Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens

Authors: CAMPOS, PHILIP - Orise Fellow; Miska, Kate; Jenkins, Mark; Yan, Xianghe; Proszkowiec-Weglarz, Monika

Submitted to: Frontiers in Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/27/2023
Publication Date: 3/20/2023
Citation: Campos, P.M., Miska, K.B., Jenkins, M.C., Yan, X., Proszkowiec-Wegla, M.K. 2023. Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens. Frontiers in Physiology. 14:1147579. https://doi.org/10.3389/fmicb.2023.1147579.
DOI: https://doi.org/10.3389/fmicb.2023.1147579

Interpretive Summary: Chickens provide a nutritious and relatively inexpensive source of meat, and the poultry industry has been expanding worldwide. However, challenges are encountered when chickens are grown intensively in large numbers. Microorganisms which typically do not cause issues when chickens are grown in small numbers can become problematic when chickens are grown on a large scale. One such disease is caused by several species of Eimeria which infects the gastrointestinal tract of chickens. In modern day farming operations these parasites cause coccidiosis, and the infection cause decrease in weight, diarrhea, loss in appetite, and sometimes even death. Though usually not deadly, coccidiosis causes losses in profits to poultry farmers. In the past, coccidiosis was treated primarily with anti-microbials, however, the use of these have been withdrawn. The need for identifying novel agents which might have anti-coccidial activity has driven coccidia related research. Because Eimeria infects the gastrointestinal tract, we have studied its effects on the microbiome (bacterial species) which resides in the gut. In this study, chickens were infected with Eimeria acervulina, and parts of the upper small intestine (duodenum and jejunum) were taken at six time points for microbiome analysis. Populations of bacteria that were attached to the gut or were present in the gut contents were analyzed separately. The bacterial sequences showed that bacteria the are attached to the wall of the intestine are different that those present in the contents of the gut. The biggest changes in the bacteria composition were centered around the peak of the infection (around seven days), when damage to the intestine is greatest. We also found that species of bacteria that are capable of making and secreting short chain fatty acids were affected by Eimeria infection. Short chain fatty acids are very important molecules because they have anti-inflammatory properties and have been shown to reduce the severity of Eimeria infection. It is possible that by decreasing the bacteria that produce short chain fatty acids, the Eimeria infection has more severe effects on the chicken. More work needs to be carried out on the effect of microbiome changes during Eimeria infection, as well as the effect of short chain fatty acids on the course of infection, however these small molecules might represent alternative therapies to anti-microbials.

Technical Abstract: The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.