Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation

Sarah Haberecht,T T Hao Van,Yadav S Bajagai,Robert J Moore,Dragana Stanley

doi:10.1186/s13568-020-01077-5

Sarah Haberecht, T T Hao Van + Show 3 more

Open Access

https://doi.org/10.1186/s13568-020-01077-5

Copy DOI

Abstract

Microbial colonisation of the gastrointestinal tract of newly hatched chicks starts at hatch, seeded from the immediate hatching environment, and quickly results in dense colonisation. The role of ecological factors in gut colonisation has been extensively investigated, as well as the role of micro- and macronutrients in supporting and selecting for bacterial species highly adapted for utilising those nutrients. However, the microbial community contained in poultry feed and its influence on colonisation and maturation of gut microbiota has not been directly addressed. In this study, we compared the microbiota found in poultry feed, with the microbiota of ileum, cecum and excreta, to identify substantial overlap in core microbiotas of the compared groups. We then investigated the microbiota present in raw feedstuffs: meat and bone meal, wheat, corn, canola, barley, soybean, millrun, sorghum, poultry oil, oats, limestone and bloodmeal from four geographically distinct feedstuff suppliers. Each of the feedstuffs had diverse microbial communities. The meat and bone meal and bloodmeal samples had the most complex and distinct microbial populations. There was substantial overlap in the phylogenetic composition found in the grain and seed samples: barley, canola, corn, millrun, oats, sorghum, soybean meal and wheat. Issues related to methodology, viability of microbial communities in the gut and feed, and the implications for biosecurity are discussed.

Highlights

Until recent advances in technology allowed us to sequence total DNA from any environmental sample and to identify almost all bacteria including uncultured, our knowledge was limited to a small proportion of bacteria we could grow and investigate using classic microbiology growth methods
The mainstream knowledge on gut microbiota came from human research, it is understood that intestinal bacterial inhabitants of chickens play both similar and poultry-specific, influential roles (Stecher and Hardt 2008; Young 2012; Zhu et al 2002)
This study brings a new dimension to the role of feed in microbiota formation, as a source of colonizing bacteria (Fig. 6)

Summary

Introduction

Until recent advances in technology allowed us to sequence total DNA from any environmental sample and to identify almost all bacteria including uncultured, our knowledge was limited to a small proportion of bacteria we could grow and investigate using classic microbiology growth methods. Instead of taking a fecal sample and pulling out only targeted bacteria on specially selected microbiological plates, we could see thousands of species in a sample and investigate their role in the gut. This revolutionised our knowledge of the intestinal microbiota and its role in health and digestion. The poultry intestinal microbiota has evolved into its present form incorporating many different communities from the environment and the animals and humans they contact This means that the phylogenetic composition of chicken gut microbiota strongly, but not entirely, overlaps with the microbiota of humans and other farmed animals. Chicks are immediately exposed to bacteria different from bacterial communities to those that were selected in chicken guts and historically adapted to chicken as host (Stanley et al 2013)

Methods

Results

Conclusion