Full Article: Salvucci. 2014. Microbiome, holobiont and the net of life. Crit Rev Microbiol.

As a continuity of the genomic landscape, the human body
contains more bacterial cells than human cells. Microbiome is
the collective indigenous microbes associated to a host
(Arumugam et al., 2011; Dominguez-Bello & Blaser, 2008;
Hooper et al., 2013; Lederberg & McCray, 2001). Human gut
microbiome is taxonomically complex and this ecologically
dynamic community participates in several processes and
mechanisms. These include vitamin production, digestion and
utilization of carbohydrates and lipids, energy homeostasis,
tryptophan metabolism regulation, integrity of intestinal
barrier and angiogenesis, promoting the correct development
of the capillaries network (Dominguez-Bello & Blaser, 2008;
El Kaoutari et al., 2013; Kau et al., 2011). The main members
are bacteria from phyla Bacteroidetes and Firmicutes
(Eckburg et al., 2005; Xu et al., 2007). The microbiome
metabolism is essential for the development, maturation and
regulation (stimulation and suppression) of the immune
system. It participates from the first day of life in the
development of Gut-associated Lymphoid Tissue (GALT)
and, particularly, in the B immune system (Hattori & Taylor,
2009; Hooper et al., 2013; Kau et al., 2011; Mai & Draganov,
2009; Mazmanian et al., 2005). Also, the dietary intake
shapes microbial community structure. Microbial signals in
the form of microbe-associated molecular patterns (MAMPs)
modify local mucosal immune responses through innate
signalling pathways such as the inflammasome (a complex
multi-protein receptor related to inflammatory or apoptosis
processes depending on the stimuli) or Toll-like receptors
(Kau et al., 2011). These interactions develop a tolerance or
recognition between the two associated counterparts.
Immune system is the evolutionary interface that was built
in a continuous feedback with the organisms and the
environment. Germ-free mice (microbiome-free mice) have
an underdeveloped immune system, lower metabolic rates and
longer digestion times than those that have a normal
microbiome. Many studies have confirmed that alterations
of this microbiome affect human health and promote disease
state or disbiosis (Evans et al., 2013; Ley et al., 2005; Rogler,
2010; Tlaskalova´-Hogenova´ et al., 2004). Microbiome and
human host have co-evolved. The hologenome theory considers
an organism and all of its associated symbiotic
microbes, including parasites, mutualists, synergists, and
amensalists as a unity called holobiont (Rosenberg &
Zilber-Rosenberg, 2011). The holobiont is a result of the
co-habitation and symbiosis of different organisms. Among
them, we can include the virome that is integral part of this
‘‘superorganism’’. In this sense, it can be considered a result
of the process known as symbiopoiesis (Margulis & Fester,
1991; Rosenberg & Zilber-Rosenberg, 2011).

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The complex
metazoans are a result of integration of systems and the close
association between living beings which implies physiological
and, ultimately, genetic integration (Gilbert et al.,
2010; Margulis & Chapman, 1998; Margulis & Fester, 1991;
Margulis & Sagan, 1995; Rohwer et al., 2009; Salvucci, 2012;
Savinov, 2012). Savinov has developed the concepts of
autocenosis and democenosis to explain these levels of
integration (Savinov, 2012). Also, he has developed the
principle of obligatoriness of symbiosis and symbiogenesis
since the evolution of all multi-cellular and most unicellular
organisms are always based on the integration with other
organisms (Savinov, 2012). Windsor (1997) remarks that the
host-symbionts unity is the real organism (which he calls
‘‘biocartel’’) and considers that single-entity free living
species are abstractions. Baluska (2009) stated that repetitive
cycles of duplication, aggregation/merging are driving the
increase in biological complexity during metazoan evolution.
These evolutionary perspectives ponders that every organism
is a result of integration and this ‘‘superorganism’’
adjusts and transforms itself according to environmental
changes causing evolution of the entire unity.