So, generally people apply 97% similarity cut-off for species/OTUs in 16S based metagenomics. As far as I know, the 97% cut-off became standard practice with full 16S sequences. However, in 16S amplicon metagenomics we usually inspect just partial 16S sequences (~200-400 bp) from some variable region. In such cases, would it not make more sense to apply a higher cut-off value for clustering. I've noticed that with our data, increasing the cut-off from 97% to 99% increases OTU count some 5-10 fold. Our samples are from deep underground, so there's little literature to go on what would be a sensible species count for a given sample, but somehow I have a feeling that e.g. 500 OTUs is more realistic than 50 OTUs. Any thoughts?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
What platform are you sequencing on? I would like to see other's responses to this... I am sequencing on Ion Torrent PGM and the difference between 94, 97 and 99% is significant. I believe even within species, sometimes you only have 97% identity, or less. I don't know if I agree with you about your sensible species count. It sounds like your environment (deep underground) would not be an ideal place for speciation to occur, or a diverse population to develop-- too little movement, very static environment. So I would think it would be unlikely that too many species would develop to fill such a small niche as you are looking at... but maybe I'm wrong.
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment