I have some mix of bacteria and would like to know which species there are exactly. Should I send them for sequencing their DNA? or what would be cheap method?
Dear David,
Use EPI 20 system or vitek system for primary identification then you can confirm your results by doing regular or real time PCR for some genes of the identified species.
Good luck
Hello David,
The chromatogram from the sequencing company will be "messy" (showing several peaks) and BLAST NCBI can only report which is the dominant bacterial strain in the mix I suggest you purify it first via Spread Plating. Once you have pure cultures, have their DNA extracted, then, it will be great to have them sequenced.
Vitek works great too, especially if you want to know more about their Biochemical characteristics. Good luck!
Regards,
NRB
What's your source? Your bacteria are cultureable or not? Or many other questions are important for you to choosing a method.
Plate on different agar will be cheap to grow culturable bacteria and use 16S PCR to identify pure isolates. Otherwise will go for 16S metagenome sequencing - this will be a slightly more expensive approach, but it will give you a better resolution on the bacteria present in the samples. The ideal method will be whole genome shotgun, will give you resolution down to species level. Hope this helps.
I feel your bacterial mix is culturable, go for 16S rDNA sequencing for idenification
In order to differentiate one type of bacteria from others it is necessary to determine their bacterioscopic, bacteriological and biochemical properties. Express methods - immunofluorescence and PCR.
Depending on the group you are interested in, but 16S rDNA can identify bacteria at least to genera, it might be a bit complicated when you are interested in identifying the organisms to species level.
You can as well use Analytical Profiling Index (API Kit).
Whole genome sequencing is something you may consider though may be expensive and time-consuming but will have high precision
You can do extraction of total DNA and amplify it by using universal bacterial starters. After this, you can use DGGE method to appreciate the bacterial ecology of your sample. The different bands can be purified, amplified and sequenced to have the exact species.
Before sequencing you can isolate bacteria on general media and perform biochemical identifications using BIOLOG system or API system.
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