Gilbert, S. F., Sapp, J. & Tauber, A. I. A symbiotic view of life: we have never been individuals. Q. Rev. Biol. 87, 325–341 (2012).
Google Scholar
Bass, D., Stentiford, G. D., Wang, H.-C., Koskella, B. & Tyler, C. R. The pathobiome in animal and plant diseases. Trends Ecol. Evol. 34, 996–1008 (2019).
Google Scholar
Husnik, F. & Keeling, P. J. The fate of obligate endosymbionts: reduction, integration, or extinction. Curr. Opin. Genet. Dev. 58-59, 1–8 (2019).
Google Scholar
Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).
Google Scholar
Kwong, W. K. & Moran, N. A. Gut microbial communities of social bees. Nat. Rev. Microbiol. 14, 374–384 (2016).
Google Scholar
Hammer, T. J., Janzen, D. H., Hallwachs, W., Jaffe, S. P. & Fierer, N. Caterpillars lack a resident gut microbiome. Proc. Nat Acad. Sci. USA 114, 9641–9646 (2017).
Google Scholar
Holt, C. C., van der Giezen, M., Daniels, C. L., Stentiford, G. D. & Bass, D. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). ISME J. 14, 531–543 (2020).
Google Scholar
Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 4921 (2018).
Google Scholar
Thomas, T. et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat. Commun. 7, 11870 (2016).
Google Scholar
Engelberts, J. P. et al. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J. 14, 1100–1110 (2020).
Google Scholar
Ley, R. E. et al. Evolution of mammals and their gut microbes. Science 320, 1647–1651 (2008).
Google Scholar
Mallot, E. K. & Amato, K. R. Host specificity of the gut microbiome. Nat. Rev. Microbiol. 19, 639–653 (2021).
Google Scholar
Colston, T. J. & Jackson, C. R. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol. Ecol. 25, 3776–3800 (2016).
Google Scholar
Levin, D. et al. Diversity and functional landscapes in the microbiota of animals in the wild. Science 372, eabb5352 (2021).
Google Scholar
Nishida, A. H. & Ochman, H. Rates of gut microbiome divergence in mammals. Mol. Ecol. 27, 1884–1897 (2013).
Google Scholar
Brooks, A. W., Kohl, K. D., Brucker, R. M., van Opstal, E. J. & Bordenstein, S. R. Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history. PLoS Biol. 14, e2000225 (2016).
Google Scholar
Mazel, F. et al. Is host filtering the main driver of phylosymbiosis across the tree of life? mSystems 3, https://doi.org/10.1128/mSystems.00097-18 (2018).
Lutz, H. L. et al. Ecology and host identity outweigh evolutionary history in shaping the bat microbiome. mBio 4, 6 (2019).
Grond, K. et al. No evidence for phylosymbiosis in Western chipmunk species. FEMS Microbiol. Ecol. 96, fiz182 (2020).
Google Scholar
Song, S. J. et al. Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats. mBio 11, 1 (2020).
Google Scholar
Trevelline, B. K., Sosa, J., Hartup, B. K. & Kohl, K. D. A bird’s-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc. R. Soc. B 287, 20192988 (2020).
Google Scholar
Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).
Google Scholar
Youngblut, N. D. et al. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat. Commun. 10, 2200 (2019).
Google Scholar
Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).
Google Scholar
Moeller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997 (2016).
Google Scholar
Eckert, E. M., Anicic, N. & Fontaneto, D. Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment. Mol. Ecol. 30, 1545–1558 (2021).
Google Scholar
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–228 (2012).
Google Scholar
Bik, H. M. Microbial metazoa are microbes too. mSystems 4, e00109–e00119 (2019).
Google Scholar
Schuelke, T., Pereira, T. J., Hardy, S. M. & Bik, H. M. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol. Ecol. 27, 1930–1951 (2018).
Google Scholar
Guidetti, R. et al. Further insights in the Tardigrada microbiome: phylogenetic position and prevalence of infection of four new Alphaproteobacteria putative endosymbionts. Zool. J. Linn. Soc. 188, 925–937 (2020).
Google Scholar
Giere, O. Meiobenthology (Springer-Verlag, 2009).
Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. R. Soc. B 286, 20190831 (2019).
Google Scholar
Hammer, T. J., Sanders, J. G. & Fierer, N. Not all animals need a microbiome. FEMS Microbiol. Lett. 366, fnz117 (2019).
Google Scholar
Alejandre-Colomo, C. et al. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME Commun. 1, 51 (2021).
Google Scholar
Husnik, F. et al. Bacterial and archaeal symbioses with protists. Curr. Biol. 31, R862–R877 (2021).
Google Scholar
Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021).
Google Scholar
Neave, M. J., Apprill, A., Ferrier-Pagès, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324 (2016).
Google Scholar
Weiland-Bräuer, N. et al. Composition of bacterial communities associated with Aurelia aurita changes with compartment, life stage, and population. Appl. Environ. Microbiol. 81, 6038–6052 (2015).
Google Scholar
Bik, E. M. et al. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat. Commun. 7, 10516 (2016).
Google Scholar
Burns, A. R. et al. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J. 10, 655–664 (2016).
Google Scholar
McFall-Ngai, M. Adaptive immunity: care for the community. Nature 445, 153 (2007).
Google Scholar
Ruehland, C. & Dubilier, N. Gamma- and epsilonproteobacterial ectosymbionts of a shallow-water marine worm are related to deep-sea hydrothermal vent ectosymbionts. Environ. Microbiol. 12, 2312–2326 (2010).
Google Scholar
Gruber-Vodicka, H. R. et al. Two intracellular and cell-type specific bacterial symbionts in the placozoan Trichoplax H2. Nat. Microbiol. 4, 1465–1474 (2019).
Google Scholar
Schockaert, E. R. in Methods for the Examination of Organismal Diversity in Soils and Sediments (ed. Hall, G. S.) 211–225 (CABI, 1996).
Higgins, R. P. in Introduction to the Study of Meiofauna (eds. Higgins, R. P. and Thiel, H.) 328–331 (SIP, 1988).
Schram, M. D. & Davison, P. G. Irwin Loops—a history and method of constructing homemade loops. Trans. Kans. Acad. Sci. 115, 35–40 (1903).
Google Scholar
Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491–499 (1988).
Google Scholar
Bower, S. M. et al. Preferential PCR amplification of parasitic protistan small subunit rDNA from metazoan tissues. J. Eukaryot. Microbiol. 51, 325–332 (2004).
Google Scholar
Comeau, A. M., Li, W. K. W., Tremblay, J.-E., Carmack, E. C. & Lovejoy, C. Arctic ocean microbial community structure before and after the 2007 record sea ice minimum. PLoS ONE 6, e27492 (2011).
Google Scholar
Zhang, R.-Y. et al. Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea. BMC Microbiol. 20, 25 (2020).
Google Scholar
Lane, D. J. in Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt, E. & Goodfellow, M) 115–175 (Wiley, 1991).
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).
Google Scholar
Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
Callahan, B. J. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Google Scholar
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).
Love, M. I., Huber, W. & Anders, S. Moderate estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Kurtz, Z. D. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput. Biol. 11, e1004226 (2015).
Google Scholar
Csardi, G. & Nepusz, T. The igraph Software Package for Complex Network Research (InterJournal, 2006).
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
Kolde, R. pheatmap: pretty heatmaps. R package version 1.0.12 https://CRAN.R-project.org/package=pheatmap (2015).
Lin, H. & Das Peddada, S. Analysis of composition of microbiomes with bias correction. Nat. Commun. 11, 3514 (2020).
Google Scholar
Oksanen, J. vegan: Community Ecology Package. R package version 2.5.7 https://CRAN.R-project.org/package=vegan (2020).
Rouse, G., Pleijel, F. & Tilic, E. Annelida (Oxford Univ. Press, 2022).
Ahmed, M. & Holovachov, O. Twenty years after De Ley and Blaxter—How far did we progress in understanding the phylogeny of the phylum Nematoda? Animals 11, 3479 (2021).
Google Scholar
Van Steenkiste, N. W. L., Herbert, E. R. & Leander, B. S. Species diversity in the marine microturbellarian Astrotorhynchus bifidus sensu lato (Platyhelminthes: Rhabdocoela) from the Northeast Pacific Ocean. Mol. Phylogenet. Evol. 120, 259–273 (2018).
