Taxonomic Analysis of Lignocellulose and Nitrogen Metabolism

R package SQMtools [64 (link)] was used to identify the taxonomic origin of genes related to lignocellulose degradation and nitrogen metabolism. Taxonomic information was extracted from the annotated dataset of each species using the subsetFun and subsetTax functions of SQMtools. Counts transformed into relative abundances were allocated to the corresponding substrates and bacterial phyla. Adjacency matrices were then generated and visualized using Circos webtool [65 (link)].

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Hui T.K., Lo I.C., Wong K.K., Tsang C.T, & Tsang L.M. (2024). Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs. BMC Microbiology, 24, 57.

Publication 2024

Corresponding Organization :

Other organizations : Chinese University of Hong Kong

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Variable analysis

independent variables

Taxonomic information extracted from the annotated dataset of each species

dependent variables

Counts transformed into relative abundances allocated to the corresponding substrates and bacterial phyla

control variables

Control variables not explicitly mentioned

controls

Positive and negative controls not explicitly mentioned

Annotations

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