Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima)
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animal Husbandry and Tissue Sampling
2.2. Identification of Stem Cells and Morphological Measurements
2.3. DNA Isolation and 16s rRNA Library Preparation
2.4. Bioinformatics and Data Processing
2.5. Statistical Analysis
3. Results
3.1. Parameters Associated with Infection and Growth
3.2. Gut Morphology
3.3. Sequencing Summary
3.4. Alpha and Beta Diversity of the Microbiota of the Small Intestine
3.5. Taxonomy
3.6. Differentially Abundant Taxa
3.7. Analysis of Predicted Functional Processes
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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J-C | J-M | IL-C | IL-M | |
---|---|---|---|---|
Number of samples | 60 | 60 | 60 | 60 |
Raw reads | 6,321,969 | 1,906,686 | 8,520,563 | 3,669,527 |
DADA2 --p-trunc-len-f | 269 | 235 | 269 | 271 |
DADA2 --p-trunc-len-r | 217 | 205 | 229 | 208 |
Reads after DADA2 | 5,212,955 | 1,312,059 | 6,443,444 | 2,663,546 |
Reads after filtering | 5,060,831 | 1,158,586 | 6,434,195 | 2,652,074 |
Reads per sample (range) | 114–256,509 | 81–255,261 | 13,847–257,570 | 197–503,642 |
Mean reads per sample | 84,347 | 19,310 | 107,237 | 44,201 |
Total number of ASVs | 1001 | 1273 | 984 | 1371 |
ASV read length (range) | 269–465 | 234–427 | 269–473 | 271–466 |
Mean ASV read length | 418 | 358 | 420 | 385 |
Sequencing depth | 27,462 | 5658 | 49,158 | 13,067 |
Day Post-Infection Infection Status | BW (kg) | BWG 2 (kg) | FI (kg) | FCR | |
---|---|---|---|---|---|
3 PI | C | 1.12 | 0.23 f | 1.36 | 1.49 c |
IF | 1.17 | 0.22 f | 1.37 | 1.55 c | |
5 PI | C | 1.23 | 0.38 e | 2.40 | 1.58 c |
IF | 1.24 | 0.37 e | 2.30 | 1.57 c | |
7 PI | C | 1.33 | 0.61 d | 3.72 | 1.54 c |
IF | 1.50 | 0.45 e | 3.77 | 2.13 ab | |
10 PI | C | 1.51 | 0.78 c | 5.77 | 1.85 abc |
IF | 2.05 | 0.63 d | 5.51 | 2.27 a | |
14 PI | C | 1.95 | 1.19 a | 7.85 | 1.65 bc |
IF | 2.05 | 1.03 b | 7.27 | 1.79 abc | |
SEM 3 | 0.12 | 0.03 | 0.29 | 0.11 | |
Main effect day PI | |||||
3 PI | 1.15 b | 0.23 e | 1.36 e | 1.52 b | |
5 PI | 1.23 b | 0.37 d | 2.35 d | 1.57 b | |
7 PI | 1.41 b | 0.53 c | 3.75 c | 1.83 ab | |
10 PI | 1.78 a | 0.70 b | 5.64 b | 2.06 a | |
14 PI | 2.00 a | 1.11 a | 7.56 a | 1.72 b | |
SEM 3 | 0.08 | 0.02 | 0.20 | 0.08 | |
Main effect infection status | |||||
C | 1.43 b | 0.64 a | 4.22 | 1.62 b | |
IF | 1.60 a | 0.54 b | 4.04 | 1.86 a | |
SEM 3 | 0.05 | 0.01 | 0.13 | 0.05 | |
Analysis of variance | Probabilities 4 | ||||
Day post-infection × infection status | 0.18 | 0.0053 | 0.82 | 0.0487 | |
Day post-infection | <0.0001 | <0.0001 | <0.0001 | 0.0001 | |
Infection status | 0.0246 | <0.0001 | 0.33 | 0.0015 |
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Miska, K.B.; Campos, P.M.; Cloft, S.E.; Jenkins, M.C.; Proszkowiec-Weglarz, M. Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima). Animals 2024, 14, 2976. https://doi.org/10.3390/ani14202976
Miska KB, Campos PM, Cloft SE, Jenkins MC, Proszkowiec-Weglarz M. Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima). Animals. 2024; 14(20):2976. https://doi.org/10.3390/ani14202976
Chicago/Turabian StyleMiska, Katarzyna B., Philip M. Campos, Sara E. Cloft, Mark C. Jenkins, and Monika Proszkowiec-Weglarz. 2024. "Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima)" Animals 14, no. 20: 2976. https://doi.org/10.3390/ani14202976
APA StyleMiska, K. B., Campos, P. M., Cloft, S. E., Jenkins, M. C., & Proszkowiec-Weglarz, M. (2024). Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima). Animals, 14(20), 2976. https://doi.org/10.3390/ani14202976