I hope this message finds you well. I am currently working on a manuscript titled “Microbial Diversity in Surface Biofilms of Primary Poultry Production Environments in Dar es Salaam” based on 16S rRNA gene sequencing performed using the Oxford Nanopore Technologies (ONT) GridION platform.
I would greatly appreciate your support in performing the necessary alpha and beta diversity analyses and relevant visualizations to complete the microbial diversity component of the study just with the data I had shared with you.
Summary of What I Already Have:
- Sequencing platform: ONT GridION
- Target: Full-length 16S rRNA (V1–V9), using primers 27F and 1492R
- Library kit: 16S Barcoding Kit 24 V14 (ONT)
- Basecalling: Super high accuracy; only reads ≥ Q15 retained
- Taxonomic classification: Using Kraken2 with NCBI_16S database
- Outputs I received:
- Abundance tables per sample
- Read quality and length distribution graphs
- Taxonomic composition (relative abundance)
- Phylogenetic trees and reports
- Alpha diversity indices:
- Shannon Index
- Simpson’s Index
- Inverse Simpson
- Berger-Parker Index
- Fisher’s alpha
- Richness
- Pielou’s Evenness
- Effective Number of Species
What I Need Help With:
1. Alpha Diversity
- Visualization:
- Boxplots or violin plots of alpha diversity metrics across different sample types/groups (e.g., cloaca, floor, drinker, feeder)
- Statistical testing:
- Kruskal-Wallis or ANOVA to compare alpha diversity across sample types
2. Beta Diversity
- Distance matrices:
- Compute Bray-Curtis, Jaccard, and (if possible) weighted/unweighted UniFrac distances
- Ordination plots:
- PCoA and/or NMDS plots showing clustering by sample type or source
- Statistical testing:
- PERMANOVA to assess differences between sample groups
3. Additional Visualizations (if possible):
- Heatmaps of top taxa (at genus or family level)
- Stacked barplots of taxonomic composition across samples
- Dendrogram or cluster analysis based on beta diversity
Notes:
- The goal is to generate figures and outputs suitable for a peer-reviewed publication (e.g., in International Journal of Microbiology or Antibiotics).
- If needed, I can provide the sample metadata and clarify groupings (e.g., biotic vs. abiotic surfaces, districts, sample sources).
Thank you very much for your time and expertise. Your assistance will be critical in finalizing the analytical part of the manuscript. My wish is to have you as my co-author for assisting me in the technical bits of the study
Warm regards,
Levi Omache
PhD Candidate – Sokoine University of Agriculture