Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
Sarah Ahannach,
Lize Delanghe,
Irina Spacova,
Stijn Wittouck,
Wannes Van Beeck,
Ilke De Boeck,
Sarah Lebeer
Affiliations
Sarah Ahannach
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Lize Delanghe
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Irina Spacova
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Stijn Wittouck
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Wannes Van Beeck
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Ilke De Boeck
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
Sarah Lebeer
Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; Corresponding author
Summary: Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition.
