January 13, 2014

Implications of the Microbiome and Metagenomics for Animal Sciences


By Larry Reynolds

The microbiome has received increasing attention in the last decade. As evidence of this, the number of papers with ‘microbiome’ or ‘metagenomic’ in the title or abstract has increased from 178 in 2004 to 3549 in 2013, according to PubMed. Animal sciences have not been immune to this interest in metagenomics – in the last three years, eleven articles related to microbiome or metagenomics have been published in the Journal of Animal Sciences, and two more will appear in the upcoming February issue.

The microbiome constitutes the repertoire of genes contained in the microbiota that inhabit the body surfaces of all vertebrate organisms, including animals.1 Similarly, the metagenome comprises all genetic material contained an environmental sample, including the various environmental ‘niches’ present in a single organism. For the most part, the microorganisms that inhabit vertebrates have a symbiotic relationship with their host, and they are especially abundant in the gut.1,2,3 More recently, bacterial DNA has also been found within host tissues including liver, adipose, and blood.3

The existence and potential importance of the microbiota to animal health has long been recognized, and rumen microbiology has been especially important in this regard.4 “Ruminant nutritionists and microbiologists have known [about the importance of the gut microbiota] for decades. You are not only feeding and dealing with the host when it comes to energy harvest, disease incidence, inflammation, etc., but with the microorganisms that inhabit the gut (and the rest of the body) too,” commented Dr. Kelly Swanson of the University of Illinois at Urban-Champaign and expert in metagenomics. However, improved methodologies, for example high throughput sequencing, advanced bioinformatics, and the application of ecological theory to individual organisms,5-10 have recently brought surprising new insights. These insights include the observation that the microbiota exist in far greater numbers, in terms of both cells and genes, than the host’s own cells and genes. For example, it is estimated that bacterial cells in and on the human body outnumber host cells by 10-fold.6,11 In addition, it has been estimated that 36% of the small molecules found in human blood originate in the gut microbiome.8

In addition, using various animal models, researchers have shown that the microbiota are strongly influenced by diet, both short and long-term (David et al., 2013).12-15 Perhaps more importantly, the gut microbiota has been shown to alter metabolism and decrease the risk of obesity in a mouse model.16 In addition, the microbiota interact with the host immune system from birth.1,3,17 Moreover, these interactions may influence such things as intestinal development and whole-organism metabolism. The microbiota also have been shown to influence host behavior, perhaps by altering metabolism, and to affect drug metabolism in the host.18-20 These observations have led some to suggest that influencing the microbiome may be an important therapeutic approach to many non-communicable diseases, which together now constitute the major cause of disease-related deaths worldwide (http://www.who.int/nmh/events/2012/discussion_paper2_20120322.pdf).8,21-24

Scientific and Media Contact:
Larry Reynolds
ASAS Media Communications


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