Female Scientist writing on Petri dish
June 21, 2022 | Genomics

Got microbial profiling questions? We’ve got you covered

We’ve got the answers to your microbial profiling questions

Identifying microbes and understanding how they affect the overall human health and disease is of utmost importance. Next-generation sequencing (NGS) allows researchers to characterize unculturable human microbes to gain deeper insights into the metagenome. But there is more to NGS profiling than meets the eye. It is critical to understand which sequencing methods will provide the relevant information and allow you to optimize the microbial workflow.
We have answered six most commonly asked questions from our webinar on microbial community profiling and metagenomics.

1. Should I use enzymatic or mechanical-based DNA fragmentation for whole genome microbial metagenomics?

Overall, enzymatic fragmentation allows for a library prep procedure that is more amenable to automation and higher throughput. If you are concerned about running many samples at once, then the enzymatic fragmentation based whole genome kit may be best for you. 

2. For NGS microbial detection using 16S sequencing, what do you recommend between screening panels and region panels?

The screening panel offers the most comprehensive approach to detecting the high level of microbial biodiversity. However, if you know that the specific bacteria you are interested in can be characterized by only a handful of regions, it can be more cost-effective to only sequence specific regions. 

3. Can one use whole genome metagenomics to look for 16S genes? What approach would you recommend?

Whole genome metagenomics amplifies the entire bacterial genome, including the 16S genes. If you are interested in looking at the 16S gene and additional genomic regions, you should use whole genome metagenomics. However, if you are interested in the 16S region, then a targeted 16S approach may be an ideal approach for you.

4. Does QIAGEN offer sample collection to library prep products for microbiome profiling?

QIAGEN offers a wide range of sample preparation products for any sample type that you may be working with, as well as NGS tools for microbial detection. For NGS workflows, the QIAseq FX DNA Library Kit provides whole genome library preparation, while the QIAseq 16S/ITS Screening Panels and Index Kits and QIA seq 16S/ITS Region Panels profile-specific bacterial and fungal communities.

Check out our workflow configurator to find the best tool for you at each step of your workflow, from sample to sequencing.

5. For detecting antimicrobial resistance (AMR) regions, which method do you recommend, 16S or whole genome? Or both?

16S sequencing will not be able to detect any antimicrobial resistance (AMR) regions. The only options for looking at AMR is whole genome metagenomics or a targeted approach that can look at AMR genes. QIAGEN has recently launched a novel targeted hybrid capture panel for AMR, which targets 2786 unique AMR genes with over 6200 unique AMR alleles. 

6. Can I automate my whole genome library preparation for metagenomic analysis?

Yes, you can find the corresponding automation platforms and scripts on the Automation Hub.  The hub also contains valuable resources to support your research, including application notes and webinars on starting the automation process for whole-genome sequencing.