16S Sequencing in Nextseq

General Discussion
#1

Is it safe to use Nextseq in 16s sequencing?

I have some ocean samples to sequence the 16s, however, due to some infrastructure limitations, I can only use a Nextseq for sequencing. Is it okay to do that? What are the best regions to use in this case? Can I use the same V3-V4 regions used in Miseq? I looked for articles that had already done this, but I found only two, that didn’t write about the difference or why they chose Nextseq, so I’m not so confident to do that.

The articles that I mentioned:
Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls - https://doi.org/10.1038/s41598-018-27314-3
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome - https://doi.org/10.1371/journal.pone.0212474

Thanks a lot!

#2

Sure, NextSeq is a good sequencer and will work just fine with about anything you sequence. You will get pretty high depth due to the large output (at least with the high output kits) with the standard primer kits so some people run custom kits to multiplex more samples (500+). V3-V4 does not make sense on NextSeq though since the longest kit is 2x150 and V3-V4 is longer than that (450bp). So you can only run V3 or V4. There seems to be a slight preference for V4 with NextSeq.
Note that the NextSeq struggles a bit more with low complexity reads so you will need larger phiX ratios (>=20%). In our case, we needed to go even higher than that to get good yields. Hopefully, somebody has run 16S on your equipment before and guide you on what works best for your setting.

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