Hi
I have used mothur to perform analysis on data from 16S data using the “mothur miseq SOP”
I have used cluster.split to cluster sequences into OTUs.
I was wondering whether the number of sequences in each of these sampels are too low?? Or is this as expected??
I was just assuming these numbers to be higher.?
The files below are stability.file…an.unique_list.0.03.cons.taxonomy
1)
OTU Size Taxonomy
Otu00001 712594 Bacteria(100);Firmicutes(100);Negativicutes(100);Selenomonadales(100);Veillonellaceae(100);Megamonas(100);
Otu00002 532468 Bacteria(100);“Proteobacteria”(100);Gammaproteobacteria(100);“Enterobacteriales”(100);Enterobacteriaceae(100);Escherichia_Shigella(100);
Otu00003 489055 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Prevotellaceae”(100);Prevotella(100);
Otu00004 443069 Bacteria(100);“Fusobacteria”(100);“Fusobacteria”(100);“Fusobacteriales”(100);“Fusobacteriaceae”(100);Fusobacterium(100);
Otu00005 403324 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Bacteroidales”_unclassified(96);“Bacteroidales”_unclassified(96);
Otu00006 313958 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);“Bacteroidales”_unclassified(100);“Bacteroidales”_unclassified(100);
Otu00007 282352 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Peptostreptococcaceae(100);Clostridium_XI(100);
Otu00008 250186 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(79);
Otu00009 236284 Bacteria(100);Firmicutes(100);Negativicutes(100);Selenomonadales(100);Acidaminococcaceae(100);Acidaminococcaceae_unclassified(100);
Otu00010 206954 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);Bacteroidaceae(100);Bacteroides(100);
Otu00011 204317 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);Bacteroidaceae(100);Bacteroides(100);
Otu00012 157666 Bacteria(100);“Proteobacteria”(100);Epsilonproteobacteria(100);Campylobacterales(100);Helicobacteraceae(100);Helicobacter(100);
Otu00013 156286 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);
Otu00014 145738 Bacteria(100);“Actinobacteria”(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);Collinsella(100);
Otu00015 140392 Bacteria(100);“Bacteroidetes”(100);“Bacteroidia”(100);“Bacteroidales”(100);Bacteroidaceae(100);Bacteroides(100);
Otu00016 125504 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiraceae_unclassified(88);
Otu00017 124767 Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);
Otu00018 123136 Bacteria(100);“Fusobacteria”(100);“Fusobacteria”(100);“Fusobacteriales”(100);"Fusobacteri
stability.file…pick.an.unique_list.0.03.cons.tax.summary
taxlevel rankID taxon daughterlevels total cDNA1 cDNA10 cDNA11 cDNA12 cDNA13 cDNA14 cDNA15 cDNA16 cDNA17 cDNA18 cDNA19 cDNA2 cDNA20 cDNA21
0 0 Root 2 968 99 104 119 190 131 159 130 119 113 108 49 124 89 84
1 0.1 Archaea 2 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0
2 0.1.1 Crenarchaeota 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0.1.1.1 Thermoprotei 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 0.1.1.1.1 Thermoprotei_unclassified 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 0.1.1.1.1.1 Thermoprotei_unclassified 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0.1.1.1.1.1.1 Thermoprotei_unclassified 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0.1.2 Euryarchaeota 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
3 0.1.2.1 Methanomicrobia 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
4 0.1.2.1.1 Methanomicrobiales 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
5 0.1.2.1.1.1 Methanomicrobiales_incertae_sedis 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
6 0.1.2.1.1.1.1 Methanolinea 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
1 0.2 Bacteria 17 966 99 104 119 190 130 159 130 119 113 108 49 124 89 84
2 0.2.1 Acidobacteria 5 18 0 2 0 0 0 0 0 0 0 0 0 0 0 0
3) similar as above, but only genus level is shown here:
taxlevel rankID taxon daughterlevels total cDNA1 cDNA10 cDNA11 cDNA12 cDNA13 cDNA14 cDNA15 cDNA16 cDNA17 cDNA18 cDNA19
6 0.2.16.2.2.6.12 Lachnospiraceae_unclassified 0 91 11 6 13 13 8 11 15 14 14 13 5
6 0.2.15.1.1.1.1 Bacteria_unclassified 0 59 1 1 2 4 2 2 3 3 0 3 0
6 0.2.16.2.2.9.9 Ruminococcaceae_unclassified 0 43 2 0 6 8 5 8 9 7 8 12 1
6 0.2.16.2.2.4.1 Clostridiales_unclassified 0 42 3 0 6 6 3 6 4 4 1 2 0
6 0.2.4.3.1.5.1 Bacteroides 0 37 7 6 11 11 12 13 9 10 9 10 7
6 0.2.4.2.1.1.1 Bacteroidetes_unclassified 0 21 1 1 1 5 3 3 2 3 0 0 0
6 0.2.2.1.2.3.1 Corynebacterium 0 16 3 1 0 6 3 1 5 1 1 0 0
6 0.2.4.3.1.1.1 Bacteroidales_unclassified 0 12 3 3 5 5 3 5 2 2 3 1 2
6 0.2.9.1.1.1.3 Fusobacterium 0 12 3 3 3 5 4 5 2 4 2 1 1
6 0.2.16.1.2.7.3 Streptococcus 0 12 2 1 1 4 4 3 0 2 1 1 2
6 0.2.16.2.2.6.2 Blautia 0 12 4 4 6 7 3 4 5 5 5 5 4
6 0.2.16.1.2.4.1 Lactobacillus 0 11 0 0 0 0 0 1 0 0 2 0 0
6 0.2.16.4.1.1.1 Firmicutes_unclassified 0 11 0 1 0 0 1 0 1 1 1 0 0
6 0.2.1.5.1.1.1 Gp6 0 10 0 0 0 0 0 0 0 0 0 0 0
6 0.2.4.3.1.2.5 Porphyromonas 0 10 2 0 3 1 4 5 1 1 1 0 2
6 0.2.2.1.2.2.1 Actinomycetales_unclassified 0 9 0 0 0 1 2 1 1 0 0 0 0
6 0.2.2.1.4.1.2 Collinsella 0 9 1 2 1 2 2 2 2 2 1 1 1
6 0.2.2.1.4.1.3 Coriobacteriaceae_unclassified 0 9 0 0 0 1 0 0 1 1 1 2 0
6 0.2.16.2.2.6.6 Clostridium_XlVb 0 9 2 0 3 4 2 1 2 2 4 4 0
6 0.2.4.3.1.3.3 Prevotella 0 8 1 1 1 1 2 1 1 1 1 1 1
6 0.2.16.2.2.1.2 Clostridium_sensu_stricto 0 8 2 4 2 2 3 1 2 1 5 3 0
6 0.2.16.2.2.8.1 Clostridium_XI 0 8 3 4 3 4 3 1 4 3 6 5 1
6 0.2.8.1.1.1.1 Deinococcus 0 7 2 1 0 0 0 0 1 0 0 0 0
6 0.2.9.1.1.1.1 Fusobacteriaceae_unclassified 0 7 1 1 1 1 1 1 1 1 1 0 1
Thank you very much!
Kristin