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Applied and Environmental Microbiology, February 2002, p. 673-690, Vol. 68, No. 2
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.2.673-690.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

Thomas D. Leser,* Joanna Z. Amenuvor, Tim K. Jensen, Rikke H. Lindecrona, Mette Boye, and Kristian Møller

Danish Veterinary Laboratory, Department of Microbiology, DK-1790 Copenhagen V, Denmark

Received 11 July 2001/ Accepted 26 November 2001

The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis. Samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. A library comprising 4,270 cloned 16S rDNA sequences obtained directly by PCR from 52 samples of either the ileum, the cecum, or the colon was constructed. In total, 375 phylotypes were identified using a 97% similarity criterion. Three hundred nine of the phylotypes (83%) had a <97% sequence similarity to any sequences in the database and may represent yet-uncharacterized bacterial genera or species. The phylotypes were affiliated with 13 major phylogenetic lineages. Three hundred four phylotypes (81%) belonged to the low-G+C gram-positive division, and 42 phylotypes (11.2%) were affiliated with the Bacteroides and Prevotella group. Four clusters of phylotypes branching off deeply within the low-G+C gram-positive bacteria and one in the Mycoplasma without any cultured representatives were found. The coverage of all the samples was 97.2%. The relative abundance of the clones approximated a lognormal distribution; however, the phylotypes detected and their abundance varied between two libraries from the same sample. The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized.

* Corresponding author. Mailing address: Danish Veterinary Laboratory, Bülowsvej 27, DK-1790 Copenhagen V, Denmark. Phone: 45 3530 0100. Fax: 45 3530 0120. E-mail: tl{at}svs.dk.

Applied and Environmental Microbiology, February 2002, p. 673-690, Vol. 68, No. 2
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.2.673-690.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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