Journal: Scientific Reports

Article Title: Bacterial bioburden and community structure of potable water used in the International Space Station

doi: 10.1038/s41598-022-19320-3

Figure Lengend Snippet: Bacterial community structure in the PWD water determined by 16S rRNA gene amplicons sequenced on Illumina MiSeq, iSeq, or Nanopore MinION.

Article Snippet: A 16S rRNA sequencing library was constructed from 10 µL of extracted DNA using the 16S barcoding kit (Oxford Nanopore Technologies).

Techniques:

Journal: Scientific Reports

Article Title: Bacterial bioburden and community structure of potable water used in the International Space Station

doi: 10.1038/s41598-022-19320-3

Figure Lengend Snippet: Relative abundance of bacterial species in the PWD water determined by 16S rRNA gene targeted amplicon sequencing with the MinION sequencer. Genus and species with an abundance >1% are presented.

Article Snippet: A 16S rRNA sequencing library was constructed from 10 µL of extracted DNA using the 16S barcoding kit (Oxford Nanopore Technologies).

Techniques: Amplification, Sequencing

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections

doi: 10.3389/fcimb.2025.1517208

Figure Lengend Snippet: Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and ONT 16S Barcoding all-in-one kit (v14). Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( Supplementary Data 3 ).

Article Snippet: Normalized extracts were amplified and barcoded using the ONT 16S Barcoding all-in-one kit (Oxford Nanopore, SQK-16S024) as per manufacturer's instructions (maximum cycle number of 25 cycles).

Techniques: Sequencing

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections

doi: 10.3389/fcimb.2025.1517208

Figure Lengend Snippet: Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and the in-house developed 16S ONT RBK method. Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and amplified in two PCRs targeting the V1-V2 and V1-V9 genomic regions of the 16S rRNA gene; analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( Supplementary data 3 ).

Article Snippet: Normalized extracts were amplified and barcoded using the ONT 16S Barcoding all-in-one kit (Oxford Nanopore, SQK-16S024) as per manufacturer's instructions (maximum cycle number of 25 cycles).

Techniques: Sequencing, Amplification

Journal: bioRxiv

Article Title: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

doi: 10.1101/073965

Figure Lengend Snippet: In-field 16S rRNA gene amplicon sequencing of cryoconite bacterial communities showing (A) phylum and family level taxonomic distribution of (B) open and closed cryoconite holes sampled on Vestre Brøggerbreen. The top image shows a “closed” cryoconite hole where the snow and superimposed ice cover has been displaced to reveal the hole, while the middle image shows a seasonally-open cryoconite hole. The bottom image shows the arrangement of equipment for DNA extraction, 16S rRNA gene PCR and nanopore sequencing in a field lab.

Article Snippet: Samples were transferred to the NERC Arctic Research Station Ny Ålesund within three hours and DNA extracted and quantified as described above within the field lab. Bacterial 16S rRNA genes were amplified from 50 ng DNA per sample diluted to 10 µL nuclease free water in 50 µL with 1 × LongAmp Taq master mix (New England Biolabs, Inc), 1 µL 16S rRNA gene barcoded primer (ONT-SQK-RAB-201, Oxford Nanopore Technologies, Ltd) and 14 µL nuclease free water.

Techniques: Amplification, Sequencing, DNA Extraction, Nanopore Sequencing

Journal: bioRxiv

Article Title: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

doi: 10.1101/073965

Figure Lengend Snippet: multivariate discrimination of cryoconite bacterial communities revealed by in-field 16S rRNA gene amplicon sequencing. Analyses are performed with data aggregated to phylum/proteobacterial class (A-B) or family-level taxa (C-D) with Hierarchical Cluster Analysis (HCA, subpanels A, C,) or Principal Cooordinates Analysis (PCoA, B,D,). Closed holes (VB1-3) and open holes (VB5-6) are ordinated by multivariate analysis of of fourth-root transformed Bray-Curtis distances of phylotype relative abundances.

Article Snippet: Samples were transferred to the NERC Arctic Research Station Ny Ålesund within three hours and DNA extracted and quantified as described above within the field lab. Bacterial 16S rRNA genes were amplified from 50 ng DNA per sample diluted to 10 µL nuclease free water in 50 µL with 1 × LongAmp Taq master mix (New England Biolabs, Inc), 1 µL 16S rRNA gene barcoded primer (ONT-SQK-RAB-201, Oxford Nanopore Technologies, Ltd) and 14 µL nuclease free water.

Techniques: Amplification, Sequencing, Transformation Assay

Journal: bioRxiv

Article Title: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

doi: 10.1101/073965

Figure Lengend Snippet: Benchmarking nanopore 16S rRNA gene amplicon sequencing of cryoconite bacterial communities by comparison with laboratory-generated data. (A) Phylum and family level taxonomic distribution of cryoconite bacterial communities and (B) phylum and (C) family level taxon distributions used for principal coordinates analysis of fourth-root transformed Bray-Curtis distances of phylotype relative abundances discriminate between Arctic and alpine cryoconite communities. Arctic glaciers (blue, AB, ML,VB) and Alpine glaciers (red, GF, RM) are clearly ordinated.

Article Snippet: Samples were transferred to the NERC Arctic Research Station Ny Ålesund within three hours and DNA extracted and quantified as described above within the field lab. Bacterial 16S rRNA genes were amplified from 50 ng DNA per sample diluted to 10 µL nuclease free water in 50 µL with 1 × LongAmp Taq master mix (New England Biolabs, Inc), 1 µL 16S rRNA gene barcoded primer (ONT-SQK-RAB-201, Oxford Nanopore Technologies, Ltd) and 14 µL nuclease free water.

Techniques: Amplification, Sequencing, Comparison, Generated, Transformation Assay

Journal: bioRxiv

Article Title: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

doi: 10.1101/073965

Figure Lengend Snippet: Benchmarking nanopore 16S rRNA gene amplicon sequencing of cryoconite bacterial communities by comparison with laboratory-generated data. Correlation of log relative abundances between (A) the ratio of Alphaproteobacteria and Betaproteobacteria (B) Cyanobacteria to Alphaproteobacteria:Betaproteobacteria and (C) key taxonomic groups revealed using nanopore and pyro-sequencing of 16S rRNA genes. Positive, significant or highly significant Pearson r correlations are observed for each taxon.

Article Snippet: Samples were transferred to the NERC Arctic Research Station Ny Ålesund within three hours and DNA extracted and quantified as described above within the field lab. Bacterial 16S rRNA genes were amplified from 50 ng DNA per sample diluted to 10 µL nuclease free water in 50 µL with 1 × LongAmp Taq master mix (New England Biolabs, Inc), 1 µL 16S rRNA gene barcoded primer (ONT-SQK-RAB-201, Oxford Nanopore Technologies, Ltd) and 14 µL nuclease free water.

Techniques: Amplification, Sequencing, Comparison, Generated

Journal: bioRxiv

Article Title: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

doi: 10.1101/073965

Figure Lengend Snippet: Benchmarking nanopore16S rRNA gene amplicon sequencing by sequencing mock communities using in-field protocols. Panel (A) shows the expected taxonomic distribution of The ZymoBIOMICS Microbial Community Standard for each sample, spiked in triplicate with Micrococcus luteus NCTC2665 genomic DNA to afford theoretical relative abundances of 16S rRNA genes in the range of 0-1.2% of the total bacterial community. Panel (B) shows shows the observed data where all reads assigned to genus level (excepting the poorly resolvable Enterobacteriaceae while Panel (C) shows all reads at the family level. The expected and observed Micrococcus luteus spike is highlighted in yellow.

Article Snippet: Samples were transferred to the NERC Arctic Research Station Ny Ålesund within three hours and DNA extracted and quantified as described above within the field lab. Bacterial 16S rRNA genes were amplified from 50 ng DNA per sample diluted to 10 µL nuclease free water in 50 µL with 1 × LongAmp Taq master mix (New England Biolabs, Inc), 1 µL 16S rRNA gene barcoded primer (ONT-SQK-RAB-201, Oxford Nanopore Technologies, Ltd) and 14 µL nuclease free water.

Techniques: Amplification, Sequencing