Comparison of the fecal microbiota in feral and domestic goats

Genes

Volumn 3, Issue 1, 2012, Pages 1-18

  de Jesus Laboy, Kassandra M ^a   Godoy Vitorino, Filipa ^a,c   Piceno, Yvette M ^b   Tom, Lauren M ^b   Pantoja Feliciano, Ida G ^a   Rivera Rivera, Michelle J ^a   Andersen, Gary L ^b   Domínguez Bello, María G ^a  

^a UNIVERSITY OF PUERTO RICO RIO PIEDRAS   (Puerto Rico)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Antibiotic; Domestic; Feral; Microbiome; Resistance

Indexed keywords

ANTIBIOTIC AGENT;

ANTIBIOTIC RESISTANCE; ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; DIET; DOMESTIC GOAT; FECES MICROFLORA; FERAL GOAT; GENE; GENETIC DIFFERENCE; GOAT; MICROBIAL COMMUNITY; NONHUMAN; PHYLUM; POLYMERASE CHAIN REACTION; PUERTO RICO; TET(M) GENE; TET(O) GENE; TET(Q) GENE; TET(S) GENE; TET(W) GENE;

ANIMALIA; BACTERIA (MICROORGANISMS); CAPRA HIRCUS; OTUS;

EID: 84858840616     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes3010001     Document Type: Article

References (43)

1. Ley, R.E.; Hamady, M.; Lozupone, C.; Turnbaugh, P.J.; Ramey, R.R.; Bircher, J.S.; Schlegel, M.L.; Tucker, T.A.; Schrenzel, M.D.; Knight, R.; Gordon, J.I. Evolution of mammals and their gut microbes. Science 2008, 320, 1647-1651.
2. Backhed, F.; Ding, H.; Wang, T.; Hooper, L.V.; Koh, G.Y.; Nagy, A.; Semenkovich, C.F.; Gordon, J.I. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 2004, 101, 15718-15723.
3. Dillon, R.J.; Vennard, C.T.; Buckling, A.; Charnley, A.K. Diversity of locust gut bacteria protects against pathogen invasion. Ecol. Lett. 2005, 8, 1291-1298.
4. Cebra, J.J. Influences of microbiota on intestinal immune system development. Am. J. Clin. Nutr. 1999, 69, 1046S-1051S.
5. Konturek, J.W.; Konturek, S.J.; Kwiecien, N.; Bielanski, W.; Pawlik, T.; Rembiasz, K.; Domschke, W. Leptin in the control of gastric secretion and gut hormones in humans infected with Helicobacter pylori. Scand. J. Gastroenterol. 2001, 36, 1148-1154.
6. Nwokolo, C.U.; Freshwater, D.A.; O'Hare, P.; Randeva, H.S. Plasma ghrelin following cure of Helicobacter pylori. Gut 2003, 52, 637-640.
7. Zoetendal, E.G.; Akkermans, A.D.L.; Akkermans-van Vliet, W.M.; de Visser, J.A.G.M.; de Vos, W.M. The host genotype affects the bacterial community in the human gastrointestinal tract. Microb. Ecol. Health Dis. 2001, 13, 129-134.
8. Macdonald, T.T.; Monteleone, G. Immunity, inflammation, and allergy in the gut. Science 2005, 307, 1920-1925.
9. Ley, R.E.; Turnbaugh, P.J.; Klein, S.; Gordon, J.I.; Microbial ecology: Human gut microbes associated with obesity. Nature 2006, 444, 1022-1023.
10. Rawls, J.F.; Samuel, B.S.; Gordon, J.I. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci. USA 2004, 101, 4596-4601.
11. Zeder, M.A.; Hesse, B. The initial domestication of goats (Capra hircus) in the zagros mountains 10,000 years ago. Science 2000, 287, 2254-2257.
12. Shrestha, J.N.B.; Fahmy, M.H. Breeding goats for meat production: A review: 1. Genetic resources, management and breed evaluation. Small Rumin. Res. 2005, 58, 93-106.
13. Glazko, V. An attempt at understanding the genetic basis of domestication. Anim. Sci. Papers Rep. 2003, 21, 109-120.
14. Khachatourians, G. Agricultural use of antibiotics and the evolution and transfer of antibiotic resistant bacteria. Can. Med. Assoc. 1998, 159, 1129-1136.
15. Butaye, P.; Devriese, L.A.; Haesebrouck, F. Antimicrobial growth promoters used in animal feed: A review of the less well known antibiotics and their effects on Gram-positive bacteria. Clin. Microbiol. Rev. 2003, 16, 175-188.
16. Heatwoke, H.; Levins, R.; Byer, M. Biogeography of the puerto rican bank. Atoll Res. Bull. 1981, 251, 1042-1055.
17. Sponenberg, D.P. Colonial spanish sheep, goats, hogs, and asses in the United States. Zootecnia 1992, 41, 415-419.
18. Yang, G.; Bao, B.; Peatman, E.; Li, H.; Huang, L.; Ren, D. Analysis of the composition of the bacterial community in puffer fish Takifugu obscurus. Aquaculture 2007, 262, 183-191.
19. Croswell, A.; Amir, E.; Teggatz, P.; Barman, M.; Salzman, N. Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric salmonella infection. Infect. Immun. 2009, 77, 2741-2753.
20. Leser, T.D.; Lindecrona, R.H.; Jensen, T.K.; Jensen, B.B.; Moller, K. Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae. Appl. Environ. Microbiol. 2000, 66, 3290-3296.
21. Meléndez-Ackerman, E.J.; Cortés, C.; Sustache, J.; Aragón, S.; Morales-Vargas, M.; García-Bermúdez, M.; Fernández, D.S. Diet of feral goats in Mona Island Reserve, Puerto Rico. Caribb. J. Sci. 2008, 44, 199-205.
22. Aminov, R.I.; Garrigues-Jeanjean, N.; Mackie, R.I. Molecular ecology of tetracycline resistance: Development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins. Appl. Environ. Microbiol. 2001, 67, 22-32.
23. Aires, J.; Doucet Populaire, F.; Butel, M.J. Tetracycline resistance mediated by tet(W), tet(M), and tet(O) genes of Bifidobacterium isolates from humans. Appl. Environ. Microbiol. 2007, 73, 2751-2754.
24. Ready, D.; Pratten, J.; Roberts, A.P.; Bedi, R.; Mullany, P.; Wilson, M. Potential role of Veillonella spp. as a reservoir of transferable tetracycline resistance in the oral cavity. Antimicrob. Agents Chemother. 2006, 50, 2866-2868.
25. Stanton, T.B.; Humphrey, S.B.; Stoffregen, W.C. Chlortetracycline-resistant intestinal bacteria in organically-raised and feral swine. Appl. Environ. Microbiol. 2011, 77, doi:10.1128/AEM.00688-11.
26. Osterblad, M.; Norrdahl, K.; Korpimaki, E.; Huovinen, P. Antibiotic resistance. How wild are wild mammals? Nature 2001, 409, 37-38.
27. Gardner, P.; Smith, D.H.; Beer, H.; Moellering, R.C., Jr. Recovery of resistance (R) factors from a drug-free community. Lancet 1969, 2, 774-776.
28. Routman, E.; Miller, R.D.; Phillips-Conroy, J.; Hartl, D.L. Antibiotic resistance and population structure in Escherichia coli from free-ranging African yellow baboons. Appl. Environ. Microbiol. 1985, 50, 749-754.
29. Gilliver, M.A.; Bennett, M.; Begon, M.; Hazel, S.M.; Hart, C.A. Antibiotic resistance found in wild rodents. Nature 1999, 401, 233-234.
30. Berg, J.; Tom-Petersen, A.; Nybroe, O. Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field. Lett. Appl. Microbiol. 2005, 40, 146-151.
31. Coates, M.D.; MK; Kon, S.K. The effect of antibiotics on the intestine of the chick. Br. J. Nutr. 1955, 9, 110-119.
32. Guillemot, D.; Carbon, C.; Balkau, B.; Geslin, P.; Lecoeur, H.; Vauzelle-Kervroëdan, F.; Bouvenot, G.; Eschwége, E. Low dosage and long treatment duration of beta-lactam: Risk factors for carriage of penicillin-resistant Streptococcus pneumoniae. J. Am. Med. Assoc. 1998, 279, 365-370.
33. DeSantis, T.Z.; Brodie, E.L.; Moberg, J.P.; Zubieta, I.X.; Piceno, Y.M.; Andersen, G.L. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 2007, 53, 371-383.
34. Brodie, E.L.; Desantis, T.Z.; Joyner, D.C.; Baek, S.M.; Larsen, J.T.; Andersen, G.L.; Hazen, T.C.; Richardson, P.M.; Herman, D.J.; Tokunaga, T.K.; et al. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 2006, 72, 6288-6298.
35. Lozupone, C.; Hamady, M.; Knight, R. UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma. 2006, 7, doi:10.1186/1471-2105-7-371.
36. Schatz, M.C.; Phillippy, A.M.; Gajer, P.; DeSantis, T.Z.; Andersen, G.L.; Ravel, J. Integrated microbial survey analysis of Prokaryotic communities for the PhyloChip microarray. Appl. Environ. Microbiol. 2010, 76, 5636-5638.
37. PhyloTrac: Environmental Sample Analysis. Available online: http://www.phylotrac.org/Home.html (accessed on 28 November 2011).
38. The R Project for Statistical Computing. Available online: http://www.R-project.org (accessed on 28 November 2011).
39. Development Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2008.
40. Dudoit, S.; Yang, Y.H.; Callow, M.J.; Speed, T.P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Tech. Rep. 2000, 12, 111-139.
41. Schnappinger, D.; Hillen, W. Tetracyclines: Antibiotic action, uptake, and resistance mechanisms. Arch. Microbiol. 1996, 165, 359-369.
42. Roberts, M.C. Update on acquired tetracycline resistance genes. FEMS Microbiol. Lett. 2005, 245, 195-203.
43. Villedieu, A.; Diaz-Torres, M.L.; Hunt, N.; McNab, R.; Spratt, D.A.; Wilson, M.; Mullany, P. Prevalence of tetracycline resistance genes in oral bacteria. Antimicrob. Agents Chemother. 2003, 47, 878-882.