Microbial Identification
Sample sheet
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ORDER (please use the sample sheet)
THE FOLLOWING OPTIONS ARE AVAILABLE, PLEASE INDICATE YOUR CHOICE ON THE SAMPLESHEET:

Identification of unknown bacteria:
-

BC-304: MicroSEQ® 500bp. The validated MicroSEQ kits and the validated MicroSEQ
databases will be used for the identification.
BC-308: Custom ID <700bp. Our own custom 16S kit will be used and the consensus
sequences will be compared to an internal database or to a public database.
BC-309: Custom ID <1400 bp. Our own custom 16S kit will be used and the consensus
sequences will be compared to an internal database or to a public database.
BC-310: Maldi-TOF. A protein spectrum created by the Maldi-TOF system will be compared to
the validated VITEK MS IVD database.
Identification of unknown fungi:
-
BC-306: MicroSEQ® D2-LSU. The validated MicroSEQ kits and the validated MicroSEQ
databases will be used for the identification.
BC-307: ITS-region. Our own custom ITS kit will be used and the consensus sequences will be
compared to a public database.
BC-310: Maldi-TOF. A protein spectrum created by the Maldi-TOF system will be compared to
the validated VITEK MS IVD database. (This service cannot be used for moulds)
RESULTS
Depending on the services requested the results will be send only by email or by email and regular mail.
BC-304, BC-306 and BC-307 will receive the results by email and by regular mail.
BC-308, BC-309 and BC-310 will receive the results only by email.
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Microbial Identification
Sample sheet
I accept the general terms and conditions of
BaseClear*
Name
: ______________________
Signature
: ______________________
Date
:__ / __/ ____
To be filled out by BaseClear:
Project Code
: __________________
Date of registration : _ _ / _ _ / _ _ _ _
*Our General Terms and Conditions apply to all projects BaseClear carries out and can be downloaded from our
website (www.baseclear.com/labservices/terms_conditions).
SAMPLES
We can only process live Class I, non-pathogenic micro-organism that are provided to us according to Dutch
regulations. In brief, this means that bacteria or fungi should be delivered on petri-dishes or on slants that are
sealed with parafilm. Sealed dishes/ slants should be wrapped in absorbing tissue, and enclosed in an
unbreakable and watertight cover. Please make sure that you clearly indicate the sample names on the petridishes. If you suspect the micro-organisms to be pathogenic please contact us beforehand so we can discuss
alternative means of transportation.
TERMS OF DELIVERY
Bacterial samples using the validated MicroSEQ® system (BC-304)
DNA-isolation, PCR, sequencing and reporting will be performed using MicroSEQ validated protocols, kits and
database. Approximately 500 base pairs of the 16S rRNA gene will be amplified and sequenced on both strands.
A full report including the homology search to the MicroSEQ validated database and sequence data will be
mailed to the client within 5 working days.
The reported result is the most likely sample identification. However, the client has to make the final conclusion
to the identity of the sample.
Bacterial samples using custom protocols (BC-308 and BC-309)
We offer two possibilities for analysis of bacterial samples using our custom kits.
For a custom ID <700bp (BC-308) approximately 600 base pairs of the 16S rRNA gene will be amplified and
sequenced on both strands. A full report including the homology search in our internal or online database and
sequence data will be mailed to the client within 5 working days.
For a custom ID <1400bp (BC-309) approximately 1400 base pairs of the 16S rRNA gene will be amplified and
sequenced on both strands. A full report including the homology search in an online database and sequence
data will be mailed to the client within 5 working days.
Because of sequence length a complete search (~1.4 kb) is more reliable than a partial search.
The reported result is the most likely sample identification. However, the client has to make the final conclusion
to the identity of the sample.
Fungal samples using the validated MicroSEQ® system (BC-306)
DNA-isolation, PCR, sequencing and reporting will be performed using MicroSEQ validated protocols, kits and
database. For fungal samples, the D2-LSU gene (BC-306) is amplified and sequenced on both strands using
validated MicroSEQ® kits and protocols. The length of the consensus sequence is approximately 200-300 bp
long. A full report including the homology search to the validated MicroSEQ database and sequence data will
be mailed to the client within 5 working days.
The reported result is the most likely sample identification. However, the client has to make the final conclusion
to the identity of the sample.
Fungal samples using custom protocols (BC-307)
Alternatively, samples can be analysed by amplification and sequencing of the internal transcribed spacer (ITS)
genes (BC-307) using custom kits and protocols, and blasting in public databases. The consensus sequence
length is about 1400 bp long. A full report including the homology search in an online database and sequence
data will be mailed to the client within 5 working days.
The reported result is the most likely sample identification. However, the client has to make the final conclusion
to the identity of the sample.
Bacterial or yeast samples using the Maldi-TOF (BC-310).
It is not possible to requests this service for mould samples, only bacterial and yeast samples will be identified
using the Maldi-TOF. Maldi-TOF identification is achieved by obtaining spectra using the Maldi-TOF technology
(Matrix Assisted Laser Desorption Ionization Time-of-Flight) and analyzing the spectra with the VITEK MS
database. The peaks from these spectra are compared to the characteristic pattern for a species, genus, of
family of micro-organism, thus resulting in an identification. If the Maldi-TOF results do not meet BaseClear
quality standard, the samples will automatically be identified using BC-308 at no extra charge.
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Microbial Identification
Sample sheet
Strain comparison (BC-360)
Additionally, generated sequencing results can be compared to each other in order to detect differences
between strains and visualize them (at additional costs). A pdf report, including visual comparison of the DNA
sequences of the strains and marked differences will be delivered.
SmartGene database (BC-314)
BaseClear has also access to the validated web-based SmartGene databases. Identification of a sample is
achieved by comparing the consensus sequence against the constantly updated reference databases. The 16S
rDNA Centroid Reference Database is a quality- controlled 16S rDNA Reference Database. The Centroid
database is built using a proprietary algorithm, to determine the most representative sequence entry for each
bacterial species; searching a sample sequence against the Centroid dataset allows to visualize in a convenient
manner the differences of the best matching species Centroid and the other closely related species, for easier
discrimination.
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Microbial Identification
Sample sheet
Bacterial identification
No.
Fungal identification
Sample name
1.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
2.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
3.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
4.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
5.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
6.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
7.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
8.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
9.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
10.
MicroSEQ® 500bp
Custom ID <700bp
Custom ID <1400 bp
Maldi-TOF
Strain
comparison
(Y/N)
Use SmartGene
Database***
(Y/N)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
MicroSEQ® D2-LSU
ITS-region
Maldi-TOF
(only for yeast samples not
for mould samples)
***For MicroSEQ samples the use of the SmartGene database is free of charge. For custom ID services the use
of the SmartGene databases will be at additional cost.
Remarks:
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