Arikawa, K., Ide, K., Kogawa, M., Saeki, T., Yoda, T., Endoh, T., Matsuhashi, A., Takeyama, H., Hosokawa, M., Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics. Microbiome, 9, 2021, 202, 10.1186/s40168-021-01152-4.
Cani, P.D., de Hase, E.M., van Hul, M., Gut microbiota and host metabolism: From proof of concept to therapeutic intervention. Microorganisms, 9, 2021, 10.3390/microorganisms9061302.
Franzosa, E.A., Huang, K., Meadow, J.F., Gevers, D., Lemon, K.P., Bohannan, B.J.M., Huttenhower, C., Identifying personal microbiomes using metagenomic codes. Proc. Natl. Acad. Sci. USA 112 (2015), E2930–E2938, 10.1073/pnas.1423854112.
Gibbons, S.M., Kearney, S.M., Smillie, C.S., Alm, E.J., Two dynamic regimes in the human gut microbiome. PLoS Comput. Biol., 13, 2017, e1005364, 10.1371/journal.pcbi.1005364.
Heintz-Buschart, A., Wilmes, P., Human Gut Microbiome: Function Matters. Trends in Microbiology 26 (2018), 563–574, 10.1016/j.tim.2017.11.002.
Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., Küsel, K., Rillig, M.C., Rivett, D.W., Salles, J.F., et al. Where less may be more: How the rare biosphere pulls ecosystems strings. ISME Journal 11 (2017), 853–862, 10.1038/ismej.2016.174.
Kostic, A.D., Howitt, M.R., Garrett, W.S., Exploring host-microbiota interactions in animal models and humans. Genes Dev. 27 (2013), 701–718, 10.1101/gad.212522.112.
Labonté, J.M., Swan, B.K., Poulos, B., Luo, H., Koren, S., Hallam, S.J., Sullivan, M.B., Woyke, T., Wommack, K.E., Stepanauskas, R., Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J. 9 (2015), 2386–2399, 10.1038/ismej.2015.48.
Milanese, A., Mende, D.R., Paoli, L., Salazar, G., Ruscheweyh, H.J., Cuenca, M., Hingamp, P., Alves, R., Costea, P.I., Coelho, L.P., et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nat. Commun., 10, 2019, 1014, 10.1038/s41467-019-08844-4.
Petrosino, J.F., The microbiome in precision medicine: The way forward. Genome Medicine, 10, 2018, 10.1186/s13073-018-0525-6.
Pryszlak, A., Wenzel, T., Seitz, K.W., Hildebrand, F., Kartal, E., Raffaele Cosenza, M., Benes, V., Merten, C., Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. Cell Reports Methods 2 (2021), 100137-1–100137-12.
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., et al. Genomic variation landscape of the human gut microbiome. Nature 493 (2013), 45–50, 10.1038/nature11711.
Shah, P., Fritz, J.V., Glaab, E., Desai, M.S., Greenhalgh, K., Frachet, A., Niegowska, M., Estes, M., Jäger, C., Seguin-Devaux, C., et al. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat. Commun., 7, 2016, 11535, 10.1038/ncomms11535.
Wampach, L., Heintz-Buschart, A., Fritz, J.V., Ramiro-Garcia, J., Habier, J., Herold, M., Narayanasamy, S., Kaysen, A., Hogan, A.H., Bindl, L., et al. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nat. Commun., 9, 2018, 5091, 10.1038/s41467-018-07631-x.