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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.


Proportions of bacterial taxa which were present in both the cheetah and the black-backed jackal with proportions ≥0.1% (pooled on host species level) at the finest taxonomic resolution. Oligotyping was performed on all 20 bacterial genera and the two bacterial families to resolve the within taxon variation of bacteria between host species on a bacterial species-like level.
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Figure 4: Proportions of bacterial taxa which were present in both the cheetah and the black-backed jackal with proportions ≥0.1% (pooled on host species level) at the finest taxonomic resolution. Oligotyping was performed on all 20 bacterial genera and the two bacterial families to resolve the within taxon variation of bacteria between host species on a bacterial species-like level.

Mentions: Oligotyping of bacterial reads extracted from 20 shared genera and two shared families (Figure 4) revealed differences in representative oligotypes and oligotype diversity between cheetahs and black-backed jackals (Table 2, Supplementary Table 2). Collinsella and Lactobacillus were the genera with the lowest and highest number of oligotypes, respectively, in both species. In general, black-backed jackals had a higher number of oligotypes for 12 out of 22 taxa, particularly in Blautia and Megamonas. Only in the genera [Eubacterium] and Phascolarctobacterium cheetahs carried a higher number of oligotypes. In Clostridium, Enterococcus, Enterobacteriaceae, Fusobacteriaceae, Peptococcus, Peptostreptococcus, [Ruminococcus], and Sutterella the number of oligotypes were identical in both species. Within each genus and within the two families of bacteria the proportions of shared oligotypes varied substantially between cheetahs and black-backed jackals, and some oligotypes were exclusively found in one species (Supplementary Figure 2). In 60% of cases the oligotype with the highest proportion was different for both species (Supplementary Figure 2). Overall, the distribution of number of oligotypes per taxon did not differ significantly between cheetahs and black-backed jackals [K-S test (1000 permutations): D = 0.18, p = 0.69]. The observed differences in proportions of oligotypes between the two species strongly varied between bacterial taxa (Figure 5). The genus Slackia exhibited the highest oligotype differences, whereas the family Enterobacteriaceae only showed a weak differentiation between the host species. Observed differences differed strongly from a random assignment of oligotypes to cheetah and black-backed jackal within each bacterial taxon (Figure 5; randomization test: p < 0.001). When we applied the oligotyping approach on the level of cheetah and black-backed jackal individuals, results were in line with the species-level comparison and individuals exhibited strong differences in oligotype profiles according to species identity (Figure 6). Nevertheless, results from oligotyping on the level of species and individuals are only comparable in a qualitative but not in a quantitative way due to differences in the data sets and parameters which were used for oligotyping.


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)

Proportions of bacterial taxa which were present in both the cheetah and the black-backed jackal with proportions ≥0.1% (pooled on host species level) at the finest taxonomic resolution. Oligotyping was performed on all 20 bacterial genera and the two bacterial families to resolve the within taxon variation of bacteria between host species on a bacterial species-like level.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Proportions of bacterial taxa which were present in both the cheetah and the black-backed jackal with proportions ≥0.1% (pooled on host species level) at the finest taxonomic resolution. Oligotyping was performed on all 20 bacterial genera and the two bacterial families to resolve the within taxon variation of bacteria between host species on a bacterial species-like level.
Mentions: Oligotyping of bacterial reads extracted from 20 shared genera and two shared families (Figure 4) revealed differences in representative oligotypes and oligotype diversity between cheetahs and black-backed jackals (Table 2, Supplementary Table 2). Collinsella and Lactobacillus were the genera with the lowest and highest number of oligotypes, respectively, in both species. In general, black-backed jackals had a higher number of oligotypes for 12 out of 22 taxa, particularly in Blautia and Megamonas. Only in the genera [Eubacterium] and Phascolarctobacterium cheetahs carried a higher number of oligotypes. In Clostridium, Enterococcus, Enterobacteriaceae, Fusobacteriaceae, Peptococcus, Peptostreptococcus, [Ruminococcus], and Sutterella the number of oligotypes were identical in both species. Within each genus and within the two families of bacteria the proportions of shared oligotypes varied substantially between cheetahs and black-backed jackals, and some oligotypes were exclusively found in one species (Supplementary Figure 2). In 60% of cases the oligotype with the highest proportion was different for both species (Supplementary Figure 2). Overall, the distribution of number of oligotypes per taxon did not differ significantly between cheetahs and black-backed jackals [K-S test (1000 permutations): D = 0.18, p = 0.69]. The observed differences in proportions of oligotypes between the two species strongly varied between bacterial taxa (Figure 5). The genus Slackia exhibited the highest oligotype differences, whereas the family Enterobacteriaceae only showed a weak differentiation between the host species. Observed differences differed strongly from a random assignment of oligotypes to cheetah and black-backed jackal within each bacterial taxon (Figure 5; randomization test: p < 0.001). When we applied the oligotyping approach on the level of cheetah and black-backed jackal individuals, results were in line with the species-level comparison and individuals exhibited strong differences in oligotype profiles according to species identity (Figure 6). Nevertheless, results from oligotyping on the level of species and individuals are only comparable in a qualitative but not in a quantitative way due to differences in the data sets and parameters which were used for oligotyping.

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.