Hologenome theory of evolution - Psilocybin Research

The hologenome theory of evolution recasts the individual animal or plant as a community or a “holobiont” – the host plus all of its symbiotic microbes. Consequently, the collective genomes of the holobiont form a “hologenome”.

Zilber-Rosenberg, I., & Rosenberg, E.. (2008). Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.. FEMS Microbiology Reviews

Plain numerical DOI: 10.1111/j.1574-6976.2008.00123.x
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“We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. the hologenome is defined as the sum of the genetic information of the host and its microbiota. the theory is based on four generalizations: (1) all animals and plants establish symbiotic relationships with microorganisms. (2) symbiotic microorganisms are transmitted between generations. (3) the association between host and symbionts affects the fitness of the holobiont within its environment. (4) variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. these points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. during periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. the distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. thus, the hologenome theory fits within the framework of the ‘superorganism’ proposed by wilson and sober.”

Rosenberg, E., Sharon, G., & Zilber-Rosenberg, I.. (2009). The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework. Environmental Microbiology

Plain numerical DOI: 10.1111/j.1462-2920.2009.01995.x
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“The hologenome theory of evolution emphasizes the role of microorganisms in the evolution of animals and plants. the theory posits that the holobiont (host plus all of its symbiont microbiota) is a unit of selection in evolution. genetic variation in the holobiont that can occur either in the host and/or in the microbial symbiont genomes (together termed hologenome) can then be transmitted to offspring. in addition to the known modes of variation, i.e. sexual recombination, chromosomal rearrangement and mutation, variation in the holobiont can occur also via two mechanisms that are specific to the hologenome theory: amplification of existing microorganisms and acquisition of novel strains from the environment. these mechanisms are lamarckian in that (i) they are regulated by ‘use and disuse’ (of microbes) and (ii) the variations in the hologenome are transmitted to offspring, thus satisfying also the lamarckian principle of ‘inheritance of acquired characteristics’. accordingly, the hologenome theory incorporates lamarckian aspects within a darwinian framework, accentuating both cooperation and competition within the holobiont and with other holobionts.”

Rosenberg, E., & Zilber-Rosenberg, I.. (2011). Symbiosis and development: The hologenome concept. Birth Defects Research Part C – Embryo Today: Reviews

Plain numerical DOI: 10.1002/bdrc.20196
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“All animals and plants establish symbiotic relationships with microorganisms; often the combined genetic information of the diverse microbiota exceeds that of the host. how the genetic wealth of the microbiota affects all aspects of the holobiont’s (host plus all of its associated microorganisms) fitness (adaptation, survival, development, growth and reproduction) and evolution is reviewed, using selected coral, insect, squid, plant, and human/mouse published experimental results. the data are discussed within the framework of the hologenome theory of evolution, which demonstrates that changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont in the short term but also can be transmitted to offspring and lead to long lasting cooperations. as acquired characteristics (microbes) are heritable, consideration of the holobiont as a unit of selection in evolution leads to neo-lamarckian principles within a darwinian framework. the potential application of these principles can be seen in the growing fields of prebiotics and probiotics.”

Rosenberg, E., Sharon, G., Atad, I., & Zilber-Rosenberg, I.. (2010). The evolution of animals and plants via symbiosis with microorganisms. Environmental Microbiology Reports

Plain numerical DOI: 10.1111/j.1758-2229.2010.00177.x
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“Animals and plants evolved from prokaryotes and have remained in close association with them. we suggest that early eukaryotic cells, formed by the fusion of two or more prokaryotes, already contained prokaryotic genetic information for aggregation and the formation of multicellular structures. the hologenome theory of evolution posits that a unit of selection in evolution is the holobiont (host plus symbionts). the hologenome is defined as the genetic information of the host and its microbiota, which function in consortium. genetic variation of the holobiont, the raw material for evolution, can arise from changes in either the host or the symbiotic microbiota genomes. changes in the hologenome can occur by two processes that are specific to holobionts: microbial amplification and acquisition of novel strains from the environment. recent data from culture-independent studies provides considerable support of the hologenome theory: (i) all animals and plants contain abundant and diverse microbiota, (ii) the symbiotic microbiota affects the fitness of their host and (iii) symbiotic microorganisms are transmitted from parent to offspring. consideration of the dynamic aspects of symbioses of hosts with their diverse microbiota leads to the conclusion that holobionts can evolve not only via darwinian but also by adaptive lamarckian principles.”

Sharon, G., Segal, D., Ringo, J. M., Hefetz, A., Zilber-Rosenberg, I., & Rosenberg, E.. (2010). Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences

Plain numerical DOI: 10.1073/pnas.1009906107
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“Development of mating preference is considered to be an early event in speciation. in this study, mating preference was achieved by dividing a population of drosophila melanogaster and rearing one part on a molasses medium and the other on a starch medium. when the isolated populations were mixed, ‘molasses flies’ preferred to mate with other molasses flies and ‘starch flies’ preferred to mate with other starch flies. the mating preference appeared after only one generation and was maintained for at least 37 generations. antibiotic treatment abolished mating preference, suggesting that the fly microbiota was responsible for the phenomenon. this was confirmed by infection experiments with microbiota obtained from the fly media (before antibiotic treatment) as well as with a mixed culture of lactobacillus species and a pure culture of lactobacillus plantarum isolated from starch flies. analytical data suggest that symbiotic bacteria can influence mating preference by changing the levels of cuticular hydrocarbon sex pheromones. the results are discussed within the framework of the hologenome theory of evolution.”

Catania, F., Krohs, U., Chittò, M., Ferro, D., Ferro, K., Lepennetier, G., … Gadau, J.. (2017). The hologenome concept: we need to incorporate function. Theory in Biosciences

Plain numerical DOI: 10.1007/s12064-016-0240-z
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“© 2016, springer-verlag berlin heidelberg. are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called ‘typical’ organisms no longer organisms in their own right? is the study of the holobiont—host plus its symbiotic microorganisms—no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? or are associated microbes merely a component of their host’s environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? this article explores different aspects of the concept of the holobiont. we focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. we conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.”

Bosch, T. C. G., & Miller, D. J.. (2016). The Holobiont Imperative. The Holobiont Imperative

Plain numerical DOI: 10.1007/978-3-7091-1896-2
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“This book examines how the growing knowledge of the huge range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. individuals from simple invertebrates to human are not solitary, homogenous entities but consist of complex communities of many species that likely evolved during a billion years of coexistence. defining the individual microbe-host conversations in these consortia, is a challenging but necessary step on the path to understanding the function of the associations as a whole. the hologenome theory of evolution considers the holobiont with its hologenome as a unit of selection in evolution. this new view may have profound impact on understanding a strictly microbe/symbiont-dependent life style and its evolutionary consequences. it may also affect the way how we approach complex environmental diseases from corals (coral bleaching) to human (inflammatory bowel disease etc). the book is written for scientists as well as medically interested persons in the field of immunobiology, microbiology, evolutionary biology, evolutionary medicine and corals.”

Jones, B. V.. (2010). The human gut mobile metagenome, a metazoan perspective. Gut Microbes

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“Using the culture independent traca system in conjunction with a comparative metagenomic approach, we have recently explored the pool of plasmids associated with the human gut mobile metagenome. this revealed that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (america, japan and europe), and are potentially unique to the human gut microbiome. functions encoded by the most widely distributed plasmid (ptraca22) were found to be enriched in the human gut microbiome when compared to microbial communities from other environments, and of particular interest was the increased prevalence of a putative relbe toxin-antitoxin (ta) addiction module. subsequent analysis revealed that this was most closely related to putative ta modules from gut associated bacteria belonging to the firmicutes, but homologues of the rele toxin were associated with all major bacterial divisions comprising the human gut microbiota. in this addendum, functions of the gut mobile metagenome are considered from the perspective of the human host, and within the context of the hologenome theory of human evolution. in doing so, our original analysis is also extended to include the gut metagenomes of a further 124 individuals comprising the metahit dataset. differences in the incidence and relative abundance of ptraca22 and associated ta modules between healthy individuals and those with inflammatory bowel diseases are explored, and potential functions of ptraca22 type relbe modules in the human gut microbiome are discussed.”