Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Metagenomic survey of gut microbiota - depth, tradeoff and num. of samples to include

    Hi there community!

    I am a student currently enrolled in a Research Traineeship Program. My lab studies Systemic Lupus Erythematosus (SLE), and as a part of this research we are investigating microbiome in SLE patients and comparing to control groups.

    So far, we've done 16S rRNA amplicon sequencing of those patients. Some data were generated while I wasn't here (34 fecal samples, 15 controls, 19 SLE patients), and some are fairly recent (75 fecal samples, 25 controls, 50 SLE patients). Still not all samples have been sequenced, some failed PCR, and we'll be soon ordering mock communities in order to enhance our analyses, as some of the outcome results are pipeline-dependent (soft for OTU picking, filtering parameters etc.).

    Since 16S rRNA seems to be inefficient in exploring this immune disease, and "predictive metagenomics" (with PICRUSt software) is far too inaccurate, since the sequences that fail to map to reference (GreenGenes) are thrown out, we've decided to go with Shotgun Sequencing.

    Having read some papers (like: "How much metagenomic sequencing is enough to achieve a given goal?"), it is recommended to use at least 7Gbp (assuming x20 coverage to enumerate gene contents of prokaryotes with relative abundance of more than 1% in the human microbiota). Having 109 samples this is far too expensive. As a first step, I though about sticking to latest dataset, with 75 samples - i.e. reducing the number of samples to sequence. But this is too expensive (75 samples * 7GBp = 525).

    I don't have that much of an experience here, therefore I'd like to ask you, dear community, to help me out here. Direct me to some materials, or provide some suggestions. I don't want to remove patients from my dataset, as statistic power would decrease, but at the same time reducing depth could lead to "shallow" data. What are you thoughts?

    I have "paid" access to Illumina machines listed below:


    Best
    Robert.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    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...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X