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Article

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations

by
Himansu Kumar
1,
Woncheol Park
1,
Krishnamoorthy Srikanth
1,
Bong-Hwan Choi
1,
Eun-Seok Cho
2,
Kyung-Tai Lee
3,
Jun-Mo Kim
4,
Kwangmin Kim
5,
Junhyung Park
5,
Dajeong Lim
1 and
Jong-Eun Park
1,*
1
Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea
2
Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
3
Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
4
Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
5
3 BIGS CO. LTD., Hwaseong 18454, Korea
*
Author to whom correspondence should be addressed.
Genes 2019, 10(5), 382; https://doi.org/10.3390/genes10050382
Submission received: 18 March 2019 / Revised: 16 May 2019 / Accepted: 16 May 2019 / Published: 20 May 2019
(This article belongs to the Section Microbial Genetics and Genomics)
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Abstract

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson’s correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.
Keywords: cecum microbiota; 16S rRNA sequencing; SILVA database cecum microbiota; 16S rRNA sequencing; SILVA database
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MDPI and ACS Style

Kumar, H.; Park, W.; Srikanth, K.; Choi, B.-H.; Cho, E.-S.; Lee, K.-T.; Kim, J.-M.; Kim, K.; Park, J.; Lim, D.; et al. Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations. Genes 2019, 10, 382. https://doi.org/10.3390/genes10050382

AMA Style

Kumar H, Park W, Srikanth K, Choi B-H, Cho E-S, Lee K-T, Kim J-M, Kim K, Park J, Lim D, et al. Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations. Genes. 2019; 10(5):382. https://doi.org/10.3390/genes10050382

Chicago/Turabian Style

Kumar, Himansu, Woncheol Park, Krishnamoorthy Srikanth, Bong-Hwan Choi, Eun-Seok Cho, Kyung-Tai Lee, Jun-Mo Kim, Kwangmin Kim, Junhyung Park, Dajeong Lim, and et al. 2019. "Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations" Genes 10, no. 5: 382. https://doi.org/10.3390/genes10050382

APA Style

Kumar, H., Park, W., Srikanth, K., Choi, B.-H., Cho, E.-S., Lee, K.-T., Kim, J.-M., Kim, K., Park, J., Lim, D., & Park, J.-E. (2019). Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations. Genes, 10(5), 382. https://doi.org/10.3390/genes10050382

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