Abstract
Necrotic enteritis (NE), an economically devastating disease of poultry caused by pathogenic Clostridium perfringens, is known to induce small intestinal lesions and dysbiosis. However, the intestinal microbes that are associated with NE severity are yet to be characterized. Here, we investigated the link between the ileal microbiota and disease severity in a chicken model of clinical NE using 16S rRNA gene sequencing. Our results indicated that richness and Shannon Index of the ileal microbiota were drastically reduced (p<0.01) as NE was exacerbated. While the relative abundance of C. perfringens increased from 0.02% in healthy chickens to 58–70% in chickens with severe infection, a majority of the ileal microbes were markedly diminished, albeit varying in their sensitivity to NE. Compositionally, a large group of ileal microbes showed a significant correlation with NE severity. Firmicutes, such as group A and B Lactobacillus, Lactobacillus reuteri, Subdoligranulum variabile, Mediterraneibacter, and Staphylococcus as well as two genera of Actinobacteria (Corynebacterium and Kocuria) and two highly related Cyanobacteria were progressively declined as NE was aggravated. Other Firmicutes, such as Weissella, Romboutsia, Kurthia, Cuneatibacter, Blautia, and Aerococcus, appeared much more sensitive and were rapidly abolished in chickens even with mild NE. On the other hand, Enterococcus cecorum and two Escherichia/Shigella species were only enriched in the ileal microbiota of chickens with extremely severe NE, while several other species such as Streptococcus gallolyticus and Bacteroides fragilis remained unaltered by NE. Functionally, secondary bile acid biosynthesis was predicted to be suppressed by NE, while biosynthesis of aromatic and branched-amino acids and metabolism of a majority of amino acids were predicted to be enhanced in the ileum of NE-afflicted chickens. These intestinal microbes showing a strong correlation with NE severity may provide important leads for the development of novel diagnostic or therapeutic approaches to NE and possibly other enteric diseases.
Highlights
Necrotic enteritis (NE), caused by Clostridium perfringens, is one of the most economically significant enteric diseases in poultry, resulting in an annual loss of approximately $6 billion to the global poultry industry (Wade and Keyburn, 2015)
After assessing relative and absolute changes in the ileal microbiome following infection, we have revealed for the first time how relative abundances of most bacteria were altered in response to NE and how dysbiosis became more pronounced as NE was exacerbated
We demonstrated for the first time a microbiota signature of disease severity-dependent reduction of a majority of commensal bacteria in the ileum of chickens in response to NE
Summary
Necrotic enteritis (NE), caused by Clostridium perfringens, is one of the most economically significant enteric diseases in poultry, resulting in an annual loss of approximately $6 billion to the global poultry industry (Wade and Keyburn, 2015). NE is a multifactorial disease, and a coccidial infection is an important predisposing factor by damaging intestinal epithelial integrity and facilitating C. perfringens colonization and translocation (Shojadoost et al, 2012; Moore, 2016). In the ileum or cecum of NE-infected chickens, lactobacilli were reduced in some studies (Zhang et al, 2018; HernandezPatlan et al, 2019; Yang et al, 2019), but enriched (Lin et al, 2017; Latorre et al, 2018; Xu et al, 2018) or unaltered (Bortoluzzi et al, 2019; Kiu et al, 2019; Lu et al, 2020) in others. There is a need to analyze the chicken microbiota separately according to their disease severities and more importantly, examine whether and how the intestinal microbiota are influenced by the severity of NE
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