Microbial Diversity and Community Variation in the Intestines of Layer Chickens

Abstract

The intestinal microbiota is increasingly recognized as an important component of host health, metabolism and immunity. Early gut colonizers are pivotal in the establishment of microbial community structures affecting the health and growth performance of chickens. White Lohmann layer is a common commercial breed. Therefore, this breed was selected to study the pattern of changes of microbiota with age. In this study, the duodenum, caecum and colorectum contents of white Lohmann layer chickens from same environment control farm were collected and analyzed using 16S rRNA sequencing to explore the spatial and temporal variations in intestinal microbiota. The results showed that the diversity of the microbial community structure in the duodenum, caecum and colorectum increased with age and tended to be stable when the layer chickens reached 50 days of age and the distinct succession patterns of the intestinal microbiota between the duodenum and large intestine (caecum and colorectum). On day 0, the diversity of microbes in the duodenum was higher than that in the caecum and colorectum, but the compositions of intestinal microbes were relatively similar, with facultative anaerobic Proteobacteria as the main microbes. However, the relative abundance of facultative anaerobic bacteria (Escherichia) gradually decreased and was replaced by anaerobic bacteria (Bacteroides and Ruminococcaceae). By day 50, the structure of intestinal microbes had gradually become stable, and Lactobacillus was the dominant bacteria in the duodenum (41.1%). The compositions of dominant microbes in the caecum and colorectum were more complex, but there were certain similarities. Bacteroides, Odoribacter and Clostridiales vadin BB60 group were dominant. The results of this study provide evidence that time and spatial factors are important factors affecting the intestinal microbiota composition. This study provides new knowledge of the intestinal microbiota colonization pattern of layer chickens in early life to improve the intestinal health of layer chickens.

Keywords: 16S rRNA; diversity and community; intestinal microbiome; white Lohmann layer chickens.

Figure 1

Longitudinal exploration of the microbiome in layer chickens. The alpha diversity indices (Chao1 and Shannon) with age across layer chickens in the duodenum, caecum and colorectum.

Figure 2

β-Diversity of the microbiota in all types of samples. Principal coordinates analysis (PCoA) plot of the Bray-Curtis dissimilarity of the bacterial communities from the layer chicken. (a) Total sample, (b) Duodenum, (c) Caecum and (d) Colorectum. Each point represents a different sample calculated using Bray-Curtis distance according to the amplicon sequence variant (ASV) compositions and abundances.

Figure 3

Relative abundance of the phylum in different types of samples. The upper part of the circle represents different days; the lower part indicates the relative abundance of microorganisms at the phylum level and the area size indicates the relative abundance, duodenum (a), caecum (b) and colorectum (c) of layer chickens.

Figure 4

Relative abundance of the genus in different types of samples. Stacked bar chart displaying the change in the average relative abundance of the top 15 genera in the duodenum (a), caecum (b) and colorectum (c) of layer chickens.

Figure 5

Bacterial taxonomic biomarkers for defining different intestinal microbiota maturation in layer chickens throughout the first 57 days of life. Heat map displaying the average relative abundance of stage-associated microbiota in duodenum (a), caecum (b) and colorectum (c) identified by LEfSe (linear discriminant analysis (LDA) > 2) in the test trial. The maturity index for the duodenum, caecum and colorectum at a given time point was calculated through the random forest model: the predicted time point was used as the Y-axis coordinate to represent the degree of maturity, while the actual time point was used as the X-axis coordinate. The temporal patterns of intestinal maturation were compared among the duodenum (d), the caecum (e) and the colorectum (f), which indicated intestinal microbiota maturation at 50 days.

Figure 6

Network of co-occurring genera within layer chicken intestines. The important correlative associations between genera were determined based on the Spearman’s algorithm. The nodes represent the genera, and the edges represent strong and significantly positive (red) or negative (green) correlations between genera. (a): Duodenum, (b): Caecum, (c): Colorectum.

Figure 7

Functional predictions for the microbiota in different samples. The result of the LEfSe analysis is based on the PICRUSt dataset, which was conducted to identify EC that differentiated functional enzymes between the caecum (a) and colorectum (b) at different time points. Modules with a linear discriminant analysis (LDA) score > 2.0 are plotted.