Review

Examining the healthy human microbiome concept.
Joos, R. ORCID: https://orcid.org/0000-0002-8124-7747, Boucher, K. ORCID: https://orcid.org/0009-0000-4381-5451, Lavelle, A., Arumugam, M. ORCID: https://orcid.org/0000-0002-0886-9101, Blaser, M.J. ORCID: https://orcid.org/0000-0003-2447-2443, Claesson, M.J., Clarke, G. ORCID: https://orcid.org/0000-0001-9771-3979, Cotter, P.D. ORCID: https://orcid.org/0000-0002-5465-9068, De Sordi, L. ORCID: https://orcid.org/0000-0002-3785-550X, Dominguez-Bello, M.G. ORCID: https://orcid.org/0000-0002-8879-6159, Dutilh, B.E. ORCID: https://orcid.org/0000-0003-2329-7890, Ehrlich, S.D., Ghosh, T.S. ORCID: https://orcid.org/0000-0001-9570-0365, Hill, C. ORCID: https://orcid.org/0000-0002-8527-1445, Junot, C. ORCID: https://orcid.org/0000-0003-0019-6827, Lahti, L. ORCID: https://orcid.org/0000-0001-5537-637X, Lawley, T.D. ORCID: https://orcid.org/0000-0002-4805-621X, Licht, T.R. ORCID: https://orcid.org/0000-0002-6399-9574, Maguin, E. ORCID: https://orcid.org/0000-0001-5452-3382, Makhalanyane, T.P. ORCID: https://orcid.org/0000-0002-8173-1678, Marchesi, J.R. ORCID: https://orcid.org/0000-0002-7994-5239, Matthijnssens, J. ORCID: https://orcid.org/0000-0003-1188-9733, Raes, J. ORCID: https://orcid.org/0000-0002-1337-041X, Ravel, J. ORCID: https://orcid.org/0000-0002-0851-2233, Salonen, A., Scanlan, P.D. ORCID: https://orcid.org/0000-0002-6733-9653, Shkoporov, A. ORCID: https://orcid.org/0000-0002-5547-8672, Stanton, C., Thiele, I., Tolstoy, I., Walter, J. ORCID: https://orcid.org/0000-0003-1754-172X, Yang, B. ORCID: https://orcid.org/0000-0002-1347-3718, Yutin, N., Zhernakova, A., Zwart, H. ORCID: https://orcid.org/0000-0001-8846-5213, Doré, J. ORCID: https://orcid.org/0000-0002-8756-0718 and Ross, R.P. ORCID: https://orcid.org/0000-0003-4876-8839
Nature Reviews Microbiology 23 (3): 192-205. March 2025

Diversity within species: interpreting strains in microbiomes.
Van Rossum, T., Ferretti, P., Maistrenko, O.M. ORCID: https://orcid.org/0000-0003-1961-7548 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nature Reviews Microbiology 18 : 491-506. September 2020

Tara Oceans: towards global ocean ecosystems biology.
Sunagawa, S. ORCID: https://orcid.org/0000-0003-3065-0314, Acinas, S.G., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Bowler, C. ORCID: https://orcid.org/0000-0003-3835-6187, Eveillard, D. ORCID: https://orcid.org/0000-0002-8162-7360, Gorsky, G. ORCID: https://orcid.org/0000-0002-1099-8711, Guidi, L. ORCID: https://orcid.org/0000-0002-6669-5744, Iudicone, D., Karsenti, E., Lombard, F. ORCID: https://orcid.org/0000-0002-8626-8782, Ogata, H. ORCID: https://orcid.org/0000-0001-6594-377X, Pesant, S., Sullivan, M.B. ORCID: https://orcid.org/0000-0001-8398-8234, Wincker, P. ORCID: https://orcid.org/0000-0001-7562-3454 and de Vargas, C.
Nature Reviews Microbiology 18 (8): 428-445. August 2020

Dual RNA-seq of pathogen and host.
Westermann, A.J., Gorski, S.A. ORCID: https://orcid.org/0000-0003-0539-3395 and Vogel, J.
Nature Reviews Microbiology 10 (9): 618-630. September 2012

Mass spectrometry tools for the classification and identification of bacteria.
Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693 and Kliem, M.
Nature Reviews Microbiology 8 (1): 74-82. 1 January 2010

Molecular eco-systems biology: towards an understanding of community function.
Raes, J. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Nature Reviews Microbiology 6 (9): 693-699. September 2008