host dna depletion  (Zymo Research)

Journal: Microbiome

Article Title: Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome

doi: 10.1186/s40168-025-02191-x

Figure Lengend Snippet: Microbial diversity and composition by extraction method in unspiked samples (16S). A Microbial richness or number of unique ASVs and B microbial diversity (Shannon entropy) differed significantly by extraction method (Richness p = 0.0018, Shannon p = 0.0091, Friedman, multiple comparisons with FDR at 0.05, Table ). Whiskers represent minimum, maximum, and median. * p < 0.05. C Microbial composition (Bray–Curtis) differed significantly by dog (PERMANOVA p = 0.001), but not extraction method (PERMANOVA p = 0.92). D When microbial composition was weighted by phylogeny (unweighted UniFrac), composition differed significantly by both extraction method (PERMANOVA p = 0.002) and by dog (PERMANOVA p = 0.001). E Bray–Curtis, F Jaccard, and G unweighted UniFrac distances from Bacteremia-extracted samples to samples of the same dog extracted via other extraction methods. E Bray–Curtis, F Jaccard, and G unweighted UniFrac distances differed significantly with DNA Microbiome samples being the most similar (shortest distance) to Bacteremia-extracted samples (Friedman, Bray–Curtis p = 0.034; Jaccard p = 0.0342; unweighted UniFrac p = 0.0071). Pairwise comparison p -values are outlined in Table . * p < 0.05. Bar represents median

Article Snippet: In this study, we assess four commercially available DNA extraction kits that include host DNA depletion (MolYsis Complete5, NEBNext Microbiome DNA Enrichment Kit, QIAamp DNA Microbiome Kit, and Zymo HostZERO) as well as a protocol using light-activated propidium monoazide and compare them to a method with no host depletion (BiOstic Bacteremia).

Techniques: Extraction, Comparison

Journal: Microbiome

Article Title: Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome

doi: 10.1186/s40168-025-02191-x

Figure Lengend Snippet: Extraction method impacted host and microbial read abundances (shotgun metagenomics). A Total sequencing reads did not vary by extraction method ( p = 0.12, Friedman). B However, microbial reads did vary significantly by extraction method ( p = 0.0039, Friedman), with DNA Microbiome, Molzym MolYsis, and Zymo HostZERO exhibiting a greater number of microbial reads compared to Bacteremia (all pairwise p = 0.01). C The proportion of microbial reads also varied significantly by extraction method, with Molzym MolYsis and Zymo HostZERO yielding the greatest proportion of microbial reads (overall p < 0.0001, all pairwise p < 0.02, Friedman). D The abundance of contaminant reads also differed significantly by extraction method (overall Friedman p = 0.014) and was lowest in DNA Microbiome (DNA Microbiome vs. Zymo HostZERO pairwise p = 0.01). Bacteremia was excluded from D because host reads accounted for 100% of all but one Bacteremia sample, which precluded processing through decontam . See Table for a list of contaminants

Article Snippet: In this study, we assess four commercially available DNA extraction kits that include host DNA depletion (MolYsis Complete5, NEBNext Microbiome DNA Enrichment Kit, QIAamp DNA Microbiome Kit, and Zymo HostZERO) as well as a protocol using light-activated propidium monoazide and compare them to a method with no host depletion (BiOstic Bacteremia).

Techniques: Extraction, Sequencing

Journal: Microbiome

Article Title: Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome

doi: 10.1186/s40168-025-02191-x

Figure Lengend Snippet: Extraction method and microbial diversity and composition (shotgun metagenomics). Microbial diversity as measured by A observed species (richness) and B Shannon entropy varied significantly by extraction method (observed species p = 0.011, Shannon entropy, p = 0.002, Friedman) with DNA Microbiome yielding significantly greater microbial diversity than other extraction methods (observed species DNA Microbiome vs. bacteremia pairwise p = 0.014, Shannon DNA Microbiome vs. all other methods (except Molzym MolYsis) pairwise p = 0.014). Microbial species were identified via MetaPhlAn4. C Microbial composition as measured by Jaccard or D Bray–Curtis differed significantly by dog (Jaccard p = 0.001, Bray–Curtis p = 0.001, PERMANOVA), but not extraction method (Jaccard p = 0.67, Bray–Curtis p = 0.96, PERMANOVA). Urine samples extracted with Bacteremia contained little microbial DNA and did not produce reads that were assignable to a taxa by MetaPhlAn4. As such, Bacteremia samples were excluded from C and D and beta-diversity testing

Article Snippet: In this study, we assess four commercially available DNA extraction kits that include host DNA depletion (MolYsis Complete5, NEBNext Microbiome DNA Enrichment Kit, QIAamp DNA Microbiome Kit, and Zymo HostZERO) as well as a protocol using light-activated propidium monoazide and compare them to a method with no host depletion (BiOstic Bacteremia).

Techniques: Extraction

Journal: bioRxiv

Article Title: Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

doi: 10.1101/2025.07.14.664698

Figure Lengend Snippet: (A) Testing different concentrations of saponin (2, 3, 4, and 5%) o see the lysis of host cells and bacterial cells. (B) Host DNA depletion of Escherichia coli and Staphylococcus aureus blood cultures using saponin and different concentrations of SAN, followed by DNA extraction. (C) Testing the effect of different salt concentrations on the activity of SAN. (D) The final optimized protocol using 4% saponin, 10 μL (250 U) of SAN, 2.5 M NaCl, and 50 mM MgCl2 for effective host DNA depletion. * 2 vs 2.5 M NaCl + 50 mM MgCl2, 2.5 M NaCl + 15 vs 50 mM MgCl2, 0.5 M NaCl + 15 mM MgCl2 vs 2.5 M NaCl + 50 mM MgCl2.

Article Snippet: The host DNA depletion in blood cultures was performed by treating the blood cultures with 4% saponin, followed by the addition of HL-SAN and M-SAN (ArcticZymes Technologies, Norway).

Techniques: Lysis, DNA Extraction, Activity Assay

Journal: bioRxiv

Article Title: Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

doi: 10.1101/2025.07.14.664698

Figure Lengend Snippet: (A) Escherichia coli (B) Staphylococcus aureus . HL-10/20 = 10/20 μL (250/500 U) HL-SAN, M- 10/20 = 10/20 μL (250/500 U) M-SAN In E. coli blood cultures, a higher yield of DNA was obtained when a lower concentration of HL- SAN and M-SAN (250 U) was used for host depletion compared to the higher enzyme concentration (500 U). A similar high DNA yield was observed in S. aureus samples when M-SAN was used for depletion. However, in S. aureus HL-SAN samples, a higher enzyme concentration (500 U) resulted in increased DNA yield (Supplementary Table 2).

Article Snippet: The host DNA depletion in blood cultures was performed by treating the blood cultures with 4% saponin, followed by the addition of HL-SAN and M-SAN (ArcticZymes Technologies, Norway).

Techniques: Concentration Assay

Journal: bioRxiv

Article Title: Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

doi: 10.1101/2025.07.14.664698

Figure Lengend Snippet: The host DNA depletion and bacterial DNA enrichment are measured as fold change. The 2.5 M NaCl concentration is used as a reference and compared with the 2 M NaCl concentration. The concentration of MgCl2 is maintained at a constant 50 mM (A) Escherichia coli and (B) Staphylococcus aureus . 2M/2.5M = NaCl

Article Snippet: The host DNA depletion in blood cultures was performed by treating the blood cultures with 4% saponin, followed by the addition of HL-SAN and M-SAN (ArcticZymes Technologies, Norway).

Techniques: Concentration Assay

Journal: bioRxiv

Article Title: Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

doi: 10.1101/2025.07.14.664698

Figure Lengend Snippet: The host DNA depletion and bacterial DNA enrichment are measured as fold change. The 50 mM MgCl2 concentration is used as a reference for comparison with the 15 mM MgCl2. The concentration of NaCl is kept constant at 2.5 M (A) Escherichia coli and (B) Staphylococcus aureus . 15mM/50mM = MgCl2

Article Snippet: The host DNA depletion in blood cultures was performed by treating the blood cultures with 4% saponin, followed by the addition of HL-SAN and M-SAN (ArcticZymes Technologies, Norway).

Techniques: Concentration Assay, Comparison

Journal: bioRxiv

Article Title: Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

doi: 10.1101/2025.07.14.664698

Figure Lengend Snippet: The host DNA depletion and bacterial DNA enrichment are measured as fold change. The 2.5 M NaCl and 50 mM MgCl2 concentrations are used as a reference control for comparison with 0.5 M NaCl 15 mM MgCl2. (A) E . coli (B) S. aureus . HL_SAN/M_SAN = 0.5 M NaCl and 15 mM MgCl2, HL_SAN/M_SAN control = 2.5 M NaCl and 50 mM MgCl2

Article Snippet: The host DNA depletion in blood cultures was performed by treating the blood cultures with 4% saponin, followed by the addition of HL-SAN and M-SAN (ArcticZymes Technologies, Norway).

Techniques: Control, Comparison