{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Donchev D"],"funding":["Biocampus Sofia Association","European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020"],"pagination":["10817"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11477342"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["25(19)"],"pubmed_abstract":["Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as <i>Polaromonas</i>, <i>Macrococcus</i>, an"],"journal":["International journal of molecular sciences"],"pubmed_title":["Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics."],"pmcid":["PMC11477342"],"funding_grant_id":["not applicable","BG05M2OP001-1.002-0001-C04"],"pubmed_authors":["Stoikov I","Ivanov IN","Donchev D","Diukendjieva A"],"additional_accession":[]},"is_claimable":false,"name":"Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.","description":"Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as <i>Polaromonas</i>, <i>Macrococcus</i>, an","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Oct","modification":"2025-04-04T02:19:56.347Z","creation":"2025-04-04T02:19:56.347Z"},"accession":"S-EPMC11477342","cross_references":{"pubmed":["39409144"],"doi":["10.3390/ijms251910817"]}}