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Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

Menke S - Front Microbiol (2014)

Bottom Line: Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host.Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles.Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research Berlin, Germany ; Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research Berlin, Germany.

ABSTRACT
Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

No MeSH data available.


Heatmap of 16S rRNA gene reads assigned to taxonomy on the bacterial phylum level. The color encodes the abundance of OTUs (log-scale of base 4) allocated to a specific phylum. Each column represents data of an individual black-backed jackal (left) or cheetah (right) based on a sub-sampling of 8000 reads per individual. The two species are similar in their phylum profiles and share all phyla with proportions above 0.2%.
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Figure 1: Heatmap of 16S rRNA gene reads assigned to taxonomy on the bacterial phylum level. The color encodes the abundance of OTUs (log-scale of base 4) allocated to a specific phylum. Each column represents data of an individual black-backed jackal (left) or cheetah (right) based on a sub-sampling of 8000 reads per individual. The two species are similar in their phylum profiles and share all phyla with proportions above 0.2%.

Mentions: Some reads could not be assigned to a phylum and thus remained on the kingdom level of bacteria (0.5% reads of cheetahs and 0.3% reads of black-backed jackals). Basically, cheetahs and black-backed jackals had the same most abundant (>0.2%) bacterial phyla (Figure 1). Cyanobacteria and Tenericutes were only represented in the black-backed jackal with proportions ≥0.1% (0.2 and 0.1%, respectively). Differences in proportions of bacterial phyla were pronounced between the species for Actinobacteria (15.5% cheetah vs. 3.8% black-backed jackals), Bacteroidetes (5.8% cheetah vs. 26.1% black-backed jackals) and Firmicutes (56.2% cheetah vs. 40.5% black-backed jackals). Cheetahs and black-backed jackals had these phyla in common with domestic cats, dogs, and other carnivores (Table 1).


Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

Menke S - Front Microbiol (2014)

Heatmap of 16S rRNA gene reads assigned to taxonomy on the bacterial phylum level. The color encodes the abundance of OTUs (log-scale of base 4) allocated to a specific phylum. Each column represents data of an individual black-backed jackal (left) or cheetah (right) based on a sub-sampling of 8000 reads per individual. The two species are similar in their phylum profiles and share all phyla with proportions above 0.2%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4196554&req=5

Figure 1: Heatmap of 16S rRNA gene reads assigned to taxonomy on the bacterial phylum level. The color encodes the abundance of OTUs (log-scale of base 4) allocated to a specific phylum. Each column represents data of an individual black-backed jackal (left) or cheetah (right) based on a sub-sampling of 8000 reads per individual. The two species are similar in their phylum profiles and share all phyla with proportions above 0.2%.
Mentions: Some reads could not be assigned to a phylum and thus remained on the kingdom level of bacteria (0.5% reads of cheetahs and 0.3% reads of black-backed jackals). Basically, cheetahs and black-backed jackals had the same most abundant (>0.2%) bacterial phyla (Figure 1). Cyanobacteria and Tenericutes were only represented in the black-backed jackal with proportions ≥0.1% (0.2 and 0.1%, respectively). Differences in proportions of bacterial phyla were pronounced between the species for Actinobacteria (15.5% cheetah vs. 3.8% black-backed jackals), Bacteroidetes (5.8% cheetah vs. 26.1% black-backed jackals) and Firmicutes (56.2% cheetah vs. 40.5% black-backed jackals). Cheetahs and black-backed jackals had these phyla in common with domestic cats, dogs, and other carnivores (Table 1).

Bottom Line: Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host.Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles.Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research Berlin, Germany ; Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research Berlin, Germany.

ABSTRACT
Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

No MeSH data available.