# Analysis of rRNA data from BSF Metatrascriptomic Study
The Black Soldier Fly (Hermetia illucens; BSF) is a useful tool in valorising organic biomass and other biodegradable wastes. In this study, the BSF larvae were bred under different diets selected based on increasing lignocellulose content. These diets were: processed chicken feed (CF), chicken manure (CM), Brewer’s spent grain (BSG), and Water Hyacinth (WH). An additional diet Feed Mix (FM), consisting of the four diets in equal proportions was also incorporated. The different metatranscriptomes were sequenced using the PCR-cDNA approach on the ONT MinION platform. While the work, using ONT, aimed to identify and functionally characterise lignocellulosic biomass-degrading microbes, the mRNA enrichment protocol still retained some rRNAs, which were filtered out using SortMeRNA (Kopylova et al., 2012). The tool takes in the corrected fastq files from the five metatranscriptomes, runs them against multiple rRNA databases, and sorts them into two separate files (the clean/ribodepleted fastq files and the rRNA fastq files). You are provided with the rRNA fastq files for this mini-project. This is an explorative study. We aim to explore what we can glean from the data. Some questions to explore:
1. What kind of rRNA data do you have?
2. What kind of organisms can you identify from the data?
3. What else can we learn from the data?
4. How does the analysis pipeline differ from short-read sequences?

## Literature
1. Bruno, D., Bonelli, M., De Filippis, F., Di Lelio, I., Tettamanti, G., Casartelli, M., Ercolini, D., & Caccia, S. (2019). The intestinal microbiota of Hermetia illucens larvae is affected by diet and shows a diverse composition in the different midgut regions. Applied and Environmental Microbiology, 85(2). https://doi.org/10.1128/AEM.01864-18
2. Klammsteiner, T., Walter, A., Bogataj, T., Heussler, C. D., Stres, B., Steiner, F. M., Schlick-Steiner, B. C., Arthofer, W., & Insam, H. (2020). The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets. Frontiers in Microbiology, 11(May), 1–14. https://doi.org/10.3389/fmicb.2020.00993
3. Sahlin, K., Sipos, B., James, P. L., & Medvedev, P. (2021). Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis. Nature Communications, 12(1). https://doi.org/10.1038/S41467-020-20340-8
4. Tanga, C. M., Waweru, J. W., Tola, Y. H., Onyoni, A. A., Khamis, F. M., Ekesi, S., & Paredes, J. C. (2021). Organic Waste Substrates Induce Important Shifts in Gut Microbiota of Black Soldier Fly (Hermetia illucens L.): Coexistence of Conserved, Variable, and Potential Pathogenic Microbes. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.635881