Identification of an intestinal microbiota signature associated with the severity of necrotic enteritis

Authors: YANG, QING - Oklahoma State University; LIU, JING - Oklahoma State University; Robinson, Kelsy; WHITMORE, MELANIE - Oklahoma State University; STEWART, SYDNEY - Oklahoma State University; ZHANG, GUOLONG - Oklahoma State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary: Necrotic enteritis (NE) is an economically devastating disease of poultry that cause small intestinal lesions, growth retardation, reduced feed efficiency and high mortality. NE is associated with disruption of the intestinal bacterial population, known as the microbiota. However, the role of the intestinal fungi, known as the mycobiota, in disease severity is unknown. Here, we examined the association between the ileal mycobiota and disease severity in a chicken model of clinical NE using ITS2 amplicon sequencing. Our results revealed that the total fungal population progressively declined as NE was exacerbated, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE. Compositionally, among 30 most abundant fungal features, 11 were diminished and 7 were enriched, while 12 remained largely unchanged in response to NE. Dysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry.

Technical Abstract: Intestinal microbiota is critical for maintaining animal health and homeostasis. However, involvement of the fungal community, also known as the mycobiota, in animal health and disease is poorly understood. This study was aimed to examine the association between the intestinal mycobiota and the severity of necrotic enteritis (NE), an economically significant poultry disease. A total of 90 day-of-hatch Cobb broilers were infected with Eimeria maxima on day 10, followed by an oral challenge with Clostridium perfringens on day 14 to induce NE, while another 10 broilers were served as mock-infected controls. On day 17, the lesions in the jejunum were scored, and the ileal digesta were subjected to DNA isolation and real-time PCR quantification of toal bacterial and fungi populations. Internal transcribed spacer 2 (ITS2) amplicon sequencing was also performed to profile the ileal mycobiota composition. Changes in the ileal mycobiota in response to NE were investigated. Spearman correlation analysis was further conducted to identify the correlations between relative abundances of individual ileal fungi and the severity of NE. While the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population was progressively declined as NE was exacerbated, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE (P = 0.06). Compositionally, among 30 most abundant fungal features, 11 were diminished and 7 were enriched (P < 0.05), while 12 remained largely unchanged in response to NE (P > 0.05). Multiple Wallemia and Aspergillus species were markedly diminished in response to NE (P < 0.05) and also showed a significant negative correlation with NE severity (P < 0.05). Dysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry.