Phylogenetic Analysis of Microbial Genomes

A maximum-likelihood phylogenetic tree was constructed using PhyloPhlAn [58 (link)] (v.1.0) with 1904 SGBs, and visualized using Evolview [59 (link)] (v.3) and iTol [60 (link)] (v.4.3.1). All genomes were annotated using GTDB-Tk [61 (link)] (v.0.1.6) based on the Genome Taxonomy Database. The CAZyme families of the 592 high-quality genomes were annotated using HMMER [47 (link)] (v.3.2.1) based on a hidden Markov model. The PUL of high-quality SGBs was predicted by following the PULpy [62 ] (v.1.0) pipeline. The KOs of the high-quality SGBs were annotated using DIAMOND [43 (link)] (v.0.9.22) based on BLASTP searches against the KEGG [45 (link)] (v.90.0) databases. Protein sequences encoded by the 592 high-quality SGBs were also screened against HydDB [63 (link)] databases to identify the catalytic subunits of the three classes of hydrogenases ([NiFe]-, [FeFe]-, and [Fe]-hydrogenases) using BLASTP with an e-value threshold of 1e - 50, coverage values exceeding 90%, and identity values exceeding 50% [2 (link)].

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Lin L., Lai Z., Zhang J., Zhu W, & Mao S. (2023). The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet. Microbiome, 11, 10.

Publication 2023

Catalytic subunits Diamond Fe hydrogenases Genomes Hydrogenases Protein sequences Pulpy Sgbs

Corresponding Organization :

Other organizations : Nanjing Agricultural University

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Variable analysis

independent variables

Maximum-likelihood phylogenetic tree construction using PhyloPhlAn (v.1.0)
Genome annotation using GTDB-Tk (v.0.1.6)
CAZyme family annotation using HMMER (v.3.2.1)
PUL prediction using PULpy (v.1.0)
KO annotation using DIAMOND (v.0.9.22) and KEGG (v.90.0)
Hydrogenase catalytic subunit identification using BLASTP against HydDB databases

dependent variables

Phylogenetic tree
Genome taxonomy
CAZyme families
Hydrogenase catalytic subunits

control variables

1904 SGBs used for phylogenetic tree construction
592 high-quality genomes used for subsequent analyses

Annotations

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