healthmedicinet

In humans, the numbers of bacterial cells outnumber human tissue cells by 10 to 1.
The skin, nasal passages, and gastrointestinal tract are all inhabited with microorganisms,
and each location has a specific microbial profile composed of microorganisms best
suited to inhabit that niche. Perhaps the most studied of these niches is the gastrointestinal
tract (GIT). From Table 1, it is clear that competition, mutualism, and co-habitation all occur within the
GIT microbial community as well as provide nutrients and vitamins to the host.

Table 1. Examples of microorganisms found within the gastrointestinal tract of the human lower
intestine, the substrates utilized by the bacteria, and products made from the substrates

The primary function of the GIT microbes is digestion of ingested food substrates.
As shown in Table 2, symbiosis between microbes and their host primarily involves nutrient acquisition.
However, beyond digestion, GIT microbes perform other functions that potentially contribute
to the overall health status of the host. A well-studied non-digestive function of
the gut microbes is the education and regulation of the immune system 1]. The commensal bacteria educate the immune system allowing the host to distinguish
commensal and pathogenic bacteria. Commensals can also regulate the immune response
in the eukaryotic host cells including the inflammatory cascade via the nuclear factor-kappaB
(NF-?B) pathway 2]. NF-?B is a transcriptional regulator that translocates to the nucleus to induce
inflammatory cytokines and recruit immune cells. This process only occurs when NF-?B
is unbound from I?B. Commensal bacteria block the NF-?B-I?B disassociation and therefore
NF-?B cannot enter the nucleus to begin the inflammatory response. Identifying these
bacteria and their products could be useful for treating inflammatory-based diseases
including inflammatory bowel disease.

Table 2. Examples of symbiotic interactions between gut bacteria and the host

Gene regulation by the GIT microbes is not limited to the inflammatory cascade. In
fact, Hooper et al. 3] reported that Bacteroides thetaiotaomicron modulates 71 intestinal genes involved in various processes including intestinal
maturation and nutrient absorption. More recently, Neufeld and Foster 4] implied that the impact of the GIT microbiome reaches beyond the intestinal tract
and even can be linked to brain development. A recent study supports this notion by
demonstrating that adult germfree mice show an exaggerated stress response versus
conventional counterparts 5]. Additionally, it is also well recognized that many gastrointestinal disorders demonstrate
a high comorbidity with psychiatric illness 4]. For this reason, emerging work involving germfree mice suggests methods targeting
systems outside of the central nervous system are potential treatment options for
psychiatric diseases.

A wealth of information regarding the functionality and impact of the gut microbiome
on human health has been obtained from clinical studies and experimental models. Currently,
studies are applying these methods to non-human animals with bias towards agricultural
taxa. Regardless, there are numerous papers available for some species, fewer for
others, and no information for some animals. The point of this review is not to provide
an exhaustive list of bacterial taxa present in every animal and the functionality
of those microbes. Rather, the aim of this review is to point out that some gut microbe
functions may be broad and applicable to many animals, while some species may contain
unique microbes performing unique functions and to use a few animal species to demonstrate
this idea. Deciphering and defining the functionality of the gut microbes can be addressed
using various methods and observations.

Changes, disruption, and absence of the normal microbiome

Assessing and determining the functionality of microbes is not an easy task. Numerous
experiments have been undertaken to understand the function of the gut microbiome
in different species. These approaches include analyzing animals reared in sterile
environments lacking any gut microbiome and transplanting microbiome from one animal
to another. Disruptions to the microbiome such as fasting or gastrointestinal infection
also provide insight regarding functionality of the commensals. Furthermore, these
types of comparisons may be made to enhance the understanding of the symbiotic balance.

Germfree

One approach to determine functionality of microbiomes is to compare sets of conventional
animals to those without microbiomes. These so-called germfree animals have been documented
as early as 1895 by Nuttall and Theirfelder 6] who intended to prove that microbes were not needed for life and were actually harmful
by creating germfree guinea pigs. Other experiments including one conducted by Cosendy
and Wollman also intended to demonstrate that animals could live without microbes
and utilized “germfree” chickens to test their hypothesis 7], 8].

It is clear from early experiments and the newest information that higher organisms
can exist without microbes. However, drastic differences are noted in germfree animals.
Germfree sea bass (Centropristis striata) had reduced mucosal linings due to an absence of microbial stimulation of mucosa
production 9]. The intestinal villi of the germfree dog are of the same length as the normal counterpart
but are thinner with pointer tips 10]. The lamina propria of germfree mice has a sparse stroma, with few lymphocytes and
macrophages, and the Peyer’s patches are smaller. In all germfree animals studied,
the turnover rate of intestinal epithelium was decreased. These histological changes
in the intestine are the result of a reduced interaction with the bacteria that stimulate
the immune system and histological development 11].

In addition to histological changes in the intestine, other organs and physiological
changes have been noted. The germfree rat has a smaller heart and a cecum that is
four to six times larger than rats with normal microbiomes 12]. This change has been explained by an accumulation of substances normally degraded
by the microbiome and histological changes of the cecum epithelial cells 13]. In germfree chicks, the body temperature is slightly higher than that of chicks
with normal flora 14]. These experiments have demonstrated the complex role that microbiomes play in host
development, not only in the gastrointestinal systems but in other organs as well.

Fasting

That fasting tends to shift the GIT bacteria populations has been demonstrated in
many animals including mice, alligators, pythons, and chickens 15]–18]. Furthermore, a feeding/fasting cycle promotes diversity of the microbiome 18]. During fasting, the lack of nutrient availability impacts the intestinal mucin layer,
as bacteria with the ability to utilize mucin will degrade it for a nutrient source
19]. Hence, when the host does not provide nutrients to the commensals, the commensals
will start to consume the host. This may be because fasting suppresses the host antibacterial
defenses 20], 21]. Interestingly, even though the protective barrier of mucin is decreased, bacterial
translocation across the epithelia may not increase 21].

Like fasting, hibernation also affects on the microbiome populations. Sonoyama et
al. 22] reported that Clostridium predominated in both active and hibernating hamsters and populations of Akkermansia muciniphila, a mucin degrader, increased in fasting but not during hibernation. An early study
of ground squirrels using culturing methods found that there was some reduction in
total numbers of viable bacteria in the cecum during hibernation, but that the profile
of the microbiota remained stable 23]. However, a more recent study using deep-sequencing methods found that the population
profiles did shift. Specifically, hibernation increased populations of Bacteroidetes and Verrucomicrobia, capable of degrading mucin, and reduced populations of Firmicutes, which prefer polysaccharides 24].

Hibernating animals typically have a hypoactive immune system. Because a hypoactive
immune system can lead to aberrant bacterial growth and inflammation, understanding
how the immune system regulates bacterial populations during hibernation is of great
interest. In their studies using hibernating leopard frogs, Gossling et al. 25] tested several hypotheses to understand this regulation, including unique circulating
antimicrobials and antibody production, but no conclusive results were able to answer
the question. More recently, Dill-McFarland 26] reported that toll-like receptors 4 and 5 (TLR4 and TLR5) are modulated in hibernating
ground squirrels. These receptors recognize microbial products and initiate host immune
responses focused on inflammation.

Compared with other animal taxa, there is little information about the gastrointestinal
microbiome found in reptiles, many of which practice an extreme feeding/fasting cycle.
Snakes are very interesting animals because many species have extreme periods of fasting
with a time span as long as 1 year between meals 27]. In addition, all snakes ingest and rapidly digest whole prey. These two facts suggest
that snakes must be very efficient at nutrient uptake, and this would hold true for
the microbiome as well. These extreme feeding regimes in the snake raise the question
of whether the microbiome impact on nutrient uptake is more dramatic in the snake
or has any affect at all. Peterson et al. 28] aimed to answer this question using African house snakes where the snakes were repeatedly
given oral dosages of antibiotics (treatment) or sterile water (control) prior to
consuming sterilized mice. Intestinal samples were obtained non-lethally each time
prior to feeding and sequencing of these samples was conducted. No differences in
energy densities of expelled mice or feces and uric acid as determined by bomb calorimetry
were reported. However, the bacteria populations present in the intestinal samples
were very different between the two groups. From the data, the authors concluded that
the bacterial microbiome had no significant impact on nutrient acquisition.

Disruptions and changes

Disruptions in the normal patterns of host microbiome may occur for a variety of reasons.
Changes in diet, antibiotic intake, or colonization by pathogens have all been demonstrated
to result in a shift in the microbiome populations 29]. In some cases, this shift results in negative health consequences, because the immune
system maintains a constant production of antibodies aimed at the normal microbiome
pattern that must be adjusted to fit the new bacterial population, and this can be
costly in terms of energy expenditures.

Normal changes in the microbiome occur overtime and can be related to factors such
as age. For example, the chicken GIT is sterile at hatch but quickly colonized by
aerobic Proteobacteria and after 12 days is dominated by anaerobic Firmicutes. Initially, the Proteobacteria stimulate the histological maturation of the GIT and
provide an ideal environment for the Firmicutes. The Proteobacteria do well in the immature GIT but are poor competitors and are
outcompeted after a mature and anaerobic gut environment is established. The succession
of bacteria is also dependent on nutrition and gut bacteria population selection,
and establishment can also be selected by feeding specific foods. This was demonstrated
in rabbits fed only milk for the first 42 days of life. These animals did not possess
cellulolytic bacteria in the cecum and could not digest plant matter 30].

Metamorphosis and the impacts of the process on intestinal populations have been demonstrated
in frogs and toads by comparing gut microbes in tadpoles versus adult forms 31]. Tadpoles have more diversity and a microbiome similar to fish, while frog GIT profiles
resemble amniotes. The differences are attributed to food preferences and GIT structure.
Like amphibians, metamorphosis of the sea lamprey and mosquito results in GIT rearrangement
and feeding preferences 32], 33]. In both species, the microbiome in the adult is substantially less diverse than
in the young. Specific to the lamprey, the sanguivore form apparently selects for
the Aeromonads because this population of bacteria increases from 4 % in the young
to 84 % in the parasitic fish. Analysis of these Aeromonads found all species and
strains were hemolytic. Like other sanguivores, Aeromonas hydrophila was consistently isolated from fecal samples of vampire bats and is thought to be
necessary for the digestion of blood 34]. The authors also suggested that acquisition of the bacterium by nursing the young
through coprophagy is essential in order to transition to the sanguivore lifestyle.

Longevity and fecundity

Commensals of the microbiome can be classified as obligate or facultative. The obligate
bacteria often have a reduced genome and are dependent on the host and the microbial
community for nutrients and other essential compounds. As an example, Lactobacillus johnsonii codes for amino acid proteases, peptidases, and phosphotransferase transporters but
not for genes necessary for biosynthetic pathways. In addition, L. johnsonii contains all of the genes necessary for the synthesis of pyrimidines but not for
the synthesis of purines, and therefore, the bacterium must acquire amino acids, peptides,
and purine nucleotides as secondary metabolites from other microorganisms or from
the human host 35]. Since obligate microbes, like L. johnsonii, are dependent on the host for survival, promoting the fitness of the host is advantageous
to the symbionts.

In humans, promoting longevity is a leading research focus, and how the microbiome
can modulate longevity is of great interest. This research area is just beginning
and some animal models have demonstrated a link between the gut microbiome and longevity.
It was reported that feeding wild-type soil bacteria Bacillus spp. to Caenorhabditis elegans versus the typical Escherichia coli lab strain increases longevity 36]. In Drosophila, infection with an avirulent Wolbachia extends life-span 37]. The mechanisms by which bacteria can extend life-span have been attributed to host
gene regulation of immune factors and cell proliferation and availability of key vitamins
and co-factors produced by the microbiome 38], 39].

Unlike humans, the goal in rearing agricultural taxa is not longevity but rather to
hasten maturity. Hastening maturation and achieving the shortest rearing period possible
to obtain harvest weight reduces production time and, in turn, drives down costs.
The rearing period of farm-raised Atlantic salmon has been cut in half by genetic
modification. A growth hormone-regulating gene from the Pacific Chinook and promoter
from the ocean pout were added to the genome of the Atlantic salmon. This modification
allows the fish to grow year-round and achieve market weight in half the time (16 months
versus 3 years).

Many agricultural animals do not need to be genetically modified to achieve accelerated
growth rate because growth promotion can be obtained through modifying the intestinal
microbiome. Delivering probiotic cultures to animals hastens the histological development
of the intestinal tract 40], 41]. The mature GIT improves nutrient uptake and increases the growth rate of the animal
40]. Studies in the pig indicate that careful selection of probiotic bacteria is crucial
because the bacterial species colonizing the intestinal tract can have a lifelong
impact on intestinal health. Shirkey et al. 42] reported differences in the gut histology and immune marker responses dependent on
which bacteria initially colonized the gut of the pigs. The group reported that single-strain
cultures affected regions of the intestines differently than mixed cultures, and it
therefore appears that microbial diversity facilitates healthy maturation of the entire
intestinal tract.

It has been argued that the effect of improved growth rate in probiotic-treated animals
is temporal, and non-treated counterparts eventually meet the same weight 43]. In fact, some studies have demonstrated that microbes have an overall deleterious
impact on growth production in chickens and pigs, where gut metabolism accounts for
20–36 % of the whole body energy expenditure 44]–46]. This is due to host-microbiota competition for nutrients, which results in a net
energy loss and decreased growth rate. Further, the microbiome stimulates the production
of IgA, IgG, and mucin secretion that can cost the animal several hundred grams of
protein over a lifetime that is not utilized for growth 47]. Considering the rearing period of a broiler chicken (42 days) and the average final
weight (3000 g), a loss of several hundred grams can be significant. Shifts in the
gut microbiome may also initiate a costly energy production because different antibodies
must be produced 48]. Sub-therapeutic doses of antibiotics delivered in feed can achieve a stable bacterial
and antibody production resulting in an increased growth rate and hence their use
in some animal production. Regardless of the energy that the microbiome may cost the
animal, it is clear that germfree production of agriculture animals to improve production
performance is not a realistic practice.

The impact of the microbiome on host fecundity has been demonstrated in a number of
insects. Insect studies suggest that oviposition rates are dictated by the volatile
compounds produced by the fecal bacteria, and these compounds are olfactory stimulants
that are used as positive cues 49]. Similarly, the volatile compounds produced by the gut microbiome can also promote
mating aggregations 50]. Rosengaus et al. 51] showed that termites treated with Rifampin reduced the number of nitrogen-fixing
bacteria and may have resulted in a loss of amino acids required for oviposition.

In higher animals, there is some evidence of amino acid provisions supplied by the
microbiome and an impact on reproduction 52]. But these and other connections between host reproduction and the microbiome are
more difficult to discern due to the complexity of higher animal systems. Studies
in cows and pigs demonstrate a shift in the GIT microbes during the gestation period,
and thesis shifts were inferred to be for fat deposition to support the developing
fetus and milk production 53], 54]. It has been suggested that changes in hormones and immune factors during gestation
cause subsequent modifications in the microbiome profiles. Thus, it appears that host
factors may modulate the microbiome in order to facilitate some physiological needs
of reproduction.

Health and disease

Of all the functions that gastrointestinal bacteria perform, promoting health and
preventing disease are likely the most studied. Commensal organisms prevent pathogens
from colonizing the host by producing antimicrobial substances (organic acids, bacteriocins)
and competing for nutrients and spaces 55]. Pathogens must compete with the commensal bacteria and devise methods to promote
infection. For example, Salmonella typhimurium induces the inflammatory pathway to reduce the microbial population 56]. Inflammation also provides reactive oxygen species that react with thiosulfate to
produce tetrathionate 57]. Tetrathionate can be used by Salmonella in the respiratory pathway, and the presence of this compound affords a selective
advantage for the pathogen.

In the health promotion framework, the concept of probiotic administration has been
extensively explored in numerous taxa to explore the efficacy and benefits of these
beneficial cultures. Some have sought probiotic cultures from unusual sources that
have unique abilities and might be applied to non-host species. Diaz et al. 58] conducted experiments to determine the ability of the Lactobacilli spp. isolated from dolphins to inhibit pathogenic growth and stimulate tumor necrosis
factor (TNF) production in human monocytoid cells. The authors concluded that many
of the strains possessed beneficial probiotic abilities, but whether or not these
abilities were active during colonization of the dolphin is still unknown.

Understanding the mechanisms of pathogenesis and how commensal microbes defend the
host can lead to therapeutic methods. Conversely, studying the relationship and identification
of pathogens can lead to unique methods for control of certain pest insects. One specific
example took advantage of ice nucleation to control the mulberry pyralid (Glyphodes pyloalis). Ice nucleation refers to the process where insects enhance their supercooling capacity
during the winter by eliminating endogenous ice nucleators, accumulating low-molecular-weight
polyols and sugars, and synthesizing hemolymph antifreeze proteins to prevent the
formation of internal ice crystals that can pierce and damage cells and tissues. In
the mulberry pyralid, active bacteria within the gut are known to increase the supercooling
points and reduce cold hardiness by expressing an ice nucleation gene. Wantbe et al.
59] colonized the gut of the mulberry pyralid with a strain of Enterobacter cloacae, having a transformed ice nucleation gene that led to increased mortality of the
insect. A second example involves the medically important triatomine bug that may
be colonized by the parasite Trypanosoma cruzi. Triatomine bugs were colonized with the mutualistic bacterium Rhodococcus rhodnii that was genetically transformed to express an antitrypanosomal peptide effectively
preventing colonization and development of the parasite population in the gut of the
insect 60].

Functional dependence for nutrients and digestion

Many herbivores do not produce endogenous cellulases, hemicellulases, and pectinases
and as such are dependent on the gut microbiomes for digestion of plant material.
Cranial fermenters utilize a rumen in the foregut for fermentation, while caudal fermenters
possess a cecum in the large intestines. The location of fermentation has an impact
on animal physiology and nutrition. Both types are dependent on the fermentative microbes
to extract energy from cellulose. However, unlike caudal fermenters, cranial fermenters
cannot utilize hexose sources directly, and these sugars are instead converted to
volatile fatty acids in the rumen. Since amino acid absorption takes place in the
small intestines, cranial fermenters can utilize the microbes themselves as a source
of protein. In fact, in cows, bacterial biomass provides about half the protein requirement
for the animal 61]. Conversely, microbial proteins are lost in caudal fermenters because the cecum is
located after the small intestines, where amino acids are absorbed. The dependence
of the cranial fermenters on microorganisms for digestion is clear when considering
the inability to produce healthy germfree adult cows. Germfree calves have been produced
and can be sustained for a short time because they feed on sterilized milk, yet adults
are nearly impossible to sustain due to the reliance on microorganisms for symbiotic
digestion of plant materials.

Although rabbits are caudal fermenters, they can still obtain microbial proteins through
cecotrophy. This process is a 2-cycle approach where the first ingestion of plant
material is fermented by bacteria in the cecum. Pellets are excreted and ingested
and proteins of microbial sources in the pellets are absorbed in the small intestines.
Cecotrophes produce two chemically distinct types of feces in order to maximize the
extraction of essential nutrients, amino acids, and vitamins from the plants. The
impact on the microbial community and the animal due to cecotrophy has been documented.
Rabbits prevented from coprophagy have sterile stomachs and may suffer from malnutrition
62].

Marsupial foregut fermenters, or macropods, are cranial fermenters like cows but with
anatomical differences (the cow has a four-chambered stomach and the kangaroo only
one). Both animals also regurgitate and re-chew food. Rumination in the cow is the
key to the digestion process as resalivation of regurgitated feed provides buffers
for the rumen that maintain the pH required by the microbiome. In kangaroos, there
is little evidence that the regurgitation of food, termed merycism in macropods, is
necessary since they eat very slowly and masticate well 63]. Unlike cattle and sheep, kangaroo digestion releases virtually no methane gas during
exhalation accomplished by unique microbes converting the hydrogen by-product of fermentation
into acetate. These microbes are being sought for use in cattle production to reduce
greenhouse gas emission, and some unique microbes of the macropod microbiome have
been identified. Pope and co-workers 64] identified bacterial populations present in the tammar wallaby and reported that
at the phylum level the Firmicutes and Bacteroides were the dominant taxa. The group also noted that the majority of the phylotypes
were unique and only distantly related to cultured bacteria. Evans et al. 65] reported unidentified methanogens and archaea isolated from the tammar wallaby that
were related to bacteria isolated from GITs. The function of these bacteria has not
been determined, but genes associated with cell aggregation were identified which
they suggested were advantageous for digestion because aggregation facilitates plant
biomass digestion.

Many other animals also depend on the gastrointestinal bacteria to digest cellulose.
For example, the cellulolytic bacterium Teredinibacter turnerae colonizes the Deshayes gland of shipworms, a common group of clams that bore into
wooden ships and piers. This bacterium produces cellulases that degrade the wood the
clams ingest 66]. The bacterium also fixes nitrogen providing a useable source of nitrogen to the
shipworm. The symbiotic dependence for nutrient acquisition in this relationship lacks
data because sequencing of the T. turnerae genome revealed no deletions in essential genes implying that the bacterium can survive
outside the shipworm host 67]. Unlike shipworms, there is plenty of evidence showing that many terrestrial termites
are highly dependent on their endosymbionts 68]. In fact, some species die of starvation when the gut microbiome is eradicated with
antibiotics 69]. Behaviors including proctodeal feeding suggest termites are aware of their dependence
on the microbiome and practice the behavior to ensure transmission of a uniform microbiome
among the individuals 70].

A recent study of the American alligator revealed the impacts of evolution on the
microbiome for digestive dependence 17]. The authors found a high proportion of Fusobacterium in the alligator gut, which is unusual because Firmicutes or Bacteroidetes typically dominate the gut bacteria populations. For this reason, the authors suggest
Fusobacterium performs functional roles including development of the digestive organs and nutrient
acquisition in the alligator. Furthermore, given that the basal position of Fusobacterium on the evolutionary tree and that the American alligator is the least evolved of
nearly all animals, the authors suggest that Fusobacterium were dominant gut microbes in some prehistoric animals.

Adaptation to environmental extremes

Marine sponges and tubeworms inhabit a wide distribution of marine environments, but
many can be found in locations near hydrothermal vents with pressures of 400 bar (395 atm)
and water temperatures up to 60 °C. This environment may also have an acidic pH and
is rich in chemicals emitted from the vents including sulfide, hydrogen, and methane.
The sponge or tubeworm absorbs chemicals, and microbial symbionts process the chemicals
into organic molecules the host needs, while the bacteria gain a stable habitat. The
dependence of the tubeworm and sponges on their symbiotic chemoautotrophic bacteria
for nutrients has been well established 71]. Studies have confirmed the microbiome of these invertebrates is distinct from the
surrounding water 72], and evidence of vertical transmission of endosymbionts exists 73]. Together, data from studies of these animals point to an adaptation of the host
to an otherwise uninhabitable environment partly facilitated by the symbiotic bacteria.

Many marine mammals also inhabit extreme environments such as the polar arctic. To
date, the few studies examining the gut microbiome of marine mammals living in these
extreme environments have identified and cataloged bacteria, but little functionality
of these bacteria has been explored. Glad et al. 74] identified the bacteria present in 10 different samples obtained from the rectums
of polar bears (Ursus maritimus; note: polar bears are considered marine mammals and protected as
such under marine mammal laws). Ogawa et al. 75] used cloning techniques to characterize gut bacteria in three different minke whales
(Balaenoptera acutorostrata). These studied animals are carnivorous, feeding primarily on fish (minke whales)
or seals (polar bears), and thus, the identification of bacteria including Bacteroidetes and Firmicutes is not surprising. Although primarily characteristic in nature, the distribution
and abundance of the bacteria in these studies may provide clues for functionality.
Firmicutes were the dominant taxa in nearly all the samples, and these bacteria have an increased
capacity to stimulate host energy storage over other phyla 76]. These animals rely heavily on fat deposition for survival not only for energy storage
but also to maintain body temperature. Thus, it is possible that some animals living
in the polar extremes rely on their gut microbes to facilitate efficient fat storage
needed for survival.

Functionality revelations by comparative analysis

Intra-species comparisons of the metagenomes of individuals have revealed the functionality
of some digestive communities. Qu et al. 77] used a chicken model to show that even though two individuals may have marked differences
in microbiomes, the functional metagenome can be the same. They concluded that in
their samples, bacterial taxa replaced other taxa without changing the overall function
of the microbiome. Conversely, comparison of rumen samples among individuals showed
marked differences in microbiomes that did result in differences in the overall functional
microbiome 78]. The conflicting results in the two studies may be attributed to diet and digestive
tract physiology.

Comparing phylogenetically divergent animals can also provide a better understanding
of how microbiomes function and evolve and are shaped by factors such as diet and
physiology. Although the cow and termite are both heavily dependent on bacteria for
celluloytic digestion, diet was the main factor that shaped the microbiomes in these
animals 78]. Comparison of the cow and hoatzin (a foregut fermenting bird) revealed that very
similar microbial compositions and organ digestive functions dictated microbial profiles
rather than phylogeny 79]. Interestingly, comparative genomic studies have demonstrated that the bacterial
profile in swine and humans are similar and harbor many of the same phylogenetic groups
primarily due to the similar gastrointestinal systems 80]. However, comparative metagenomic analysis of the pig, chicken ceca, cow rumen, and
human fecal microbiomes showed that the metagenomes of the pig aligned more closely
with the cow and chicken than with the human microbiome 81]. The results imply that agricultural taxa possess bacterial metagenomes that have
been selected as a result of a very consistent and narrowly defined diet and rearing
environment.