Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird

Applied and Environmental Microbiology

Volumn 74, Issue 19, 2008, Pages 5905-5912

  Godoy Vitorino, Filipa ^a   Ley, Ruth E ^b   Gao, Zhan ^c   Pei, Zhiheng ^c   Ortiz Zuazaga, Humberto ^a   Pericchi, Luis R ^a   Garcia Amado, Maria A ^d   Michelangeli, Fabian ^d   Blaser, Martin J ^c   Gordon, Jeffrey I ^b   Domínguez Bello, Maria G ^a  

^a UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d INSTITUTO VENEZOLANO DE INVESTIGACIONES CIENTÍFICAS   (Venezuela)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; CROPS;

16S RRNA GENE SEQUENCES; ACTINOBACTERIA; AVIAN SPECIES; BACTERIAL COMMUNITIES; BACTERIAL POPULATIONS; COVERAGE ESTIMATORS; FIRMICUTES; INTERESTING MODELS; MICROBIOTA; OPERATIONAL TAXONOMIC UNITS; PHYLOTYPES; PROTEOBACTERIA; SPECIES RICHNESSES;

ECOLOGY;

RIBOSOME RNA; BACTERIAL DNA; BACTERIAL RNA; RIBOSOME DNA; RNA 16S;

BACTERIUM; BIRD; CELLULOSE; DIGESTION; DOMINANCE; FOOD SELECTION; MICROBIAL COMMUNITY; RNA; SPECIES RICHNESS; TAXONOMY;

ACTINOBACTERIA; AMINANAEROBIA; ANIMAL EXPERIMENT; ARTICLE; BACILLI; BACTEROIDETES; BIRD; CONTROLLED STUDY; ECOSYSTEM; FIRMICUTES; FOLIVORE; GENE SEQUENCE; HOATZIN; INTESTINE FLORA; LENTISPHAERAE; MICROBIAL COMMUNITY; MOLLICUTES; NEOTROPICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEOBACTERIA; SPIROCHETE; TAXONOMY; VERRUCOMICROBIA; ANIMAL; AVIAN CROP; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE HOMOLOGY;

ACTINOBACTERIA; AVES; BACILLI (CLASS); BACTERIA (MICROORGANISMS); BACTEROIDALES; BACTEROIDETES; CLOSTRIDIA; FIRMICUTES; LENTISPHAERAE; MOLLICUTES; OPISTHOCOMIDAE; PROTEOBACTERIA; SPIROCHAETES; VERRUCOMICROBIA;

ANIMALS; BACTERIA; BIODIVERSITY; BIRDS; CROP, AVIAN; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 54449098594     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00574-08     Document Type: Article

References (53)

1. An, D., X. Dong, and Z. Dong. 2005. Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. Anaerobe 11:207-215.
2. Chao, A., and T.-J. Shen. 2003. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ. Ecol. Stat. 10:429-443.
3. Clarke, A., and P. Rothery. 2008. Scaling of body temperature in mammals and birds. Funct. Ecol. 22:58-67.
4. Collinson, M. E., and J. J. Hooker. 1991. Fossil evidence of interactions between plants and plant-eating mammals. Philos. Trans. R. Soc. Lond. B 333:197-208.
5. Cracraft, J. 1971. A new family of hoatzin-like birds (order Opisthocomiformes) from the Eocene of South America. Ibis 113:229-233.
6. Demment, M. W., and P. J. Van Soest. 1985. A nutritional explanation for body-size patterns of ruminant and nonruminant herbivores. Am. Nat. 125:641-672.
7. DeSantis, T. Z., Jr., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394-W399.
8. Domínguez-Bello, M. G., M. Lovera, P. Suárez, and F. Michelangeli. 1993. Microbial digestive symbionts of the crop of the hoatzin (Opisthocomus hoazin): the only foregut fermenter avian. Physiol. Zool. 66:374-383.
9. Domínguez-Bello, M. G., F. Michelangeli, M. C. Ruiz, A. Garcia, and E. Rodriguez. 1994. Ecology of the folivorous hoatzin (Opisthocomus hoazin) on the Venezuelan plains. Auk 111:643-651.
10. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
11. Garcia-Amado, M. A., F. Michelangeli, P. Gueneau, and M. E. Perez. 2007. Bacterial detoxification of saponins in the crop of the avian foregut fermenter Opisthocomus hoazin. J. Anim. Feed Sci. 16:82-85.
12. Good, I. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
13. Grajal, A. 1991. Digestive efficiency of the hoatzin (Opisthocomus hoatzin), a folivorous bird with foregut fermentation. University of Florida, Gainesville.
14. Grajal, A. 1995. Structure and function of the digestive tract of the hoatzin (Opisthocomus hoazin): a folivorous bird with foregut fermentation. Auk 112:20-28.
15. Grajal, A., and O. Parra. 1995. Passage rates of digesta markers in the gut of the hoatzin, a folivorous bird with foregut fermentation. Condor 97:675-683.
16. Grajal, A., S. Strahl, R. Parra, M. G. Dominguez, and A. Neher. 1989. Foregut fermentation in the hoatzin, a neotropical leave-eating bird. Science 245:1236-1238.
17. Grajal, A., and S. Strahl. 1991. A bird with the guts to eat leaves. Nat. His. 100:48-55.
18. Hedges, S. B., M. D. Simmons, M. A. van Dijk, G. J. Caspers, W. W. de Jong, and C. G. Sibley. 1995. Phylogenetic relationships of the hoatzin, an enigmatic South American bird. Proc. Natl. Acad. Sci. USA 92:11662-11665.
19. Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.
20. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:REVIEWS0003.
21. Hughes, J. M., and A. J. Baker. 1999. Phylogenetic relationships of the enigmatic hoatzin (Opisthocomus hoazin) resolved using mitochondrial and nuclear gene sequences. Mol. Biol. Evol. 16:1300-1307.
22. Hungate, R. E. 1950. The anaerobic mesophilic cellulolytic bacteria. Bacteriol. Rev. 14:1-49.
23. Hungate, R. E. 1966. The rumen and its microbes. Academic Press, New York, NY.
24. Jones, R. J., M. A. G. Amado, and M. G. Dominguez-Bello. 2000. Comparison of the digestive ability of crop fluid from the folivorous hoatzin (Opisthocomus hoazin) and cow rumen fluid with seven tropical forages. Anim. Feed Sci. Technol. 87:287-296.
25. Karnati, S. K., J. T. Sylvester, S. M. Noftsger, Z. Yu, N. R. St.-Pierre, and J. L. Firkins. 2007. Assessment of ruminal bacterial populations and protozoal generation time in cows fed different methionine sources. J. Dairy Sci. 90:798-809.
26. Kleiber, M. 1961. The fire of life. Wiley, New York, NY.
27. Konstantinidis, K. T., and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102:2567-2572.
28. Kornegay, J. R. 1996. Molecular genetics and evolution of stomach and nonstomach lysozymes in the hoatzin. J. Mol. Evol. 42:676-684.
29. Kornegay, J. R., J. W. Schilling, and A. C. Wilson. 1994. Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin. Mol. Biol. Evol. 11:921-928.
30. Larue, R., Z. Yu, V. A. Parisi, A. R. Egan, and M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7:530-543.
31. Ley, R. E., F. Backhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight, and J. I. Gordon. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:11070-11075.
32. Löffler, F. E., K. M. Ritalahti, and J. M. Tiedje. 1997. Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens. Appl. Environ. Microbiol. 63:4982-4985.
33. Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
34. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
35. Mackie, R. I., R. I. Aminov, W. Hu, A. V. Klieve, D. Ouwerkerk, M. A. Sundset, and Y. Kamagata. 2003. Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl. Environ. Microbiol. 69:6808-6815.
36. Milton, K., and R. H. McBee. 1983. Structural carbohydrate digestion in a new world primate, Alouatta palliata Gray. Comp. Biochem. Physiol. 74:29-31.
37. Muizon, C., and R. L. Cifelli. 2000. The "condylarths" (archaic Ungulata, Mammalia) from the early Palaeocene of Tiupampa (Bolivia): implications on the origin of the South American ungulates. Geodiversitas 22:47-150.
38. Pei, Z., E. Bini, L. Yang, M. Zhou, F. Francois, and M. Blaser. 2004. Bacterial biota in the human distal esophagus. Proc. Natl. Acad. Sci. USA 101:4250-4255.
39. Pielou, E. C. 1966. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13:131-144.
40. Rattray, R. M., and A. M. Craig. 2007. Molecular characterization of sheep ruminal enrichments that detoxify pyrrolizidine alkaloids by denaturing gradient gel electrophoresis and cloning. Microb. Ecol. 54:264-275.
41. Ruiz, M., M. Dominguez-Bello, and F. Michelangeli. 1994. Gastric lysozyme in the hoatzin (Opisthocomus hoazin), an avian folivore. Experientia 50:499-501.
42. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
43. Schloss, P., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
44. Scupham, J. A., T. G. Patton, E. Bent, and D. O. Bayles. 2008. Comparison of the cecal microbiota of domestic and wild turkeys. Microb. Ecol. 56:322-331.
45. Shannon, C. E., and W. Weaver. 1963. The mathematical theory of communication. University of Illinois Press, Urbana, IL.
46. Simpson, E. H. 1949. Measurement of diversity. Nature 163:688.
47. Sorenson, M. D., E. Oneal, J. Garcia-Moreno, and D. P. Mindell. 2003. More taxa, more characters: the hoatzin problem is still unresolved. Mol. Biol. Evol. 20:1484-1498.
48. Springer, M. S., W. J. Murphy, E. Eizirik, and S. J. O'Brien. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. USA 100:1056-1061.
49. Stevens, C. E., and I. D. Hume. 1998. Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients. Physiol. Rev. 78:393-427.
50. Sundset, M., K. Praesteng, I. Cann, S. Mathiesen, and M. R. I. 2007. Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb. Ecol. 54:424-438.
51. Tajima, K., R. I. Aminov, T. Nagamine, H. Matsui, M. Nakamura, and Y. Benno. 2001. Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl. Environ. Microbiol. 67:2766-2774.
52. Van Soest, P. J. 1994. Nutritional ecology of the ruminant, 2nd ed. Comstock, Ithaca, NY.
53. Zhu, X. Y., T. Zhong, Y. Pandya, and R. D. Joerger. 2002. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol. 68:124-137.