With the involvement of NGS, most of the researchers have moved to desk than to bench. At bench we understand the biological entity with chemicals and pipettes by monitoring them at specific laboratory conditions day over night, at desk we hypothesize of a biological relevance using the arsenal of computational tools of biology. I myself do microbial ecology but I wonder, are we unnoticing and losing those so called uncultured entities who are definitely of significance.
What would be the push towards making the uncultivable cultivable ??
http://www.nature.com/nature/journal/v517/n7535/full/nature14098.html
Hello Rajal,
According to me, for the isolation of unculturable microorganism we can use two approaches. one is to mimic environmental condition in laboratory which is not easy because we even dont know the complete environmental conditions and various factors present in natural environment, then how can we mimic it completely. So the next option that we have is in situ cultivation, based on the principle of diffusion chamber. So i think all these methods are only hit and trial based because in diffusion chamber also, condition will not be 100% similar to natural ecological niche.
Thanks Hani, Jay, Saurav for the input. I was aware of the ICHIP technology and the discovery of teixobactin. But I was more looking forward to the alternative approaches and principle. Thanks Hani for the book reference. I liked it.
This is the constant challenge in Microbial Ecology of course, but one way to develop a better understanding of what uncultured microbes in nature are doing is to survey their genomic potential through single cell genomics. This method anonymously sorts cells and then screens the single cells for 16S genes of interest to then develop genomic sequencing datasets from those cells of interest. See this link for what you can learn.
http://www.nature.com/nature/journal/v499/n7459/full/nature12352.html
In viral ecology, we face even a more daunting challenge as getting viruses into culture requires first having their hosts in culture. Currently ~85% of 1100 sequenced phage genomes derive from only 3 of 45 bacterial phyla (much worse for archaea) and this leads to viral metagenomic surveys where 63-93% of the reads are new to science. One way forward is mining single cell, complete and draft microbial genomes for viral signal to at least get sequence data on the viruses. Simon Roux in my group has done this even on important uncultivated microbes (SUP05, chemoautrophs dominating marine oxygen minimum ones) and has developed an automated tool for anyone in the community to do this. See the below links for details:
https://peerj.com/articles/985/
http://elifesciences.org/content/3/e03125
Aloha Rajal, what type of unculturable microbe are ya attempting to culture and isolate, and what ecological niche does it employ? I have led research in the past on endophytic microbes within native and indigenous botanical specimens, and have done a lot of work culturing microbes that would otherwise be difficult to isolate. I am very active in indigenous microbial analysis in various locations, and have been very successful in culturing microbes from environments ranging from the desert to tropical forests. I would spend more time becoming familiar with the biological aspects that your microbe of interest employs in its niche, then based off location, habitat, and selected food source, ya should be able to determine the right media for your needs. As aforementioned, it is very difficult to mimic nature, but it is still capable of being accomplished, just takes patience and time. Good luck on the endeavor!
Hi dear, For sure, it's a trial & error approach that needs patience. Try to similate the environment in lab. focussing on co-culture with other organisms in that same environ.
There may aslo some factors be involed that are host associated (if any). You may refer to the attached link. Good luck. http://jb.asm.org/content/194/16/4151.full
I agree with mimic approach to give same environment where microbes are growing naturally. I used Baiting techniques for my difficult mold species. Getting same water or soil or host and add new host/media. After several transfers you may expect to see some new cells from desired microbial spp. I am not from this university but am an independent Mycologist working for my own company in Hayward, CA . (TBON LAB, LLC)
Rajal- great point. i am one from the crowd who is just isolating total microbial DNA, and analyze by qPCR and NGS. dont have any expertise with culturing. the only thing i know- there is a huge number of microbes that cant be cultured at the moment, and its obvioulsy not trivial to address at the moment. but should be done one way or another
I'm not sure if you have seen the iChip http://www.northeastern.edu/magazine/how-the-ichip-works/ or if it is even relevant here.
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