I am looking to amplify a region that can be used to group the gut bacteria into higher taxa like phyla or classes. The target has to be a region that is relatively conserved within the phylum or class but variable between these groups.
I hope some here who have done studies in this area can give me recommendations on which primer sequences worked best for you. Thanks!
Hi Ferdinand Mendoza
We study the V3-V4 region.
V3-V4 Region: This is a widely used region known to provide profiles representative of diverse gut microbial communities at the genus level. It's a good starting point offering a balance of accuracy and practicality.
- Title: "Dietary Fiber Modulates Gut Microbiota Composition and Function in High-Fat Diet-Fed Mice" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234870/)
- Authors: Yuanyuan Li, et al.
- Journal: Nutrients (2020)
- Abstract: This study investigated the impact of dietary fiber on the gut microbiome of mice fed a high-fat diet. Fecal samples were collected and analyzed using V3-V4 16S rRNA gene sequencing.
- Title: "Antimicrobial Treatment Alters the Gut Microbiota and Promotes Fatty Liver Disease in Mice" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9034083/)
- Authors: Yuanyuan Mao, et al.
- Journal: Cell Reports (2018)
- Abstract: This research explored the link between antibiotic treatment and the development of fatty liver disease in mice. V3-V4 16S rRNA gene sequencing was used to analyze the gut microbiome composition from fecal samples.
- Title: "Association between Gut Microbiota and Response to Anti-PD-1 Therapy in Tumor-Bearing Mice" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035070/)
- Authors: Wenbo Zhang, et al.
- Journal: Frontiers in Immunology (2020)
- Abstract: This study examined the potential link between gut microbiota and the effectiveness of anti-PD-1 immunotherapy in mice with tumors. The gut microbiome of the mice was analyzed using V3-V4 16S rRNA gene sequencing of fecal samples.
You can check the sequence from the following studies.
Thanks,
For human gut microbiome diversity studies using 16S rRNA gene sequencing, the choice of primers is crucial for accurately capturing the microbial diversity. The following primer pairs are commonly used and recommended:
V3-V4 Region Primers
These primers are widely used due to their ability to provide a good balance between coverage and resolution of microbial communities.
V4 Region Primers
Primers targeting the V4 region are popular because this region is relatively short, making it suitable for high-throughput sequencing platforms like Illumina MiSeq.
V1-V2 Region Primers
These primers are used for capturing a broader range of bacteria, though they may not cover as many taxa as the V3-V4 or V4 regions.
V1-V3 Region Primers
Targeting the V1-V3 regions can provide a comprehensive view of the bacterial diversity, although the longer amplicon size might pose challenges for some sequencing platforms.