Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets.

Gresse Gresse,Blanquet-Diot Blanquet-Diot,Chaucheyras Durand Chaucheyras Durand,Dunière Dunière,Forano Forano

doi:10.3390/microorganisms7090343

Gresse Gresse, Blanquet-Diot Blanquet-Diot + Show 3 more

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https://doi.org/10.3390/microorganisms7090343

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Abstract

Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions.

Highlights

In intensive swine production, early weaned piglets encounter social, environmental and dietary stresses generated by handling, transport, mixing litters, separation from the mother and the transition from a milk-based diet to a solid-based diet [1]
Weaning transition in the piglet is associated with diarrhea and enteric infections which are the main causes of piglet death [6] and could be a direct consequence of microbial shifts observed at this critical period
The main feature reported in the present study was a clear separation between the upper part and the lower part of the piglet gastrointestinal tract (GIT), suggesting that characterization of fecal microbiota could be inadequate to investigate post-weaning infections etiology due to the fact numbers of pathogen infection or multiplication sites are located in the jejunum, ileum, or the colon segments

Summary

Introduction

Early weaned piglets encounter social, environmental and dietary stresses generated by handling, transport, mixing litters, separation from the mother and the transition from a milk-based diet to a solid-based diet [1]. A few studies describe the microbial populations longitudinally harbored in the weaning piglet GIT using next-generation sequencing techniques and revealed distinct location-specific differences in microbial composition inside the different gut compartments [16,17,18,19,20]. Among these studies, four out of five used animals raised in a controlled laboratory environment [16,17,18]. As microbial population colonizing the intestine is impacted by the environment, including the use of commercial pigs in such research is of great interest to be representative of swine industry conditions

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