the human microbiome, Genome Biology, vol.12, issue.5, p.21624126, 2011.
DOI : 10.1093/bioinformatics/btq461

T. Yatsunenko, F. Rey, M. Manary, I. Trehan, M. Dominguez-bello et al., Human gut microbiome viewed across age and geography, Nature, vol.2, issue.7402, pp.222-227, 2012.
DOI : 10.1038/nature11053

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376388

E. Costello, C. Lauber, M. Hamady, N. Fierer, J. Gordon et al., Bacterial Community Variation in Human Body Habitats Across Space and Time, Science, vol.127, issue.2, pp.1694-1697, 2009.
DOI : 10.1016/j.cell.2006.08.043

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602444

M. Claesson, S. Cusack, O. Sullivan, O. Greene-diniz, R. De-weerd et al., Composition, variability, and temporal stability of the intestinal microbiota of the elderly, Proceedings of the National Academy of Sciences, vol.4, issue.1, pp.4586-4591, 2011.
DOI : 10.1038/ismej.2009.97

D. Gevers, R. Knight, J. Petrosino, K. Huang, A. Mcguire et al., The human microbiome project: a community resource for the healthy human microbiome):e1001377. https, PLoS biology, vol.10, issue.8, p.22904687, 2012.

M. Arthur and R. , SPECIES PACKING, AND WHAT COMPETITION MINIMIZES, Proceedings of the National Academy of Sciences, pp.1369-1371, 1969.
DOI : 10.1073/pnas.64.4.1369

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC223294/pdf

R. Macarthur, Species packing and competitive equilibrium for many species Theoretical population biology, pp.1-110040, 1970.

P. Chesson, MacArthur's consumer-resource model, Theoretical Population Biology, vol.37, issue.1, pp.26-380040, 1990.
DOI : 10.1016/0040-5809(90)90025-Q

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.361.5142

J. Wright, Plant diversity in tropical forests: a review of mechanisms of species coexistence, Oecologia, vol.130, issue.1, pp.1-14, 2002.
DOI : 10.1007/s004420100809

C. Shannon, A mathematical theory of communication, ACM SIGMOBILE Mobile Computing and Communications Review, vol.5, issue.1, pp.3-55, 2001.
DOI : 10.1145/584091.584093

R. Macarthur, Fluctuations of Animal Populations and a Measure of Community Stability, Ecology, vol.36, issue.3, pp.533-536, 1955.
DOI : 10.2307/1929601

B. Flury, Two generalizations of the common principal component model, Biometrika, vol.74, issue.1, pp.59-69, 1987.
DOI : 10.1093/biomet/74.1.59

R. Vollgraf and K. Obermayer, Quadratic optimization for simultaneous matrix diagonalization, IEEE Transactions on Signal Processing, vol.54, issue.9, pp.3270-3278, 2006.
DOI : 10.1109/TSP.2006.877673

N. Trendafilov, Stepwise estimation of common principal components, Computational Statistics & Data Analysis, vol.54, issue.12, pp.3446-3457, 2010.
DOI : 10.1016/j.csda.2010.03.010

M. Udell, C. Horn, R. Zadeh, and S. Boyd, Generalized low rank models. arXiv preprint arXiv:14100342, 2014.
DOI : 10.1561/2200000055

URL : http://arxiv.org/abs/1410.0342

A. Cutler and L. Breiman, Archetypal Analysis, Technometrics, vol.4, issue.4, pp.338-347, 1994.
DOI : 10.1080/00401706.1994.10485840

C. Bauckhage, k-Means Clustering Is Matrix Factorization. arXiv preprint arXiv:151207548, 2015.

J. Bray and J. Curtis, An Ordination of the Upland Forest Communities of Southern Wisconsin, Ecological Monographs, vol.27, issue.4, pp.325-349, 1957.
DOI : 10.2307/1942268

C. Lozupone and R. Knight, UniFrac: a new phylogenetic method for comparing microbial communities Applied and environmental microbiology, pp.8228-8235, 2005.
DOI : 10.1128/aem.71.12.8228-8235.2005

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317376

J. Kruskal and M. Wish, Multidimensional scaling, Sage, vol.11, 1978.
DOI : 10.4135/9781412985130

H. Wang, A. Banerjee, and D. Boley, Common component analysis for multiple covariance matrices, Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining, KDD '11, pp.956-964, 2011.
DOI : 10.1145/2020408.2020565

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.297.5300

S. Federhen, The NCBI taxonomy database Nucleic acids research, pp.136-143, 2012.

M. Kanehisa and S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102409/pdf

V. Mazumdar, S. Amar, and D. Segrè, Metabolic Proximity in the Order of Colonization of a Microbial Community, PLoS ONE, vol.102, issue.10, pp.77617-24204896, 2013.
DOI : 10.1371/journal.pone.0077617.s002

M. Langille, J. Zaneveld, J. Caporaso, D. Mcdonald, D. Knights et al., Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nature Biotechnology, vol.51, issue.9, pp.814-821, 2013.
DOI : 10.1093/nar/gkr1178

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819121

K. Aßhauer, B. Wemheuer, R. Daniel, and P. Meinicke, Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1., Bioinformatics, vol.31, issue.17, pp.2882-2884, 2015.
DOI : 10.1093/bioinformatics/btv287

C. Fisher and P. Mehta, Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics, Bioinformatics, vol.31, issue.11, p.25619995
DOI : 10.1093/bioinformatics/btv037

C. Fisher and P. Mehta, Bayesian feature selection with strongly-regularizing priors maps to the Ising Model. arXiv preprint arXiv:14110591, 2014.
DOI : 10.1162/neco_a_00780

URL : http://arxiv.org/abs/1411.0591

C. Smillie, M. Smith, J. Friedman, O. Cordero, L. David et al., Ecology drives a global network of gene exchange connecting the human microbiome, Nature, vol.37, issue.7376, pp.241-244, 2011.
DOI : 10.1038/nature10571

M. Tikhonov, R. Leach, and N. Wingreen, Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution, The ISME Journal, vol.28, issue.1, pp.68-80, 2015.
DOI : 10.1038/ismej.2014.117

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274427

A. Koeppel and M. Wu, Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic acids research. 2013; p. gkt241. https
DOI : 10.1093/nar/gkt241

URL : http://doi.org/10.1093/nar/gkt241

L. Philippot, S. Andersson, T. Battin, J. Prosser, J. Schimel et al., The ecological coherence of high bacterial taxonomic ranks, Nature Reviews Microbiology, vol.444, issue.7, pp.523-529, 2010.
DOI : 10.4319/lo.2002.47.2.0453

W. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2128, 1999.
DOI : 10.1126/science.284.5423.2124

A. Bashan, T. Gibson, J. Friedman, V. Carey, S. Weiss et al., Universality of human microbial dynamics, Nature, vol.3, issue.7606, pp.259-262, 2016.
DOI : 10.1038/nature18301

A. Wilke, J. Bischof, T. Harrison, T. Brettin, D. Souza et al., A RESTful API for accessing microbial community data for MG-RAST):e1004008. https, PLoS Comput Biol, vol.11, issue.1, p.25569221, 2015.
DOI : 10.1371/journal.pcbi.1004008

URL : http://doi.org/10.1371/journal.pcbi.1004008

E. Glass, J. Wilkening, A. Wilke, D. Antonopoulos, and F. Meyer, Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes, Cold Spring Harbor Protocols, vol.2010, issue.1, pp.5368-20150127, 2010.
DOI : 10.1101/pdb.prot5368

A. Wilke, E. Glass, J. Bischof, D. Braithwaite, M. Souza et al., MG-RAST technical report and manual for version 3, pp.6-7