Metabolic Teamwork between

Gut Microbes and Hosts

In processing energy, furnishing key nutrients, and detoxifying
xenobiotics, microbial diversity matters for hosts
William H. Karasov and Hannah V. Carey

ymbiotic relationships between microbes and their animal and plant

hosts shape our world. Interest in these
host-microbial interactions is intensifying, and researchers from many
disciplines within biology are striving to understand their functional and evolutionary significance.
Those of us studying animal feeding, digestion, and nutrition appreciate the key role microbes played in shaping the biodiversity of vertebrates. For instance, microbial fermentations
unlock energy from cellulose, the most abundant organic compound on Earth. Thus, gut
microbes enable animals to thrive as herbivores,
a primordial step that led to a huge diversification of animal species. Modern molecular analytic techniques make it possible for us to learn
more about these important symbioses.

Summary
Microbial diversity in the gut tremendously increases metabolic pathways accessible to hosts
for energy, essential nutrients, and detoxifying
xenobiotics.

Differences in gut structure yield diverse niches

and microbiota.

Diversity at the microbial species level sometimes lacks functional significance because of
redundancies in the metagenome.

Specificity within the microbiota matters in certain cases, such as glycan processing by acetogens versus methanogens and the detoxification
of particular xenobiotics.

Biodiversity in Host-Microbial Systems

Phylogenetic analyses indicate that fermentative
digestion evolved repeatedly and independently
in vertebrates. Further, herbivores have diverse
gut structures, thereby providing many different
environmental situations for gut microbes (Fig.
1). Consider three distinct examples.
In herbivores with foregut fermentation, the
microbial fermentation chamber is proximal to
the small intestine. This configuration developed independently in four clades of mammals,
including ruminants such as cows and deer,
colubid monkeys, sloths, macropod marsupials
such as the kangaroo, and at least once in birds,
including the hoatzin, Opisthocomus hoazin in
South America. These groups all share a key
feature: their resident microbial communities
have first crack at ingested nutrients before any
food reaches the host small intestine. Yet, as
described below, there are some examples
that illustrate important differences among
foregut fermenters.
The nutritional milieu of foregut fermenters differs from that of hindgut fermenters,
animals in which the fermentation chamber
is distal to the stomach and small intestine
(Fig. 1). Because the small intestine absorbs
most soluble carbohydrates, proteins, and
lipids, the residue that arrives at the hindgut
contains lower levels of those nutrients but
more of structural materials such as cell
walls. Thus, microbes in hindguts receive
the dregs compared with what microbes in
foreguts receive, a fact with important implications for host-microbial processing.
Some vertebrate hosts process food
much more slowly than others because of

William H. Karasov
is Professor in the
Department of Forest and Wildlife
Ecology, University
of Wisconsin, Madison, and Hannah V.
Carey is Professor
in the Department
of Comparative Biosciences, School of
Veterinary Medicine, University of
Wisconsin, Madison

Volume 4, Number 7, 2009 / Microbe Y 323

microbial community that these hosts

can sustain.
In general, reptiles operate at lower
and more variable body temperatures
than do mammals and birds, another
host variable that may influence gut microbiota. Differences in nutrient milieu,
retention time, and temperature can foster diverse microbial niches and mixtures
that older culture-based methods vastly
underestimate. Recent efforts to reevaluate microbial richness in the rumen, for
example, by analyzing 16S rRNA gene
sequences suggest that the typical rumen
contains 300 400 bacterial species,
on the basis of operational taxonomic
units (OTUs)a figure that is about 10
times higher than culture-based estimates.
Furthermore, similar analyses of gut
microbial communities in the fermentative chambers of previously unexamined
herbivores typically indicate high proportions of previously undescribed sequences, suggesting the presence of novel
microbial species. Indeed, on average,
62% of OTUs within guts of mammalian
hosts were not observed in any other species, according to a recent survey across
60 mammal species by Ruth Ley, Jeffrey
Gordon, and their collaborators at Washington University in St. Louis, Mo.
Besides differences among animal
species, microbial biodiversity can vary
among populations within species and
even among individuals within populations. The genetic, developmental, and
All vertebrates have a small intestine but vary as to whether they possess other
compartments such as crop, forestomach, stomach, cecum, and large intestine/colon.
environmental (e.g., diet) determinants
As a general rule, catalytic enzymatic reactions occur in the small intestine, whereas
of all this microbial biodiversity in guts
microbial fermentation can occur in the forestomach, cecum, and large intestine/colon
remain to be determined. Interpreting
(shown with dotted areas). Foregut fermentation occurs in four major clades of mammals
and in at least one avian species (the Hoatzin). Hindgut fermentation, either in the cecum
the functional significance of this mior large intestine/colon, occurs in many clades of mammals, birds, and reptiles.
crobial biodiversity will require a detailed understanding of processes in
which microbes are involved. One of
differences in gut morphology or metabolic
the better understood of those processes is fermode. The period that digesta remains in the
mentative digestion of cellulose.
gut is called digesta retention time and is
typically measured with marked food particles. For instance, reptiles have digesta retenCellulose Fermentations Involving
tion times 510 times longer than those of
Microbial Consortia
similar-sized mammals. Among mammals, sloths
have particularly long retention times. Such differWhen microbial communities living within the
ences have important implications for the kinds of
rumen of herbivores degrade cellulose and other
FIGURE 1

324 Y Microbe / Volume 4, Number 7, 2009

glycans, they yield short-chain fatty acFIGURE 2

ids (SCFAs), including acetate, propionate, and butyrate, for the host to absorb to meet its energy needs (Fig. 2).
The metabolic pathways that produce
SCFAs involve sequential fermentations by several microbial taxa in consortia.
These pathways are part of a complex ecological food web whose microbial members exchange intermediates. When more than one microbial
species within a community performs
the same reactions, they create a functional redundancy. Thus, the overall
degradative process goes on, even
though some species may replace others with similar metabolic roles. Indeed, some fraction of microbial
biodiversity may have relatively little
functional significance.
A few decades ago, some ecologists
fermented plant foods in vitro to estimate the digestive efficiency of wild ruminants, namely that fraction of the
energy or nutrients in food available to
its consumer. This approach to measuring digestive efficiencies is cheaper than
is capturing wild animals and then collecting both their food and excreta to
The pathways for the anaerobic degradations of organic materials involve the combined
action of many microorganisms. Green arrows refer to microbially produced energy
determine what they digested. Resubstrates absorbed and used by the host. Numbered blue (1) and red (2) arrows refer to
searchers validate in vitro fermentation
alternative pathways that remove H, whose formation can retard fermentation. Not all
estimates by comparing them with
the pathways shown occur in the gut of all vertebrate hosts.
whole-animal studies (Fig. 3).
Surprisingly, whether the rumen inoculum was from a deer or a cow and
of acetogenic bacteria with shorter generation
regardless of the diet consumed, the results are
times. They produce acetate, which hosts can
about the same across several dozen of these
absorb for use as an energy source.
studies. However, our recently developed view
of how high gut microbial biodiversity creates
Biodiversity Matters for
functional redundancy helps to explain these
Foregut Fermenters
results.
In other cases, differences in gut microbial
Ruminants such as cows and macropod marsucommunities lead to important functional difpials such as kangaroos are both foregut ferferences. For example, microbes may be inmenters. However, kangaroos apparently convolved in removing hydrogen that builds up in
tain no methanogenic microbes and produce
these systems through one of several alternative
relatively little methane, whereas 10 15% of
pathways (Fig. 2). One such group includes
the energy flow for ruminants is lost as methane
methanogens that reduce hydrogen to methane,
gas.
which vertebrate hosts cannot use as an energy
Differences in gut morphology help to acsource. Many methanogens are members of the
count for this difference. The ruminant foregut
archaea, with relatively long generation times.
is like a continuous stirred-tank reactor that
Another group for removing hydrogen consists
retains food particles until they are small enough

Volume 4, Number 7, 2009 / Microbe Y 325

roos provoke other questions. For instance, are kangaroos more efficient
than ruminants at extracting energy
from food? Kangaroos are less efficient
at digesting Lucerne hay, which is
mainly cellulose, because shorter digesta retention times provide less contact between fermentative microbes and
this food, according to Ian Hume of the
University of Sydney in Australia. That
loss puts kangaroos on an equal footing
with sheep in overall digestive efficiency.
Such differences have economic implications. Livestock producers would
like to reduce methane losses from ruminants while increasing their efficiency in converting plant materials
into milk and meat products. There are
also global implications. The 1.5 billion
cattle on the planet generate more than
100 million tons of methane per year,
which is about 20% of emissions contributing to global warming. Conservation researchers in Australia suggest
that shifting from ruminant cattle and
sheep to kangaroos for meat could be
useful for decreasing the Australian
contributions to greenhouse gases.

FIGURE 3

Rumen microbial inoculum can be used to estimate diet digestibility in wild ruminants.
Digestibility, which is the proportion or percentage of food material actually digested, can
vary among diets of herbivores because of different amounts of refractory plant cell wall
material in foods and differences in digestive processes including the extent and rate of
microbial fermentation. This plot shows the digestibility of five different foods consumed
by white-tailed deer measured in whole-animal feeding trials with deer (in vivo, x axis) or
estimated using in vitro fermentation (y axis). The source of the microbial inoculum for
the fermentations are shown as different symbols. In many studies, as in this one, the
inoculum source seems not to make a great difference. (Data from C. T. Robbins et al.
J. Wildlife Management 39:6779, 1975.)

to exit. In contrast, the macropod marsupial

foregut is tubular, with outpouches that retard
flow but nothing like the particle size-dependent
mechanism in ruminants. Thus, digesta retention times are much shorter in marsupials than
in similar-sized ruminants. Microbes that attach
to particles can persist in chambers if their generation times are shorter than the mean retention times of digesta. The longer retention times
of ruminants appear to favor methanogenic archaea that grow more slowly and have longer
generation times than do acetogenic bacteria.
Differences between ruminants and kanga-

326 Y Microbe / Volume 4, Number 7, 2009

Host-Microbial Nutrient
Processing

Microbes provide their vertebrate hosts

with more than energy-rich fermentation products. They also synthesize nutrients, including essential amino acids,
that are absorbed directly or during recycling when the host degrades and absorbs the microbes.
Of the 20 amino acids that are critical for
vertebrates, 10 are considered essential because
the vertebrates cannot synthesize them at all or
in adequate amounts. Vertebrates can obtain
essential amino acids, such as lysine, from their
diet, but there is evidence that they also obtain
them from their gut microbes (Fig. 4). For example, after urea containing the nitrogen-15 isotope is administered orally to cows, lysine containing that same isotope is found in proteins
within tissues of those animals (Fig. 4, top).
Because cows cannot produce the amino acid
directly, they must have depended on microbes

in the rumen to convert the labeled urea

into lysine, which then is incorporated
into microbial protein. When the microbes move from the rumen into the
acidic part of the cow stomach and then
to the intestine, cow enzymes digest the
protein, enabling the animals to absorb
the nitrogen-15 lysine.
Nonruminant animals such as rats
depend on the microbial community in
the cecum and colon to incorporate isotope-labeled urea nitrogen into lysine.
When rats reingest feces (coprophagy,
or cecotrophy in rabbits), they digest
and absorb labeled amino acid from
those microbial proteins (Fig. 4, bottom). However, germ-free rats cannot
incorporate isotope-labeled urea nitrogen into lysine.
In theory, humans cannot incorporate lysine that might derive from isotope-labeled urea through proteins that
the hindgut microbial community produces because they are hindgut fermenters and do not reingest feces. Amazingly, however, nitrogen-15 labeled
lysine appears in human plasma proteins hours after labeled urea is administered. Thus, amino acids and perhaps
other nitrogen-containing compounds
may be cycling between humans and
their microbiota, a process that could
reduce dietary requirements for those
nutrients. However, whether the fluxes
of those amino acids or other essential
nutrients between microbes and humans are great enough to contribute
significantly to nutritional requirements is unresolved.

FIGURE 4

Pathways of amino acid recycling depend on gut design and animal behavior. In foregut
fermenting herbivores (top schematic), ingested sources of nitrogen (N) can be incorporated into host protein as essential amino acids such as lysine because the microbes can
synthesize this amino acid (the vertebrate host cannot). The host breaks down the
microbial wall with lysozyme and digestion and absorption of microbial protein occurs in
the small intestine, followed by absorption of the amino acid, which enters the hosts
amino acid pool. In hindgut fermenters (lower figure), such recycling can occur if the host
reingests the feces (called coprophagy or cecotorphy), breaks down the microbes
perhaps with intestinal lysozyme, and then digests and absorbs microbial protein that
contains the new essential amino acids. Many details remain to be elaborated, such as
the location and magnitude of lysozyme capacity. Also, recent work with pigs and
humans that do not reingest feces demonstrates that there is another unknown pathway
for absorption of microbially produced essential nutrients.

Host-Microbial Processing
of Toxins
Gut microbes modify not only nutrients but
xenobiotics such as toxins. For example, the
fast-growing tropical legume Leucaena leucocephala is rich in nitrogen and hence is used as a
feed supplement for cattle. However, its tissues
contain mimosine, an amino acid that is toxic
and that foregut microbes can transform into
other toxic metabolites that intoxicate ruminants.
In 1982, Australian ecologist Raymond Jones
determined that Leucaena leaves are toxic for

Australian goats but not Hawaiian goats. However, when Australian goats are inoculated with
ruminal fluid from Hawaiian goats, the recolonized Australian goats become tolerant to mimosine. The bacterium that degrades and thus
detoxifies mimosine metabolites was isolated
from the rumen of the resistant goats and was
subsequently named Synergistes jonesii. Once
established, S. jonesii spreads readily among
members of a herd. Hence, S. jonesii is being
used to inoculate ruminants throughout the
world, making it safe for them to eat Leucaena
spp.

Volume 4, Number 7, 2009 / Microbe Y 327

Biodiversity and Superorganisms

A striking picture emerges from studying hostmicrobial processing of energy, nutrients, and
toxins. The gut microbial metagenome tremendously increases the diversity of metabolic pathways accessible to animal hosts, enabling them
to metabolize many things that they otherwise
could not.
Perhaps most importantly, gut microbes enable some animals to partake of cellulose, the
single largest nutritional energy source on the
planet. More generally, gut microbes enable animals to survive on diets with low levels of
particular nutrients and high levels of particular
toxins. In this sense, vertebrates become nutri-

tional superorganisms, with microbial biodiversity providing the metagenome.

Diversity in gut structure and function, in
diet, and in other features of animal hosts creates differences in nutrient milieu, digesta retention times, and temperatures that create diverse
microbial niches and inhabitants. Sometimes
that diversity lacks functional significance because of redundancies in the metagenome of gut
microbiota. At other times, however, diversity
matters, such as in processing glycans or specific
xenobiotics. With new molecular tools for
studying microbial communities, determining
the details of gut microbial diversity will depend
on scientists from different disciplines forming
symbioses of their own.

ACKNOWLEDGMENTS
Dr. Carlos Martinez del Rio (University of Wyoming-Laramie) and Dr. Karen Cloud-Hansen (University of WisconsinMadison) graciously shared material and their perspectives and offered comments on drafts of this manuscript. Preparation of
the manuscript was supported in part from a grant from the National Science Foundation (IOB-0615678 to W.H.K).
SUGGESTED READING
Edwards, J. E., S. A. Huws, E. J. Kim, M. R. F. Lee, A. H. Kingston-Smith, and N. D. Scollan. 2008. Advances in microbial
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Gill, S. R., M. Pop, R. T. DeBoy, P. B. Eckburg, P. J. Turnbaugh, S. S. Buck, J. I. Gordon, D. A. Relman, C. M. Fraser-Liggett,
and K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:13551359.
Karasov, W. H., and C. Martinez del Rio. 2007. Physiological ecology: How animals process energy, nutrients, and toxins.
Princeton University Press, Princeton, N.J.
Ley, R. E., M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey, J. S. Bercher, M. L. Schlegel, T. A. Tucker, M. D.
Schrenzel, and R. Knight, and J. I. Gordon. 2008. Evolution of mammals and their gut microbes. Science 320:16471651.
Metges, C. C., M. Eberhard, and K. J. Petzke. 2006. Synthesis and absorption of intestinal microbial lysine in humans and
non-ruminant animals and impact on humans estimated average requirement of dietary lysine. Curr. Opinion Clin Nutrition
Metabolic Care 9:37 41.
Ouwerkerk, D., A. J. Maguire, L. McMillen, and A. V. Klieve. 2007. Why kangaroos do not produce methane. Recent Adv.
Animal Nutrition Australia 16:101104.
Stevens, C. E., and I. D. Hume. 1995. Comparative physiology of the vertebrate digestive system. Cambridge University Press,
Cambridge.
Wallace, R. J. 2008. Gut microbiology broad genetic diversity, yet specific metabolic niches. Animal 2:661 668.
Wilson G. R., and M. J. Edwards. 2008. Native wildlife on rangelands to minimize methane and produce lower-emission meat:
kangaroos versus livestock. Conservation Lett. 1:119 128.

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