Powerbead solution

Manufactured by Qiagen

Sourced in Germany, United States

The PowerBead solution is a reagent designed for the mechanical lysis of samples, facilitating the extraction and purification of nucleic acids. It is a core component in various nucleic acid isolation and purification workflows. The solution contains specially engineered beads that disrupt cell walls and membranes, enabling the release of genetic material for further downstream processing.

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Lab products found in correlation

Dneasy powerplant pro htp 96 kit, by Qiagen (2 mentions) Zirconia silica bead, by Biospec (2 mentions) Rnase a, by Qiagen (1 mentions) Zymobiomics microbial community standard, by Zymo Research (1 mentions) Dneasy powersoil kit, by Qiagen (1 mentions) Mini beadbeater 8, by Biospec (1 mentions) Eb buffer, by Qiagen (1 mentions) Minelute pcr purification kit, by Qiagen (1 mentions) Proteinase k, by Qiagen (1 mentions) Powerbead tube, by Qiagen (1 mentions) Dneasy ultraclean microbial kit, by Qiagen (1 mentions) Fastidious anaerobe agar, by Neogen (1 mentions)

10 protocols using powerbead solution

Optimized DNA Extraction from Rhizosphere, Spermosphere, and Plant Tissues

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After thawing, rhizosphere and spermosphere washes were concentrated by centrifugation at 15,000 g for 15 min, generating a pellet. The supernatant was removed, and the process repeated until 3 ml of sample had been processed. The pellet was re-suspended in an additional 1 ml of spermosphere or rhizosphere wash, before proceeding with DNA extraction. In contrast, after thawing, 50-ml conical tubes containing roots, shoots, or seeds received five 6.35-mm carbon steel ball bearings and 1 ml of sterile distilled water and were then vigorously shaken by hand until the supernatant obtained the consistency of a thick soup.
Then, 400 μl of these liquid samples was transferred to a 2-ml Eppendorf tube containing five 2.3-mm zirconia/silica beads (Cat#11079125z, Biospec Products, United States) along with 500 μl of Qiagen Powerbead solution, RNAse A, Phenolics Blocker, and Solution SL (Qiagen, United States). These were shaken for 20 min in a Harbil 5G-HD 5 Gallon Shaker (Part#32940, Fluid Management, United States) and then centrifuged at 13,000 RCF for 2 min before up to 700 μl was aspirated off with a pipette and added to buffer IL. The rest of the protocol was followed as per Qiagen instructions with the DNeasy PowerPlant Pro HTP 96 Kit (Qiagen, United States).

Johnston-Monje D., Gutiérrez J.P, & Lopez-Lavalle L.A. (2021). Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes. Frontiers in Microbiology, 12, 737616.

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Microbial Cell Extraction from Frozen Samples

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Frozen liquid samples (spermospheres and rhizospheres) were centrifuged at 15,000× g for 5 min to concentrate microbial cells as a pellet. Supernatant was taken off and the procedure repeated until 3 mL of sample had been concentrated. The resulting microbial pellet was resuspended in an additional 1 mL of unfrozen rhizosphere or spermosphere. On the other hand, after unfreezing, 1 mL of sterile, distilled water and five 6.35 mm carbon steel ball bearings were added to shoots, roots and seeds in tubes, followed by hand-shaking until the liquid took on the consistency of thick soup.
A total of 400 uL was taken from these slurries and transferred to 2 mL microcentrifuge tubes containing five 2.3 mm zirconia/silica beads (Cat#11079125z, Biospec Products, Bartlesville, OK, USA) and RNAse A, Phenolics Blocker, and Solution SL 500 uL of Qiagen Powerbead solution (Qiagen, Germantown, MD, USA). For 20 min, these samples were shaken using a Harbil 5G-HD 5 Gallon Shaker (Part#32940, Fluid Management, Wheeling, IL, USA), followed by centrifugation for 2 min at 13,000 RCF. A total of 700 µL of the supernatant was transferred to a fresh tube. The rest of the protocol was followed as per Qiagen instructions with the DNeasy PowerPlant Pro HTP 96 Kit (Qiagen, USA).

Johnston-Monje D., Gutiérrez J.P, & Becerra Lopez-Lavalle L.A. (2022). Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants. Life, 12(9), 1372.

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Skin Microbiome Sampling Protocol

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Study participants did not bathe for at least 24 hours prior to sampling. On the day of sampling, the subject’s arms and back were fitted with pre-constructed, raised grids of waterproof medical tape (Nexcare Absolute Waterproof, 3M; S1 Photo; Fig 1). Baseline samples (Ba, Bb;Fig 1) from the arms (Ba) and back (Bb) were obtained by vigorously rubbing the designated 2.5 cm x 3.0 cm grid-squares for 30 seconds with dampened swabs. For all adjacent samples, swabs of one grid-square in went in 1 mL Amies for culture, and the other grid-square in 0.5 mL of PowerBead solution (Qiagen) for PCR. Culture and PCR methods are outlined in detail in the following sections.

Perin B., Addetia A, & Qin X. (2019). Transfer of skin microbiota between two dissimilar autologous microenvironments: A pilot study. PLoS ONE, 14(12), e0226857.

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Surface Microbiome Sampling and Extraction

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Surface samples were collected for three surface types at each station: kiosks, railings, and benches. A nylon, flocked swab (Copan eSwab 490 CE.A, Copan Diagnostics, CA, USA) wetted in Amies liquid medium, was used to swab the surface for 3 min, covering an area as large as possible. The swab was placed in a 15-mL centrifuge tube and stored in a transport cooler with ice packs before they were transferred to − 80 °C upon return to the laboratory. DNA was isolated according to the DNeasy PowerSoil Kit (Qiagen) protocol, except that the standard PowerBead Tubes were replaced with the customized bead tubes described above for air samples. Swabs were cut with sterilized scissors into bead tubes filled with PowerBead Solution (550 μL, Qiagen) and Solution C1 (60 μL, Qiagen) before tubes were bead beaten (1 min, maximum intensity) in a Mini-Beadbeater-8 (BioSpec Products). Negative controls (reagents) were prepared by cutting clean swabs into bead tubes and performing DNA isolation.
ZymoBIOMICS Microbial Community Standard (10 μL, Zymo Research) was added to one bead tube before DNA isolation (isolated according the protocol described above), which served as a positive control.

Gohli J., Bøifot K.O., Moen L.V., Pastuszek P., Skogan G., Udekwu K.I, & Dybwad M. (2019). The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities. Microbiome, 7, 160.

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Saliva and Subgingival Plaque Sampling

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Samples for shotgun sequencing were collected between 2 and 5 pm, and before any dental treatment had been performed. Participants were asked to refrain from coffee, cheese, and chlorhexidine usage and stay sober 1 h before sample collection. A modified protocol from Belstrøm et al. 2017 was used [36 (link)]. First, 2–5 mL stimulated saliva was collected after 30 s of chewing on a parafilm. Next, subgingival plaque samples were taken from the deepest PPD with bleeding using sterile paper points, as previously described [36 (link)]. We tried to choose standardized sites for collection of the subgingival microbiome. Samples were directly stored on ice in sterile Powerbead Solution (Qiagen, Hilden, Germany). Microbial analysis was performed on pooled subgingival samples (i.e., combining paper points from each site in the same tube).

Plachokova A.S., Andreu-Sánchez S., Noz M.P., Fu J, & Riksen N.P. (2021). Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation. International Journal of Molecular Sciences, 22(11), 5876.

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Buccal Microbiome Sampling Protocol

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We collected two buccal swabs from each of the 17 participants, one pre-POIT and another post-POIT, as described above. Samples were collected by inserting the sterile Hydraflock swab with break point (Puritan, Guilford, ME, USA) on one side of the mouth between the inside of the cheek and the upper gum. The swab was pressed firmly and twirled against the inside of the inner cheek for 30 s to collect cells, using an up and down motion from front to back and back to front. After collection, the swab was placed in a 750-µL volume of PowerBead Solution (Qiagen, Hilden, Germany), labeled, and sent to the Texas Children’s Microbiome Center (TCMC) for microbiome characterization. Buccal samples were stored at −80 °C until further processing.

Blackman A.C., Thapa S., Venkatachalam A., Horvath T.D., Runge J.K., Haidacher S.J., Hoch K.M., Haag A.M., Luna R.A, & Anagnostou A. (2022). Insights into Microbiome and Metabolic Signatures of Children Undergoing Peanut Oral Immunotherapy. Children, 9(8), 1192.

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Infant Microbiome Longitudinal Cohort Study

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The Wisconsin Infant Study Cohort (WISC) is an ongoing observational birth cohort established in 2013 and has been previously described [68 (link)]. Participants born between 2013–18 were concurrently recruited and enrolled at two study sites, Marshfield Clinic and LaFarge Medical Clinic (part of Vernon Memorial Healthcare). Collection kits were from a centralized site with rigorous lot tracking. Oral and nasal microbiome specimens used in this study were collected during routine surveillance timepoints between 2015–2021 from enrolled 24-month-old infants. Specimens were collected by trained research coordinators. Oral specimens were collected using a Catch-All Sample Collection Swab to swab the entire area of both the left and right buccal mucosa for 10 seconds per side. After pressing the swab against the cryovial wall for greater than 20 seconds, specimens were stored at −80ºC in PowerBead Solution (Qiagen). Nasal specimens were obtained by swabbing (Copan #56750CS01) the anterior nasal passage, immersing the swab in Amies media, and then cryopreserving it until extraction and culture. Written informed consent was obtained from primary guardians. The WISC study was approved by the Human Subjects Committee at the Marshfield Clinic Health System and University of Wisconsin-Madison (IRB approvals: KEI10613 and 2017–1454).

Zelasko S., Swaney M.H., Sandstrom S., Davenport T.C., Seroogy C.M., Gern J.E., Kalan L.R, & Currie C.R. (2024). Upper respiratory microbial communities of healthy populations are shaped by niche and age. bioRxiv.

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Coprolite DNA Extraction Protocol

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All work was conducted at University of Oklahoma LMAMR ancient DNA laboratory according to the following protocols for coprolite-derived materials.
For DNA extraction, approximately 200 mg were subsampled from each sample material and incubated on a rotator with 400 µl of 0.5 M EDTA and 100 µl of proteinase K (QIAGEN) for 4 h. After that, the samples were subjected to bead-beating with 750 µl of PowerBead solution (QIAGEN) and then extracted using the MinElute PCR Purification kit (QIAGEN) with a modified protocol (method B) described in Hagan et al.^{77 (link)} and based on Dabney et al.^{78 (link)}, including two cleaning steps before final elution into two 30 μl of EB buffer (QIAGEN).

Rampelli S., Turroni S., Mallol C., Hernandez C., Galván B., Sistiaga A., Biagi E., Astolfi A., Brigidi P., Benazzi S., Lewis CM J.r., Warinner C., Hofman C.A., Schnorr S.L, & Candela M. (2021). Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Communications Biology, 4, 169.

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Nanotrap Processing for Nucleic Acid Extraction

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Nanotrap samples were processed for plating experiments such as “bacteria incubated with Nanotraps”, and were then processed for nucleic acid extraction using the DNeasy UltraClean Microbial kit with the following modifications: DPBS was added 4:1 to blood Nanotrap samples. Samples were vortexed to reconstitute solidified blood and centrifuged following the kit protocol. Supernatant was removed. Washed samples were resuspended in the same volume of DPBS, centrifuged, and supernatant was removed. The particle pellet was resuspended in 300 µL PowerBead solution and Qiagen protocol was continued as instructed.

Ii A.N., Lin S.C., Lepene B., Zhou W., Kehn-Hall K, & van Hoek M.L. (2021). Use of magnetic nanotrap particles in capturing Yersinia pestis virulence factors, nucleic acids and bacteria. Journal of Nanobiotechnology, 19, 186.

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Bacterial DNA Extraction Protocol

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Isolates had been stored frozen (-80°C) and were recovered on Fastidious Anaerobe Agar (Neogen®, Auchincruive, Scotland) with the addition of 5% horse blood. DNA from 24-hour cultures was manually extracted using the DNeasy UltraClean Microbial Kit (Qiagen, Hilden, Germany), with the following modified pre-step: one-third of a 10 μL loop of cultured bacteria was added to 300 μL PowerBead solution in a PowerBead tube (Qiagen). Thereafter, 50 μL SL solution (part of DNeasy UltraClean Microbial Kit) was added, vortexed briefly and incubated at 95°C for 5 minutes. The tubes were vortexed for 20 minutes and then centrifuged at 10,000×g for 2 minutes and then processed according to the manufacturer’s instructions and eluted in 50 μL.

Werner A., Mölling P., Fagerström A., Dyrkell F., Arnellos D., Johansson K., Sundqvist M, & Norén T. (2020). Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans. PLoS ONE, 15(12), e0244227.

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