What is the Hologenome?

New scientific findings indicate the necessity of a revision of our understanding of a complex creature. Until recently, an organism was considered as a singular entity loosely associated with   various individual microbes. However, current research reveals that all complex creatures are a combination of innate and microbial cells as a vast collaborative, co-dependent and competitive network of interlinked ecologies…… a microcosm within.   The extent of this collaboration is so extensive that the volume of microbial cells within and on an organism outnumbers its innate cells by a factor of 10 to 1. Further, the amount of microbial genetic material overwhelms  intrinsic cellular DNA by a factor of 100 to 1. This degree of interdependence requires a new vision of an organism….. neither ‘host’ nor ‘symbiont’ but essential constituents of a ‘holobiont’ as a hologenome.  ‘The hologenome’ references the overarching concept of  the totality of all the holobionts that constitute the biologic system on our planet

Why does ‘the hologenome’ matter?

The recognition that all complex organisms are holobionts (hologenomes as vast collaborative networks of collaborative, co-dependent and competitive co-linked ecologies which only seems to us as unitary organisms) impels a complete reorganization of evolutionary thinking.

  • Since all organisms are holobionts, nature is clearly interested in the collaborative relationships at every scale that creates holobionts, not just genes. Evolution is about cellular cooperation and connections as well as competition.
  • As holobionts are vast linkages of environments, genes exist to serve forms by faithfully reproducing the localized, linked, co-dependent and competitive ecologies constituting a holobiont.
  • These cellular ecologies are the result of cellular cognition limited to their scale and the preferences that  they can therefore express within their limits. Cellular awareness and intentionality exist to make forms that serve the constituent cells and  it is by this means that complexity arises. This is not a random process, contradicting standard neoDarwinism.
  • As all organisms are holobionts, and since holobionts can only exist based on complex immunologic interplay, immunology rules in evolution as well as infectious disease.  Importantly then, the origin of species is an immunological event.

There are multiple critically important practical implications of the hologenome.

  • The field of medicine requires redirection towards exploring the actual range of interactions between the microbial life that is part of us and health. Chronic diseases such as obesity, diabetes, arthritic disorders, and ‘autoimmune’ diseases need to be thoroughly reevaluated. New companies are forming to provide early diagnosis and treatment of critical health issues based on our emerging understanding of our microbiome.
  • The risks of genetic therapies are not fully appreciated since the basic structure of complex organisms and the proper reasons for evolutionary development have been  critically misunderstood. Therefore, the appropriate framework for evaluating those genetic manipulations for the risks of unintended consequences is not yet in place.
  •  Changing climate considerations have concentrated on the superficial and readily observable aspects of rising sea levels or melting polar ice. The much more important narrative for climate change, whenever it occurs or by any means, will be most critically felt in a changing distribution and incidence of infectious disease and the world wide distribution and concentration of that genetic interchange. This issue has received scant notice, despite instances of such shifts changing the distribution of West Nile Virus in the U.S. or malaria in Africa.

What is metagenomics?

Metagenomics is the study of genetic material recovered directly from environmental samples. The field is the investigation of the full microbiotic community and its genetic complement. The microbial ecological communities within any environment have traditionally been vastly underestimated due to the limitations of standard culture methods. Instead of relying on traditional microbiological cultures, metagenomics employs microbial genome sequencing, cultivated clonal cultures, and exhaustive environmental gene sequencing (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. This research has revealed that the vast majority of microbial biodiversity had been missed by prior standard methods although previously thought to be fully representative of the entire panoply of microbes that might interact with an organism. By this means, a previously hidden diversity of microscopic life has been revealed.  Metagenomics offers a powerful new means of understanding the underlying complexity of microbial life that is an obligatory part of all holobionts and the hologenome

 

Importance of the Microbiome

A microbiome is the entirety of the microbial life that is a part of the ecological communities comprising all complex creatures. For example, the bacterial colonization of the intestine that begins at birth is a process of considerable interest to science and medicine. Numerous studies have shown that there are differences between the gut microbiota of babies born transvaginally and are therefore exposed to maternal vaginal bacteria compared with those born via Caesarean section. In the latter instance, neonate gut microbiota bacteria is less diverse during the first months of life. Now, a new study has analysed the evolution of the gut microbiota of low-birth weight infants and premature babies. This research has identified that immediately after birth the mouth microbiota is similar to that of the gut in these babies, but that it differs substantially after three weeks of  life. The study, published in the latest edition of the American Academy of Microbiology journal ‘mBio’, is the first to analyse the time dependent differentiation of the exact composition of the microbiota in varying body sites of newborn infants. http://mbio.asm.org/content/4/6/e00782-13 Important implications include the differing susceptibility of low birth weight newborns to necrotizing enterocolitis compared to normal birth weight newborns.