Bacterial diversity of smoked and smoked‐dried fish from West Africa: A metagenomic approach

Abstract

This study aimed to explore the bacterial diversity of smoked fish and smoked‐dried fish. Forty‐eight fish samples were collected from various processing sites and markets in Benin. The bacterial diversity was analyzed using high‐throughput sequencing of the 16S rRNA gene on the Illumina MiSeq platform. In total, 16 bacterial phyla were identified across all samples, with the majority of sequences belonging to Firmicutes (43.3%) and Proteobacteria (43.6%). Families, Staphylococcaceae, Moraxellaceae, Planococcaceae, Enterobacteriaceae, Vibrionaceae, and Bartonellaceae, were well represented. A total of 384 distinct genera was identified, with the most abundant represented by the Gram‐negative, Acinetobacter, Bartonella, Enterobacter, Morganella, and Photobacterium, and the Gram‐positive, Aerococcus, Bacillus, Kurthia, Macrococcus, Staphylococcus, and Weissella. OTUs related to pathogenic bacteria, such as Salmonella spp., Staphylococcus aureus, and Listeria monocytogenes, were not detected in these popular foods sold in street markets in Benin. However, the presence of potentially harmful histamine‐producing bacteria has been revealed. Practical application In West Africa, fish is mainly preserved by hot smoking, which can be followed by an additional drying step using the heat that emanates from the kiln. Although several studies have investigated the microbiological quality of smoked and smoked‐dried fish, their overall microbial diversity has remained so far poorly explored. Therefore, this study has investigated the bacterial diversity of these popular foods. The results of this work provide useful information on bacteria potentially participating in food spoilage or compromising the safety of these popular foods and can be useful for improving their quality and safety.

Comparative analyses of the bacterial communities present in the spontaneously fermented milk products of Northeast India and West Africa

“…The precipitated DNA pellets were dissolved in 50 μl of TE buffer. The metagenomic DNA of Wagashi cheese samples was extracted as described earlier (Anihouvi et al, 2021 ) using the NucleoSpin ® Food (Macherey-Nagel GmbH&Co.) following the manufacturer's instructions. Qualitative (A260/280) and quantitative estimations of the extracted DNA of both food types were performed using a spectrophotometer (NanoDrop ND-1000, United States).…”

“…A further MG-RAST pipeline was used at a 97% similarity threshold against the M5RNA database for the generation of OTU tables at different taxonomic levels. For the Wagashi cheese samples of Benin, the V1-V2 region of the 16S rRNA gene was targeted using the forward primer 28F (5′-GAGTTTGATCNTGGCTCAG−3′) and reverse primer 388R (5′-TGCTGCCTCCCGTAGGAGT-3′) with Illumina adapter and barcodes (Anihouvi et al, 2021 ). The target was PCR amplified in an ABI Verti-thermocycler, purified, pooled in equimolar proportion after quantification using a Qubit assay, and sequenced on Illumina MiSeq at RTL Genomics (Lubbock, TX, United States) as described earlier (Anihouvi et al, 2021 ).…”

“…For the Wagashi cheese samples of Benin, the V1-V2 region of the 16S rRNA gene was targeted using the forward primer 28F (5′-GAGTTTGATCNTGGCTCAG−3′) and reverse primer 388R (5′-TGCTGCCTCCCGTAGGAGT-3′) with Illumina adapter and barcodes (Anihouvi et al, 2021 ). The target was PCR amplified in an ABI Verti-thermocycler, purified, pooled in equimolar proportion after quantification using a Qubit assay, and sequenced on Illumina MiSeq at RTL Genomics (Lubbock, TX, United States) as described earlier (Anihouvi et al, 2021 ). The sequence data were processed by PEAR sequence merger, USEARCH clustering and alignment algorithm, and UPARSE algorithm for OTU generation at different taxa levels.…”

“…The precipitated DNA pellets were dissolved in 50 µl of TE buffer. The metagenomic DNA of Wagashi cheese samples was extracted as described earlier (Anihouvi et al, 2021) using the NucleoSpin R Food (Macherey-Nagel GmbH&Co.)…”

“…(5 ′ -TGCTGCCTCCCGTAGGAGT-3 ′ ) with Illumina adapter and barcodes (Anihouvi et al, 2021). The target was PCR amplified in an ABI Verti-thermocycler, purified, pooled in equimolar proportion after quantification using a Qubit assay, and sequenced on Illumina MiSeq at RTL Genomics (Lubbock, TX, United States) as described earlier (Anihouvi et al, 2021).…”