A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal

Abstract

Natural spices play an essential role in human nutrition and well-being. However, their processing on different scales can expose them to potential sources of contamination. This study aimed to describe the bacterial community genomic footprint in spices sold in Senegal. Spice samples were collected in August 2022 in Saint-Louis, Senegal. The genomic region coding bacterial 16S rRNA was then amplified and sequenced using Oxford Nanopore Technology (ONT). Sequencing was carried out on two batches of samples, one containing part of the "Local Spices or Herbs" (n = 10), and the other, a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Results showed high bacterial diversity and the predominance of Escherichia coli and Salmonella enterica in samples, with total reads of 65,744 and 165,325 for the two batches, respectively. The sample category "Homemade mixture of food condiments ", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme. Also, the different categories of spices studied show similarities in their bacterial composition. These results highlight the microbial community's highly diverse genomic profile, including pathogenic bacteria, in spice samples.

Keywords: Bacterial community; Metagenomic; Sequencing; Spices.

Figure 1

Relative distribution of bacterial species in samples. This figure was produced using Microsoft Excel 2016. It describes the relative abundance of bacterial species in each spice sample studied. The “others” section contains bacterial with less than 1% abundance.

Figure 2

Alpha-diversity analysis. This figure was produced using R software version 4.1.3 to observe alpha-diversity, representing the diversity of bacterial species within a single spice group such as Curcuma, 7 spice, local spices or thyme. This alpha diversity is observed through its different parameters: the “observed species” (Fig. 2a) gives the number of bacterial species observed in each spice group considered; the chao1 index (Fig. 2b) gives the actual number of bacterial species in the environment based on the previously estimated number; the Shannon index (Fig. 2c), which shows the main differences in the diversity of the spice groups studied, as the higher the index, the greater the diversity; the Simpson index (Fig. 2d), which completes the interpretation of alpha diversity, as it varies between 0 and 1, showing maximum diversity if it tends towards 1 and minimum if it tends towards 0.

Figure 3

Beta-diversity analysis. This figure was produced using R software version 4.1.3. The aim is to compare bacterial diversity in the different spice groups studied using Jaccard and Bray Curtis distances.

Figure 4

Hierarchical clustering of samples.