Analysis of swine fecal microbiota at various growth stages

Archives of Microbiology

Volumn 197, Issue 6, 2015, Pages 753-759

  Kim, Jungman ^a   Nguyen, Son G ^a,b   Guevarra, Robin B ^a   Lee, Iljoo ^c   Unno, Tatsuya ^a  

^a Jeju National University   (South Korea)

^b INSTITUTE OF ECOLOGY AND BIOLOGICAL RESOURCES   (Viet Nam)

^c Darby Genetics Inc   (South Korea)

Author keywords

Antibiotics; Fecal microbiota; MiSeq; Mothur; Swine

Indexed keywords

RNA 16S; ANTIINFECTIVE AGENT; BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; BACTEROIDETES; DNA EXTRACTION; FECES MICROFLORA; FIRMICUTES; GENE SEQUENCE; GROWTH CURVE; LACHNOSPIRACEAE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL GROWTH; NONHUMAN; POPULATION ABUNDANCE; PREVOTELLA; PREVOTELLACEAE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES RICHNESS; TAXONOMY; ANIMAL; BACTERIUM; CLASSIFICATION; FECES; GENETICS; MICROBIOLOGY; MICROFLORA; PIG;

BACTERIA (MICROORGANISMS); BACTEROIDETES; OTUS; RODENTIA; SUIDAE;

ANIMALS; ANTI-BACTERIAL AGENTS; BACTERIA; BACTEROIDETES; DNA, BACTERIAL; FECES; MICROBIOTA; RNA, RIBOSOMAL, 16S; SWINE;

EID: 84937815087     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-015-1108-1     Document Type: Article

References (44)

1. Arnal ME, Zhang J, Messori S, Bosi P, Smidt H, Lalles JP (2014) Early changes in microbial colonization selectively modulate intestinal enzymes, but not inducible heat shock proteins in young adult swine. PLoS One 9:e87967. doi:10.1371/journal.pone.0087967
2. Caporaso JG et al (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 108(Suppl 1):4516–4522. doi:10.1073/pnas.1000080107
3. Caporaso JG et al (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624. doi:10.1038/ismej.2012.8
4. Casewell M, Friis C, Marco E, McMullin P, Phillips I (2003) The European ban on growth-promoting antibiotics and emerging consequences for human and animal health. J Antimicrob Chemother 52:159–161. doi:10.1093/jac/dkg313
5. Cole JR et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145. doi:10.1093/nar/gkn879
6. Degnan PH, Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6:183–194. doi:10.1038/ismej.2011.74
7. Donatin E, Drancourt M (2012) Optimized microbial DNA extraction from diarrheic stools. BMC Res Notes 5:702. doi:10.1186/1756-0500-5-702
8. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32:1720–1724. doi:10.1038/ijo.2008.155
9. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi:10.1093/bioinformatics/btr381
10. Ferrand J, Patron K, Legrand-Frossi C, Frippiat JP, Merlin C, Alauzet C, Lozniewski A (2014) Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice. J Microbiol Methods 105:180–185. doi:10.1016/j.mimet.2014.07.029
11. Flint HJ (2012) The impact of nutrition on the human microbiome. Nutr Rev 70(Suppl 1):S10–S13. doi:10.1111/j.1753-4887.2012.00499.x
12. Paulson J, Pop M, Bravo H (2011) Metastats: an improved statistical method for analysis of metagenomic data Genome biology 12:1–17
13. Gihring TM, Green SJ, Schadt CW (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14:285–290. doi:10.1111/j.1462-2920.2011.02550.x
14. Heinritz SN, Mosenthin R, Weiss E (2013) Use of pigs as a potential model for research into dietary modulation of the human gut microbiota. Nutr Res Rev 26:191–209. doi:10.1017/S0954422413000152
15. Hijova E, Chmelarova A (2007) Short chain fatty acids and colonic health. Bratisl Lek Listy 108:354–358
16. Iijima K, Asano S, Suzuki K, Ogata T, Kitagawa Y (2008) Modified multiplex PCR methods for comprehensive detection of Pectinatus and beer-spoilage cocci. Biosci Biotechnol Biochem 72:2764–2766. doi:10.1271/bbb.80297
17. Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Nunez G (2012) Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336:1325–1329. doi:10.1126/science.1222195
18. Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD (2014) Evaluating bias of illumina-based bacterial 16S rRNA gene profiles. Appl Environ Microbiol 80:5717–5722. doi:10.1128/AEM.01451-14
19. Konstantinov SR et al (2008) Feeding of Lactobacillus sobrius reduces Escherichia coli F4 levels in the gut and promotes growth of infected piglets. FEMS Microbiol Ecol 66:599–607. doi:10.1111/j.1574-6941.2008.00517.x
20. Koren O et al (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150:470–480. doi:10.1016/j.cell.2012.07.008
21. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, 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 79:5112–5120. doi:10.1128/AEM.01043-13
22. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123. doi:10.1111/j.1462-2920.2009.02051.x
23. Lalles JP (2010) Intestinal alkaline phosphatase: multiple biological roles in maintenance of intestinal homeostasis and modulation by diet. Nutr Rev 68:323–332. doi:10.1111/j.1753-4887.2010.00292.x
24. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023. doi:10.1038/4441022a
25. Li X, Yin J, Li D, Chen X, Zang J, Zhou X (2006) Dietary supplementation with zinc oxide increases Igf-I and Igf-I receptor gene expression in the small intestine of weanling piglets. J Nutr 136:1786–1791
26. Liu Z, DeSantis TZ, Andersen GL, Knight R (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res 36:e120. doi:10.1093/nar/gkn491
27. Mizrahi-Man O, Davenport ER, Gilad Y (2013) Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One 8:e53608. doi:10.1371/journal.pone.0053608
28. Pang X et al (2007) Inter-species transplantation of gut microbiota from human to pigs. ISME J 1:156–162. doi:10.1038/ismej.2007.23
29. Quast C et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. doi:10.1093/nar/gks1219
30. Rapp D, Waller J, Brightwell G, Muirhead RW (2010) Lyophilization prior to direct DNA extraction from bovine feces improves the quantification of Escherichia coli O157:H7 and Campylobacter jejuni. Appl Environ Microbiol 76:1686–1688. doi:10.1128/AEM.01866-09
31. Redondo LM, Chacana PA, Dominguez JE, Fernandez Miyakawa ME (2014) Perspectives in the use of tannins as alternative to antimicrobial growth promoter factors in poultry. Front Microbiol 5:118. doi:10.3389/fmicb.2014.00118
32. Salipante SJ et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol 80:7583–7591. doi:10.1128/AEM.02206-14
33. Santacruz A et al (2010) Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr 104:83–92. doi:10.1017/S0007114510000176
34. Schloss PD et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/AEM.01541-09
35. Shannon P et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504. doi:10.1101/gr.1239303
36. Thacker PA (2013) Alternatives to antibiotics as growth promoters for use in swine production: a review. J Anim Sci Biotechnol 4:35. doi:10.1186/2049-1891-4-35
37. Thompson CL, Wang B, Holmes AJ (2008) The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J 2:739–748. doi:10.1038/ismej.2008.29
38. Tremaroli V, Backhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242–249. doi:10.1038/nature11552
39. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031. doi:10.1038/nature05414
40. Turnbaugh PJ et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484. doi:10.1038/nature07540
41. Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R (2011) PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics 27:1159–1161. doi:10.1093/bioinformatics/btr087
42. Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Ponten T, Gupta R, Licht TR (2014) Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2:19. doi:10.1186/2049-2618-2-19
43. Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS (2009) Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 75:5227–5236. doi:10.1128/AEM.00592-09
44. Zhang J, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614–620. doi:10.1093/bioinformatics/btt593