Molzym Blog

Impact of Host DNA in Detection of AMR Genes in Milk Production

01 February 2021

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The vast amount of host (bovine) DNA compared to microbial DNA in milk products is a challenge for metagenomic analysis. Therefore, the authors of this study investigated the impact of two different host DNA depletion techniques, sequencing depths and milk production matrices to obtain valuable data about the microbiome and antimicrobial resistance (AMR) genes.

Aliquots of bulk tank milk and in-line milk filter were treated with i) MolYsis™ Basic5 kit (Molzym, Germany) and DNeasy Blood and Tissue kit (Qiagen, Germany) or with ii) the DNeasy Blood and Tissue kit (Qiagen, Gemernay) and the NEBNext Microbiome DNA Enrichment Kit (New England Biolabs, USA) or iii) were left untreated. After library preparation the samples were sequenced on an Illumina NovaSeq 6000 platform with a sequencing depth of either 120 million paired-end (PE) reads or 60 million PE reads.

For the untreated aliquots, both from milk and filter, the higher sequencing depth revealed more microbial taxa than the lower. However, for the aliquots with depleted host DNA, the lower sequencing depth appeared to perform as well as the higher one. Comparing the performance of the two host DNA depletion kits, the MolYsis™ Basic 5 kit was significantly more effective than the NEBNext Microbiome DNA Enrichment kit in reducing the percentage of host DNA related reads which was associated with a higher detection of microbial taxa and AMR determinants. For the milk aliquots, only aliquots treated with the MolYsis™ kit resulted in the detection of AMR genes.

The authors summarized that, considering the different matrices, sequencing depths and microbial enrichment methods, the samples treated with MolYsis™ kits and a sequencing depth of 60 million PE reads appeared to be more suitable for a deep taxonomic and AMR gene content profiling.


[1] Rubiola S, Chiesa F, Dalmasso A, Di Ciccio P, Civera T (2020) Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth.

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