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Comparison of Fecal Microbial Communities between White and Black Pigs
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 Title & Authors
Comparison of Fecal Microbial Communities between White and Black Pigs
Guevarra, Robin B.; Kim, Jungman; Nguyen, Son G.; Unno, Tatsuya;
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 Abstract
Meat from black pigs (BP) is in high demand compared with that from modern white pig (WP) breeds such as Landrace pigs owing to its high quality. However, the growth rate of black pigs is slower than that of white pig breeds. We investigated differences in the fecal microbial composition between white and black pigs to explore whether these breeds differed in the composition of their gut microbial communities. The swine gut microbiota was investigated using Illumina's MiSeq-based sequencing technology by targeting the V4 region of the 16S rRNA gene. Our results showed that the composition of the gut microbiota was significantly different between the two pig breeds. While the composition of the WP microbiota shifted according to the growth stage, fewer shifts in composition were observed for the BP gut microbiota. In addition, the WP gut microbiota showed a higher Firmicutes/Bacteroidetes ratio compared with that of BP. A high ratio between these phyla was previously reported as an obesity-linked microbiota composition. Moreover, the WP microbiota contained a significantly higher abundance of cellulolytic bacteria, suggesting a possibility of higher fiber digestion efficiency in WP compared to BP. These findings may be important factors affecting growth performance and energy-harvesting capacities in pigs. Our findings of differences in the gut microbiota composition between the two breeds may provide new leads to understand growth rate variation across pig breeds.
 Keywords
cellulolytic microorganisms;feces;growth rate;gut flora;pig breeds;
 Language
English
 Cited by
 References
1.
Adesehinwa AOK (2008) Energy and protein requirements of pigs and the utilization of fibrous feedstuffs in Nigeria: A review. Afr J Biotech 7, 4798-806.

2.
Cai S and Dong X (2010) Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov. Int J Syst Evol Microbiol 60, 845-9. crossref(new window)

3.
Cai S, Li J, Hu FZ, Zhang K, Luo Y, Janto B et al. (2010) Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. Appl Environ Microbiol 76, 3818-24. crossref(new window)

4.
Choct M, Dersjant-Li Y, McLeish J, and Peisker M (2010) Soy Oligosaccharides and Soluble Non-starch Polysaccharides:A Review of Digestion, Nutritive and Anti-nutritive Effects in Pigs and Poultry. Asian-Aust. Journal of Animal Science 23, 1386-98. crossref(new window)

5.
Cluny NL, Eller LK, Keenan CM, Reimer RA, and Sharkey KA (2015) Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats. Obesity (Silver Spring) 23, 769-78. crossref(new window)

6.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, D141-5. crossref(new window)

7.
Degnan PH and Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6, 183-94. crossref(new window)

8.
de La Serre CB, Ellis CL, Lee J, Hartman AL, Rutledge JC, and Raybould HE (2010) Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am J Physiol Gastrointest Liver Physiol 299, G440-8. crossref(new window)

9.
DiBaise JK, Frank DN, and Mathur R (2012) Impact of the Gut Microbiota on the Development of Obesity: Current Concepts. Am J Gastroenterol Suppl 1, 22-7. crossref(new window)

10.
Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P et al. (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32, 1720-4. crossref(new window)

11.
Edgar RC, Haas BJ, Clemente JC, Quince C, and Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-200. crossref(new window)

12.
Fisher AR (2012) Comparison of the gut microbiome of pigs, mice and humans. George Mason University, USA.

13.
Foster EK (2003) METASTATS: behavioral science statistics for Microsoft Windows and the HP49G programmable calculator. Behav Res Methods Instrum Comput 35, 325-8. crossref(new window)

14.
Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, and Martin JF (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245. crossref(new window)

15.
Guo X, Xia X, Tang R, and Wang K (2008) Real-time PCR quantification of the predominant bacterial divisions in the distal gut of Meishan and Landrace pigs. Anaerobe 14, 224-8. crossref(new window)

16.
Hampson DJ and Ahmed N (2009) Spirochaetes as intestinal pathogens: Lessons from a Brachyspira genome. Gut Pathog 1, 1-3. crossref(new window)

17.
Hijova E and Chmelarova A (2007) Short chain fatty acids and colonic health. Bratisl Lek Listy 108, 354-8.

18.
Holman DB, Baurhoo B, and Chenier MR (2014) Temporal analysis of the effect of extruded flaxseed on the swine gut microbiota. Can J Microbiol 60, 649-59. crossref(new window)

19.
Isaacson R and Kim HB (2012) The intestinal microbiome of the pig. Anim Health Res Rev 13, 100-9. crossref(new window)

20.
JC Y and MK C (2005) A similarity measure based on species proportions. Comm Statist Theory Methods 34, 2123-31. crossref(new window)

21.
Kim J, Nguyen SG, Guevarra RB, Lee I, and Unno T (2015) Analysis of swine fecal microbiota at various growth stages. Arch Microbiol 197, 753-9. crossref(new window)

22.
Kim KS, Yeo JS, and Kim JW (2002) Assessment of genetic diversity of Korean native pig (Sus scrofa) using AFLP markers. Genes Genet Syst 77, 361-8. crossref(new window)

23.
Kim M, Lee KH, Yoon SW, Kim BS, Chun J, and Yi H (2013) Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform 11, 102-13. crossref(new window)

24.
Kim TH, Kim KS, Choi BH, Yoon DH, Jang GW, Lee KT et al. (2005) Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 83, 2255-63. crossref(new window)

25.
Kinyon JM and Harris DL (1979) Treponema innocens, a new species of intestinal bacteria, and emended description of the type strain of Treponema hyodysenteriae. Int J Syst Bacteriol 29, 102-9. crossref(new window)

26.
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, and Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79, 5112-20. crossref(new window)

27.
Krajmalnik-Brown R, Ilhan ZE, Kang DW, and DiBaise JK (2012) Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract 27, 201-14. crossref(new window)

28.
Lahteinen T, Lindholm A, Rinttila T, Junnikkala S, Kant R, Pietila TE et al. (2014) Effect of Lactobacillus brevis ATCC 8287 as a feeding supplement on the performance and immune function of piglets. Vet Immunol Immunopathol 158, 14-25. crossref(new window)

29.
Lamendella R, Domingo JW, Ghosh S, Martinson J, and Oerther DB (2011) Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol 11, 103. crossref(new window)

30.
Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, and Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102, 11070-5. crossref(new window)

31.
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS et al. (2008) Evolution of mammals and their gut microbes. Science 320, 1647-51. crossref(new window)

32.
Ley RE, Turnbaugh PJ, Klein S, and Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022-3. crossref(new window)

33.
Liao X, Wu R, Ma G, Zhao L, Zheng Z, and Zhang R (2015) Effects of Clostridium butyricum on antioxidant properties, meat quality and fatty acid composition of broiler birds. Lipids Health Dis 14, 36. crossref(new window)

34.
Liu J, Wang JK, Zhu W, Pu YY, Guan LL, and Liu JX (2014) Monitoring the rumen pectinolytic bacteria Treponema saccharophilum using real-time PCR. FEMS Microbiol Ecol 87, 576-85. crossref(new window)

35.
Luo Y, Su Y, Wright AG, Zhang L, Smidt H, and Zhu W (2012) Lean Breed Landrace Pigs Harbor FecalMethanogens at Higher Diversity and Density than Obese Breed Erhualian Pigs. Hindawi Publishing Corporation 1-9.

36.
Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F et al. (2010) Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 59, 1635-42. crossref(new window)

37.
Norris V, Molina F, and Gewirtz AT (2013) Hypothesis: bacteria control host appetites. J Bacteriol 195, 411-6. crossref(new window)

38.
Paulson J, Pop M, and Bravo H (2011) Metastats: an improved statistical method for analysis of metagenomic data. Genome Biology 12, P17. crossref(new window)

39.
Pedersen R, Ingerslev HC, Sturek M, Alloosh M, Cirera S, Christoffersen BO et al. (2013) Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome. PloS one 8, e56612. crossref(new window)

40.
Pramanik P and Kim PJ (2014) Evaluating changes in cellulolytic bacterial population to explain methane emissions from air-dried and composted manure treated rice paddy soils. Sci Total Environ 470-471, 1307-12. crossref(new window)

41.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41, D590-6. crossref(new window)

42.
Samuel BS and Gordon JI (2006) A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103, 10011-6. crossref(new window)

43.
Sanz Y, Santacruz A, and De Palma G (2008) Insights into the roles of gut microbes in obesity. Interdiscip Perspect Infect Dis 2008, 829101.

44.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75, 7537-41. crossref(new window)

45.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-504. crossref(new window)

46.
Song GL, Li DF, Piao XS, Chi F, and Yang WJ (2003) Apparent ileal digestibility of amino acids and the digestible and metabolizable energy content of high-oil corn varieties and its effects on growth performance of pigs. Arch Tierernahr 57, 297-306.

47.
Teeling H and Glockner FO (2012) Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform 13, 728-42. crossref(new window)

48.
Thompson CL, Wang B, and Holmes AJ (2008) The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J 2, 739-48. crossref(new window)

49.
Tilg H (2010) Obesity, metabolic syndrome, and microbiota: multiple interactions. J Clin Gastroenterol 44 Suppl 1, S16-8. crossref(new window)

50.
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, and Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-31. crossref(new window)

51.
Turroni F, Ribbera A, Foroni E, van Sinderen D, and Ventura M (2008) Human gut microbiota and bifidobacteria: from composition to functionality. Antonie Van Leeuwenhoek 94, 35-50. crossref(new window)

52.
Wang JP, Lee JH, Yoo JS, Cho JH, Kim HJ, and Kim IH (2010) Effects of phenyllactic acid on growth performance, intestinal microbiota, relative organ weight, blood characteristics, and meat quality of broiler chicks. Poult Sci 89, 1549-55. crossref(new window)

53.
Yan L, Wang JP, Kim HJ, Meng QW, Ao X, Hong SM et al. (2010) Influence of essential oil supplementation and diets with different nutrient densities on growth performance, nutrient digestibility, blood characteristics, meat quality and fecal noxious gas content in grower-finisher pigs. Livestock Science 128, 115-22. crossref(new window)

54.
Yang L, Bian G, Su Y, and Zhu W (2014) Comparison of faecal microbial community of lantang, bama, erhualian, meishan, xiaomeishan, duroc, landrace, and yorkshire sows. Asian-Australas J Anim Sci 27, 898-906. crossref(new window)

55.
Zentek J, Ferrara F, Pieper R, Tedin L, Meyer W, and Vahjen W (2013) Effects of dietary combinations of organic acids and medium chain fatty acids on the gastrointestinal microbial ecology and bacterial metabolites in the digestive tract of weaning piglets. J Anim Sci 91, 3200-10. crossref(new window)

56.
Zhang J, Kobert K, Flouri T, and Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614-20. crossref(new window)

57.
Ziemer CJ, Kerr BJ, Weber TE, Arcidiacono S, Morrison M, and Ragauskas A (2012) Effects of feeding fiber-fermenting bacteria to pigs on nutrient digestion, fecal output, and plasma energy metabolites. J Anim Sci 90, 4020-7. crossref(new window)