Detection of microorganisms in food samples and food processing facilities

A method comprising:

• (a) adding a first barcode to a first plurality of nucleic acid sequences from a sample, wherein said sample is a food sample or an environmental sample from a food processing facility, wherein said plurality of nucleic acid sequences comprise a mixture of cDNA, RNA, and gDNA sequences, thereby providing a first plurality of barcoded nucleic acid sequences;
• and
• (b) performing a first pore sequencing reaction on said first plurality of barcoded nucleic acid sequences, wherein said pore sequencing reaction is performed on a sequencing apparatus comprising a flow cell;
• (c) adding a second barcode to a second plurality of nucleic acid sequences from a second sample, wherein said sample is a food sample or an environmental sample from a food processing facility, wherein said plurality of nucleic acid sequences comprise a mixture of cDNA, RNA, and gDNA sequences, thereby providing a second plurality of barcoded nucleic acid sequences;
• and
• (d) performing a second pore sequencing reaction on said second plurality of barcoded nucleic acid sequences, wherein said second pore sequencing reaction is performed on said sequencing apparatus comprising said flow cell, thereby reusing said flow cell.