The wealth of genome data for host-adapted bacteria have made it possible to re-examine and quantify the level of integration between bacteria and their hosts.
For genera with multiple hosts there seems to be a correlation between host range, host population size and the repertoire of bacterial outer surface proteins.
Shifts in bacterial lifestyle towards greater interaction with the host are mediated by mechanisms such as gain of new functions through horizontal gene transfer and duplication and functional divergence of existing genes.
Bacteria from many different phyla have established relationships with animals, plants and invertebrates. Mutualistic relationships are mostly seen in invertebrates, suggesting that plants and animals present barriers to obligate mutualism that are difficult to overcome.
Secretion systems in bacteria are essential for the interaction with their eukaryotic hosts. Horizontal gene transfer events, functional diversification and innovation through gene duplication of these systems have made it possible for bacteria to adapt to their host in various ways, giving rise to pathogenic or mutualistic relationships.
Obligate mutualistic bacteria with highly eroded genomes have survived owing to selective pressure on the essential function they contribute to eukaryotic fitness. This contribution has resulted in intimate relationships, in which some bacteria have transferred their genes to the host nuclear genome or established consortia with other co-habiting symbionts for the benefit of the host.
Host-adapted bacteria include mutualists and pathogens of animals, plants and insects. Their study is therefore important for biotechnology, biodiversity and human health. The recent rapid expansion in bacterial genome data has provided insights into the adaptive, diversifying and reductive evolutionary processes that occur during host adaptation. The results have challenged many pre-existing concepts built from studies of laboratory bacterial strains. Furthermore, recent studies have revealed genetic changes associated with transitions from parasitism to mutualism and opened new research avenues to understand the functional reshaping of bacteria as they adapt to growth in the cytoplasm of a eukaryotic host.
Your institute does not have access to this article
Open Access articles citing this article.
Nature Microbiology Open Access 07 July 2022
Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency in Streptomyces
Journal of Genetic Engineering and Biotechnology Open Access 03 January 2022
Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication
The ISME Journal Open Access 16 July 2021
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
McCutcheon, J. P., McDonald, B. R. & Moran, N. A. Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet. 5, e1000565 (2009). This paper reports the most reduced bacterial genome identified to date. Like many mitochondrial genomes, the genetic code is altered, possibly owing to the loss of a reduced set of ribosome release factors.
Nakabachi, A. et al. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314, 267 (2006).
Tamas, I. et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296, 2376–2379 (2002).
Moran, N. A., McLaughlin, H. J. & Sorek, R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323, 379–382 (2009).
Fuxelius, H. H., Darby, A. C., Cho, N. H. & Andersson, S. G. Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol. 9, R42 (2008).
Cole, S. T. et al. Massive gene decay in the leprosy bacillus. Nature 409, 1007–1011 (2001).
Andersson, S. G. et al. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 133–140 (1998).
Cho, N. H. et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc. Natl Acad. Sci. USA 104, 7981–7986 (2007).
Klasson, L. et al. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc. Natl Acad. Sci. USA 106, 5725–5730 (2009).
Moya, A., Pereto, J., Gil, R. & Latorre, A. Learning how to live together: genomic insights into prokaryote–animal symbioses. Nature Rev. Genet. 9, 218–229 (2008).
Corsaro, D., Venditti, D., Padula, M. & Valassina, M. Intracellular life. Crit. Rev. Microbiol. 25, 39–79 (1999).
Boussau, B., Karlberg, E. O., Frank, A. C., Legault, B. A. & Andersson, S. G. Computational inference of scenarios for α-proteobacterial genome evolution. Proc. Natl Acad. Sci. USA 101, 9722–9727 (2004).
Snel, B., Bork, P. & Huynen, M. A. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12, 17–25 (2002).
Paulsen, I. T. et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl Acad. Sci. USA 99, 13148–13153 (2002).
Buchner, P. Endosymbiosis of Animals With Plant Microorganisms (Interscience New York, 1965).
Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Rev. Microbiol. 6, 776–788 (2008).
Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010).
Casadevall, A. Evolution of intracellular pathogens. Annu. Rev. Microbiol. 62, 19–33 (2008).
Albert-Weissenberger, C., Cazalet, C. & Buchrieser, C. Legionella pneumophila — a human pathogen that co-evolved with fresh water protozoa. Cell. Mol. Life Sci. 64, 432–448 (2007).
Thomas, V. & McDonnell, G. Relationship between mycobacteria and amoebae: ecological and epidemiological concerns. Lett. Appl. Microbiol. 45, 349–357 (2007).
Ogata, H. et al. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet. 2, e76 (2006).
Salah, I. B., Ghigo, E. & Drancourt, M. Free-living amoebae, a training field for macrophage resistance of mycobacteria. Clin. Microbiol. Infect. 15, 894–905 (2009).
Schmitz-Esser, S. et al. The genome of the amoeba symbiont “Candidatus Amoebophilus asiaticus” reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J. Bacteriol. 192, 1045–1057 (2010).
Birtles, R. J. et al. 'Candidatus Odyssella thessalonicensis' gen. nov., sp. nov., an obligate intracellular parasite of Acanthamoeba species. Int. J. Syst. Evol. Microbiol. 50, 63–72 (2000).
Fritsche, T. R. et al. In situ detection of novel bacterial endosymbionts of Acanthamoeba spp. phylogenetically related to members of the order Rickettsiales. Appl. Environ. Microbiol. 65, 206–212 (1999).
Horn, M., Fritsche, T. R., Gautom, R. K., Schleifer, K. H. & Wagner, M. Novel bacterial endosymbionts of Acanthamoeba spp. related to the Paramecium caudatum symbiont Caedibacter caryophilus. Environ. Microbiol. 1, 357–367 (1999).
Horn, M. et al. Obligate bacterial endosymbionts of Acanthamoeba spp. related to the β-Proteobacteria: proposal of 'Candidatus Procabacter acanthamoebae' gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 52, 599–605 (2002).
Horn, M. et al. Members of the Cytophaga-Flavobacterium-Bacteroides phylum as intracellular bacteria of acanthamoebae: proposal of 'Candidatus Amoebophilus asiaticus'. Environ. Microbiol. 3, 440–449 (2001).
Amann, R. et al. Obligate intracellular bacterial parasites of acanthamoebae related to Chlamydia spp. Appl. Environ. Microbiol. 63, 115–121 (1997).
Birtles, R. J., Rowbotham, T. J., Storey, C., Marrie, T. J. & Raoult, D. Chlamydia-like obligate parasite of free-living amoebae. Lancet 349, 925–926 (1997).
Pine, L., George, J. R., Reeves, M. W. & Harrell, W. K. Development of a chemically defined liquid medium for growth of Legionella pneumophila. J. Clin. Microbiol. 9, 615–626 (1979).
Skrodzki, E. F. tularensis cultures on agar-peptone medium. Biul. Inst. Med. Morsk. Gdansk. 17, 471–478 (1966).
Wong, M. T., Thornton, D. C., Kennedy, R. C. & Dolan, M. J. A chemically defined liquid medium that supports primary isolation of Rochalimaea (Bartonella) henselae from blood and tissue specimens. J. Clin. Microbiol. 33, 742–744 (1995).
Winkler, H. H. Rickettsia species (as organisms). Annu. Rev. Microbiol. 44, 131–153 (1990).
Stephens, R. S. Chlamydia: Intracellular Biology, Pathogenesis, and Immunity (Amer Society for Microbiology, Washington, D.C, 1999).
Hybiske, K. & Stephens, R. S. Mechanisms of host cell exit by the intracellular bacterium Chlamydia. Proc. Natl Acad. Sci. USA 104, 11430–11435 (2007).
Baca, O. G. & Paretsky, D. Q fever and Coxiella burnetii: a model for host-parasite interactions. Microbiol. Rev. 47, 127–149 (1983).
Munson, M. A. et al. Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. J. Bacteriol. 173, 6321–6324 (1991).
Clark, M. A., Moran, N. A., Baumann, P. & Wernegreen, J. J. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 54, 517–525 (2000).
Moran, N. A. & Wernegreen, J. J. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol. Evol. 15, 321–326 (2000).
Mikkola, R. & Kurland, C. G. Selection of laboratory wild-type phenotype from natural isolates of Escherichia coli in chemostats. Mol. Biol. Evol. 9, 394–402 (1992).
Zhu, P. et al. Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc. Natl Acad. Sci. USA 98, 5234–5239 (2001).
Falush, D. Toward the use of genomics to study microevolutionary change in bacteria. PLoS Genet. 5, e1000627 (2009).
Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science 273, 1516–1517 (1996).
Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243–1247 (2009).
Zhong, S., Miller, S. P., Dykhuizen, D. E. & Dean, A. M. Transcription, translation, and the evolution of specialists and generalists. Mol. Biol. Evol. 26, 2661–2678 (2009).
Dethlefsen, L. & Schmidt, T. M. Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol. 189, 3237–3245 (2007).
Andersson, S. G. & Kurland, C. G. Reductive evolution of resident genomes. Trends Microbiol. 6, 263–268 (1998).
Moran, N. A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).
Funk, D. J., Wernegreen, J. J. & Moran, N. A. Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association. Genetics 157, 477–489 (2001).
Bordenstein, S. R. & Reznikoff, W. S. Mobile DNA in obligate intracellular bacteria. Nature Rev. Microbiol. 3, 688–699 (2005).
Williams, T. A., Codoner, F. M., Toft, C. & Fares, M. A. Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet. 26, 47–51 (2009).
McNally, D. & Fares, M. A. In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae. BMC Evol. Biol. 7, 81 (2007).
Enninga, J. & Rosenshine, I. Imaging the assembly, structure and activity of type III secretion systems. Cell. Microbiol. 11, 1462–1470 (2009).
Fronzes, R., Christie, P. J. & Waksman, G. The structural biology of type IV secretion systems. Nature Rev. Microbiol. 7, 703–714 (2009).
Ma, W., Dong, F. F., Stavrinides, J. & Guttman, D. S. Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race. PLoS Genet. 2, e209 (2006).
Frank, A. C., Alsmark, C. M., Thollesson, M. & Andersson, S. G. Functional divergence and horizontal transfer of type IV secretion systems. Mol. Biol. Evol. 22, 1325–1336 (2005).
Toft, C., Williams, T. A. & Fares, M. A. Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PLoS Comput. Biol. 5, e1000344 (2009).
Maezawa, K. et al. Hundreds of flagellar basal bodies cover the cell surface of the endosymbiotic bacterium Buchnera aphidicola sp. strain APS. J. Bacteriol. 188, 6539–6543 (2006).
Toft, C. & Fares, M. A. The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Mol. Biol. Evol. 25, 2069–2076 (2008).
Quebatte, M. et al. The BatR/BatS two component regulatory system controls the adaptive response of Bartonella henselae during human endothelial cell infection. J. Bacteriol. 23 Apr 2010 (doi:10.1128/JB.01676-09).
Seubert, A., Hiestand, R., de la Cruz, F. & Dehio, C. A bacterial conjugation machinery recruited for pathogenesis. Mol. Microbiol. 49, 1253–1266 (2003).
Nystedt, B., Frank, A. C., Thollesson, M. & Andersson, S. G. Diversifying selection and concerted evolution of a type IV secretion system in Bartonella. Mol. Biol. Evol. 25, 287–300 (2008).
Dobrindt, U., Hochhut, B., Hentschel, U. & Hacker, J. Genomic islands in pathogenic and environmental microorganisms. Nature Rev. Microbiol. 2, 414–424 (2004).
Dale, C. & Moran, N. A. Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453–465 (2006).
Berglund, E. C. et al. Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PLoS Genet. 5, e1000546 (2009). This paper shows that a chromosomal segment of several hundred kilobases which contains gene clusters for various secretion systems is amplified and packaged into bacteriophage particles. The site covering the origin of the amplification process and the genes encoding the phage particles are conserved across strains, showing selection for mobility.
Klasson, L. et al. Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol. Biol. Evol. 25, 1877–1887 (2008).
Wu, M. et al. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2, E69 (2004).
Nogueira, T. et al. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr. Biol. 19, 1683–1691 (2009). This paper shows that genes for secreted proteins tend to be located near mobile elements. It is thought that mobile elements enforce cooperation by reintroducing genes for secreted proteins into cheater cells in the populations that have lost these traits.
Mira, A., Ochman, H. & Moran, N. A. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17, 589–596 (2001).
Hillesland, K. L. & Stahl, D. A. Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proc. Natl Acad. Sci. USA 107, 2124–2129 (2010). The authors carried out a laboratory study of the evolution of a mutualistic relationship between sulphate-reducing and methanogenic microorganisms. The results contribute to the understanding of the evolutionary processes leading to the emergence and persistence of mutualistic associations.
Sachs, J. L., Mueller, U. G., Wilcox, T. P. & Bull., J. J. The evolution of cooperation. Q. Rev. Biol. 79, 135–160 (2004).
Frank, S. A. Host-symbiont conflict over the mixing of symbiotic lineages. Proc. Biol. Sci. 263, 339–344 (1996).
Sachs, J. L. & Simms, E. L. Pathways to mutualism breakdown. Trends Ecol. Evol. 21, 585–592 (2006).
Marchetti, M. et al. Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol. 8, e1000280 (2010). This paper shows that the transition from a pathogenic to a mutualistic relationship requires the acquisition of symbiotic genes and the modification of pre-existing functions through key mutations in regulatory and structural genes. The results reveal the role of adaptive changes in the recipient genome following horizontal transfers of symbiotic plasmids for the evolution of nodulation in Rhizobia.
Sachs, J. L., Ehinger, M. O. & Simms, E. L. Origins of cheating and loss of symbiosis in wild Bradyrhizobium. J. Evol. Biol. 23, 1075–1089 (2010).
Werren, J. H., Baldo, L. & Clark, M. E. Wolbachia: master manipulators of invertebrate biology. Nature Rev. Microbiol. 6, 741–751 (2008).
Stouthamer, R., Breeuwer, J. A. & Hurst, G. D. Wolbachia pipientis: microbial manipulator of arthropod reproduction. Annu. Rev. Microbiol. 53, 71–102 (1999).
Langworthy, N. G. et al. Macrofilaricidal activity of tetracycline against the filarial nematode Onchocerca ochengi: elimination of Wolbachia precedes worm death and suggests a dependent relationship. Proc. Biol. Sci. 267, 1063–1069 (2000).
Stevens, L., Giordano, R. & Fialho, R. F. Male-killing, nematode infections, bacteriophage infection, and virulence of cytoplasmic bacteria in the genus Wolbachia. Annu. Rev. Ecol. Syst. 32, 519–545 (2001).
Foster, J. et al. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 3, e121 (2005).
Hosokawa, T., Koga, R., Kikuchi, Y., Meng, X. Y. & Fukatsu, T. Wolbachia as a bacteriocyte-associated nutritional mutualist. Proc. Natl Acad. Sci. USA 107, 769–774 (2010). The first report of obligate bacteriocyte-associated nutritional mutualism in insect-infecting Wolbachia strains. As all previously described strains of Wolbachia associated with insects show commensal or parasitic relationships, the results reinforce the hypothesis that pathogens can evolve to mutualists, given the right conditions.
Perlman, S. J., Hunter, M. S. & Zchori-Fein, E. The emerging diversity of Rickettsia. Proc. Biol. Sci. 273, 2097–2106 (2006).
Perotti, M. A., Clarke, H. K., Turner, B. D. & Braig, H. R. Rickettsia as obligate and mycetomic bacteria. FASEB J. 20, 2372–2374 (2006).
Darby, A. C., Cho, N. H., Fuxelius, H. H., Westberg, J. & Andersson, S. G. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23, 511–520 (2007).
Perez-Brocal, V. et al. A small microbial genome: the end of a long symbiotic relationship? Science 314, 312–313 (2006).
Gosalbes, M. J., Lamelas, A., Moya, A. & Latorre, A. The striking case of tryptophan provision in the cedar aphid Cinara cedri. J. Bacteriol. 190, 6026–6029 (2008).
Toft, C. & Fares, M. A. Selection for translational robustness in Buchnera aphidicola, endosymbiotic bacteria of aphids. Mol. Biol. Evol. 26, 743–751 (2009).
Tamames, J. et al. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol. Biol. 7, 181 (2007).
Hotopp, J. C. et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317, 1753–1756 (2007). Evidence for the presence of DNA inserts of Wolbachia spp. in the nuclear genomes of four insects and four nematode hosts. The results show that bacterial genes of endosymbiotic bacteria can be transferred to the nuclear genomes of their hosts.
Timmis, J. N., Ayliffe, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Rev. Genet. 5, 123–135 (2004).
Nikoh, N. & Nakabachi, A. Aphids acquired symbiotic genes via lateral gene transfer. BMC Biol. 7, 12 (2009).
Nikoh, N. et al. Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host. PLoS Genet. 6, e1000827 (2010).
Woyke, T. et al. One bacterial cell, one complete genome. PLoS One 5, e10314 (2010).
Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods 6, 377–382 (2009).
Bergelson, J., Dwyer, G. & Emerson, J. J. Models and data on plant–enemy coevolution. Annu. Rev. Genet. 35, 469–499 (2001).
Dawkins, R. & Krebs, J. R. Arms races between and within species. Proc. R. Soc. Lond. B. Biol. Sci. 205, 489–511 (1979).
Clay, K. & Kover, P. X. The Red Queen Hypothesis and plant/pathogen interactions. Annu. Rev. Phytopathol. 34, 29–50 (1996).
Stavrinides, J., Ma, W. & Guttman, D. S. Terminal reassortment drives the quantum evolution of type III effectors in bacterial pathogens. PLoS Pathog. 2, e104 (2006).
Goldman, N. & Yang, Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725–736 (1994).
Crandall, K. A., Kelsey, C. R., Imamichi, H., Lane, H. C. & Salzman, N. P. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16, 372–382 (1999).
Gu, X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16, 1664–1674 (1999).
Gu, X. Mathematical modeling for functional divergence after gene duplication. J. Comput. Biol. 8, 221–234 (2001).
Gu, X. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18, 453–464 (2001).
Van der Goot, F. G. Pore-Forming Toxins (Springer Verlag, Berlin, 2001).
Gonzalez, M. R., Bischofberger, M., Pernot, L., van der Goot, F. G. & Freche, B. Bacterial pore-forming toxins: the (w)hole story? Cell. Mol. Life Sci. 65, 493–507 (2008).
Galan, J. E. & Collmer, A. Type III secretion machines: bacterial devices for protein delivery into host cells. Science 284, 1322–1328 (1999).
Cornelis, G. R. The type III secretion injectisome. Nature Rev. Microbiol. 4, 811–825 (2006).
Gophna, U., Ron, E. Z. & Graur, D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312, 151–163 (2003).
Alvarez-Martinez, C. E. & Christie, P. J. Biological diversity of prokaryotic type IV secretion systems. Microbiol. Mol. Biol. Rev. 73, 775–808 (2009).
Stebbins, C. E. & Galan, J. E. Structural mimicry in bacterial virulence. Nature 412, 701–705 (2001).
Galan, J. E. Common themes in the design and function of bacterial effectors. Cell Host Microbe 5, 571–579 (2009).
Price, C. T. et al. Molecular mimicry by an F-box effector of Legionella pneumophila hijacks a conserved polyubiquitination machinery within macrophages and protozoa. PLoS Pathog. 5, e1000704 (2009).
Yarbrough, M. L. et al. AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science 323, 269–272 (2009).
Ishoey, T., Woyke, T., Stepanauskas, R., Novotny, M. & Lasken, R. S. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11, 198–204 (2008).
Rodrigue, S. et al. Whole genome amplification and de novo assembly of single bacterial cells. PLoS One 4, e6864 (2009).
Lasken, R. S. & Stockwell, T. B. Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnol. 7, 19 (2007).
Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).
Wooley, J. C., Godzik, A. & Friedberg, I. A primer on metagenomics. PLoS Comput. Biol. 6, e1000667 (2010).
Guell, M. et al. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268–1271 (2009).
Kuhner, S. et al. Proteome organization in a genome-reduced bacterium. Science 326, 1235–1240 (2009).
Yus, E. et al. Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263–1268 (2009). In references 120–122, the metabolic, interactomic and transcriptomic maps are deciphered in the cell-surface parasite Mycoplasma pneumoniae . The authors show protein multi-functionality, explaining how cellular functions can be maintained despite a small gene set.
Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215–1220 (2008).
Gibson, D. G. et al. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl Acad. Sci. USA 105, 20404–20409 (2008).
Lartigue, C. et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693–1696 (2009).
Klasson, L. & Andersson, S. G. Research on small genomes: implications for synthetic biology. Bioessays 32, 288–295 (2010).
Pal, C. et al. Chance and necessity in the evolution of minimal metabolic networks. Nature 440, 667–670 (2006).
Wu, D. et al. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462, 1056–1060 (2009).
This work was supported by grants to S.G.E.A. from the Swedish Research Council, the Göran Gustafsson Foundation, the Swedish Foundation for Strategic Research and the Knut and Alice Wallenberg Foundation.
The authors declare no competing financial interests.
- Mutualistic relationship
A symbiosis in which both species increase their fitness.
- Pathogenic relationship
A symbiosis in which one species increases its fitness while the fitness of the other species is adversely affected.
- Commensal relationship
A symbiosis in which one partner increases its fitness without affecting the other species.
An intracellular organism that contributes to the survival of the host cell and depends on the host for its own persistence. The relationship can be either mutualistic or commensalistic.
A single-celled (usually microscopic) eukaryotic organism. The name originates from the Greek words 'proton' and 'zoa', meaning first and animals, respectively.
- Horizontal gene transfer
The transfer of genetic material between the genomes of two organisms not through the normal parent–progeny transmission during cell division.
The process whereby changes in the coding region of a gene that disrupt the function of the gene lead to its inactivation.
- Endosymbiotic bacterium
A non-pathogenic bacterium that lives inside host cells.
A specialised host cell that houses obligate mutualistic bacteria.
The physical joining of two bacterial cells to transfer genetic material from the donor cell to the recipient cell through a pilus.
- Coefficient of variation
A normalized measure of dispersion of a probability distribution.
- Genomic island
A region of the genome that has been acquired through a horizontal event.
A virus that infects bacteria and can serve as a vector of novel genetic material.
The genome of a bacteriophage when it is integrated into the chromosome of the host bacterium.
- Secondary symbiont
A facultative bacterial symbiont that is not essential for host survival and reproduction.
- tRNA isoacceptor
One of a group of tRNA species that can bind to different codons for the same amino acid residue.
One of a group of nitrogen-fixing bacteria that have symbiotic associations with plants.
The ability to cause disease by breaking down the protective mechanisms of the host.
- Primary endosymbiont
An obligate mutualistic endosymbiont that is essential for host survival and reproduction. Primary endosymbionts are often located in bacteriocytes and are maternally transmitted between host generations.
Small sap-sucking insects, also known as 'jumping plant lice'.
The functional and sequence-based analysis of the collective microbial genomes contained in an environmental sample.
About this article
Cite this article
Toft, C., Andersson, S. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 11, 465–475 (2010). https://doi.org/10.1038/nrg2798
Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency in Streptomyces
Journal of Genetic Engineering and Biotechnology (2022)
Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication
The ISME Journal (2022)
Nature Microbiology (2022)
Mining the diversity and functional profile of bacterial symbionts from the larvae of Chironomus circumdatus (bloodworms)
Folia Microbiologica (2022)
BMC Ecology and Evolution (2021)