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Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag082","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T12:51:48Z","timestamp":1774615908000},"source":"Crossref","is-referenced-by-count":1,"title":["Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case"],"prefix":"10.1093","volume":"6","author":[{"given":"Philipp","family":"Schmelz","sequence":"first","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna 1030 ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Eckensperger","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"River Ecosystems Laboratory, Alpine and Polar Environmental Research Centre, School of Architecture, Civil and Environmental Engineering, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne , Sion 1950 ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay","family":"Osvatic","sequence":"additional","affiliation":[{"name":"Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"Department of Laboratory Medicine, Medical University of Vienna , Vienna 1090 ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3951-3674","authenticated-orcid":false,"given":"Joana","family":"S\u00e9neca","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"Department of Laboratory Medicine, Medical University of Vienna , Vienna 1090 ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanin","family":"Alzubaidy","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna 1030 ,","place":["Austria"]},{"name":"Marine Evolutionary Ecology, GEOMAR Helmholtz-Center for Ocean Research Kiel , Kiel 24148 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