Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Animals, Experimental Design, and Housing
2.2. Sampling
2.3. DNA Isolation
2.4. 16S rRNA Gene Amplification and Sequencing
2.5. Bioinformatic Analysis
2.6. Statistical Analysis
3. Results
3.1. Synbiotic Impact on Microbial Diversity
3.2. Synbiotic Impacts on Taxonomic Composition
3.3. Synbiotic Effect on Predicted Microbial Functionality across the Body Sites
4. Discussion
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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Body Site | Synbiotic | Genus | logFC 1 | logCPM 1 | LR 1 | p-Value | FDR 1 |
---|---|---|---|---|---|---|---|
oropharyngeal cavity | Bacillus-based synbiotic supplementation | Campylobacter | −3.19 | 13.17 | 19.98 | 7.83 × 10−6 | 1.02 × 10−3 |
Megasphaera | 6.09 | 6.16 | 12.29 | 4.55 × 10−4 | 2.95 × 10−2 | ||
Unclassified Porphyromonadaceae | −7.59 | 8.32 | 9.19 | 2.43 × 10−3 | 1.05 × 10−1 | ||
Unclassified Clostridiales | −1.46 | 13.78 | 8.42 | 3.71 × 10−3 | 1.21 × 10−1 | ||
oropharyngeal cavity | Lactobacillus-based synbiotic supplementation | Unclassified Deltaproteobacteria | 7.39 | 6.79 | 14.56 | 1.36 × 10−4 | 1.76 × 10−2 |
Lactobacillus | −7.28 | 8.12 | 9.84 | 1.71 × 10−3 | 1.11 × 10−1 | ||
Proximal colon | Lactobacillus-based synbiotic supplementation | Unclassified Tremblayales | 10.44 | 9.76 | 24.38 | 7.89 × 10−7 | 8.13 × 10−5 |
Unclassified Lactobacillales | 7.11 | 7.74 | 11.99 | 5.35 × 10−4 | 2.76 × 10−2 | ||
Lactobacillus | 1.69 | 15.84 | 8.46 | 3.62 × 10−3 | 1.24 × 10−1 | ||
Streptococcus | −1.92 | 16.63 | 7.85 | 5.09 × 10−3 | 1.31 × 10−1 | ||
Vaginal canal | Bacillus-based synbiotic supplementation | Filifactor | −10.41 | 10.76 | 28.22 | 1.08 × 10−7 | 2.85 × 10−5 |
Clostridium | 6.27 | 6.05 | 20.52 | 5.91 × 10−6 | 7.77 × 10−4 | ||
Halalkalibacillus | 7.12 | 6.59 | 17.94 | 2.28 × 10−5 | 2.00 × 10−3 | ||
Veillonella | −4.24 | 14.03 | 11.77 | 6.02 × 10−4 | 3.96 × 10−2 | ||
Leifsonia | 7.46 | 6.84 | 10.80 | 1.01 × 10−3 | 5.33 × 10−2 | ||
Unclassified Fusobacteriaceae | −3.36 | 16.06 | 10.02 | 1.55 × 10−3 | 5.89 × 10−2 | ||
Unclassified Clostridiales | −2.64 | 16.00 | 10.00 | 1.57 × 10−3 | 5.89 × 10−2 | ||
Bacteroides | −3.40 | 16.48 | 9.08 | 2.58 × 10−3 | 8.48 × 10−2 | ||
Paraeggerthella | −5.06 | 9.24 | 8.62 | 3.32 × 10−3 | 9.17 × 10−2 | ||
Clostridium | −5.27 | 10.71 | 8.53 | 3.49 × 10−3 | 9.17 × 10−2 | ||
Unclassified Bacteroidales | −2.05 | 17.53 | 7.92 | 4.90 × 10−3 | 1.17 × 10−1 | ||
Peptostreptococcus | −2.96 | 12.62 | 7.65 | 5.66 × 10−3 | 1.24 × 10−1 | ||
Unclassified Bacteria | −2.41 | 15.66 | 7.23 | 7.18 × 10−3 | 1.38 × 10−1 | ||
Megamonas | 4.84 | 5.39 | 7.18 | 7.36 × 10−3 | 1.38 × 10−1 | ||
Finegoldia | 2.71 | 11.79 | 7.02 | 8.07 × 10−3 | 1.41 × 10−1 | ||
Weissella | −5.82 | 6.60 | 6.87 | 8.74 × 10−3 | 1.43 × 10−1 | ||
Unclassified Dermatophilaceae | 5.31 | 6.93 | 6.77 | 9.25 × 10−3 | 1.43 × 10−1 | ||
Campylobacter | −1.93 | 15.48 | 6.61 | 1.01 × 10−2 | 1.48 × 10−1 | ||
Vaginal canal | Lactobacillus-based synbiotic supplementation | Haemophilus | 10.11 | 8.82 | 20.36 | 6.42 × 10−6 | 1.69 × 10−3 |
Oribacterium | 7.74 | 6.77 | 10.23 | 1.38 × 10−3 | 1.75 × 10−1 |
Body Site | Synbiotic | Superpathway Class | Pathway Name | Log FC * | Log CPM * | LR * | p-Value | FDR * |
---|---|---|---|---|---|---|---|---|
oropharyngeal cavity | Bacillus-based synbiotic | Carbohydrate Biosynthesis | superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis | −3.12 | 8.61 | 28.72 | 8.37 × 10−8 | 2.84 × 10−5 |
Cofactor, Carrier, and Vitamin Biosynthesis | superpathway of menaquinol-8 biosynthesis II | −3.11 | 7.65 | 24.24 | 8.51 × 10−7 | 1.44 × 10−4 | ||
Carbohydrate Biosynthesis | CMP-pseudaminate biosynthesis | −3.30 | 6.13 | 17.80 | 2.46 × 10−5 | 1.50 × 10−3 | ||
Carbohydrate Biosynthesis | protein N-glycosylation (bacterial) | −3.36 | 6.21 | 18.32 | 1.86 × 10−5 | 1.50 × 10−3 | ||
Cofactor, Carrier, and Vitamin Biosynthesis | 1,4-dihydroxy-6-naphthoate biosynthesis II | −3.22 | 6.19 | 17.65 | 2.66 × 10−5 | 1.50 × 10−3 | ||
Cofactor, Carrier, and Vitamin Biosynthesis | superpathway of demethylmenaquinol-6 biosynthesis II | −3.22 | 6.19 | 17.68 | 2.62 × 10−5 | 1.50 × 10−3 | ||
Amine and Polyamine Biosynthesis | ectoine biosynthesis | 7.29 | −0.15 | 15.64 | 7.65 × 10−5 | 3.70 × 10−3 | ||
Proximal colon | Lactobacillus-based synbiotic | Fatty Acid and Lipid Biosynthesis | (5Z)-dodecenoate biosynthesis I | −1.47 | 11.22 | 22.44 | 2.17 × 10−6 | 7.39 × 10−4 |
Vaginal canal | Bacillus-based synbiotic | Degradation/Utilization/Assimilation-Other | caprolactam degradation | 7.24 | −0.16 | 17.29 | 3.20 × 10−5 | 1.56 × 10−3 |
Nucleosides and Nucleotides Degradation | adenosine nucleotides degradation IV | 6.84 | −0.42 | 20.11 | 7.33 × 10−6 | 5.73 × 10−4 | ||
Fatty Acid and Lipids Degradation | phospholipase pathway | 6.28 | −0.77 | 15.00 | 1.08 × 10−4 | 2.81 × 10−3 | ||
Aromatic Compounds Degradation | gallate degradation I | 4.36 | 0.81 | 11.17 | 8.32 × 10−4 | 9.30 × 10−3 | ||
Aromatic Compounds Degradation | vanillin and vanillate degradation I | 4.20 | 1.36 | 9.40 | 2.17 × 10−3 | 1.70 × 10−2 | ||
Aromatic Compounds Degradation | superpathway of vanillin and vanillate degradation | 4.20 | 1.36 | 9.45 | 2.11 × 10−3 | 1.70 × 10−2 | ||
Aromatic Compounds Degradation | vanillin and vanillate degradation II | 4.20 | 1.51 | 9.24 | 2.37 × 10−3 | 1.82 × 10−2 | ||
Carbohydrates Biosynthesis | CMP-legionaminate biosynthesis I | 2.05 | 6.61 | 7.77 | 5.31 × 10−3 | 3.26 × 10−2 | ||
Aromatic Compounds Degradation | catechol degradation to β-ketoadipate | 1.66 | 7.67 | 7.34 | 6.75 × 10−3 | 3.88 × 10−2 | ||
Aromatic Compounds Degradation | protocatechuate degradation II (ortho-cleavage pathway) | 1.63 | 8.39 | 9.81 | 1.74 × 10−3 | 1.48 × 10−2 | ||
Cell Structures Biosynthesis | peptidoglycan biosynthesis II (staphylococci) | 1.61 | 9.61 | 10.88 | 9.70 × 10−4 | 9.65 × 10−3 | ||
Superpathways | superpathway of 2,3-butanediol biosynthesis | 1.57 | 7.46 | 8.42 | 3.71 × 10−3 | 2.57 × 10−2 | ||
Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis | mycothiol biosynthesis | 1.39 | 8.07 | 7.86 | 5.05 × 10−3 | 3.23 × 10−2 | ||
Secondary Metabolite Biosynthesis | mevalonate pathway I (eukaryotes and bacteria) | 1.19 | 9.90 | 11.49 | 6.99 × 10−4 | 8.54 × 10−3 | ||
Secondary Metabolite Biosynthesis | superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) | 1.11 | 10.30 | 12.44 | 4.21 × 10−4 | 6.58 × 10−3 | ||
Amino Acid Degradation | L-lysine fermentation to acetate and butanoate | −1.03 | 11.14 | 11.54 | 6.79 × 10−4 | 8.54 × 10−3 | ||
Amino Acid Degradation | L-glutamate degradation V (via hydroxyglutarate) | −1.06 | 10.24 | 8.19 | 4.21 × 10−3 | 2.79 × 10−2 |
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Bugenyi, A.W.; Song, K.-D.; Lee, H.-K.; Heo, J. Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs. Fermentation 2023, 9, 359. https://doi.org/10.3390/fermentation9040359
Bugenyi AW, Song K-D, Lee H-K, Heo J. Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs. Fermentation. 2023; 9(4):359. https://doi.org/10.3390/fermentation9040359
Chicago/Turabian StyleBugenyi, Andrew Wange, Ki-Duk Song, Hak-Kyo Lee, and Jaeyoung Heo. 2023. "Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs" Fermentation 9, no. 4: 359. https://doi.org/10.3390/fermentation9040359