Phylogenetic Evidence for Lateral Gene Transfer in the Intestine of Marine Iguanas

Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, USA.
PLoS ONE (Impact Factor: 3.23). 05/2010; 5(5):e10785. DOI: 10.1371/journal.pone.0010785
Source: PubMed


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.
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.
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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Available from: David Nelson, Jul 21, 2015
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    • "Although seven genomes contained butyrate kinase, they appear to have potentially acquired the corresponding gene laterally from other members of class Clostridia (supplementary fig. S1, Supplementary Material online), a group associated with frequent LGT events (Beiko et al. 2005; Sebaihia et al. 2006; Nelson et al. 2010), especially within GI tracts (Meehan and Beiko 2012). LGT has also contributed to the distribution of the BCoAT-mediated pathway, the main route for butyric acid production within the human GI tract (Louis et al. 2004; Louis and Flint 2009). "
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    ABSTRACT: Several bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of many species within the group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer. An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation while other members of this family lack key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity and bovine rumen. Our analysis demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and lateral gene transfer.
    Genome Biology and Evolution 03/2014; 6(3). DOI:10.1093/gbe/evu050 · 4.23 Impact Factor
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    • "A previous attempt to isolate novel bacteria from Galápagos marine iguana feces resulted in a range of Clostridia isolated from media containing different carbohydrate sources, and these isolates await full identification and characterization (Mackie, unpublished data). In a separate enrichment culture that actively degraded agar by rapid liquefaction, repeated attempts to isolate pure cultures of the agar-degraders failed, suggesting novel metabolic and functional pathways, operating synergistically , that require further elucidation before subsequent isolation attempts (Nelson et al., 2010). "
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    The ISME Journal 03/2011; 5(9):1461-70. DOI:10.1038/ismej.2011.33 · 9.30 Impact Factor
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