Currently, I am doing an experiment related to microbiome analysis from environment. However, I face technical problem related to NGS analysis that I have to wait for the analysis for around 2 months, cause the company needs to collect enough sample for one time running. I want to ask is there any faster method to do the microbiome analysis other than NGS?
I read that MALDI-TOF is fast, accurate, and reliable method for microbiome analysis. But from what I read, for this method we need to culture the bacteria and analyze each colony in different running time. Is that correct? If so, then how to analyze uncultured bacteria that might be exist in our sample? because for NGS, we extract the DNA of all types of bacteria including the uncultured one.
Or is there any method to estimate the diversity of bacteria cells in our sample?
Greetings Surono.
What do you mean by NGS? Do you mean rRNA16S sequentiation or metagenomics analysis of your samples? Either way, if your purpose is to estimate the relative abundance and have metrics on the proportions and families of bacterial species you could go for 16S. This is a reliable technique that could suit your environmental samples. From other hand if what you want is to understand, more than just bacterial abundance of ASV´s (The way of calling species in metagenomics or 16S sequencing), and identify genes related to a specific environment or treatment the way to go is metagenomics.
Finally, if you want to identify, quickly and with high certainty your PURE CULTURES of you environmental sample, your can use MALDI TOF.
For what you ask, rRNA 16S sequencing of V3 and V4 regions could be suitable for your needs in matter of bacterial diversity.
Cheers!
Hi Alejandro Mejia Muñoz,
Thank you so much for your brief explanation. Sorry, I might not describe my questions accordingly. I was just curious if we could identify or estimate bacterial composition in my samples without relying on the NGS.
I read that MALDI-TOF is quite reliable for bacterial identification, but it needs a single or pure bacteria colony. So, it would be hard to identify bacteria that are still unculturable. I understand that the majority of bacteria from environmental samples are still uncultured or unculturable.
Anyway, thank you for your insight.
Regards!
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