Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Microbial Ecology

Volumn 69, Issue 1, 2015, Pages 25-36

  Li, Tongtong ^a,b   Long, Meng ^a,b   Gatesoupe, François Joël ^c   Zhang, Qianqian ^a,b   Li, Aihua ^a   Gong, Xiaoning ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c IFREMER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CARASSIUS; CARASSIUS CUVIERI; CETOBACTERIUM; CTENOPHARYNGODON; CTENOPHARYNGODON IDELLA; CYPRINIDAE; FIRMICUTES; FUSOBACTERIA; HYPOPHTHALMICHTHYS; HYPOPHTHALMICHTHYS NOBILIS; PROTEOBACTERIA;

RNA 16S;

ANIMAL; BACTERIUM; BACTEROIDETES; CARP; CLASSIFICATION; GENETICS; INTESTINE; MICROBIOLOGY; PHYLOGENY; PROTEOBACTERIA;

ANIMALS; BACTERIA; BACTEROIDETES; CARPS; INTESTINES; PHYLOGENY; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S;

EID: 84920852587     PISSN: 00953628     EISSN: 1432184X     Source Type: Journal    
DOI: 10.1007/s00248-014-0480-8     Document Type: Article

References (57)

1. Walter J, Britton RA, Roos S (2011) Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A 108:4645–4652
2. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776–788
3. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6:121–131
4. 12-producing ability of the intestinal microflora of freshwater fish. Aquaculture 92:267–276
5. Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5:1595–1608
6. Wu S, Gao T, Zheng Y, Wang W, Cheng Y, Wang G (2010) Microbial diversity of intestinal contents and mucus in yellow catfish (Pelteobagrus fulvidraco). Aquaculture 303:1–7
7. Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquac Res 41:1553–1573
8. Sullam KE, Essinger SD, Lozupone CA, O’CONNOR MP, Rosen GL, Knight R, Kilham SS, Russell JA (2012) Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol 21:3363–3378
9. Greetham H, Giffard C, Hutson R, Collins M, Gibson G (2002) Bacteriology of the Labrador dog gut: a cultural and genotypic approach. J Appl Microbiol 93:640–646
10. Kim DH, Brunt J, Austin B (2007) Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 102:1654–1664
11. Spanggaard B, Huber I, Nielsen J, Nielsen T, Appel K, Gram L (2000) The microflora of rainbow trout intestine: a comparison of traditional and molecular identification. Aquaculture 182:1–15
12. Wu S, Wang G, Angert ER, Wang W, Li W, Zou H (2012) Composition, diversity, and origin of the bacterial community in grass carp intestine. PLoS One 7:e30440. doi:10.1371/journal.pone.0030440
13. Navarrete P, Magne F, Araneda C, Fuentes P, Barros L, Opazo R, Espejo R, Romero J (2012) PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PLoS One 7:e31335. doi:10.1371/journal.pone.0031335
14. Li X, Yu Y, Feng W, Yan Q, Gong Y (2012) Host species as a strong determinant of the intestinal microbiota of fish larvae. J Microbiol 50:29–37
15. Cardenas E, Tiedje JM (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19:544–549
16. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nat Methods 5:235
17. Nam Y-D, Jung M-J, Roh SW, Kim M-S, Bae J-W (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6:e22109. doi:10.1371/journal.pone.0022109
18. Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL (2012) Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity 20:738–747
19. Wong S, Waldrop T, Summerfelt S, Davidson J, Barrows F, Kenney PB, Welch T, Wiens GD, Snekvik K, Rawls JF (2013) Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol 79:4974–4984
20. MoA BoF (2011) China fisheries statistical yearbook 2011. China Agriculture Press, Beijing
21. BillaRd R, BeRni P (2004) Trends in cyprinid polyculture. Cybium 28:255–261
22. Ringø E, Sperstad S, Myklebust R, Refstie S, Krogdahl Å (2006) Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.): the effect of fish meal, standard soybean meal and a bioprocessed soybean meal. Aquaculture 261:829–841
23. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108:4516–4522
24. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35:e120
25. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
26. Schloss PD (2009) A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One 4:e8230
27. Gaspar JM, Thomas WK (2013) Assessing the consequences of denoising marker-based metagenomic data. PLoS One 8:e60458. doi:10.1371/journal.pone.0060458
28. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
29. Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4:e6669. doi:10.1371/journal.pone.0006669
30. Lozupone C, Hamady M, Knight R (2006) UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma 7:371. doi:10.1186/1471-2105-7-371
31. Kemp PF, Aller JY (2004) Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnol Oceanogr Methods 2:114–125
32. Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849
33. Piao Z, Yang L, Zhao L, Yin S (2008) Actinobacterial community structure in soils receiving long-term organic and inorganic amendments. Appl Environ Microbiol 74:526–530
34. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484
35. Sekirov I, Russell SL, Antunes LCM, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90:859–904
36. Gatesoupe FJ, Covès D, Ortega A, Papandroulakis N, Vadstein O, Gándara F (2013) A spatiotemporal study of bacterial community profiles associated with Atlantic bluefin tuna larvae, Thunnus thynnus L., in three Mediterranean hatcheries. Aquac Res 44:1511–1523
37. Larsen AM, Mohammed HH, Arias CR (2014) Characterization of the gut microbiota of three commercially valuable warmwater fish species. J Appl Microbiol 116:1396–1404
38. Ye L, Amberg J, Chapman D, Gaikowski M, Liu W-T (2013) Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish. ISME J 8:541–551
39. van Kessel MA, Dutilh BE, Neveling K, Kwint MP, Veltman JA, Flik G, Jetten MS, Klaren PH, den Camp HJO (2011) Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express 1:1–9. doi:10.1186/2191-0855-1-41
40. Finegold SM, Vaisanen M-L, Molitoris DR, Tomzynski TJ, Song Y, Liu C, Collins MD, Lawson PA (2003) Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium. Syst Appl Microbiol 26:177–181
41. Ni J, Yu Y, Zhang T, Gao L (2012) Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats. Chin J Oceanol Limnol 30:757–765
42. Zhou, Z., He, S., Liu, Y., Shi, P., Yao, B., Ringø, E. (2012). Do stocking densities affect the gut microbiota of gibel carp Carassius auratus gibelio cultured in ponds? J Aquacult Res Development 3. doi:10.4172/2155-9546.S1-003
43. Dominika Ś, Arjan N, Karyn RP, Henryk K (2011) The study on the impact of glycated pea proteins on human intestinal bacteria. Int J Food Microbiol 145:267–272
44. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107:14691–14696
45. Uffen R (1997) Xylan degradation: a glimpse at microbial diversity. J Ind Microbiol Biotechnol 19:1–6
46. Uz I, Ogram AV (2006) Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades. FEMS Microbiol Ecol 57:396–408
47. Schwab C, Cristescu B, Northrup JM, Stenhouse GB, Gänzle M (2011) Diet and environment shape fecal bacterial microbiota composition and enteric pathogen load of grizzly bears. PLoS One 6:e27905. doi:10.1371/journal.pone.0027905
48. Lubbs D, Vester B, Fastinger N, Swanson K (2009) Dietary protein concentration affects intestinal microbiota of adult cats: a study using DGGE and qPCR to evaluate differences in microbial populations in the feline gastrointestinal tract. J Anim Physiol Anim Nutr 93:113–121
49. Pikuta EV, Hoover RB, Marsic D, Whitman WB, Lupa B, Tang J, Krader P (2009) Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano. Int J Syst Evol Microbiol 59:2302–2307
50. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W (2000) Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev 64:655–671
51. Tetlock A, Yost CK, Stavrinides J, Manzon RG (2012) Changes in the gut microbiome of the sea lamprey during metamorphosis. Appl Environ Microbiol 78:7638–7644
52. Pond MJ, Stone DM, Alderman DJ (2006) Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout (Oncorhynchus mykiss). Aquaculture 261:194–203
53. Namba A, Mano N, Hirose H (2007) Phylogenetic analysis of intestinal bacteria and their adhesive capability in relation to the intestinal mucus of carp. J Appl Microbiol 102:1307–1317
54. Ringø E, Olsen RE, Mayhew TM, Myklebust R (2003) Electron microscopy of the intestinal microflora of fish. Aquaculture 227:395–415
55. Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9:279–290
56. Petnicki-Ocwieja T, Hrncir T, Liu Y-J, Biswas A, Hudcovic T, Tlaskalova-Hogenova H, Kobayashi KS (2009) Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A 106:15813–15818
57. Palma G, Capilla A, Nadal I, Nova E, Pozo T, Varea V, Polanco I, Castillejo G, López A, Garrote JA (2010) Interplay between human leukocyte antigen genes and the microbial colonization process of the newborn intestine. Curr Issues Mol Biol 12:1–10