Computational protocol: Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

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Protocol publication

[…] The overlap between the forward and reverse reads was 180–190 bp approximately. The minimum quality score was 25 when merge the Illumina reads and the minimum overlap was 10 bp. The preprocessing of sequences was performed mainly by using MOTHUR 1.35.1 (University of Michigan, Ann Arbor, MI, USA) and by following the MiSeq analysis pipeline outlined in http://www.mothur.org/wiki/MiSeq_SOP []. Operational taxonomic units (OTUs) are defined as groups among which sequence similarities were greater than 97%. The species richness estimators (the abundance-based coverage estimator ACE, Jackknife and Chao1), Shannon diversity index, and Simpson diversity index were calculated. In this study, data preprocessing and OTU-based analysis were performed by MOTHUR (University of Michigan, Ann Arbor, MI, USA). Canoco 4.5 (Microcomputer Power, Ithaca, NY, USA) was used with Monte Carlo permutation test to perform the redundancy analysis (RDA) based on population abundance and environment factors. LEfSe (University of Auckland, Auckland, New Zealand) was used to find indicator bacterial groups specific to the sediment samples []. The statistical analysis was performed using SPSS 20.0 (International Business Machines Corporation, Armonk, NY, USA). […]

Pipeline specifications

Software tools mothur, LEfSe, SPSS
Applications Miscellaneous, Metagenomic sequencing analysis
Organisms Hemisus marmoratus
Diseases Water Intoxication