From the Editor

Gut microbiota, diet, and health:

Application to livestock and companion animals
Kelly S. Swanson
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA

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Gastrointestinal (GI) microbes play a fundamental role in the health in newfound knowledge in the field. A majority of the progress initially
and disease of animals and humans, participating in immune system devel- came from large international microbiome projects such as the Human
opment, production of bioactive compounds, harvesting energy, and many Microbiome Project (HMP; http://www.hmpdacc.org) and the Metage-
other processes. For decades, the microbiology field was hampered by the nomics of the Human Intestinal Tract (MetaHIT; http://www.metahit.eu).
lack of research tools and an inability to culture and study the majority Initial phases of these projects produced reference genomes and estab-
of microbes present in the GI tract. With the advent of high-throughput lished a framework for subsequent metagenomic analysis and microbiome
DNA-based sequencing methods, coupled with new bioinformatic devel- structure and function studies. These large, multifaceted projects laid the
opments that allow for the identification and characterization of microbes foundation for future microbiome studies that could be conducted by large
and their genes (microbiome) in and on the body, there has been an upsurge and small research groups alike and applied to many scientific realms.
The buzz surrounding the microbiome field has led to significant re-
© Swanson search investments by federal agencies, private foundations, and industry.
doi:10.2527/af.2016-0027 Recent microbiome studies in humans have not only associated micro-

4 Animal Frontiers
biota with GI diseases (Dicksved et al., 2008), but also with a wide range
of other diseases, including obesity (Ley, 2010), diabetes (Larsen et al.,
2010), and allergies (Round and Mazmanian, 2009). A similar invest-
ment has been made into livestock and companion animal species. This
research is providing a better understanding of the taxonomy, dynamics,
and functions of GI microbial communities, the relationships between mi-
crobial members, the substances produced and consumed by microbes,
the influence of environmental factors on microbial activity, microbe–host
interactions, and the differences between healthy and diseased animal
populations. Most of this work has animal health implications. Given the
exchange of microbes among humans, pets, and livestock, however, such
research may have relevance to human health as well.
This issue of Animal Frontiers explores the importance of the GI mi-
crobiota of several livestock and companion animal species as well as

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humans, with application to host metabolism, growth performance, and
overall health. Depending on the situation, GI microbiota may enhance or
hinder performance and/or host health. While ruminants and large herbi-
vores rely heavily on microbial fermentation to meet energy and nutrient
needs, the resources required to protect the body from pathogenic bacteria
Source: © 2015 Ronnachai Palas/stock.adobe.com
and the toxins they may produce can be quite costly. To ease this burden
on the body, sub-therapeutic antibiotic growth promoters have been ef-
crobe symbiosis for decades. Loor et al. (2016) discuss the dietary impacts
fectively used in the livestock industry for more than 60 years. Due to
on rumen microbiota, with application to both beef and dairy production.
the concerns over antibiotic-resistant bacteria and possible transmission
Given the highly-fibrous nature of their diet, the host–microbe symbio-
to humans, medicated feeds have been phased out in Europe and are now
sis that exists in ruminants is crucial for meeting energy and essential
being phased out in the US. This issue begins with Cox (2016), who dis-
nutrient needs. Forage quality, forage:concentrate ratios, and ionophores
cusses the use of sub-therapeutic antibiotic growth promoters in livestock
have long been studied to improve productive efficiency and growth per-
production, including the reasons for their use and the concerns that come
formance. Those relevant topics and specific topics of interest, including
with them. In addition to a brief history of their use in livestock species,
dairy calves, transition (peripartum) cows, subacute ruminal acidosis, and
recent research using rodent models is presented and discussed. This work
milkfat depression, were discussed. Microbial methodological advance-
shows that the timing of antibiotic administration may shape host me-
ments and how a systems biology approach may be used to fill in knowl-
tabolism and have lasting effects over generations. The article ends with
edge gaps, also were highlighted.
its application not only to food animals, but human health, and includes
The nutritional strategies of non-ruminants differ substantially from
economic considerations and alternative strategies for growth promotion.
that of ruminants, but the GI microbiota are still of critical importance
Whether it is due to its relevance to global warming, the energy harvest
when it comes to the immunological development, physiological func-
of livestock species, or human gastrointestinal disease, methane production
tion, and nutritional and health status. Fouhse et al. (2016) discuss the
is always a popular topic of debate. Hoedt et al. (2016) review the impor-
importance of the GI microbiota in regards to swine health and produc-
tance of methane production in the agricultural, environmental, and bio-
tion. The increased emphasis on the GI microbiota comes at an interest-
medical sectors of society. Although the global demand for milk and meat
ing time in the history of swine production, a time when medicated feeds
continues to increase, with beef and dairy cattle contributing greatly in this
have recently been or are currently being phased out throughout the world
regard, the environmental impacts of these industries are highly scrutinized.
and a wide variety of highly fibrous byproduct feeds are available for
The production of methane, which is the principal method by which rumi-
use. Many of the great challenges facing today’s swine producers, such as
nant livestock dispose of hydrogen, is often the reason cattle are painted in
minimizing dysbiosis and post-weaning diarrhea, maximizing growth per-
such a negative light when it comes to the environment. Although agricul-
formance and feed efficiency, and maintaining human food safety, pertain
ture’s contribution to greenhouse gases is typically overblown, researchers
to the GI microbiota and their management and/or manipulation. Potential
are exploring novel approaches to manage livestock methane emissions.
solutions may include prebiotics and dietary fibers, probiotics/direct-fed
Because energy is lost through the production of methane, these strategies
microbials, and possibly others but require significant investment in re-
may not only reduce the carbon footprint of ruminant livestock production,
gards to research and may be met with stringent regulatory agencies in
but may increase productive efficiency. Methanogens also are present in
many countries around the world.
the human GI tract and have been associated with several disease states,
Dogs and cats evolved as members of Carnivora and have tradition-
including constipation, colorectal cancer, and inflammatory bowel diseases.
ally relied on high-protein, high-fat diets containing relatively low fiber
Looking forward, a comparative research approach that considers a variety
concentrations. Despite having a relatively simple GI tract designed to
of animal species, dietary strategies, and human disease conditions, may
digest such diets, a rich microbial community exists. Today’s pet dogs and
have wide-reaching implications to animal agriculture and human health.
cats live in close proximity to humans and have similar environmental
Despite the recent excitement surrounding the GI microbiome as it
exposures, serving as potential vectors for pathogen exposure. Dogs and
pertains to human health, livestock producers, ruminant nutritionists, and
cats are also afflicted by many of the same complex diseases present in
rumen microbiologists alike have appreciated the importance of host–mi-

July 2016, Vol. 6, No. 3 5

humans, including obesity, diabetes, inflammatory bowel diseases, and measured in terms of growth or feed efficiency as it is for the livestock spe-
cancers, all of which may be influenced by diet and GI microbiota. Given cies mentioned above, numerous stressors and challenges exist. Laminitis,
their proximity to humans, similar disease incidence and etiology, and travel stress, and GI diseases such as colic, all of which may contribute to or
unique metabolism, microbiome research in dogs and cats may not only be affected by GI microbiota, are major sources of morbidity and mortality
lead to improved pet nutrition and veterinary care, but may increase our in horses and economically important to the equine industry. Gastrointesti-
understanding of host–microbe interactions, with relevance to human me- nal microbiota populations are known to change with increased age, some-
tabolism and diseases and public health at large. Blake and Suchodolski thing that is shared with dogs, cats, and humans, but rarely of concern in the
(2016) review the existing microbiome literature pertaining to dogs and production livestock species. Probiotics and other medications have been
cats. Like other host species, the composition and activities of the canine used to improve or stabilize equine GI microbiota populations, but results
and feline GI microbiota are impacted by dietary macronutrient profile, have been inconsistent and may soon be scrutinized by regulatory bodies.
including protein:carbohydrate ratio and the type and amount of dietary fi- In closing, this timely issue of Animal Frontiers focuses on the char-
ber. As is done in non-ruminant livestock species, the inclusion of specific acterization and importance of the GI microbiota in several livestock
ingredients such as prebiotics and probiotics is common as a means to and companion animal species as well as in humans, touching on several
improve gastrointestinal health but come with mixed results experimen- important agricultural, environmental, and biomedical issues. The micro-

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tally. Finally, the GI microbiota shifts associated with disease have been biome field is a buzz, and for good reason, but it is still in its infancy
studied recently, with many of the phylogenetic and functional changes stage. Given the financial investments being made by federal agencies,
of dogs and cats being similar to that noted in humans, suggesting a core private foundations, and industry, and the high-throughput and molecular
microbiome among host species. experimental tools and bioinformatics strategies that are now available, it
The issue wraps up with a review of a host species viewed to be both should continue to be an exciting field
livestock and companion animal, depending on the audience. Venable to watch in the coming years.
et al. (2016) discusses the recent microbiome literature applied to equine
health and disease. Horses rely heavily on microbial fermentation to
meet energy needs but are hindgut fermenters that have an enlarged
cecum for this purpose. Despite the importance of the GI micro-
biota to the horse, a relatively small number of studies have
been performed in this species using high-throughput se-
quencing techniques. The impact of dietary ingredient and/
or nutrients on GI microbiota have been measured but have
typically focused on fecal populations that may or may
not have relevance to the composition and activity in the
cecum. Although performance in horses is typically not

Source: © 2015 Ronnachai Palas/stock.adobe.com

6 Animal Frontiers
 Horse with fistula (source: ©

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2015 Kelby Fenton).

About the Author

Kelly S. Swanson received his Ph.D. in nu-
tritional sciences at the University of Illinois Literature Cited
at Urbana-Champaign (UIUC) in 2002. Fol- Blake, A.B., and J.S. Suchodolski. 2016. Importance of gut microbiota for the health
lowing post-doctoral training in functional and disease of dogs and cats. Anim. Front. 6(3):37–42.
genomics, he became Assistant Professor Cox, L.M. 2016. Antibiotics shape microbiota and weight gain across the animal king-
at UIUC in 2004 and has since been pro- dom. Anim. Front. 6(3): 8–14.
moted to Associate (2009) and Full Profes- Dicksved, J., J. Halfvarson, M. Rosenquist, G. Järnerot, C. Tysk, J. Apajalahti, L. Eng-
sor (2014). His lab studies the effects of strand, and J.K. Jansson. 2008. Molecular analysis of the gut microbiota of identical
nutritional intervention on canine and feline twins with Crohn’s disease. ISME J. 2:716–727.
health, identifying mechanisms by which Fouhse, J.M., R.T. Zijlstra, and B.P. Willing. 2016. The role of gut microbiota in the
health and disease of pigs. Anim. Front. 6(3):30–36.
nutrients impact gene expression and host
Hoedt, E.C., P.O. Cuiv, and M. Morrison. 2016. Methane matters: From blue-tinged
physiology, with emphasis on gastrointesti- moos, to boozy roos, and the health of humans too. Anim. Front. 6(3):15–21.
nal health and obesity. He has established an Larsen, N., F.K. Vogensen, F.W. van den Berg, D.S. Nielsen, A.S. Andreasen, B.K.
internationally recognized research program, highlighted by more than $9 mil- Pedersen, W.A. Al-Soud, S.J. Sørensen, L.H. Hansen, and M. Jakobsen. 2010. Gut
lion in research support, 90 invited lectures in 11 countries around the world, 135 microbiota in human adults with type 2 diabetes differs from non-diabetic adults.
peer-reviewed publications, and 11 research and teaching awards. He has trained PLoS ONE 5:e9085.
24 graduate students and post-doctoral fellows, hosted 11 international visiting Ley, R.E. 2010. Obesity and the human microbiome. Curr. Opin. Gastroenterol. 26:5–11.
scholars/interns, and mentored 23 undergraduate research projects. Dr. Swanson Loor, J.J., A. Elolimy, and J.C. McCann. 2016. Dietary impacts on rumen microbiota in
teaches three courses pertaining to companion animal nutrition to veterinary, un- beef and dairy production. Anim. Front. 6(3):22–29.
Round, J.L., and S.K. Mazmanian. 2009. The gut microbiota shapes intestinal immune
dergraduate, and graduate students annually and serves on many committees at
responses during health and disease. Nat. Rev. Immunol. 9:313–323.
the departmental, college, and campus level, including the Institutional Animal Venable, E., J. McPherson, J. Francis, and S. Bland. 2016. Role of the gut microbiota in
Care and Use Committee. Correspondence: ksswanso@illinois.edu equine health and disease. Anim. Front. 6(3):43–49.

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