At least some of the advantages that come from larger size can be achieved simply by multiple cells existing as colonies. These colonies can be achieved by a failure of daughter cells to fully separate following either binary fission (for bacteria) or mitosis (for eukaryotes). Colonies, essentially by definition, display little differentiation, other than cells being in different physiological states based upon their access to nutrients. Advantages may include protection from predation or more effective access to resources (e.g., due to competition by shading). Thus, biofilms, for example, represent colonial living, but not multicellularity. In addition, there are a number of varieties of relatively simple eukaryotic algae that are more reasonably or at least traditionally described as colonies of individual organisms rather than as multicellular organisms unto themselves (Kirk, 2005) . The distinction is not unambiguous, but ultimately a multicellular organism, versus colony of unicellular organisms, must display not just some collective advantage that comes from not existing as separate individuals but also some degree of coordination of functions and, perhaps especially, cellular differentiation.
Sheathed bacteria may exemplify an intermediate state between colonial and multicellular. Here macroscopic sheaths surround elongated colonies where the sheath serves a protective function that may not be available (or as available) to individual bacteria. Sheathed bacteria additionally do not necessarily lack differentiation—i.e., they are more multicellular-like than my description so far may suggest—since the sheathed colonies can be attached at one end to solid substrates, e.g., rocks in a stream. That is, at a minimum one cell is attached to both substrate and bacteria while the rest of the members of the colony are attached only to fellow bacteria. These sheathed bacteria also differentiate into sheathed versus swarmer cells, where the latter are the dissemination stage. Additional bacteria, not colonial, also can be differentiated into a stationary, or stalked stage along with a flagellated swarmer stage involved in dissemination, e.g., Caulobacter.
Beyond protection from predation, sheaths may supply mechanical support that allows greater physical separation between the colony's holdfast and the point of release of swarmer cells, perhaps providing swarmer release into more or different dissemination-promoting currents. Even greater elaboration is seen with Myxococcus where a vegetative swarmer stage alternates with a differentiated fruiting body stage, the latter presumably allowing for more efficient microcyst dissemination on air currents and/or protection from hazards found closer to ground level. That is, Myxococcus displays at least three differentiated states: swarmer cells along with fruiting body as well as microcyst cells that are found together. This differentiation is seemingly analogous to that seen in Caulobacter, with the stalk cells or sheathed cells equivalent to the fruiting body cells of Micrococcus but with the Myxococcus microcyst stage skipped in favor of direct differentiation into swarmer cells. The difference probably has an ecological explanation where microcysts represent adaptations to airborne dissemination while flagellated swarmer cells are better suited to dissemination in an aquatic environment. A key distinction, nonetheless, is that with Myxococcus – as also with the fruiting body-forming cellular (i.e., dictyostelid) slime molds – the differentiated colonies form not by cell division but instead via cellular aggregation.
In general, colonial living might be seen as advantageous, given levels of organization that are more than just a failure of sister cells to fully separate, if individual cells are unable to perform essential functions that the rest of the colony can compensate for. An example of such a function is flagella possession, which various protists employ for resource acquisition, e.g., algae swimming towards light or phagocytosis as performed by choanoflagellates. The problem is that mitotic division conflicts with flagella possession or use (Nedelcu and Michod, 2004) . Thus, cell division comes at a resource-acquisition cost. By existing within a colony, particularly one in which cell division is not synchronized, however, then resource acquisition may be retained despite some (but not all) cells undergoing mitosis. This group-mediated compensation might be especially useful given existence within more marginal environments where accumulation of reserves to allow for mitosis in the absence of simultaneous resource acquisition may be more difficult . Note that another example of such dependence can be germ-line cell dependence on somatic cells, e.g., designated swarmer cells may not simultaneously be highly effective at resource acquisition. Thus, a colony can be viewed in at least some cases as an entity that serves to support certain cells over spans during which those cells are vulnerable but nevertheless still useful.
An alternative form of colonial living, one that also can be viewed as intermediate in complexity between simple colonies and true multicellular organisms, is seen with various multinucleated coenocytic or plasmodial organisms, i.e., various algae, fungi, and slime molds. These organisms are able to capitalize on certain cellular efficiencies while expanding on those efficiencies by possessing multiple nuclei. That is, they have genes that are dispersed throughout the cytoplasm, rather than located more or less centrally, where lack of close, physical access to genetic material may be viewed as another mechanism that could serve to limit cell size. In fact, even some unicellular organisms, i.e., ciliates possess more than one nucleus, which also could serve as a means of easing the burden of expressing genes throughout relatively large volumes, including by possessing greater numbers of otherwise centrally located genes. Among bacteria, members of genus Epulopiscium are unusually large – i.e., with multiple dimensions in the range of or exceeding 100-fold the size of a typical E. coli — but seem to compensate for their large size by possessing multiple genomes, numbering in the thousands per cell. These bacteria also display a form of cellular reproduction that is more elaborate than the simple binary fission displayed by most bacteria. Nonetheless, even though these various multinucleated or, at least, multi-genomed organisms often display impressive cellular complexity, they are still less complex than organisms that have achieved a true multicellularity, which can be said to involve not only multiple, somewhat-separated cell cytoplasms but also significant cellular differentiation.
While size alone can be an advantage of multicellularity, such as if it serves as a deterrent to predation or if it results in a greater potential to share an extended phenotype with clones (e.g., such as extracellular hydrolytic enzymes), in fact it is through cellular differentiation that many additional benefits of multicellularity may be realized. It is through cellular differentiation, in fact, that true multicellularity (versus simply colonial living) may be possible at all. Starting with the first point, i.e., that of additional benefits, with multicellularity there is a potential for greater metabolic diversity, greater morphological diversity, and greater functional diversity. In part these are consequences of cells being able to specialize on a particular function rather than all of the cells expressing all of an organism's functions all the time. Furthermore, it is not just specializing on different functions but in fact specializing on functions that may not even be possible for a cell to get away with without the support of the rest of a multicellular body (particularly, this could be any function that substantially interferes with basic resource acquisition).
The consequence of this specialization is that organisms can become modular in the sense that they may be built up of different cell-type building blocks, and these building blocks then can be arranged in innumerable ways. Benefits include having tissues with different functions found on the inside versus the outside of an organism, or even having a front or a back (or a top or a bottom). Different cells can be involved in protection, circulation, resource acquisition, digestion, etc. Indeed, without differentiation of cell types, multicellular organisms presumably would display morphological complexity which isn't too much greater than the morphological complexity seen, for example, among bacteria. Note though that even among bacteria there exist examples of cellular differentiation, most notably the existence of nitrogen-fixing heterocysts in certain colonial cyanobacteria (see also "More than Colonial", above).
The cellular differentiation that may be most necessary for the stability of multicellularity as an evolutionary strategy is the sequestration of the germ line. This sequestration can be viewed as a mechanism of cooperation assurance since non-germ line defector cell lineages will have an opportunity to contribute to the next generation only if they do not detract too greatly from the functioning of the germ line. Indeed, one can view sequestered germ lines from the perspective of inclusive fitness where the long-term survival of all cells making up a multicellular organism is dependent entirely on the fate of the sequestered germ line, thus enforcing cooperation within these organisms, or at least preventing the propagation of cheating genotypes (see also "Greater Size and Complexity: Problems in Multicellularity: Germ Lines").
A somewhat recent addition to the concept of the individual is that of microbiome. A microbiome can be viewed as an organism's extracellular genome, that is, the genomes associated with an individual's microflora. The concept in its more modern sense is closely associated with genomic and especially metagenomic study, but obviously is built upon our understanding of normal flora and therefore, more generally, upon the ideas of microorganism-macroorganism symbioses. As such, the concept of the microbiome is relevant from two perspectives. The first is that normal flora represent a yet additional means by which macroorganisms can display increased complexity. The second is that the existence of a well-defined and functioning microbiome, one which may be acquired vertically as well as horizontally, challenges our ideas of just what it means to be an individual.