Dissection of the cecal microbial community in chickens after Eimeria tenella infection

Abstract

Background: Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

Methods: We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted.

Results: We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection.

Conclusions: Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.

Keywords: 16S rRNA; Alternative therapeutics; Cecal microbiota; Chicken coccidiosis; Eimeria tenella.

Fig. 1

Histopathological images of the cecum in AA broiler chickens from each group. a Section of the cecum from the uninfected chickens. b Section of the cecum from the 105 hpi chickens in group M. c Section of the cecum from the 144 hpi chickens in group G; visible gametocytes are indicated by arrows. d Section of the cecum from the 214 hpi chickens in group O; visible oocysts are indicated by arrows. Abbreviations: EC, epithelial cell; LP, lamina propria; SM, submucosa. Magnifications: ×200 and ×400. Scale-bars: 200 μm

Fig. 2

Curves for the OTUs obtained from 20 samples. a Good’s coverage analysis of sequencing data. b Rarefaction curves. c Shannon-Wiener curves. d Species accumulation curves. Abbreviations: C, samples from the control group; M, samples from the merozoite reproduction group; G, samples from the gametocyte reproduction group; O, samples from the oocyst shedding group

Fig. 3

Analysis of alpha-diversity in the four experimental groups. Chao1 (a) and observed number of species (b) were used as richness estimators. Shannon-Wiener index (c) was used as a diversity estimator

Fig. 4

Principal coordinates analysis of the structure of the gut microbiota. Abbreviations: C, samples from the control group; M, samples from the merozoite reproduction group; G, samples from the gametocyte reproduction group; O, samples from the oocyst shedding group

Fig. 5

The relative abundances of the cecal microbiota at the phylum (a) and genus (b) levels. The relative abundances of the gut bacteria presented here were calculated by averaging the data obtained from the five replicates within each group. Abbreviations: C, control group; M, merozoite reproduction group; G, gametocyte reproduction group; O, oocyst shedding group

Fig. 6

Heatmap plot depicting the relative abundance of each bacterial genus. Abbreviations: C, control group; M, merozoite reproduction group; G, gametocyte reproduction group; O, oocyst shedding group

Fig. 7

Cladogram of the LEfSe analysis of the gut microbiota in different groups. The microbial compositions were compared at different evolutionary levels

Fig. 8

LDA scores obtained from the LEfSe analysis of the gut microbiota in different groups. An LDA effect size of greater than 3 was used as a threshold for the LEfSe analysis. Abbreviations: C, control group; M, merozoite reproduction group; G, gametocyte reproduction group; O, oocyst shedding group

Fig. 9

Eimeria tenella infection significantly decreased the abundances of Ruminococcaceae UCG-013 spp. (a), Romboutsia spp. (b) and Shuttleworthina spp. (c). Abbreviations: C, control group; M, merozoite reproduction group; G, gametocyte reproduction group; O, oocyst shedding group. The solid lines represent the mean values of relative abundance and the dotted lines represent the median values

Fig. 10

Eimeria tenella infection significantly increased the abundance of Enterococcus spp. (a), Streptococcus spp. (b) and Bisophila spp. (c). Abbreviations: C, control group; M, merozoite reproduction group; G, gametocyte reproduction group; O, oocyst shedding group. The solid lines represent the mean values of relative abundance and the dotted lines represent the median values

Fig. 11

Co-occurrence network diagram of Firmicutes and Bacteroidetes