Identification of intestinal microbiota and mycobiota signatures associated with the severity of necrotic enteritis

Necrotic enteritis (NE) is known to induce intestinal 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/mycobiota and disease severity in a chicken model of clinical NE using 16S rRNA gene and ITS2 sequencing. Our results indicated that, while the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population progressively declined in exacerbated NE, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. The C. perfringens population was increased from 0.02% in healthy chickens to 58 to 70% in chickens with severe infection, with most the ileal microbes being markedly diminished. Compositionally, a large group of ileal microbes showed a significant positive or negative correlation with NE severity. Firmicutes, such as group A and B Lactobacillus, Lactobacillus reuteri, Subdoligranulum variabile, Mediterraneibacter, and Staphylococcus as well as 2 genera of Actinobacteria (Corynebacterium and Kocuria) and 2 closely 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 2 Escherichia/Shigella species were only enriched in the ileal microbiota of chickens with extremely severe NE. Multiple fungi such as members of the Wallemia and Aspergillus species were obviously diminished in response to NE. Functionally, secondary bile acid biosynthesis was predicted to be suppressed by NE, while biosynthesis of aromatic and branched-amino acids and metabolism of most amino acids were enhanced. 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.

Key Words: necrotic enteritis, microbiome, mycobiome, dysbiosis, Clostridium perfringens.

Presented at the 9th Symposium on Gut Health in Production of Food Animals, St. Louis, USA, 2021. For information on the next edition, click here.