This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Hill, J. E. Articles by Hemmingsen, S. M. Search for Related Content PubMed PubMed Citation Articles by Hill, J. E. Articles by Hemmingsen, S. M. Agricola Articles by Hill, J. E. Articles by Hemmingsen, S. M.

Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing

National Research Council Plant Biotechnology Institute,¹ Department of Poultry and Animal Sciences,² Department of Biochemistry,³ Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada⁴

Received 10 January 2002/ Accepted 12 March 2002

Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.

This article has been cited by other articles:

• Willing, B. P., Van Kessel, A. G. (2007). Enterocyte proliferation and apoptosis in the caudal small intestine is influenced by the composition of colonizing commensal bacteria in the neonatal gnotobiotic pig. J ANIM SCI 85: 3256-3266 [Abstract] [Full Text]  
• Shirkey, T. W., Siggers, R. H., Goldade, B. G., Marshall, J. K., Drew, M. D., Laarveld, B., Van Kessel, A. G. (2006). Effects of Commensal Bacteria on Intestinal Morphology and Expression of Proinflammatory Cytokines in the Gnotobiotic Pig. Exp. Biol. Med. 231: 1333-1345 [Abstract] [Full Text]  
• Dumonceaux, T. J., Hill, J. E., Hemmingsen, S. M., Van Kessel, A. G. (2006). Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken. Appl. Environ. Microbiol. 72: 2815-2823 [Abstract] [Full Text]  
• Hill, J. E., Paccagnella, A., Law, K., Melito, P. L., Woodward, D. L., Price, L., Leung, A. H., Ng, L.-K., Hemmingsen, S. M., Goh, S. H. (2006). Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database.. J Med Microbiol 55: 393-399 [Abstract] [Full Text]  
• Maynard, C., Berthiaume, F., Lemarchand, K., Harel, J., Payment, P., Bayardelle, P., Masson, L., Brousseau, R. (2005). Waterborne Pathogen Detection by Use of Oligonucleotide-Based Microarrays. Appl. Environ. Microbiol. 71: 8548-8557 [Abstract] [Full Text]  
• Hill, J. E., Hemmingsen, S. M., Goldade, B. G., Dumonceaux, T. J., Klassen, J., Zijlstra, R. T., Goh, S. H., Van Kessel, A. G. (2005). Comparison of Ileum Microflora of Pigs Fed Corn-, Wheat-, or Barley-Based Diets by Chaperonin-60 Sequencing and Quantitative PCR. Appl. Environ. Microbiol. 71: 867-875 [Abstract] [Full Text]  
• Ventura, M., Canchaya, C., Zink, R., Fitzgerald, G. F., van Sinderen, D. (2004). Characterization of the groEL and groES Loci in Bifidobacterium breve UCC 2003: Genetic, Transcriptional, and Phylogenetic Analyses. Appl. Environ. Microbiol. 70: 6197-6209 [Abstract] [Full Text]  
• Hill, J. E., Penny, S. L., Crowell, K. G., Goh, S. H., Hemmingsen, S. M. (2004). cpnDB: A Chaperonin Sequence Database. Genome Res. 14: 1669-1675 [Abstract] [Full Text]  
• Konstantinov, S. R., Awati, A., Smidt, H., Williams, B. A., Akkermans, A. D. L., de Vos, W. M. (2004). Specific Response of a Novel and Abundant Lactobacillus amylovorus-Like Phylotype to Dietary Prebiotics in the Guts of Weaning Piglets. Appl. Environ. Microbiol. 70: 3821-3830 [Abstract] [Full Text]  
• Mai, V., Morris, J. G. Jr. (2004). Colonic Bacterial Flora: Changing Understandings in the Molecular Age. J. Nutr. 134: 459-464 [Abstract] [Full Text]