mock community controls  (Zymo Research)

Journal: Bioinformatics

Article Title: MHASS: Microbiome HiFi Amplicon Sequencing Simulator

doi: 10.1093/bioinformatics/btaf656

Figure Lengend Snippet: Edit distance distribution from read to nearest reference ASV by genome for both real and MHASS-simulated reads, with length 1400–1700 for 16S and 2000–3000 for Titan-1. Each panel corresponds to a different mock community: Zymo/Titan-1 (top), ATCC/16S (middle), and Phylotag/16S (bottom). Left violins show distributions from real CCS data; right violins show MHASS-simulated reads. Total number of reads surviving QC steps for each dataset are indicated in the top left. No misassignment of simulated reads occurred; all simulated reads were found to be closest to the original ASV sequences from which they were simulated.

Article Snippet: In contrast, the ATCC/16S mock community exhibited unimodal distributions across genomes, reflecting the more conserved and less variable nature of the 16S amplicon sequences.

Techniques:

Journal: MicrobiologyOpen

Article Title: Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification

doi: 10.1002/mbo3.70194

Figure Lengend Snippet: Quantification of the ttr gene following MDA. Quantitative PCR assay results for the Salmonella ‐specific ttr gene in MDA outputs from (a) no competition, pure Isolate (100% Salmonella ) (b) even competition, Zymo mixed‐microbial (10% Salmonella ) and (c) varying competition, ATCC environmental mixed‐microbial (0.1%–90.6% Salmonella ) starting input communities. Mean ttr copy numbers based on sample duplicates are given for (a) isolate and (b) Zymo communities. B.D. indicates below detection limit. Left y ‐axis is the log10 output ttr copies/µL and right y‐axis is the log10 fold change in copies/µL between MDA input and output. Sample names for the (a) isolate and (b) Zymo community correspond to the log10 order of the Salmonella genome copy number and the percent of Salmonella in the total MDA community inputs. Sample names for the (c) ATCC environmental community correspond to the log10 order of the Salmonella genome copy number, the percent of Salmonella in the total MDA community, and the initial mass (ng DNA) input of the ATCC environmental community before being spiked with the Salmonella isolate.

Article Snippet: LT2 (ATCC 19585) DNA and two synthetic environmental, mock DNA communities, ZymoBIOMICS Microbial Community Standard (catalog no. D6305, Zymo) and ATCC ABRF‐MGRG 10 strain even mix (catalog no. MSA‐3001, ATCC), were used to simulate pathogens in the environment for MDA evaluation.

Techniques: Real-time Polymerase Chain Reaction

Journal: MicrobiologyOpen

Article Title: Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification

doi: 10.1002/mbo3.70194

Figure Lengend Snippet: Effect of input Salmonella copy numbers on community composition following MDA. Taxonomic composition of (a) isolate (100% Salmonella ) (b) Zymo (10% Salmonella ) and (c) ATCC environmental (mixed % Salmonella ) communities based on relative abundances of mapped reads. Reads were multi‐mapped using Fastq‐Screen and a customized database, which included the appropriate community references and common nontarget contaminants. The predicted community composition (Expected) and a non‐MDA sequencing control that did not undergo MDA (Actual) are included for comparison. Reads that did not map (No Hit) and reads that mapped to more than one reference genome (Multi‐Hit) in the database are also included. Sample names for the (a) isolate and (b) Zymo community correspond to the log10 order of the Salmonella genome copy number and the percent of Salmonella in the total MDA community inputs. Sample names for the (c) ATCC environmental community correspond to the log10 order of the Salmonella genome copy number, the percent of Salmonella in the total MDA community, and the initial mass (ng DNA) input of the ATCC environmental community before being spiked with the Salmonella isolate.

Article Snippet: LT2 (ATCC 19585) DNA and two synthetic environmental, mock DNA communities, ZymoBIOMICS Microbial Community Standard (catalog no. D6305, Zymo) and ATCC ABRF‐MGRG 10 strain even mix (catalog no. MSA‐3001, ATCC), were used to simulate pathogens in the environment for MDA evaluation.

Techniques: Sequencing, Control, Comparison

Journal: MicrobiologyOpen

Article Title: Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification

doi: 10.1002/mbo3.70194

Figure Lengend Snippet: Performance metrics of Salmonella spp. genome in MDA communities at varying sequencing depths. Breadth of coverage, mean read depth and uniformity of coverage (CV) of Salmonella spp. in MDA isolate and mixed‐microbial mock communities based on reads mapped to the Salmonella LT2 (Isolate and ATCC) or FDAARGOS (Zymo) reference genome. Sample names for the isolate and Zymo community correspond to the log10 order of the Salmonella genome copy number and the percent of Salmonella in the total MDA community inputs. Sample names for the (c) ATCC environmental community correspond to the log10 order of the Salmonella genome copy number, the percent of Salmonella in the total MDA community, and the initial mass (ng DNA) input of the ATCC environmental community before being spiked with the Salmonella isolate.

Article Snippet: LT2 (ATCC 19585) DNA and two synthetic environmental, mock DNA communities, ZymoBIOMICS Microbial Community Standard (catalog no. D6305, Zymo) and ATCC ABRF‐MGRG 10 strain even mix (catalog no. MSA‐3001, ATCC), were used to simulate pathogens in the environment for MDA evaluation.

Techniques: Sequencing

Journal: MicrobiologyOpen

Article Title: Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification

doi: 10.1002/mbo3.70194

Figure Lengend Snippet: Effect of MDA for different starting input DNA amounts on %GC coverage. %GC bias curves based on output sequencing normalized coverage results for starting MDA inputs of 10 1 –10 4 and 10 6 copy numbers of Salmonella LT2 in the isolate WGA community samples. A non‐MDA sequencing control (No MDA) for the Salmonella LT2 isolate is shown for comparison. A 200‐bp sliding window was selected to determine the fraction of normalized coverage mapped to the Salmonella LT2 reference genome. A horizontal line at 1 for the fraction of normalized coverage (all 200 bp windows covered equally at all GC percentages) indicates no %GC bias; steeper curves indicate greater %GC bias. Sample names indicate the log10 order of the Salmonella genome copy number and the percent of Salmonella in the total MDA inputs.

Article Snippet: LT2 (ATCC 19585) DNA and two synthetic environmental, mock DNA communities, ZymoBIOMICS Microbial Community Standard (catalog no. D6305, Zymo) and ATCC ABRF‐MGRG 10 strain even mix (catalog no. MSA‐3001, ATCC), were used to simulate pathogens in the environment for MDA evaluation.

Techniques: Sequencing, Control, Comparison