1.Blaser, M. J. & Falkow, S. What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894 (2009).CAS
PubMed
Article
PubMed Central
Google Scholar
2.Friesen, M. L. et al. Microbially mediated plant functional traits. Annu. Rev. Ecol. Evol. Syst. 42, 23–46 (2011).Article
Google Scholar
3.McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. 110, 3229–3236 (2013).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
4.Douglas, A. E. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a016113 (2014).5.Stappenbeck, T. S. & Virgin, H. W. Accounting for reciprocal host-microbiome interactions in experimental science. Nature 534, 191–199 (2016).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
6.Moran, N. A. & Sloan, D. B. The hologenome concept: helpful or hollow? PLoS Biol. 13, e1002311 (2015).PubMed
Article
CAS
PubMed Central
Google Scholar
7.Douglas, A. E. & Werren, J. H. Holes in the hologenome: why host-microbe symbioses are not holobionts. MBio 7, e02099 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
8.Koskella, B., Hall, L. J. & Metcalf, C. J. E. The microbiome beyond the horizon of ecological and evolutionary theory. Nat. Ecol. Evol. 1, 1606–1615 (2017).PubMed
Article
PubMed Central
Google Scholar
9.Morimoto, J. & Baltrus, D. A. The extended genotype: to what extent? A comment on Carthey et al. Trends Ecol. Evol. 34, 186–187 (2019).10.Scheuring, I. & Yu, D. W. How to assemble a beneficial microbiome in three easy steps. Ecol. Lett. 15, 1300–1307 (2012).PubMed
Article
PubMed Central
Google Scholar
11.Dawkins, R. The Extended Phenotype: The Long Reach of the Gene. (Oxford University Press, USA, 1982).12.Whitham, T. G. et al. A framework for community and ecosystem genetics: from genes to ecosystems. Nat. Rev. Genet. 7, 510–523 (2006).CAS
PubMed
Article
PubMed Central
Google Scholar
13.Mueller, U. G. & Sachs, J. L. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol 23, 606–617 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
14.Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735 (2008).CAS
PubMed
Article
PubMed Central
Google Scholar
15.Bordenstein, S. R. & Theis, K. R. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol. 13, e1002226 (2015).PubMed
Article
CAS
PubMed Central
Google Scholar
16.Alberdi, A., Aizpurua, O., Bohmann, K., Zepeda-Mendoza, M. L. & Gilbert, M. T. P. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol. Evol. 31, 689–699 (2016).PubMed
Article
PubMed Central
Google Scholar
17.Shapira, M. Gut Microbiotas and host evolution: scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016).PubMed
Article
PubMed Central
Google Scholar
18.Carrier, T. J. & Reitzel, A. M. The hologenome across environments and the implications of a host-associated microbial repertoire. Front. Microbiol. 8, 802 (2017).PubMed
Article
PubMed Central
Google Scholar
19.Hurst, G. D. D. Extended genomes: symbiosis and evolution. Interface Focus 7, 20170001 (2017).20.Sudakaran, S., Kost, C. & Kaltenpoth, M. Symbiont acquisition and replacement as a source of ecological innovation. Trends Microbiol 25, 375–390 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
21.Carthey, A. J. R., Gillings, M. R. & Blumstein, D. T. The extended genotype: microbially mediated olfactory communication. Trends Ecol. Evol. 33, 885–894 (2018).PubMed
Article
PubMed Central
Google Scholar
22.Rosenberg, E. & Zilber-Rosenberg, I. The hologenome concept of evolution after 10 years. Microbiome 6, 78 (2018).PubMed
Article
PubMed Central
Google Scholar
23.Futuyma, D. J. & Moreno, G. The evolution of ecological specialization. Annu. Rev. Ecol. Syst. 19, 207–233 (1988).Article
Google Scholar
24.Piersma, T. & Drent, J. Phenotypic flexibility and the evolution of organismal design. Trends Ecol. Evol. 18, 228–233 (2003).Article
Google Scholar
25.Lande, R. Natural selection and random genetic drift in phenotypic. Evolution. Evolution 30, 314–334 (1976).PubMed
Article
PubMed Central
Google Scholar
26.West-Eberhard, M. J. Phenotypic plasticity and the origins of diversity. Annu. Rev. Ecol. Syst. 20, 249–278 (1989).Article
Google Scholar
27.Ghalambor, C. K., McKay, J. K., Carroll, S. P. & Reznick, D. N. Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Funct. Ecol. 21, 394–407 (2007).Article
Google Scholar
28.Bolnick, D. I. et al. Why intraspecific trait variation matters in community ecology. Trends Ecol. Evol. 26, 183–192 (2011).PubMed
Article
PubMed Central
Google Scholar
29.Metcalf, C. J. E. & Koskella, B. Protective microbiomes can limit the evolution of host pathogen defense. Evol. Lett. 3, 534–543 (2019).PubMed
Article
PubMed Central
Google Scholar
30.Rosenberg, E., Koren, O., Reshef, L., Efrony, R. & Zilber-Rosenberg, I. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355–362 (2007).CAS
PubMed
Article
Google Scholar
31.Theis, K. R. et al. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1, e00028 (2016).32.Funkhouser, L. J. & Bordenstein, S. R. Mom knows best: the universality of maternal microbial transmission. PLoS Biol. 11, e1001631 (2013).CAS
PubMed
Article
PubMed Central
Google Scholar
33.Salem, H., Florez, L., Gerardo, N. & Kaltenpoth, M. An out-of-body experience: the extracellular dimension for the transmission of mutualistic bacteria in insects. Proc. R. Soc. Lond. B. 282, 20142957 (2015).34.Vacher, C. et al. The phyllosphere: microbial jungle at the plant–climate interface. Annu. Rev. Ecol. Evol. Syst. 47, 1–24 (2016).Article
Google Scholar
35.Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).ADS
CAS
PubMed
Article
Google Scholar
36.Grieneisen, L. E. et al. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc. R. Soc. B: Biol. Sci. 286, 20190431 (2019).Article
Google Scholar
37.McKenney, E. A., Koelle, K., Dunn, R. R. & Yoder, A. D. The ecosystem services of animal microbiomes. Mol. Ecol. 27, 2164–2172 (2018).CAS
PubMed
Article
Google Scholar
38.Sprockett, D., Fukami, T. & Relman, D. A. Role of priority effects in the early-life assembly of the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 15, 197–205 (2018).PubMed
Article
PubMed Central
Google Scholar
39.Uhr, G. T., Dohnalová, L. & Thaiss, C. A. The dimension of time in host-microbiome interactions. mSystems 4, e00216–18 (2019).40.van Vliet, S. & Doebeli, M. The role of multilevel selection in host microbiome evolution. Proc. Natl Acad. Sci. U.S.A. 116, 20591–20597 (2019).PubMed
Article
CAS
PubMed Central
Google Scholar
41.Benson, A. K. The gut microbiome—an emerging complex trait. Nat. Genet. 48, 1301 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
42.van Opstal, E. J. & Bordenstein, S. R. Rethinking heritability of the microbiome. Science 349, 1172–1173 (2015).ADS
PubMed
Article
Google Scholar
43.Beilsmith, K. et al. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host–microbe interactions. Plant J. 97, 164–181 (2019).44.Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789–799 (2014).CAS
PubMed
Article
PubMed Central
Google Scholar
45.Goodrich, J. K. et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19, 731–743 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
46.Early, A. M., Shanmugarajah, N., Buchon, N. & Clark, A. G. Drosophila genotype influences commensal bacterial levels. PLoS ONE 12, e0170332 (2017).PubMed
Article
CAS
PubMed Central
Google Scholar
47.Walters, W. A. et al. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc. Natl Acad. Sci. U. S. A. 115, 7368–7373 (2018).PubMed
Article
PubMed Central
Google Scholar
48.Camarinha-Silva, A. et al. Host genome influence on gut microbial composition and microbial prediction of complex traits in pigs. Genetics 206, 1637–1644 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
49.Difford, G. F. et al. Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows. PLoS Genet 14, e1007580 (2018).PubMed
Article
CAS
PubMed Central
Google Scholar
50.Koga, R., Meng, X.-Y., Tsuchida, T. & Fukatsu, T. Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte–embryo interface. Proc. Natl Acad. Sci. U.S.A. 109, E1230–E1237 (2012).CAS
PubMed
Article
PubMed Central
Google Scholar
51.Nyholm, S. V. & McFall-Ngai, M. The winnowing: establishing the squid–vibrio symbiosis. Nat. Rev. Microbiol. 2, 632–642 (2004).CAS
PubMed
Article
PubMed Central
Google Scholar
52.Kaltenpoth, M., Göttler, W., Herzner, G. & Strohm, E. Symbiotic bacteria protect wasp larvae from fungal infestation. Curr. Biol. 15, 475–479 (2005).CAS
PubMed
Article
PubMed Central
Google Scholar
53.Clark, R. I. et al. Distinct shifts in microbiota composition during Drosophila aging impair intestinal function and drive mortality. Cell Rep. 12, 1656–1667 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
54.Franzosa, E. A. et al. Identifying personal microbiomes using metagenomic codes. Proc. Natl Acad. Sci. U.S.A. 112, E2930–E2938 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
55.Lokmer, A. et al. Spatial and temporal dynamics of pacific oyster hemolymph microbiota across multiple scales. Front. Microbiol. 7, 1367 (2016).PubMed
Article
PubMed Central
Google Scholar
56.Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4, 457–469 (2003).CAS
PubMed
Article
PubMed Central
Google Scholar
57.Lapierre, P. & Gogarten, J. P. Estimating the size of the bacterial pan-genome. Trends Genet 25, 107–110 (2009).CAS
PubMed
Article
PubMed Central
Google Scholar
58.Koonin, E. V. & Wolf, Y. I. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front. Cell. Infect. Microbiol. 2, 119 (2012).PubMed
Article
PubMed Central
Google Scholar
59.Ferreiro, A., Crook, N., Gasparrini, A. J. & Dantas, G. Multiscale evolutionary dynamics of host-associated microbiomes. Cell 172, 1216–1227 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
60.Kikuchi, Y., Hosokawa, T. & Fukatsu, T. Specific developmental window for establishment of an insect-microbe gut symbiosis. Appl. Environ. Microbiol. 77, 4075–4081 (2011).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
61.Kikuchi, Y. et al. Symbiont-mediated insecticide resistance. Proc. Natl Acad. Sci. U.S.A. 109, 8618–8622 (2012).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
62.Itoh, H. et al. Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying. ISME J. 12, 909–920 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
63.Kohl, K. D. & Dearing, M. D. The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins. Front. Microbiol. 7, 1165 (2016).PubMed
PubMed Central
Google Scholar
64.Kohl, K. D., Weiss, R. B., Cox, J., Dale, C. & Dearing, M. D. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol. Lett. 17, 1238–1246 (2014).PubMed
Article
PubMed Central
Google Scholar
65.Miller, A. W., Kohl, K. D. & Dearing, M. D. The gastrointestinal tract of the white-throated Woodrat (Neotoma albigula) harbors distinct consortia of oxalate-degrading bacteria. Appl. Environ. Microbiol. 80, 1595–1601 (2014).ADS
PubMed
Article
CAS
PubMed Central
Google Scholar
66.Miller, A. W., Oakeson, K. F., Dale, C. & Dearing, M. D. Effect of dietary oxalate on the gut microbiota of the mammalian herbivore Neotoma albigula. Appl. Environ. Microbiol. 82, 2669–2675 (2016).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
67.Kohl, K. D., Stengel, A. & Dearing, M. D. Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets. Environ. Microbiol. 18, 1720–1729 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
68.Kohl, K. D. & Dearing, M. D. Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores. Ecol. Lett. 15, 1008–1015 (2012).PubMed
Article
PubMed Central
Google Scholar
69.Redman, R. S., Sheehan, K. B., Stout, R. G., Rodriguez, R. J. & Henson, J. M. Thermotolerance generated by plant/fungal symbiosis. Science 298, 1581 (2002).CAS
PubMed
Article
PubMed Central
Google Scholar
70.Rodriguez, R. J. et al. Stress tolerance in plants via habitat-adapted symbiosis. ISME J. 2, 404–416 (2008).PubMed
Article
PubMed Central
Google Scholar
71.Miller, E. T., Svanbäck, R. & Bohannan, B. J. M. Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. Trends Ecol. Evol. 33, 926–935 (2018).PubMed
Article
PubMed Central
Google Scholar
72.Newell, P. D. & Douglas, A. E. Interspecies interactions determine the impact of the gut microbiota on nutrient allocation in Drosophila melanogaster. Appl. Environ. Microbiol. 80, 788–796 (2014).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
73.Keebaugh, E. S., Yamada, R., Obadia, B., Ludington, W. B. & Ja, W. W. Microbial quantity impacts drosophila nutrition, development, and lifespan. Science 4, 247–259 (2018).CAS
Google Scholar
74.Gould, A. L. et al. Microbiome interactions shape host fitness. Proc. Natl Acad. Sci. U.S.A. 115, E11951–E11960 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
75.Mushegian, A. A., Walser, J.-C., Sullam, K. E. & Ebert, D. The microbiota of diapause: How host-microbe associations are formed after dormancy in an aquatic crustacean. J. Anim. Ecol. 87, 400–413 (2017).PubMed
Article
PubMed Central
Google Scholar
76.Panke-Buisse, K., Poole, A. C., Goodrich, J. K., Ley, R. E. & Kao-Kniffin, J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 9, 980–989 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
77.Rolig, A. S., Parthasarathy, R., Burns, A. R., Bohannan, B. J. M. & Guillemin, K. Individual members of the microbiota disproportionately modulate host innate immune responses. Cell Host Microbe 18, 613–620 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
78.Webster, N. S. & Reusch, T. B. H. Microbial contributions to the persistence of coral reefs. ISME J. 11, 2167–2174 (2017).PubMed
Article
PubMed Central
Google Scholar
79.Bourne, D. G., Morrow, K. M. & Webster, N. S. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu. Rev. Microbiol. 70, 317–340 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
80.Ainsworth, T. D., Thurber, R. V. & Gates, R. D. The future of coral reefs: a microbial perspective. Trends Ecol. Evol. 25, 233–240 (2010).PubMed
Article
PubMed Central
Google Scholar
81.Sommer, F. et al. The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep. 14, 1655–1661 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
82.Metcalf, C. J. E., Henry, L. P., Rebolleda-Gómez, M. & Koskella, B. Why evolve reliance on the microbiome for timing of ontogeny? MBio 10, e01496-19 (2019).83.Gilbert, S. F., Bosch, T. C. G. & Ledón-Rettig, C. Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents. Nat. Rev. Genet. 16, 611–622 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
84.Philippi, T. & Seger, J. Hedging one’s evolutionary bets, revisited. Trends Ecol. Evol. 4, 41–44 (1989).CAS
PubMed
Article
PubMed Central
Google Scholar
85.Storelli, G. et al. Lactobacillus plantarum promotes Drosophila systemic growth by modulating hormonal signals through TOR-dependent nutrient sensing. Cell Metab. 14, 403–414 (2011).CAS
PubMed
Article
PubMed Central
Google Scholar
86.Bruijning, M., Henry, L. P., Forsberg, S. K. G., Metcalf, C. J. E. & Ayroles, J. F. When the microbiome defines the host phenotype: selection on vertical transmission in varying environments. bioRxiv 2020.09.02.280040 (2020) https://doi.org/10.1101/2020.09.02.280040.87.Boone, C. K. et al. Bacteria associated with a tree-killing insect reduce concentrations of plant defense compounds. J. Chem. Ecol. 39, 1003–1006 (2013).CAS
PubMed
Article
PubMed Central
Google Scholar
88.Berasategui, A. et al. Gut microbiota of the pine weevil degrades conifer diterpenes and increases insect fitness. Mol. Ecol. 26, 4099–4110 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
89.Ceja-Navarro, J. A. et al. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nat. Commun. 6, 7618 (2015).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
90.Berasategui, A. et al. The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles. Mol. Ecol. 25, 4014–4031 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
91.Sachs, J. L., Skophammer, R. G. & Regus, J. U. Evolutionary transitions in bacterial symbiosis. Proc. Natl Acad. Sci. U.S.A 108, 10800–10807 (2011).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
92.Ohbayashi, T. et al. Insect’s intestinal organ for symbiont sorting. Proc. Natl Acad. Sci. U.S.A 112, E5179–E5188 (2015).CAS
PubMed
Article
PubMed Central
Google Scholar
93.Itoh, H. et al. Host–symbiont specificity determined by microbe–microbe competition in an insect gut. Proc. Natl Acad. Sci. U.S.A. 116, 22673–22682 (2019).CAS
PubMed
Article
PubMed Central
Google Scholar
94.Bennett, G. M. & Moran, N. A. Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole. Proc. Natl Acad. Sci. 112, 10169–10176 (2015).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
95.Knight, R. et al. Best practices for analysing microbiomes. Nat. Rev. Microbiol. 16, 410–422 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
96.Klassen, J. L. Defining microbiome function. Nat. Microbiol 3, 864–869 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
97.Lau, J. A. & Lennon, J. T. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl Acad. Sci. U.S.A. 109, 14058–14062 (2012).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
98.Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl Acad. Sci. U.S.A 115, E4284–E4293 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
99.Cho, I. & Blaser, M. J. The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260–270 (2012).CAS
PubMed
Article
PubMed Central
Google Scholar
100.Raymann, K., Bobay, L.-M. & Moran, N. A. Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome. Mol. Ecol. 27, 2057–2066 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
101.David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
102.Ziegler, M., Seneca, F. O., Yum, L. K., Palumbi, S. R. & Voolstra, C. R. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat. Commun. 8, 14213 (2017).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
103.Pollock, J., Glendinning, L., Wisedchanwet, T. & Watson, M. The madness of microbiome: attempting to find consensus ‘best practice’ for 16S microbiome studies. Appl. Environ. Microbiol. 84, e02627–17 (2018).PubMed
Article
PubMed Central
Google Scholar
104.Roth-Schulze, A. J. et al. Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga Ulva spp. Mol. Ecol. 27, 1952–1965 (2018).PubMed
Article
PubMed Central
Google Scholar
105.Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
106.Meaden, S., Metcalf, C. J. E. & Koskella, B. The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur). Environ. Microbiol. Rep. 8, 649–658 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
107.Lambais, M. R., Barrera, S. E., Santos, E. C., Crowley, D. E. & Jumpponen, A. Phyllosphere metaproteomes of trees from the Brazilian atlantic forest show high levels of functional redundancy. Microb. Ecol. 73, 123–134 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
108.Kwong, W. K. & Moran, N. A. Gut microbial communities of social bees. Nat. Rev. Microbiol. 14, 374–384 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
109.Oh, J. et al. Temporal stability of the human skin microbiome. Cell 165, 854–866 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
110.Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).PubMed
Article
PubMed Central
Google Scholar
111.Asnicar, F. et al. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling. mSystems 2, e00164–16 (2017).112.Yassour, M. et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe 24, 146–154.e4 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
113.Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
114.Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392–400 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
115.Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).CAS
PubMed
Article
PubMed Central
Google Scholar
116.Jorth, P. et al. Metatranscriptomics of the human oral microbiome during health and disease. MBio 5, e01012–e01014 (2014).PubMed
Article
PubMed Central
Google Scholar
117.Bashiardes, S., Zilberman-Schapira, G. & Elinav, E. Use of metatranscriptomics in microbiome research. Bioinform. Biol. Insights 10, 19–25 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
118.Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. U.S.A. 111, E2329–E2338 (2014).CAS
PubMed
Article
PubMed Central
Google Scholar
119.Abu-Ali, G. S. et al. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat. Microbiol. 3, 356–366 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
120.Hoang, K. L., Morran, L. T. & Gerardo, N. M. Experimental evolution as an underutilized tool for studying beneficial animal–microbe interactions. Front. Microbiol. 7, 1444 (2016).121.Martino, M. E. et al. Bacterial adaptation to the host’s diet is a key evolutionary force shaping drosophila-lactobacillus symbiosis. Cell Host Microbe 24, 109–119.e6 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
122.Schlötterer, C., Kofler, R., Versace, E., Tobler, R. & Franssen, S. U. Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 114, 431–440 (2015).PubMed
Article
PubMed Central
Google Scholar
123.Henry, L. P. & Ayroles, J. F. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC Microbiol 21, 108 (2021).CAS
PubMed
Article
PubMed Central
Google Scholar
124.Wagner, M. R. et al. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol. Lett. 17, 717–726 (2014).PubMed
Article
PubMed Central
Google Scholar
125.Hendry, A. P. Eco-evolutionary Dynamics. (Princeton University Press, 2017).126.Bang, C. et al. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology 127, 1–19 (2018).PubMed
Article
PubMed Central
Google Scholar
127.Hoyt, J. R. et al. Bacteria isolated from bats inhibit the growth of Pseudogymnoascus destructans, the causative agent of white-nose syndrome. PLoS ONE 10, e0121329 (2015).PubMed
Article
CAS
PubMed Central
Google Scholar
128.Cheng, T. L. et al. Efficacy of a probiotic bacterium to treat bats affected by the disease white-nose syndrome. J. Appl. Ecol. 54, 701–708 (2016).Article
Google Scholar
129.Woodhams, D. C., Bletz, M., Kueneman, J. & McKenzie, V. Managing amphibian disease with skin microbiota. Trends Microbiol. 24, 161–164 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
130.Weiss, B. & Aksoy, S. Microbiome influences on insect host vector competence. Trends Parasitol. 27, 514–522 (2011).CAS
PubMed
Article
PubMed Central
Google Scholar
131.Zitvogel, L., Ma, Y., Raoult, D., Kroemer, G. & Gajewski, T. F. The microbiome in cancer immunotherapy: diagnostic tools and therapeutic strategies. Science 359, 1366–1370 (2018).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
132.Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).PubMed
Article
PubMed Central
Google Scholar
133.Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255–1262 (2012).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
134.Christian, N., Whitaker, B. K. & Clay, K. Microbiomes: unifying animal and plant systems through the lens of community ecology theory. Front. Microbiol. 6, 869 (2015).PubMed
Article
PubMed Central
Google Scholar
135.Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc. Biol. Sci. 286, 20182448 (2019).PubMed
PubMed Central
Google Scholar
136.Mueller, E. A., Wisnoski, N. I., Peralta, A. L. & Lennon, J. T. Microbial rescue effects: how microbiomes can save hosts from extinction. Funct. Ecol. 34, 2055-2064 (2020).137.Hird, S. M. Evolutionary biology needs wild microbiomes. Front. Microbiol. 8, 725 (2017).PubMed
Article
PubMed Central
Google Scholar
138.Wade, M. J. The co-evolutionary genetics of ecological communities. Nat. Rev. Genet. 8, 185–195 (2007).CAS
PubMed
Article
PubMed Central
Google Scholar
139.Hammer, T. J., Janzen, D. H., Hallwachs, W., Jaffe, S. P. & Fierer, N. Caterpillars lack a resident gut microbiome. Proc. Natl Acad. Sci. 114, 9641–9646 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
140.Hammer, T. J., Sanders, J. G. & Fierer, N. Not all animals need a microbiome. FEMS Microbiol. Lett. 366, fnz117 (2019).141.Heath, K. D. & Stinchcombe, J. R. Explaining mutualism variation: a new evolutionary paradox? Evolution 68, 309–317 (2014).PubMed
Article
PubMed Central
Google Scholar
142.Sandoval-Motta, S., Aldana, M., Martínez-Romero, E. & Frank, A. The human microbiome and the missing heritability problem. Front. Genet. 8, 80 (2017).PubMed
Article
CAS
PubMed Central
Google Scholar
143.Wallace, R. J. et al. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci. Adv. 5, eaav8391 (2019).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
144.Vollmar, S. et al. The gut microbial architecture of efficiency traits in the domestic poultry model species japanese quail (Coturnix japonica) assessed by mixed linear models. G3 10, 2553–2562 (2020).CAS
PubMed
Article
PubMed Central
Google Scholar
145.Hoffmann, A. A., Sgrò, C. M. & Kristensen, T. N. Revisiting adaptive potential, population size, and conservation. Trends Ecol. Evol. 32, 506–517 (2017).PubMed
Article
PubMed Central
Google Scholar
146.Bruijning, M., Metcalf, C. J. E., Jongejans, E. & Ayroles, J. F. The evolution of variance control. Trends Ecol. Evol. 35, 22–33 (2020).PubMed
Article
PubMed Central
Google Scholar
147.Douglas, G. M., Bielawski, J. P. & Langille, M. G. I. Re-evaluating the relationship between missing heritability and the microbiome. Microbiome 8, 87 (2020).PubMed
Article
PubMed Central
Google Scholar
148.Johannes, F., Colot, V. & Jansen, R. C. Epigenome dynamics: a quantitative genetics perspective. Nat. Rev. Genet. 9, 883–890 (2008).CAS
PubMed
Article
PubMed Central
Google Scholar
149.Slatkin, M. Epigenetic inheritance and the missing heritability problem. Genetics 182, 845–850 (2009).PubMed
Article
PubMed Central
Google Scholar
150.Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J. & Marques-Bonet, T. DNA methylation: insights into human evolution. PLoS Genet 11, e1005661 (2015).PubMed
Article
CAS
PubMed Central
Google Scholar
151.Pujol, B. et al. The missing response to selection in the wild. Trends Ecol. Evol. 33, 337–346 (2018).PubMed
Article
PubMed Central
Google Scholar
152.Shaw, R. G. From the past to the future: considering the value and limits of evolutionary prediction. Am. Nat. 193, 1–10 (2019).PubMed
Article
PubMed Central
Google Scholar
153.Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol.17, e3000102 (2019).154.Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626–638 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
155.Spor, A., Koren, O. & Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9, 279–290 (2011).CAS
PubMed
Article
Google Scholar
156.Guo, Y. et al. Networks underpinning symbiosis revealed through cross-species eQTL mapping. Genetics 206, 2175–2184 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
157.Kohl, K. D. An introductory ‘how-to’ guide for incorporating microbiome research into integrative and comparative biology. Integr. Comp. Biol. 57, 674–681 (2017).PubMed
Article
Google Scholar
158.Marchesi, J. R. & Ravel, J. The vocabulary of microbiome research: a proposal. Microbiome 3, 31 (2015).PubMed
Article
PubMed Central
Google Scholar More