Miseq 16s

Manufactured by Illumina

The MiSeq 16S is a sequencing instrument designed for targeted amplicon sequencing. It utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality, short-read sequencing data. The MiSeq 16S is optimized for analysis of 16S rRNA gene amplicons, which are commonly used for microbial community profiling.

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Lab products found in correlation

Barcoded primer, by Illumina (1 mentions) Quant it dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Qubit fluorimeter, by Thermo Fisher Scientific (1 mentions) Fastdna spin kit for soil, by Qiagen (1 mentions)

Spelling variants of this product

MiSeq 16S Metagenomic Sequencing Library Preparation protocol (9 citations) MiSeq 16S Metagenomic Sequencing Library Preparation (6 citations) MiSeq 16S Sequencing Library Protocol (4 citations) MiSeq 16S rRNA (4 citations) Miseq 16S rRNA sequencing (2 citations)

4 protocols using miseq 16s

16S rRNA Sequencing of Low DNA Samples

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Illumina MiSeq 16S (V3-V4 region of 16S rRNA gene) libraries were generated following standard protocol (16S Metagenomic Sequencing Library Preparation, Part # 15044223 Rev. B) with modifications described in Bruno et al. (2017) (link), due to the low DNA concentrations. DNA extracts were normalized on Ct values of Real Time PCR with the same primer pairs, instead of measuring the total amount of microbial DNA with fluorometric/spectrophotometric methods. Negative controls were included in library preparation.
Samples were sequenced using the 2 × 300 paired-end chemistry (MiSeq Reagent Kit v3). Technical replicates were included to verify the sequencing reproducibility (84 samples in total). The sequencing process was conducted by National Research Council, Institute of Biomedical Technologies (CNR-ITB, Italy).

Bruno A., Sandionigi A., Bernasconi M., Panio A., Labra M, & Casiraghi M. (2018). Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy). Frontiers in Microbiology, 9, 2557.

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Microbiome Diversity Assessment Protocol

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The DNA from each 0.22 μm pore filter was extracted and purified with a DNA Isolation PowerWater kit (MO BIO Laboratory, Inc.). Extraction procedures were identical for all samples. DNA concentration was determined using a NanoDrop 2000p. The diversity of uncultured microeukaryotes and bacteria was assessed by Illumina MiSeq 16S and 18S rRNA gene amplicon sequencing. The amplification and sequencing of the V3–V4 regions of the 16S rRNA gene (forward sequence CCTACGGGNGGCWGCAG; reverse sequence GACTACHVGGGTATCTAATC) were performed to identify bacteria. Microeukaryotes were identified by amplification and sequencing of the V4–V5 regions of the 18S rRNA gene (forward sequence GCCAGCAVCYGCGGTAAY; reverse sequence CCGTCAATTHCTTYAART).

Ruiz-Blas F., Muñoz-Hisado V., Garcia-Lopez E., Moreno A., Bartolomé M., Leunda M., Martinez-Alonso E., Alcázar A, & Cid C. (2023). The hidden microbial ecosystem in the perennial ice from a Pyrenean ice cave. Frontiers in Microbiology, 14, 1110091.

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Illumina-Based Microbiome Profiling and Analysis

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We utilize state-of-the-art methods developed and benchmarked by our collaborating laboratory [29 (link)–31 (link)]. Briefly, bacterial genomic DNA is extracted and amplified with Illumina barcoded primers and analyzed on the Illumina MiSeq (16S) and HiSeq (WGS) platforms. Bacterial mock community samples (QC standards) are routinely included in each run. Alpha and beta (within and between sample) diversity analyses are performed to assess community diversity and richness by calculating the number of observed species for each sample at various sequencing depths. ANOVA and supervised machine learning techniques are used to identify taxa at the level of phylum, class, genus and species that differ significantly in abundance and discriminate between defined parameters. Various clustering algorithms assess whether distinct microbiome clusters or community types are formed.

Zhang X., Browman G., Siu W., Basen-Engquist K.M., Hanash S.M., Hoffman K.L., Okhuysen P.C., Scheet P., Petrosino J.F., Kopetz S, & Daniel C.R. (2019). The BE GONE trial study protocol: a randomized crossover dietary intervention of dry beans targeting the gut microbiome of overweight and obese patients with a history of colorectal polyps or cancer. BMC Cancer, 19, 1233.

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Diversity of Microbes in Pyroclastic Deposits

Cited 2 times

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DNA was sequenced from 5 samples belonging to either pyroclastic density current deposits (partially consolidated) or loose pyroclastic lapilli-size deposits (Table 1). Approximately 500 mg of each sample was used for DNA extraction. Samples NB1_S2, DIVOL_12A and DIPV_36_S3 were representative of the first group, and samples DIVOL_4A and DIVOL_23 were representative of the second group. DNA was extracted from one aliquot from each volcanic rock (only the inner fraction) using FastDNA™ SPIN Kit for Soil (QIAGEN, Hilden, Germany). DNA quantification was carried out with the commercial Quant-iT™ dsDNA HS Assay kit (Invitrogen™, Waltham, MA, USA). Its concentration was determined with the Qubit™ fluorimeter (Invitrogen™). The diversity of uncultured microeukaryotes and bacteria was assessed by Illumina MiSeq 16S and 18S rRNA gene amplicon sequencing [57 (link)]. The amplification and sequencing of the V3-V4 regions of the 16S rRNA gene (forward sequence CCTACGGGNGGCWGCAG; reverse sequence GACTACHVGGGTATCTAATC) were performed to identify bacteria. Microeukaryotes were identified by amplification and sequencing of the V4-V5 regions of the 18S rRNA gene (forward sequence GCCAGCAVCYGCGGTAAY; reverse sequence CCGTCAATTHCTTYAART) [58 (link)].

Hidalgo-Arias A., Muñoz-Hisado V., Valles P., Geyer A., Garcia-Lopez E, & Cid C. (2023). Adaptation of the Endolithic Biome in Antarctic Volcanic Rocks. International Journal of Molecular Sciences, 24(18), 13824.

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