of Dogs and Cats:
a Bigger World than
Jan S. Suchodolski, med vet, Dr med vet, PhD
Recent molecular studies have revealed that the mammalian gastrointestinal (GI) tract
harbors a highly complex microbiota that includes bacteria, archaea, fungi, protozoa,
and viruses. The total microbial load in the intestine is estimated to range between
1012to 1014organisms, about 10 times the number of host cells. It is estimated that
several thousand bacterial phylotypes reside in the GI tract.1–3The gene content of
these microbes is defined as the intestinal microbiome. Gut microbes play a crucial
role in the regulation of host health, by stimulating the immune system and develop-
ment of gut structure, aiding in the defense against invading pathogens and providing
nutritional benefit to the host (ie, production of short chain fatty acids, vitamin B12). In
contrast, a microbial dysbiosis has been identified in dogs and cats with GI disease
This review summarizes current information about the intestinal microbial
ecosystem in dogs and cats.
Methods for Characterization of the Intestinal Microbiome
Cultivation methods are most useful when targeting a specific pathogen in clinical
specimens (eg, Salmonella). Culture assesses the viability of organisms and allows
antimicrobial susceptibility testing. Isolates can be genotyped for epidemiologic
studies. Culture is also valuable for characterizing the metabolic properties of isolates
and their virulence factors.
The author has nothing to disclose.
Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory,College of Veterinary
Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843‑4474, USA
E-mail address: firstname.lastname@example.org
? Feline ? Canine ? Gastrointestinal ? 16S rRNA gene
?Microflora ?Microbiota ?Gastrointestinal tract
Vet Clin Small Anim 41 (2011) 261–272
0195-5616/11/$ – see front matter ? 2011 Elsevier Inc. All rights reserved.
Alterations in bacterial groups observed in dogs and cats with GI disease
Refs.Sample MaterialDiagnosisMethod Microbial Alterations
Suchodolski et al4
Duodenal biopsiesIBD Comparative 16S rRNA gene analysis
Allenspach et al48
GSD with food- or antibiotic-
Comparative 16S rRNA gene analysis
Jergens et al35
Duodenal biopsies IBD 16S rRNA gene 454-pyrosequencing
YClostridium cluster XIVa and IV
Ruminococcus, Dorea spp)
Xenoulis et al5
IBDComparative 16S rRNA gene analysis
Craven et al49
Duodenal biopsiesChronic enteropathies (steroid-,
food-, and antibiotic-responsive)
16S rRNA gene
Simpson et al50
Colonic biopsiesBoxer dogs with
Fluorescence in-situ hybridization Intraepithelial invasion of
adherent and invasive E coli
Jia et al9
Bell et al7
FecesChronic diarrhea Fluorescence in-situ hybridization
FecesDiarrhea Terminal restriction fragment
Janeczko et al6
IBD Fluorescence in-situ hybridization
Inness et al8
FecesSmall and large bowel IBD Fluorescence in-situ hybridization
Ytotal bacterial load
YBifidobacterium spp, Bacteroides
Abbreviations: GSD, German Shepherd dog; IBD, irritable bowel disease.
It is now well recognized that bacterial cultivation techniques do not yield sufficient
information about the microbial diversity in complex biologic ecosystems because of
their significant limitations. Firstly, there is currently not enough information available
about the optimal growth requirements of most microorganisms, which explains why
only a minority of intestinal microbes can be recovered on culture mediums. Secondly,
the GI tract harbors predominantly anaerobic bacteria, which may be more prone to
damage during sample handling. Thirdly, many microbes live in mutualistic interac-
tions with other microorganisms or the host, and this hinders their growth on culture
media. Additionally, many selective culture media lack sufficient specificity and often
other organisms than the targets are enumerated.10Finally, phenotypic and biochem-
ical identification systems frequently fail to accurately classify many microorganisms
residing in the gut. Therefore, DNA sequencing of culture isolates is often required.
Because of these limitations, it is estimated that only a small fraction (<5%) of intes-
tinal bacteria can be cultivated, and a much smaller fraction can be correctly identified
Because bacterial culture underestimates microbial diversity in the GI tract, molec-
ular tools have now become the standard approach in gut microbial ecology.1,2,11–14
For molecular analysis, DNA or RNA is extracted from intestinal samples (eg, feces,
biopsy specimen, luminal content). For phylogenetic identification or for molecular
fingerprinting, a specific gene is amplified using universal primers (either bacterial,
fungal, or archaeal) that target conserved regions within these genes. The conserved
regions flank variable gene regions, which when sequenced allow the phylogenetic
identification of the present organisms. For bacterial and archaeal identification,
the 16S ribosomal RNA (16S rRNA) gene is most commonly targeted. Other targets
include the 16S-23S internal transcribed spacer (ITS) region and the chaperonin
Molecular fingerprinting Molecularfingerprintingisusedtoseparateamixtureofpoly-
a fingerprint, which is representative of the bacterial community within the sample.
Different techniques include denaturing gradient gel electrophoresis (DGGE), tempera-
ture gradient gel electrophoresis (TGGE), and terminal restriction fragment length
polymorphism (T-RFLP).7,15–19In DGGE and TGGE, differences in nucleotide
composition result inuniquemeltingbehaviorsoftheindividualPCRamplicons,gener-
ating a banding pattern that illustrates the bacterial diversity in the sample. DGGE and
TGGE are inexpensive and can be rapidly performed. However, DGGE and TGGE only
allow a limited resolution of PCR amplicons because many bacterial phylotypes may
have similar melting behaviors. Therefore, these techniques capture only changes in
primer are fragmented in different sizes using sequence specific restriction enzymes,
again yielding a characteristic fingerprint of the microbial community.7
Identification of bacterial groups For identification of individual bacterial phylotypes,
PCR amplicons generated using universal bacterial primers need to be separated and
sequenced, which can be achieved by construction of 16S rRNA gene clone
libraries,11,12,20or more recently by an automated high-throughput sequencing plat-
form (eg, 454-pyrosequencing). This platform allows several thousand sequences to
be analyzed within a few hours, yielding deep phylogenetic information about the
Intestinal Microbiota of Dogs and Cats
Quantification of bacterial groups Commonly used methods for quantification of
bacterial groups are quantitative real-time PCR (qPCR)12,18and fluorescent in-situ
hybridization (FISH).6The use of FISH is currently considered to be the most accurate
method for quantification of bacterial groups because it allows direct microscopic
counting of fluorescence-labeled bacteria. Furthermore, the location of bacteria with
regard to the epithelium (ie, intracellular, adherent, or invasive) can be visualized.
Limitations of molecular methods It is important to realize that molecular methods
have some limitations. The use of different DNA extraction methods (eg, bead beating
steps, heating in lysis buffer)1,13and the use of different PCR primers will yield slightly
underestimate the presence of specific bacterial groups, especially those with a high
guanine-cytosine content (eg, Bifidobacterium spp),11,21and some investigators use
either a primer mix or group-specific primers for more accurate amplification.22
tute such a low proportion of total bacteria that they escape identification even when
high-throughput sequencing techniques using broad-range primers are employed.
The additional use of group-specific PCR assays is needed to detect these groups of
interest. Furthermore, PCR can exhibit bias in quantification of specific bacterial
groups. For example, the bacterial 16S rRNA gene is organized in so-called operons.
These operons can vary in number from 1 to 15 within individual bacterial phylotypes.
The operon number may also change during the growth phase and changed activity of
tion method exists for accurate characterization of all microorganisms, and the various
methods available should be used complementarily.
Metagenomics and transcriptomics The amplification of a specific gene (eg, 16S rRNA
gene) allows identification of intestinal bacteria and has yielded comprehensive infor-
mation about which bacterial groups are present in the canine and feline GI tract.
However, because only one single gene is evaluated in comparative 16S rRNA gene
analysis, these methods yield only phylogenetic information (answering the question:
who is there?). They do not provide information about the functional properties of the
intestinal microbiome. The microbiota differs substantially at the species and strain
level in each individual animal.2,15,17Despite these phylogenetic differences, the meta-
bolic end products of the gastrointestinal microbiome are similar between individuals.
Also, although some environmental influences (eg, diet, fasting) may lead to changes
in bacterial groups, these changes are not immediately associated with any major
alterations in gut physiology in healthy animals. For example, antibiotic administration
has a profound impact on the composition of gut microbiota but these microbial
changes do not correlate with gut function.1,24Therefore, for a better understanding
of microbial-host interactions in health and disease, the functionality of the intestinal
microbiome needs to be explored. New high-throughput sequencing platforms facili-
tate rapid sequencing of total genomic DNA or mRNA without prior amplification of
specific genes. Therefore, inaddition to phylogenetic identification ofmicroorganisms,
these techniques yield information about the gene content (metagenomics) or the
expressed genes (transcriptomics) within the microbiome, and may therefore define
the functional potential of the microbiome.14,25Metagenomic approaches have
revealed the existence of a core microbiome in the mammalian intestine. Despite
differences in abundance and prevalence of specific bacterial phylotypes, individuals
possess similar microbial genes and metabolic pathways,14,25which indicates a func-
tional redundancy of the gastrointestinal microbiota.24The various members of the
microbial community perform similar functions, and if one group is depressed
because of external factors (eg, antibiotic therapy), other members of the community
are capable of maintaining the functionality within the ecosystem. These findings
emphasize the need for evaluating both phylogenetic relationships and metabolic
functions (ie, metagenomics and transcriptomics) of the intestinal microbiome.
Bacteria in the GI tract of dogs and cats
Cultivation results Much of the published data describing the composition of the
gastrointestinal microbial ecosystem in dogs and cats has been generated using
bacterial cultivation techniques.26–30These studies have revealed that total bacterial
counts in the stomach range between 101and 106cfu/g or ml.26The bacterial load
in the duodenum and jejunum of dogs and cats shows pronounced individual varia-
tions. Duodenal bacterial counts are low in most dogs (<103cfu/g or ml of duodenal
aspirates), but they may reach up 109cfu/g or ml in some dogs.29,30The feline
duodenum reportedly harbors higher bacterial counts (105–108cfu/g or ml), and
anaerobic bacteria (Bacteroides spp, Fusobacterium spp, Eubacterium spp) appear
to predominate unlike in dogs.29The bacterial counts found in the proximal small
intestine of some healthy dogs and cats are substantially higher than typically found
in humans, where bacterial counts greater than 105cfu/g or ml of small bowel aspi-
rates indicate small intestinal bacterial overgrowth (SIBO). Although initial studies in
dogs defined SIBO based on the same numerical criteria as in humans (bacterial
counts >105cfu/g or ml for aerobes or >104cfu/g or ml for anaerobes),31subsequent
investigations showed that healthy dogs can have bacterial counts that by far exceed
those proposed cutoffs.30Therefore, the use of the term SIBO is now controversial in
dogs, and authors prefer the terms antibiotic-responsive diarrhea or small intestinal
dysbiosis. SIBO has not been reported in the cat based on the higher physiologic
bacterial counts found in that species.28
Bacterial concentrations increase aborally along the length of the gastrointestinal
tract. The ileum harbors approx. 107cfu/g or ml, whereas bacterial counts in the colon
of dogs and cats range between 109and 1011cfu/g or ml of intestinal content. Bacter-
oides, Clostridium, Lactobacillus, Bifidobacterium spp, and Enterobacteriaceae are
the predominant bacterial groups that have been cultured from canine and feline
Molecular tools Molecular tools have revealed high numbers of previously unrecog-
nized species in the mammalian GI tract. It isestimated that several thousand bacterial
phylotypes inhabit the human colon.32Recent high-throughput sequencing studies
(based on 454 pyrosequencing of the 16S rRNA gene) have estimated that approxi-
mately 200 bacterial species and 900 bacterial strains reside in the canine jejunum1;
whereas, several thousand phylotypes are thought to be present in fecal samples of
dogs and cats.2Ten to 12 different bacterial phyla are routinely identified in the
mammalian GI tract.2,12,13,21Of these, the phyla Firmicutes, Bacteroidetes, and Fuso-
bacteria makethe majority of gut microbiota (approximately 95%), followed by Proteo-
bacteria and Actinobacteria, which constitute typically 1% to 5% of total bacteria
identified by sequencing.2,13The phyla Spirochaetes, Tenericutes, Verrucomicrobia,
TM7, Cyanobacteria, Chloroflexi, Planctomycetes, and a few currently unclassified
bacterial lineages constitute typically less than 1% of obtained bacterial sequences.
The abundance of these bacterial groups varies along the length of the GI tract as
shown by 16S rRNA gene analysis. In the stomach, Helicobacter spp represented 99%
Intestinal Microbiota of Dogs and Cats
tified in the proximal small intestine of dogs1and cats (Suchodolski, unpublished data,
2010), respectively. Firmicutes (mainly Clostridiales and Lactobacillales), Bacteroidetes,
Proteobacteria, and Actinobacteria constituted approximately 95% of sequences.
Firmicutes (mainly Clostridiales), Bacteroides, and Fusobacteria have been
reported to be the predominant bacterial phyla in the colon and feces of dogs and
cats.2,11,13,14,20,21However, the observed abundance of these bacterial groups differs
between studies. For example, percentages of Firmicutes range between 25% and
95% of obtained 16S rRNA gene sequencing tags.2,13These wide ranges are most
likely caused by differences in DNA extraction methods and selection of different
universal PCR primers. In contrast to results from 16S rRNA gene-based studies, Acti-
nobacteria were documented to be abundant in feline feces in a comparative chaper-
onin 60 gene analysis.12This finding is not surprising because it has been shown that
16S rRNA gene approaches routinely underestimate the abundance of Actinobacteria
in intestinal samples when universal bacterial primers are used.21In contrast, the use
of group-specific primers for Bifidobacterium spp, members of the phylum Actinobac-
teria, or the use of FISH analysis with Bifidobacterium species-specific probes confirm
that this bacterial group is present in the intestinal tract of the majority of dogs and
cats.8,9,21In a recent metagenomic study, the Bacteroidetes/Chlorobi group and Fir-
micutes represented each approximately 35% of sequences obtained from canine
feces, followed by Proteobacteria (15%) and Fusobacteria (8%). Actinobacteria
(including Bifidobacterium spp) represented only 1% of obtained sequences.14Similar
results were observed in feline fecal samples analyzed by a metagenomic approach.34
feline gastrointestinal tract, are represented mainly by the bacterial order Clostridiales,
ters differ in abundance among the differentparts of theintestine.11,20Clostridiumclus-
ters XIVa and IV make up approximately 60% of all Clostridiales, and encompass many
important short-chain fatty acids producing bacteria, such as Ruminococcus spp, Fae-
depleted in humans and dogs with acute or chronic enteropathies, emphasizing the
importance of these bacterial groups in intestinal health (see Table 1).4,35,36
Molecular fingerprinting has also demonstrated that every individual dog and cat
has a unique and stable microbial ecosystem.15,17,21All animals harbor similar bacte-
rial groups when analyzed on a higher phylogenetic level (ie, family or genus level), but
the microbiome of each animal differs substantially on a species/strain level, with typi-
cally only a 5% to 20% overlap of bacterial species between individual animals. For
example, a recent study has shown that only a small percentage (<30%) of dogs
and cats harbored the same species of Bifidobacterium spp.2,21
OTHER MEMBERS OF THE INTESTINAL ECOSYSTEM
In addition to bacteria, the mammalian gastrointestinal tract harbors a diverse mixture
of microorganisms, including fungi, archaea, protozoa, and viruses (mostly bacterio-
phages). Molecular tools have provided information about the species richness of
these microbes, but their role in gastrointestinal health needs to be further elucidated.
Cultivation studies have documented the presence of yeasts and molds in the intes-
tine of approximately 25% of healthy Beagle dogs, with fungal counts ranging from
101cfu/g jejunal content to 105cfu/g of feces, respectively.26,27,37Using a PCR assay
with universal fungal primers targeting the ITS region, fungal DNA was detected in the
small intestine in 39 of 64 (61%) healthy dogs and in 54 of 71 (76%) dogs with chronic
enteropathies.38Marked differences in the prevalence of different fungi was observed
between animals. A total of 51 different fungal phylotypes were identified across all
135 dogs, with the majority harboring only 1.38Saccharomycetes were the most
commonly identified fungal class, and no significant differences in the prevalence of
specific fungal phylotypes were observed between healthy and diseased dogs.38
Fungi were found to adhere to the intestinal mucosa more frequently than they were
detected in the luminal content.38,39
Recent high-throughput sequencing data based on 454 pyrosequencing of the 18S
rRNA gene revealed 4 fungal phyla in canine and feline fecal samples, with the majority
of sequences belonging to the phyla Ascomycota (>90%) and Neocallimastigomycota
(>5%).40Fungi were present in all 19 evaluated animals, with each animal harboring
multiple fungal species, with a median of 40 phylotypes (Table 2).40Remarkable intera-
nimal differences were observed as each dog harbored a unique profile. Although most
dogs harbored similar fungal phyla, each animal had a unique species population.40
There is no data describing the precise abundance of fungi in the gastrointestinal
tract of healthy dogs and cats. Studies in humans using FISH analysis have estimated
fungal abundance as less than 0.3% of the total fecal microbiota.41In a recent meta-
genomic study,14the numerical abundance of fungi in canine fecal samples was esti-
mated to be approximately 0.01% of obtained sequences. A similar abundance was
observed in a metagenomic analysis of feline feces.34
Archaea are evolutionarily distinct from bacteria and eukaryotes, and are classified as
the third domain of life. Archaea are obligate anaerobes. They are part of the normal
Predominant fungal families identified in feces of 12 dogs
Fungal FamilyMean of Total Fungal Sequences (%)Number of Dogs Positive
Hypocreaceae 1.78 6
Data was obtained using high-throughput pyrosequencing of the fungal 18S rRNA gene.
Abbreviation: N/A, not applicable.
Intestinal Microbiota of Dogs and Cats
intestinal flora in ruminants and have also been characterized in human intestinal
samples, with Methanobacteria being the predominant form.42The role of archaea
in gastrointestinal health is unclear. Hydrogen is an end product generated by other
intestinal microbes as a result of microbial fermentation and is metabolized by metha-
nogens and sulfate-reducing bacteria (SRB), which produce methane and hydrogen
sulfite, respectively. Hydrogen consumption by methanogens and SRB is an important
scavenging pathway. An abnormal accumulation of hydrogen would inhibit further
microbial fermentation, resulting in a decreased production of short-chain fatty acids.
An imbalance of SRB to methanogens may result in increased production of hydrogen
sulfite, which has the potential to damage epithelial cells.43Initial studies have
revealed a higher abundance of sulfite-producing bacteria in the colon of cats with
inflammatory bowel disease (IBD).8
In a comparative 16S rRNA gene analysis with universal archaeal primers, 2
archaeal phyla were observed in the intestine of dogs and cats: Crenarchaeota and
Euryarchaeota (Suchodolski and colleagues, unpublished data, 2010). Similar to
humans, Methanobacteria (ie, Methanosphaera, Methanobrevibacter) were the most
abundant archaeal class (Box 1). Recent metagenomic studies in fecal samples of
Archaeal genera identified in canine and feline fecal samples by 16S rRNA gene sequencing
or metagenomic approaches
Archaeal genera identified in canine and feline fecal samples
dogs and cats revealed the numerical abundance of archaea as 1.1% of total
microbiota.14Methanogens were the most abundant and diverse group.
Because of the heterogeneity of viruses (ie, DNA viruses, RNA viruses, ssDNA viruses),
an approach with universal primers, the preferred method for bacteria, archaea, and
fungi, is not possible. Therefore, it remains challenging to characterize the viral
communities present in the intestine of dogs and cats. Reported viral phylotypes
include rotavirus, coronavirus, parvovirus, norovirus, astrovirus, distemper virus,
and paramyxovirus.44–46The coinfection rate with multiple viruses is suspected to
be low. In a recent study using electron microscopy, only 6.5% of 935 evaluated fecal
samples contained more than 1 virus.44However, recent metagenomic studies in
humans revealed a highly diverse viral community in the gastrointestinal tract, with
several hundred different genotypes, with the vast majority of these genotypes repre-
senting bacteriophages.47New metagenomic studies have described dsDNA viruses
in fecal samples of dogs and cats.14,34Approx. 0.38% of all obtained sequences rep-
resented dsDNA viruses, with the vast majority representing bacteriophages. Future
studies will require more detailed characterization of the viral metagenomes for better
understanding of their contributions to gastrointestinal health and disease.
Although molecular-phylogenetic and metagenomic studies have brought insight into
the complexity of gut microbes, the medical importance of other members of the intes-
tinal ecosystem, such as fungi, archaea, and viruses, needs to be further evaluated.
New technological advances (ie, high-throughput sequencing techniques) will allow
not only exploring the presence of microbes in the GI tract but also their metabolic
functions. These approaches may yield a better understanding of microbial-host rela-
Intestinal microbiotaCollection of all microorganisms residing in the GI tract
Intestinal microbiome The collection of all microbial genes in the GI tract
PhylotypeA phylotype defines a microbe by its phylogenetic relationship to
other microbes. In molecular studies, a phylotype is defined as an
organism that is different from all other organisms at a specific
cutoff (for example: 95%, 97%, or 99% genetic similarity for
genus, species or strain, respectively).
Metagenomics The metagenome is defined as the collection of all host and microbial
genes in the GI tract. In metagenomics, DNA extracted from
intestinal samples is sequenced randomly (ie, without
amplification of specific genes), which provides characterization of
all genes (host and microbial) present in the sample, providing
a snap shot of the functional property of the metagenome.
TranscriptomicsThe meta-transcriptome is defined as the collection of all expressed
host and microbial genes in the GI tract. In transcriptomics, mRNA
extracted from intestinal samples is sequenced randomly (ie,
without amplification of specific genes), which provides
characterization of expressed genes present in the sample.
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