We have lab established culture setup of marine synechococcus PCC 7002 sp. and heterotrophic bacteria. Recently we did metagenomic analysis of it (sequencing was done by an outside reputed company). According to the metagenomic analysis our sample contains other cynaobacterial algae corrosponding to synechococcus and Lyngbia genera (taking upto less than 1 to 2% of the reads for different samples from same culture).

We tried to identify this other algae morphologically using microscopy, flowcytometry and plate culture method but at no point we observed any other algal cells than Synechococcus PCC 7002. 16S amplicon sequencing also did not show any presence of other algae.

What might be the reason for such a different result from metagenomic ( apart from the assumption that contamination were introduced while sequencing as the company is reputed and we have sequenced different samples processed from same culture system)?

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