Re: 16SRNA sequencing to determine differences between bacteria species

up to you. If you're not trying to conserve plates I'd do a swab per
plate just to keep them isolated.

Pretty close to a lab protocol at Washington U that a bit of google-fu
turned up, btw: www.nslc.wustl.edu/elgin/genomics/bio3055/idunknbacteria06.pdf

--Derek

On Dec 1, 10:57 pm, Koz <kozovsk...@gmail.com> wrote:
> Thanks for the link up Nathan, some super useful info there.
>
> Derek to your point,
> I will start with some 20 or so TSA plates and see what grows per each
> swab and then attempt to isolate.
> Any suggestions on culturing? Should I split each petri in 4?
>
> Alexander
>
> On Dec 2, 1:22 am, Derek <dere...@gmail.com> wrote:
>
>
>
>
>
>
>
> > very true if trying to identify a pure colony- cheap and easy. If
> > instead you are trying to identify species distribution from a swab
> > then my understanding is that the pcr step is largely the same but
> > that you'll have such a mix of species that you can no longer depend
> > on a simple sanger sequencing. I believe multi-tag pyrosequencing in a
> > 454 run is the current preferred approach in determining species
> > distribution, but at $4k a run that's definitely not what you're
> > looking for.
>
> > If I'm wrong and there's a simpler way to do species distribution from
> > swab samples please let me know!
>
> > Otherwise, you may be best off in attempting to isolate colonies
> > inoculated from your swabs onto petri dishes and sanger sequencing
> > individual colonies at $10 a pop or so. That won't give you
> > distributions but will at least distinctly identify some individual
> > bacteria.
>
> > --Derek
>
> > On Dec 1, 8:16 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
>
> > > (Specifically Patrik's response):
> > > On Oct 6, 12:00 am, Nathan McCorkle <nmz...@gmail.com> wrote:
>
> > > > I was thinking that colony PCR is really quite easy, are there
> > > > universal primers for 16S? I could get some in the mail in a few days
> > > > for not more than $5-$15... not sure if I really need that level
> > > > though, since I think this Prof is a "very very fair" grader.
>
> > > JGI typically uses universal primers 27F/1391R for bacterial 16S rRNA:http://my.jgi.doe.gov/general/protocols/SOP_16S18S_rRNA_PCR_Library_C...
> > > The Wikipedia page actually has a table with universal primers as
> > > well:http://en.wikipedia.org/wiki/16S_ribosomal_RNA#Universal_Primers
> > > 16S is such a common target in microbiology, that chances are somebody
> > > at your lab may have some primers available that you could use. Ask
> > > around among the grad students and postdocs...
>
> > > On Thu, Dec 1, 2011 at 11:15 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> > > > See this recent thread, you'll need lab access and tools to perform PCR:
>
> > > > How to perform bacterial ID (I am trying to determine a Bacillus species)
> > > >http://groups.google.com/group/diybio/browse_thread/thread/449334a66c...
>
> > > > On Thu, Dec 1, 2011 at 9:58 PM, Koz <kozovsk...@gmail.com> wrote:
> > > >> Hi ,
>
> > > >> I want to do a fairly simple test and determine specific species of
> > > >> bacteria that exist on different surfaces.
> > > >> The agar plate/phenotype test does not give me enough precise data, so
> > > >> I was wondering if there is a relatively inexpensive way to sequence
> > > >> microorganisms from a collection of swabs?
> > > >> Pretty new to this and have very limited access to basic lab equipment
> > > >> so supposedly I would need to send this out.
> > > >> Any suggestions?
>
> > > >> Alexander
>
> > > >> --
> > > >> You received this message because you are subscribed to the Google Groups "DIYbio" group.
> > > >> To post to this group, send email to diybio@googlegroups.com.
> > > >> To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
> > > >> For more options, visit this group athttp://groups.google.com/group/diybio?hl=en.
>
> > > > --
> > > > Nathan McCorkle
> > > > Rochester Institute of Technology
> > > > College of Science, Biotechnology/Bioinformatics
>
> > > --
> > > Nathan McCorkle
> > > Rochester Institute of Technology
> > > College of Science, Biotechnology/Bioinformatics

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