karegapauline/Mangrove_microbiome_metagenomics_project

Microbiome metagenomics analysis of Kilifi creek mangrove sediments # Mangrove_microbiome_metagenomics_project ## Introduction. Mangrove forests can be divided two regions.; Indo-West Pacific (IWP) or the Old world mangroves that comprises Eastern Africa, Australasia, southern Japan and the West Pacific Islands; and the Atlantic-East Pacific (AEP) also referred to as the New world mangroves that includes the mangroves of Americas and West Africa. In Kenya, mangroves cover approximately 54,000 ha, most of which are in Lamu and Tana River. There are 9 mangrove species in Kenya, with the dominant species Rhizophora mucronata and Ceriops tagal making 70 % of the formation . ## Aim of the study. To do microbiome analysis of two mangrove species, Sonneratia alba Sm. and Rhizophora mucronata mangrove, collected from two sites, one disturbed and one undisturbed. ## Methodology. Obtain raw sequences. (10 sequences obtained) Perform quality control and trimming of data. Analyze data using Qiime 2 package version 2019.4. Perform OTU picking and generate OTU table. Use the R package Phyloseq to further analyse the data generated using Qiime. ## Tools used. Bash. R. ## Members. Elizabeth Mwangi Shaban Mziray Stanslaus Musyoki Karega Pauline