Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas - PubMed (original) (raw)

Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas

David M Nelson et al. PLoS One. 2010.

Abstract

Background: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood.

Methodology/principal findings: We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT.

Conclusion: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Phylogenetic relationships of 16S rRNA gene sequences among the fosmids, clone library, and Clostridium clusters.

Clone library sequences start with “M.” The numbers in parentheses following some of the marine iguana sequences indicate the number of times that a particular sequence was obtained. Only representatives of the major Clostridium clusters, and limited representatives of the Bacteroidetes and Coriobacteriales, are shown. The tree was inferred using the neighbor joining approach. The numbers at the nodes represent bootstrap values. The bar represents 0.02 substitutions per nucleotide position. The outgroup is Aquifex pyrophilus.

Figure 2

Figure 2. BLASTP result distribution across fosmids 7–14 and 7–25.

a) The X-axis indicates genera with at least 10 BLASTP hits throughout the ORFeome of the analyzed fosmids. Using a previously published approach the organism distribution on a genus level was identified for each coding gene, e-values were grouped into ranges, and threshold levels were defined for minimum overall frequency. Genera are phylogenetically sorted. The Y-axis indicates respective e-value ranges. The frequency of hits for each genus in each e-value range (log scale) is shown by color coding and corresponding values are indicated in the figure. All BLASTP hits per genus per ORF were accepted. b) Same as a), except that custom databases of species from phylogenetically defined Clostridium clusters were used.

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