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

Abstract

Natural spices are reputed to play an essential role in human nutrition and well-being due to their organoleptic and therapeutic properties. Moreover, they are increasingly being processed on various scales, exposing them to potential sources of contamination. This study aimed to describe the bacterial community in spices sold in Senegal. Thyme, Curcuma, a mixture of 7 spices and "Local Spices or Herbs" (LSH) samples were collected in selected open-air markets in August 2022 in Saint-Louis, Senegal. DNA extraction was performed using the Omega E.N.Z.A Food DNA kit. PCR assays were based on a genomic fragment encoding bacterial 16S rRNA, which was subsequently 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) designated as "a mixture of food seasonings", and the other, samples of a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Analysis of the sequencing data showed high bacterial diversity and the predominance of Escherichia coli, Salmonella enterica and Escherichia marmotae in the samples, with a total number of reads of 65744 and 165325 for the two batches, respectively. The sample category "Homemade mixture of food condiments (ready to use)", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme, respectively. These results highlight a highly diverse genomic profile of the microbial community, including pathogenic bacteria, in spice samples. This is the first metagenomic study to assess microbial diversity and analyze microbial community structures in spices in Senegal.