Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania

Abstract

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

Figure 1

Samples from wildlife species collected from the Western Serengeti. (A) Samples were collected from three districts surrounding the Serengeti National Park (blue): Bunda (light green), Serengeti (medium green), Tarime (dark green). (B) The bar graphs represent the number of samples collected in each district (Fresh – Gray; Processed – Green shade) from wildebeest (WB), buffalo (BF), and less prevalent species (Other).

Figure 2

Phylum-level alpha diversity. The Shannon Diversity Index (species richness) shows no significant differences in the alpha diversity of phyla between different (A) wildlife species, (B) seasons, and (C) sample conditions. In the boxplot, the median is represented by the middle line, the first and third quartiles by the box and the range by the whiskers. The violin plots demonstrate the distribution of the Shannon Diversity Indices for the different variables, including buffalo (blue), wildebeest (green), Other (red). The overall Shannon Diversity Index for seasons and sample condition is represented in gray.

Figure 3

Hierarchical clustering of samples based on the relative abundance of phyla. (A) Hierarchical clustering grouped the samples into six clusters: C-I (Blue), C-II (Pink), C-III (Gray), and C-IV (Green), C-V (Purple), C-VI (Orange). (B) The stacked bar graphs represent the relative abundance of phyla in each sample. The colors are representative of the respective phyla in the legend. (C) The heatmap includes descriptive characteristics of each sample, including species, condition, season, and region, colored according to the legend. The approximately unbiased (AU) p-value and bootstrap probability (BP) for the respective nodes are noted (AU > 95 are statistically significant).

Figure 4

The Principal Coordinates Analysis of the microbiota at the phylum level. The beta diversity of the samples was represented in Principal Coordinate Analysis using the Bray-Curtis diversity matrix. Since there are multiple variables the four plots illustrate the same visualization of the beta diversity but colored differently according to each characteristic examined: (A) species, (B) region, (C) condition, and (D) season. In (A), the red square represents buffalo, the green circle represents other species, and the blue triangle represent wildebeest. In (B) the same symbols represent the Bunda, Serengeti, and Tarime districts, respectively. In (C,D), the red square represents fresh samples and dry season, respectively and the blue circle represents processed samples and rainy season, respectively. The variability explained by the first two components are represented by the percentage on each axis. The ellipses, represent the 95% confidence interval of the clustering, is represented as the respective colors in each sample series and the centers of the ellipses (or average value of the groups) are reported with the asterisk.

Figure 5

Select agents present in the bushmeat samples. The heatmap demonstrates the relative abundance of the genera of federal select agents (Bacillus, Brucella, Burkholderia, Clostridium, Coxiella, Francisella, Mycoplasma, Ralstonia, Rickettsia, Staphylococcus, Xanthomonas, and Yersinia) in the bushmeat samples. The relative abundance ranges from low (blue) to high (red). The gray color represents samples where the respective select agent is not present.