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

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.

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

“…However, the observed similarities between the oligotypes from sewage and those from feces of swine, cats, and dogs suggest that any indicators developed should be tested thoroughly against feces from a wider selection of these hosts to ensure their specificity or high degree of preference for sewage. Although the differentiation of animal sources was not the focus of this study, similarities (shared oligotypes) were common among hosts with similar diets and/or physiologies, such as humans (sewage) and swine or deer and cows, as has been observed in other studies (10,25,45). This suggests that a more comprehensive sampling effort with respect to particular animals of interest would also yield hostspecific oligotypes for tracking animal fecal pollution.…”

“…Our recent analysis of fecal community profiles using this approach with sequences that mapped to the genus Blautia revealed a high degree of host preference and host specificity for both humans and other animals at the oligotype level (35). Another recent study by Menke et al also demonstrated the efficacy of Blautia at distinguishing two free-ranging sympatric carnivore host species (45). Our current study expanded upon this effort and examined eight fecal taxa, in addition to Blautia (32,35) and the widely studied Bacteroides (8,13,15,16,44), that are relatively unexplored in terms of source tracking to determine the potential of each of these taxa to provide novel targets for use as alternative indicators.…”

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources

“…Firmicutes is the only phylum universally shared in mammals (Ley et al. ) and in some carnivore species and human Firmicutes has a relative abundance of >60% (Menke et al., , ).…”

Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens

“…The laboratory work including DNA extraction, PCR protocol, purification, library generation and sequencing was as described in detail by Menke et al. (). All individuals were run in duplicate in independent PCRs labelled with different barcodes and were processed for library preparation and paired‐end sequencing in a single run of next‐generation sequencing (NGS) Illumina ® MiSeq.…”