Journal: Applied and Environmental Microbiology

Article Title: Ethanolamine Utilization Contributes to Proliferation of Salmonella enterica Serovar Typhimurium in Food and in Nematodes

doi: 10.1128/AEM.01403-10

Figure Lengend Snippet: Bacterial strains and plasmids used in this study

Article Snippet: In Salmonella enterica subsp. enterica serovar Paratyphi B strain SPB7, Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67, S. enterica subsp. enterica serovar Paratyphi strain AKU_12601, S. enterica subsp. enterica serovar Agona strain SL483, S. enterica serovar Typhi strain CT18, S. enterica subsp. enterica serovar Paratyphi A strain ATCC 9150, S. enterica subsp. enterica serovar Weltevreden strain HI_NO5-537, S. enterica subsp. enterica serovar Virchow strain SL491, S. enterica subsp. enterica serovar Newport strain SL317, and S . enterica subsp. arizonae strain RSK2980, the genetic organization of the eut , pdu , and cob gene cluster is essentially similar to that of the clusters in the reference strain S . Typhimurium LT2, and the encoded amino acid sequences are homologous with at least 95% identity to the LT2 counterparts.

Techniques: Plasmid Preparation, Mutagenesis

Journal: Applied and Environmental Microbiology

Article Title: Ethanolamine Utilization Contributes to Proliferation of Salmonella enterica Serovar Typhimurium in Food and in Nematodes

doi: 10.1128/AEM.01403-10

Figure Lengend Snippet: Genetic organization of the eut, pdu, and cob-cbi genes in S. Typhimurium LT2. The genomes of the S. enterica serovars tested (Table ​(Table1)1) carry intact operons with most of the genes homologous to each other (filled arrows). The cob and pdu operons in the genome of S. Gallinarum strain 287/91 lack the cbiOKDC and pocR genes (open arrows). The organization of the eut operon within most Salmonella serovars is also shown. An exception is the eut operon of S. Choleraesuis strain SC-B67, lacking eutACK. Shaded arrows indicate gene replacement with respect to the LT2 genome.

Article Snippet: In Salmonella enterica subsp. enterica serovar Paratyphi B strain SPB7, Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67, S. enterica subsp. enterica serovar Paratyphi strain AKU_12601, S. enterica subsp. enterica serovar Agona strain SL483, S. enterica serovar Typhi strain CT18, S. enterica subsp. enterica serovar Paratyphi A strain ATCC 9150, S. enterica subsp. enterica serovar Weltevreden strain HI_NO5-537, S. enterica subsp. enterica serovar Virchow strain SL491, S. enterica subsp. enterica serovar Newport strain SL317, and S . enterica subsp. arizonae strain RSK2980, the genetic organization of the eut , pdu , and cob gene cluster is essentially similar to that of the clusters in the reference strain S . Typhimurium LT2, and the encoded amino acid sequences are homologous with at least 95% identity to the LT2 counterparts.

Techniques:

Journal: Bioinformatics

Article Title: Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

doi: 10.1093/bioinformatics/btu641

Figure Lengend Snippet: Comparison of Sigma, Pathoscope, MetaPhlAn, and MEGAN in strain-level identification and quantification using a 5-genome synthetic community. (RA%: relative abundance in percentage)

Article Snippet: S.enterica serovar Paratyphi A strain ATCC 9150 , 60 , S.enterica serovar Paratyphi A strain ATCC 9150 , 59.85 , S.enterica serovar Paratyphi A strain ATCC 9150 , 60.11 , S.enterica serovar Paratyphi A , 1.58 , S.enterica , 31.05.

Techniques:

Journal: Bioinformatics

Article Title: Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

doi: 10.1093/bioinformatics/btu641

Figure Lengend Snippet: Identification of a Salmonella enterica strain at a serial dilution of relative abundances in a human fecal microbiota background. ( a ) Likelihood ratios of all aligned Salmonella enterica strains. Only the correct strain (highlighted in red outline) has statistically significant identification with <0.01 p -value down to the 0.001% dataset. (b) Estimated and expected relative abundances (RA) of the spike-in Salmonella enterica strain. Point estimates (red dots) were bracketed by 95% confidence intervals (blue error bars) with small relative standard deviations (RSD) down to 0.001% (0.027X coverage depth).

Article Snippet: S.enterica serovar Paratyphi A strain ATCC 9150 , 60 , S.enterica serovar Paratyphi A strain ATCC 9150 , 59.85 , S.enterica serovar Paratyphi A strain ATCC 9150 , 60.11 , S.enterica serovar Paratyphi A , 1.58 , S.enterica , 31.05.

Techniques: Serial Dilution