No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chicken Breed and Experimental Design
2.2. Sample Collection
2.3. Extraction of Total Nucleic Acid from Feces
2.4. 16S rRNA Gene Amplification and Sequencing
2.5. Bioinformatic and Statistical Analyses
3. Results
3.1. Taxonomic Richness and Structure of Chicken Cloaca Bacteriobiome
3.2. OTU Relative Abundance in the Chicken Cloaca Bacteriobiome
3.3. Biodiversity Indices of the Chicken Cloaca Bacteriobiome
3.4. Production Performance of Chickens
4. Discussion
4.1. Taxonomic Richness and Structure of the Chicken Cloaca Bacteriobiome
4.2. Alpha-Biodiversity Indices of the Chicken Cloaca Bacteriobiome
4.3. Cloaca Bacteriobiome Diversity and Chickens’ Production Performance
4.4. General Comments
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Ingredients, g/kg | Day 1–28 | Day 29–42 |
---|---|---|
Wheat | 0.392 | 0.537 |
Soya beans | 0.240 | 0.254 |
Soyabean meal | 0.150 | 0.112 |
Sunflower oil | 0.075 | 0.060 |
Sunflower seed millcake | 0.100 | 0 |
Methionine | 0.003 | 0.003 |
Lysine | 0.003 | 0.003 |
Sodium chloride | 0.003 | 0.003 |
Calcium monophosphate | 0.012 | 0.012 |
Limestone powder | 0.012 | 0.007 |
Premix 1 | 0.010 | 0.010 |
Crude protein, % | 23 | 21 |
Metabolic energy, MJ/kg | 13.0 | 13.2 |
Taxon Level | Taxonomic Attribution | |||
---|---|---|---|---|
All OTUs | Dominant OTUs | |||
Both Groups | Antibiotic-Receiving | Prebiotic-Receiving | ||
Phylum | 9 | 3 | 3 | 2 |
Class | 17 | 4 | 4 | 3 |
Order | 26 | 6 | 8 | 3 |
Family | 41 | 8 | 8 | 5 |
Genus | 96 | 12 | 10 | 7 |
OTU | 397 | 18 | 12 | 7 |
OTU | Antibiotic Group | Prebiotic Group | |
---|---|---|---|
Males | |||
1 | Escherichia/Shigella sp. | 7.1 (20.6) | 24.5 (42.5) |
2 | Alistipes sp. | 20.4 (35.8) | 14.0 (28.1) |
3 | Enterococcus sp. | 0.0 (0.0) | 4.9 (22.4) |
4 | Lactobacillus sp. | 6.3 (28.4) | 3.6 (9.7) |
5 | Romboutsia timonensis | 1.9 (5.8) | 4.8 (3.0) |
6 | Lactobacillus sp. | 2.1 (4.6) | 2.5 (5.4) |
7 | Faecalibacterium prausnitzii | 1.3 (4.0) | 2.4 (5.6) |
8 | un. 1 Clostridiaceae | 0.1 (3.2) | 1.5 (3.9) |
9 | Ligilactobacillus sp. | 4.9 (5.9) | 0.6 (0.5) |
10 | un. Lachnospiraceae | 0.9 (3.3) | 2.0 (4.1) |
12 | un. Muribaculaceae | 3.6 (9.3) | 0.8 (2.3) |
13 | Streptococcus sp. | 0.0 (0.0) | 1.9 (3.5) |
15 | un. Ruminococcaceae | 0.3 (1.1) | 1.0 (1.8) |
17 | Limosilactobacillus sp. | 1.6 (17.1) | 0.8 (1.7) |
26 | un. Lachnospiraceae | 1.1 (2.0) | 1.2 (2.1) |
Females | |||
1 | Escherichia/Shigella sp. | 4.6 (15.6) | 20.4 (32.2) |
2 | Alistipes sp. | 23.2 (21.3) | 0.0 (19.4) |
3 | Enterococcus sp. | 0.00 (0.0) | 23.6 (39.7) |
4 | Lactobacillus sp. | 3.2 (19.2) | 2.4 (6.4) |
5 | Romboutsia timonensis | 0.8 (3.3) | 6.6 (14.9) |
7 | Faecalibacterium prausnitzii | 5.1 (7.3) | 0.0 (2.1) |
8 | un. Clostridiaceae | 0.2 (0.6) | 2.8 (5.8) |
10 | un. Lachnospiraceae | 5.7 (3.9) | 0.0 (1.4) |
12 | un. Muribaculaceae | 2.5 (4.2) | 0.4 (3.1) |
13 | Streptococcus sp. | 0.0 (0.1) | 4.0 (2.2) |
14 | un. Bacteroides | 1.6 (1.3) | 0.0 (1.0) |
16 | un. Clostridiales | 2.7 (3.2) | 0.0 (0.05) |
17 | Limosilactobacillus sp. | 1.7 (5.1) | 1.7 (0.9) |
20 | Blautia sp. | 1.0 (0.6) | 0.4 (1.4) |
23 | un. Ruminococcaceae | 1.0 (1.0) | 0.00 (0.1) |
26 | un. Lachnospiraceae | 3.6 (2.1) | 0.3 (0.6) |
OTU | Factor | |||
---|---|---|---|---|
Prebiotic | Sex | Prebiotic × Sex | ||
3 | Enterococcus sp. | 30.7 1 | 3.4 | 3.4 |
9 | Ligilactobacillus sp. | 25.6 | 8.2 | 6.6 |
13 | Streptococcus sp. | 56.2 | 0.5 | 0.3 |
16 | un. 2 Clostridiales | 28.0 | 5.9 | 14.0 |
22 | Clostridium spiroforme | 14.1 3 | 14.1 | 21.3 |
23 | un. Ruminococcaceae | 28.0 | 3.0 | 6.1 |
24 | Bifidobacterium pullorum | 39.8 | 1.0 | 1.8 |
26 | un. Lachnospiraceae | 24.1 | 3.9 | 27.2 |
29 | un. Clostridiales | 0.1 | 1.7 | 37.8 |
34 | un. Lachnospiraceae | 6.6 | 0.4 | 29.9 |
46 | Butyricicoccus pullicaecorum | 31.2 | 3.0 | 8.1 |
51 | un. Ruminococcaceae | 25.4 | 5.6 | 19.5 |
52 | un. Firmicutes | 30.6 | 13.0 | 7.0 |
54 | un. Clostridium XVIII | 45.5 | 8.3 | 18.8 |
59 | un. Clostridiales | 29.6 | 6.3 | 10.4 |
71 | Negativibacillus massiliensis | 18.1 | 0.9 | 24.1 |
78 | un. Clostridiales | 26.6 | 3.3 | 9.0 |
87 | Bifidobacterium sp. | 48.4 | 1.0 | 1.0 |
93 | Anaeromassilibacillus sp. | 0.7 | 2.5 | 27.7 |
98 | un. Firmicutes | 28.9 | 10.9 | 24.0 |
114 | Massilimicrobiota timonensis | 33.9 | 18.3 | 28.2 |
126 | Monoglobus sp. | 22.3 | 9.1 | 19.1 |
136 | un. Lachnospiraceae | 4.5 | 1.4 | 29.6 |
140 | Blautia hydrogenotrophica | 0.4 | 0.9 | 37.6 |
143 | un. Lachnospiraceae | 20.3 | 3.1 | 27.3 |
152 | Clostridium colinum | 27.6 | 2.2 | 1.6 |
157 | un. Lachnospiraceae | 0.2 | 1.2 | 35.7 |
158 | un. Ruminococcaceae | 1.3 | 12.7 | 38.0 |
169 | un. Clostridiales | 27.9 | 3.3 | 14.0 |
183 | Ligilactobacillus agilis | 42.6 | 5.0 | 4.0 |
194 | un. Ruminococcaceae | 15.2 | 18.3 | 25.1 |
203 | un. Firmicutes | 28.1 | 2.8 | 24.6 |
224 | un. Lachnospiraceae | 19.5 | 9.8 | 21.6 |
228 | Staphylococcus sp. | 30.5 | 1.9 | 1.9 |
231 | un. Clostridium IV | 29.6 | 0.0 | 0.0 |
246 | un. Lachnospiraceae | 23.2 | 0.6 | 18.4 |
251 | un. Clostridiales | 32.6 | 0.0 | 0.8 |
257 | un. Lachnospiraceae | 27.0 | 3.7 | 9.5 |
339 | Butyricicoccus sp. | 37.6 | 0.1 | 0.5 |
347 | Paludicola sp. | 30.9 | 0.6 | 0.6 |
357 | un. Firmicutes | 25.6 | 13.7 | 24.5 |
374 | un. Ruminococcaceae | 22.7 | 22.7 | 22.7 |
OTU | Antibiotic Group | Prebiotic Group | |||
---|---|---|---|---|---|
Male | Female | Male | Female | ||
3 | Enterococcus sp. | 0.0 a 1 | 0.0 a | 11.6 b | 23.2 b |
9 | Ligilactobacillus sp. | 4.3 b | 1.7 ab | 0.6 a | 0.5 a |
13 | Streptococcus sp. | 0.0 a | 0.1 a | 3.0 b | 3.5 b |
16 | un. 2 Clostridiales | 0.9 ab | 2.6 b | 0.4 a | 0.0 a |
22 | Clostridium spiroforme | 0.2 a | 0.9 b | 0.2 a | 0.2 a |
23 | un. Ruminococcaceae | 0.9 b | 1.0 b | 0.6 ab | 0.1 a |
24 | Bifidobacterium pullorum | 0.4 ab | 0.5 b | 0.1 a | 0.1 a |
26 | un. Lachnospiraceae | 1.2 a | 3.2 b | 1.3 a | 0.3 a |
29 | un. 2 Clostridiales | 0.1 a | 0.4 ab | 0.4 b | 0.0 a |
34 | un. Lachnospiraceae | 0.2 b | 0.6 b | 0.4 b | 0.1 a |
46 | Butyricicoccus pullicaecorum | 0.5 ab | 1.1 b | 0.2 a | 0.0 a |
51 | un. Ruminococcaceae | 0.1 a | 0.2 b | 0.1 a | 0.0 a |
52 | un. Firmicutes | 0.2 a | 0.5 b | 0.0 a | 0.1 a |
54 | un. Clostridium XVIII | 0.11 a | 0.26 b | 0.05 a | 0.02 a |
59 | un. Clostridiales | 0.08 ab | 0.22 b | 0.03 a | 0.01 a |
71 | Negativibacillus massiliensis | 0.17 a | 0.44 b | 0.20 ab | 0.06 a |
78 | un. Clostridiales | 0.41 ab | 0.85 b | 0.21 a | 0.11 a |
87 | Bifidobacterium sp. | 0.00 a | 0.00 a | 0.13 b | 0.17 b |
93 | Anaeromassilibacillus sp. | 0.2 a | 0.9 a | 0.1 a | 0.1 a |
98 | un. Firmicutes | 0.03 a | 0.11 b | 0.03 a | 0.01 a |
114 | Massilimicrobiota timonensis | 0.02 a | 0.10 b | 0.02 a | 0.01 a |
126 | Monoglobus sp. | 0.02 a | 0.07 b | 0.02 a | 0.01 a |
140 | Blautia hydrogenotrophica | 0.01 a | 0.04 ab | 0.05 b | 0.01 a |
143 | un. Lachnospiraceae | 0.03 a | 0.11 b | 0.04 a | 0.00 a |
152 | Clostridium colinum | 0.05 b | 0.03 a | 0.00 a | 0.00 a |
157 | un. Lachnospiraceae | 0.01 a | 0.03 b | 0.03 b | 0.00 a |
158 | un. Ruminococcaceae | 0.01 a | 0.07 b | 0.04 a | 0.02 a |
169 | un. Clostridiales | 0.03 ab | 0.07 b | 0.01 a | 0.00 a |
183 | Ligilactobacillus agilis | 0.04 b | 0.02 a | 0.00 a | 0.00 a |
194 | un. Ruminococcaceae | 0.00 a | 0.03 b | 0.01 a | 0.00 a |
203 | un. Firmicutes | 0.01 a | 0.03 b | 0.01 a | 0.00 a |
224 | un. Lachnospiraceae | 0.03 a | 0.08 b | 0.03 a | 0.02 a |
228 | Staphylococcus sp. | 0.00 a | 0.00 a | 0.02 b | 0.03 b |
231 | un. ClostridiumIV | 0.01 b | 0.01 b | 0.00 a | 0.00 a |
246 | un. Lachnospiraceae | 0.045 ab | 0.096 b | 0.040 ab | 0.004 a |
251 | un. Clostridiales | 0.01 a | 0.01 a | 0.00 a | 0.00 a |
257 | un. Lachnospiraceae | 0.005 ab | 0.013 b | 0.002 a | 0.000 a |
339 | Butyricicoccus sp. | 0.03 a | 0.03 a | 0.00 a | 0.00 a |
347 | Paludicola sp. | 0.005 a | 0.004 a | 0.000 a | 0.000 a |
357 | un. Firmicutes | 0.00 a | 0.01 b | 0.00 a | 0.00 a |
374 | un. Ruminococcaceae | 0.000 a | 0.003 b | 0.000 a | 0.000 a |
Index | Factor | ||
---|---|---|---|
Prebiotic | Sex | Prebiotic × Sex | |
Total number of identified OTUs | 19.3 | 0.0 | 10.6 |
Chao-1 | 26.3 | 0.0 | 7.8 |
Simpson (1-D) | 9.1 | 1.0 | 17.4 |
Shannon | 9.0 | 0.5 | 13.7 |
Equitability | 1.9 | 1.7 | 16.7 |
Dominance (D) | 9.2 | 1.0 | 17.3 |
Berger–Parker | 4.8 | 3.0 | 32.6 |
Index | Antibiotic Group | Prebiotic Group | ||
---|---|---|---|---|
Male | Female | Male | Female | |
Number of identified OTUs | 202 ab 1 | 269 b | 178 ab | 112 a |
Chao-1 | 249 ab | 307 b | 199 ab | 139 a |
Simpson (1-D) | 0.78 | 0.87 | 0.80 | 0.75 |
Shannon | 2.5 | 3.2 | 2.6 | 2.1 |
Equitability | 0.47 | 0.57 | 0.52 | 0.47 |
Dominance (D) | 0.22 | 0.13 | 0.20 | 0.25 |
Berger–Parker | 0.43 b | 0.29 a | 0.37 ab | 0.44 b |
Index | Antibiotic Group | Prebiotic Group | ||
---|---|---|---|---|
Male | Female | Male | Female | |
Living mass of a 42-day-old chickens, g/bird | 2210.1 c 1 | 1832.7 a | 2352.8 d | 1939.7 b |
Average daily gain, g/bird per day | 51.6 c | 42.6 a | 55.0 d | 45.2 b |
Characteristic | Antibiotic Group | Prebiotic Group |
---|---|---|
Living mass of 1-day-old chickens, g/bird | 43.3 ± 0.3 | 43.2 ± 0.3 |
Living mass of 42-day-old chickens, g/bird3 | 2021.4 ± 21.4 | 2144.3 ± 30.5 |
Average daily gain, g/bird per day | 47.1 ± 2.1 | 50.03 ± 2.3 |
Feed intake, kg/kg bird mass | 2.04 | 1.93 |
Survival over 42 days, % | 94 | 99 |
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Lysko, S.B.; Baturina, O.A.; Naumova, N.B.; Lescheva, N.A.; Pleshakova, V.I.; Kabilov, M.R. No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens. Agriculture 2022, 12, 24. https://doi.org/10.3390/agriculture12010024
Lysko SB, Baturina OA, Naumova NB, Lescheva NA, Pleshakova VI, Kabilov MR. No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens. Agriculture. 2022; 12(1):24. https://doi.org/10.3390/agriculture12010024
Chicago/Turabian StyleLysko, Svetlana B., Olga A. Baturina, Natalia B. Naumova, Nadezhda A. Lescheva, Valentina I. Pleshakova, and Marsel R. Kabilov. 2022. "No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens" Agriculture 12, no. 1: 24. https://doi.org/10.3390/agriculture12010024