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Microbial Ecology

, Volume 63, Issue 4, pp 719–725 | Cite as

Bacterial Diversity in the Cecum of the World’s Largest Living Rodent (Hydrochoerus hydrochaeris)

  • M. Alexandra García-Amado
  • Filipa Godoy-Vitorino
  • Yvette M. Piceno
  • Lauren M. Tom
  • Gary L. Andersen
  • Emilio A. Herrera
  • Maria G. Domínguez-BelloEmail author
Notes and Short Communications

Abstract

The capybara (Hydrochoerus hydrochaeris) is the world’s largest living rodent. Native to South America, this hindgut fermenter is herbivorous and coprophagous and uses its enlarged cecum to digest dietary plant material. The microbiota of specialized hindgut fermenters has remained largely unexplored. The aim of this work was to describe the composition of the bacterial community in the fermenting cecum of wild capybaras. The analysis of bacterial communities in the capybara cecum is a first step towards the functional characterization of microbial fermentation in this model of hindgut fermentation. We sampled cecal contents from five wild adult capybaras (three males and two females) in the Venezuelan plains. DNA from cecal contents was extracted, the 16S rDNA was amplified, and the amplicons were hybridized onto a DNA microarray (G2 PhyloChip). We found 933 bacterial operational taxonomic units (OTUs) from 182 families in 21 bacterial phyla in the capybara cecum. The core bacterial microbiota (present in at least four animals) was represented by 575 OTUs. About 86% of the cecal bacterial OTUs belong to only five phyla, namely, Firmicutes (322 OTUs), Proteobacteria (301 OTUs), Bacteroidetes (76 OTUs), Actinobacteria (69 OTUs), and Sphirochaetes (37 OTUs). The capybara harbors a diverse bacterial community that includes lineages involved in fiber degradation and nitrogen fixation in other herbivorous animals.

Keywords

Bacterial Community Proteobacteria Actinobacteria Firmicutes Bacteroidetes 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported by grants from CREST HRD0206200, UPR grant FIPI- 8–80314, US DOE/UC Berkeley/LBNL under contract DE-AC02-05CH11231, the Venezuelan Institute for Scientific Research-IVIC (Caracas, Venezuela), and Universidad Simón Bolívar (Caracas, Venezuela).

Supplementary material

248_2011_9963_MOESM1_ESM.doc (373 kb)
Table S1 Numbers of bacterial OTUs by family in the cecum of individual capybaras. The most abundant families appear in red. (DOC 373 kb)
248_2011_9963_MOESM2_ESM.doc (48 kb)
Table S2 Distance matrix of UNIFRAC community distances between individuals (DOC 48 kb)
248_2011_9963_MOESM3_ESM.jpg (64 kb)
Fig. S1 Principal coordinate analysis of bacterial communities from cecal contents from five capybaras. Female communities are shown in red and those of male communities in blue. Variability explained by each principal component is indicated in parentheses (JPEG 64 kb)

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • M. Alexandra García-Amado
    • 1
  • Filipa Godoy-Vitorino
    • 2
    • 3
  • Yvette M. Piceno
    • 4
  • Lauren M. Tom
    • 4
  • Gary L. Andersen
    • 4
  • Emilio A. Herrera
    • 5
  • Maria G. Domínguez-Bello
    • 2
    Email author
  1. 1.Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y BioquímicaInstituto Venezolano de Investigaciones CientíficasCaracasVenezuela
  2. 2.Department of BiologyUniversity of Puerto RicoSan JuanPuerto Rico
  3. 3.Metagenome Systems ProgramDOE Joint Genome InstituteWalnut CreekUSA
  4. 4.Ecology Department, Earth Sciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  5. 5.Departamento de Estudios AmbientalesUniversidad Simón BolívarCaracasVenezuela

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