LOW-BIOMASS CONTAMINANT (LBC)
DATABASE
One problem with using the sensitive PCR reaction to examine 16S sequences in low biomass samples is contamination, which can lead to misinterpretation of the data. This is particularly important in samples from nutrient limited environments, as oligotrophic organisms often comprise the majority of laboratory contaminant sequences. While we have eliminated many sources of contamination our DNA extraction procedures, if PCR products are found in our negative controls, they are cloned, sequenced, and entered into this laboratory contaminant database.
This database contains the phylotypes either we, or other investigators, have identified as contaminants to be excluded from further analysis (or at least regarded with a high level of skepticism!) Our data contains the name of the organism, original NCBI acession number, and the original data as a FASTA or ARB-aligned sequence. All phylotypes are also uploaded to the on-line NCBI sequence database. We encourage all investigators to add their sequences to this expanding database. Intstructions for how to use the contaminant database are below.
|
Phylogenetic Group |
Clone |
Clones / Group |
Closest identified relative |
% Sequence identity |
NCBI Accession Number |
ARB
Aligned |
|
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|
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Alphaproteobacteria |
NMT_Ct2 |
1/10 |
Brevundimonas nasdae |
99% |
|
|
|
|
NMT_Ct12 |
2/10 |
Methylobacterium aminovarians |
99% |
|
|
|
|
NMT_Ct17 |
2/10 |
Methylobacterium extorquens |
99% |
|
|
|
|
CDBL_C9 |
2/10 |
Methylobacterium extorquens |
95% |
||
|
|
CDBL_C1 |
2/10 |
Sphingomonas sp. |
98% |
||
|
|
CDBL_B9 |
1/10 |
Agrobacterium tumefaciens |
99% |
||
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Betaproteobacteria |
NMT_Ct3 |
1/30 |
Ralstonia sp. |
96% |
||
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|
NMT_Ct4 |
2/30 |
Comamonas sp. |
98% |
||
|
|
NMT_Ct10 |
2/30 |
Cupriavidus respiraculi |
99% |
||
|
|
NMT_Ct22 |
1/30 |
Massilia sp. |
97% |
||
|
|
CDBL_C3 |
1/30 |
Ralstonia eutrophus |
97% |
||
|
|
CDBL_D6 |
4/30 |
Acidovorax temperans |
98% |
ARB CDBLD6 | |
|
|
MT14 |
3/30 |
Leptothrix cholodnii |
97% |
||
|
|
MT18 |
14/30 |
Duganella zoogloeoides |
100% |
||
|
|
MT22 |
2/30 |
Herbaspirillum seropedicae |
99% |
||
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Gammaproteobacteria |
NMT_WFC6 |
2/17 |
Haemophilus influenzae |
91% |
ARB WFC6 | |
|
|
CDBL_F5 |
5/17 |
Acinetobacter johnsonii |
99% |
ARB CDBLF5 | |
|
|
NMT_WFC5 |
2/17 |
Salmonella typhimurium LT2* |
100% |
||
|
|
MT3 |
2/17 |
Stenotrophomonas maltophilia |
98% |
||
|
|
MT6 |
4/17 |
Acinetobacter sp. |
100% |
||
|
|
MT9 |
2/17 |
Escherichia coli* |
98% |
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Frrmicutes |
CDBL_B8 |
1/1 |
Peptostreptococcus micro |
98% |
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Actinobacteria |
NMT_Ct9 |
1/1 |
Banisveld landfill bacterium |
93% |
ARB_CT9 | |
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|
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Crytophagales |
NMT_Ct5 |
1/1 |
Bacteroidetes sp. |
93% |
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* Laboratory DNA control strain
There are a number of ways of using the LBC database; however, if you just wish to confirm whether an identified phylotype represents an actual species or a contaminant, we recommend carrying out a two-sequence BLAST (bla2seq). Directly align your phylotype of interest against the identified contaminant. If they have >98% identity, we assume that the phylotype represents a contaminant. Where the test sequence appears numerous times in your clone library (>3 occurrences in a 96 clone library) you may assume it does not represent a contaminating sequence.