Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics and Approval Statement
2.2. Animal Handling and Sampling
2.3. DNA Extraction, 16S rRNA Gene Amplification and Illumina MiSeq Sequencing
2.4. Bioinformatics and Statistical Analyses
2.5. Co-Occurrence Network Analysis
3. Results
3.1. Sequencing Data and Differences in the Alpha and Beta Diversity
3.2. Gut Microbiota Composition at Phylum Level
3.3. Gut Microbiota Composition at Genus Level
3.4. Correlation between Gut Microbiota and BW
3.5. Analysis of Co-Occurrence Patterns
4. Discussion
4.1. Diversity of Gut Microbiota
4.2. Composition of Gut Microbiota in the Different Sampling Places
4.3. BW-Related Differences of the Gut Microbiota
4.4. Analysis of Co-Occurrence Patterns
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SP | BW | Diversity Indices (Mean) | ||||
---|---|---|---|---|---|---|
OTU | Chao1 | Shannon | Simpson | PD | ||
JC | LBW | 105 | 106 | 2.86 | 0.71 | 38.0 |
HBW | 122 | 122 | 3.17 | 0.72 | 41.8 | |
JM | LBW | 345 | 346 | 5.11 | 0.82 | 101.6 |
HBW | 360 | 361 | 6.45 | 0.97 | 109.2 | |
CC | LBW | 362 | 363 | 6.10 | 0.963 | 97.9 |
HBW | 350 | 351 | 5.98 | 0.955 | 97.5 | |
JC | 111 b | 111 b | 2.08 b | 0.71 b | 39.9 b | |
JM | 345 a | 346 a | 3.97 a | 0.89 a | 105.4 a | |
CC | 355 a | 357 a | 4.18 a | 0.96 a | 97.7 a | |
LBW | 269 | 270 | 3.24 | 0.83 | 79.2 | |
HBW | 272 | 272 | 3.59 | 0.88 | 82.9 | |
Pooled SEM | 23.67 | 23.74 | 0.31 | 0.03 | 6.25 | |
p-Values | SP | <0.001 | <0.001 | <0.001 | <0.001 | <0.001 |
BW | 0.779 | 0.780 | 0.162 | 0.256 | 0.589 | |
SP × BW | 0.860 | 0.863 | 0.247 | 0.311 | 0.891 |
Body Weight | Sampling Place | Mean (BW) | FDR p-Values | |||||
---|---|---|---|---|---|---|---|---|
Jejunal Chymus | Jejunal Mucosa | Caecum Chymus | SP | BW | SP × BW | |||
Actinobacteria | LBW | 2.54 | 1.55 | 0.38 | 1.49 | 0.188 | 0.898 | 0.681 |
HBW | 4.40 | 0.46 | 0.17 | 1.67 | ||||
Mean (SP) | 3.47 | 1.00 | 0.28 | |||||
Bacteroidetes | LBW | 0.38 | 20.83 B | 45.25 | 22.15 B | <0.001 | 0.029 | 0.109 |
HBW | 1.18 | 39.99 A | 51.61 | 30.93 A | ||||
Mean (SP) | 0.78 c | 30.41 b | 48.43 a | |||||
Cyanobacteria | LBW | 4.82 | 0.47 | 0.05 | 1.78 | 0.163 | 0.990 | 0.878 |
HBW | 3.76 | 1.47 | 0.06 | 1.76 | ||||
Mean (SP) | 4.29 | 0.97 | 0.06 | |||||
Deinococcus Thermus | LBW | 0.04 | 0.02 | 0.00 | 0.02 | 0.406 | 0.532 | 0.843 |
HBW | 0.02 | 0.00 | 0.00 | 0.01 | ||||
Mean (SP) | 0.03 | 0.01 | 0.00 | |||||
Epsilonbacteraeota | LBW | 0.00 | 0.00 | 0.00 | 0.00 | 0.567 | 0.525 | 0.580 |
HBW | 0.01 | 0.11 | 0.00 | 0.04 | ||||
Mean (SP) | 0.01 | 0.06 | 0.00 | |||||
Firmicutes | LBW | 88.16 | 74.76 A | 51.77 | 71.57 A | <0.001 | 0.053 T | 0.532 |
HBW | 76.67 | 54.78 B | 46.92 | 59.46 B | ||||
Mean (SP) | 82.42 a | 64.77 b | 49.35 c | |||||
Patescibacteria | LBW | 0.25 | 0.05 | 0.00 | 0.1 | 0.530 | 0.530 | 0.559 |
HBW | 4.03 | 0.12 | 0.00 | 1.38 | ||||
Mean (SP) | 2.14 | 0.09 | 0.00 | |||||
Proteobacteria | LBW | 3.78 | 2.25 | 2.39 | 2.81 | 0.045 | 0.399 | 0.170 |
HBW | 9.88 | 2.72 | 0.98 | 4.53 | ||||
Mean (SP) | 6.83 a | 2.48 b | 1.68 b | |||||
Tenericutes | LBW | 0.01 | 0.08 B | 0.15 B | 0.08 B | 0.056 T | 0.068 T | 0.406 |
HBW | 0.05 | 0.34 A | 0.25 A | 0.21 A | ||||
Mean (SP) | 0.03 b | 0.21 a | 0.20 a | |||||
B/F Ratio | LBW | 0.00 | 0.32 B | 0.89 | 0.40 B | <0.001 | 0.029 | 0.188 |
HBW | 0.02 | 0.76 A | 1.13 | 0.64 A | ||||
Mean (SP) | 0.01 c | 0.54 b | 1.01 a |
Genus | Body Weight | Sampling Place | Mean (BW) | FDR p-Values | ||||
---|---|---|---|---|---|---|---|---|
Jejunal Chymus | Jejunal Mucosa | Caecum Chymus | SP | BW | SP × BW | |||
Alistipes | LBW | 0.00 | 0.64 | 0.82 B | 0.48 B | 0.451 | ||
HBW | 0.03 | 1.71 | 2.48 A | 1.41 A | 0.081 T | |||
Mean (SP) | 0.01 b | 1.17 a | 1.65 a | 0.017 | ||||
Bacteroides | LBW | 0.11 | 19.06 B | 42.39 | 20.52 B | 0.280 | ||
HBW | 0.76 | 34.28 A | 46.27 | 27.10 A | 0.098 T | |||
Mean (SP) | 0.43 c | 26.67 b | 44.33 a | 0.000 | ||||
Enterococcus | LBW | 0.02 B | 0.03 | 0.00 | 0.02 B | 0.001 | ||
HBW | 0.22 A | 0.02 | 0.00 | 0.08 A | 0.012 | |||
Mean (SP) | 0.123 a | 0.025 b | 0.002 b | 0.000 | ||||
Ruminococcaceae UCG-010 | LBW | 0.00 | 0.09 B | 0.19 | 0.09 B | 0.472 | ||
HBW | 0.00 | 0.24 A | 0.29 | 0.18 A | 0.083 T | |||
Mean (SP) | 0.00 b | 0.17 a | 0.24 a | 0.000 | ||||
Ruminococcaceae UCG-013 | LBW | 0.01 | 0.09 | 0.39 A | 0.17 A | 0.026 | ||
HBW | 0.01 | 0.06 | 0.18 B | 0.08 B | 0.020 | |||
Mean (SP) | 0.010 b | 0.078 b | 0.285 a | 0.000 |
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Farkas, V.; Csitári, G.; Menyhárt, L.; Such, N.; Pál, L.; Husvéth, F.; Rawash, M.A.; Mezőlaki, Á.; Dublecz, K. Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens. Animals 2022, 12, 1296. https://doi.org/10.3390/ani12101296
Farkas V, Csitári G, Menyhárt L, Such N, Pál L, Husvéth F, Rawash MA, Mezőlaki Á, Dublecz K. Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens. Animals. 2022; 12(10):1296. https://doi.org/10.3390/ani12101296
Chicago/Turabian StyleFarkas, Valéria, Gábor Csitári, László Menyhárt, Nikoletta Such, László Pál, Ferenc Husvéth, Mohamed Ali Rawash, Ákos Mezőlaki, and Károly Dublecz. 2022. "Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens" Animals 12, no. 10: 1296. https://doi.org/10.3390/ani12101296
APA StyleFarkas, V., Csitári, G., Menyhárt, L., Such, N., Pál, L., Husvéth, F., Rawash, M. A., Mezőlaki, Á., & Dublecz, K. (2022). Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens. Animals, 12(10), 1296. https://doi.org/10.3390/ani12101296