Denaturing Gradient Gel Electrophoresis:Article Title: Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing.
Article Snippet: .. As the DGGE analysis is now the most widely applied for comparative analysis of parallel samples, results of the barcoded pyrosequencing analysis were compared with the findings with DGGE, for which the bulk community DNAs Table 2 Comparison of phylotype coverage and diversity estimation of the 16S rRNA gene libraries from the pyrosequencing analysis Sample Reads OTUa Goodb Chao1 ACE Jackknife Shannon Simpson Archaea J1 388 83 79.5 160 193 172 2.59 0.207 J2 2132 282 84.4 561 570 663 2.91 0.277 J3 3258 340 83.5 547 541 672 2.75 0.336 J4 1116 200 78.5 324 367 365 3.17 0.219 J5 788 155 83.2 310 320 388 2.98 0.199 J6 3279 332 83.7 532 522 667 2.75 0.35 J7 1074 269 80.7 540 545 4334 3.95 0.061 Bacteria J1 78 8 87.5 11 17 12 1.22 0.367 J2 171 21 100 87 43 67 1.56 0.424 J3 146 18 88.9 30 31 30 1.74 0.3 J4 54 13 92.3 27 40 27 1.92 0.191 J5 129 21 90.5 61 77 67 1.55 0.335 J6 593 56 80.4 88 98 87 1.97 0.275 J7 166 21 85.7 38 47 37 1.32 0.527 aThe operational taxonomic units (OTU) were defined with 1% dissimilarity. bThe coverage percentages (Good), richness estimators (ACE, Chao1, and Jackknife) and diversity indices (Shannon and Simpson) were calculated using Good’s method (Good, 1953) and the DOTUR program (Schloss and Handelsman, 2005). ..
Article Title: Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples
Article Snippet: .. DGGE fingerprinting was used prior to pyrosequencing, to compare archaeal community compositions among samples, and later, the data were complemented with a more-in-depth barcoded pyrosequencing analysis of composite samples (13). .. PCR-DGGE mixtures (25 l) consisted of 1 l of the first nested PCR product (ARC344f-mod/Arch958R-mod), 1 PCR buffer (Fermentas, Vilnius, Lithuania), 0.2 mM dNTPs, 2.75 mM MgCl2, 8% (vol/vol) acetamide, 0.2 M primers 524F-10 and Arch958R-mod (GC), and 2.5 U Dream Taq polymerase (Fermentas).
Comparison:Article Title: Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing.
Article Snippet: .. As the DGGE analysis is now the most widely applied for comparative analysis of parallel samples, results of the barcoded pyrosequencing analysis were compared with the findings with DGGE, for which the bulk community DNAs Table 2 Comparison of phylotype coverage and diversity estimation of the 16S rRNA gene libraries from the pyrosequencing analysis Sample Reads OTUa Goodb Chao1 ACE Jackknife Shannon Simpson Archaea J1 388 83 79.5 160 193 172 2.59 0.207 J2 2132 282 84.4 561 570 663 2.91 0.277 J3 3258 340 83.5 547 541 672 2.75 0.336 J4 1116 200 78.5 324 367 365 3.17 0.219 J5 788 155 83.2 310 320 388 2.98 0.199 J6 3279 332 83.7 532 522 667 2.75 0.35 J7 1074 269 80.7 540 545 4334 3.95 0.061 Bacteria J1 78 8 87.5 11 17 12 1.22 0.367 J2 171 21 100 87 43 67 1.56 0.424 J3 146 18 88.9 30 31 30 1.74 0.3 J4 54 13 92.3 27 40 27 1.92 0.191 J5 129 21 90.5 61 77 67 1.55 0.335 J6 593 56 80.4 88 98 87 1.97 0.275 J7 166 21 85.7 38 47 37 1.32 0.527 aThe operational taxonomic units (OTU) were defined with 1% dissimilarity. bThe coverage percentages (Good), richness estimators (ACE, Chao1, and Jackknife) and diversity indices (Shannon and Simpson) were calculated using Good’s method (Good, 1953) and the DOTUR program (Schloss and Handelsman, 2005). ..
Bacteria:Article Title: Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing.
Article Snippet: .. As the DGGE analysis is now the most widely applied for comparative analysis of parallel samples, results of the barcoded pyrosequencing analysis were compared with the findings with DGGE, for which the bulk community DNAs Table 2 Comparison of phylotype coverage and diversity estimation of the 16S rRNA gene libraries from the pyrosequencing analysis Sample Reads OTUa Goodb Chao1 ACE Jackknife Shannon Simpson Archaea J1 388 83 79.5 160 193 172 2.59 0.207 J2 2132 282 84.4 561 570 663 2.91 0.277 J3 3258 340 83.5 547 541 672 2.75 0.336 J4 1116 200 78.5 324 367 365 3.17 0.219 J5 788 155 83.2 310 320 388 2.98 0.199 J6 3279 332 83.7 532 522 667 2.75 0.35 J7 1074 269 80.7 540 545 4334 3.95 0.061 Bacteria J1 78 8 87.5 11 17 12 1.22 0.367 J2 171 21 100 87 43 67 1.56 0.424 J3 146 18 88.9 30 31 30 1.74 0.3 J4 54 13 92.3 27 40 27 1.92 0.191 J5 129 21 90.5 61 77 67 1.55 0.335 J6 593 56 80.4 88 98 87 1.97 0.275 J7 166 21 85.7 38 47 37 1.32 0.527 aThe operational taxonomic units (OTU) were defined with 1% dissimilarity. bThe coverage percentages (Good), richness estimators (ACE, Chao1, and Jackknife) and diversity indices (Shannon and Simpson) were calculated using Good’s method (Good, 1953) and the DOTUR program (Schloss and Handelsman, 2005). ..
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