Genomic Characterization of KD337-16 Strain

A QIAamp PowerFecal Pro DNA Kit (Qiagen, Hilden, Germany) was employed to extract genomic DNA from the KD337-16^T strain. Subsequently, the SQK-LSK109 Ligation Sequencing Kit on a PromethION Flow Cell (R9.4.1) and Illumina NovaSeq 6000 in paired-end (2 × 151 bp) mode was used for Oxford Nanopore Technologies (ONT) sequencing. After the sequences had been decoded and refined, Flye version 2.8.3 was employed for assembly of the valid ONT sequences. The primary contigs were polished with Racon v1.4.22 and the Illumina read alignment results constructed using Minimap2 v2.17. The DDBJ Fast Annotation and Submission Tool was used to annotate the genome [35 (link)]. Methods described elsewhere [36 (link),37 (link),38 (link)] were employed to quantify the digital DNA–DNA hybridization (dDDH), the amino acid identity (AAI), and average nucleotide identity (ANI). The up-to-date bacterial core genes pipeline (http://leb.snu.ac.kr/ubcg2, accessed on 28 October 2022) [39 (link)] and EDGAR platform were utilized to construct phylogenomic trees [40 (link)], whereas the 3ggNOG 4.5 database and carbohydrate-active enzyme (CAZy) database were employed for functional assignment [41 (link),42 (link)]. The OrthoVenn2 webserver was used for pangenome analysis [43 (link)]. Finally, AntiSMASH software (v. 6.0) was employed to predict putative biosynthetic gene clusters [44 (link)].

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Lee A.Y., Chen C.H., Liou J.S., Lin Y.C., Hamada M., Wang Y.T., Peng L.L., Chang S.C., Chen C.C., Lin C.F., Huang L, & Huang C.H. (2022). Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa). Life, 12(11), 1749.

Publication 2022

QIAamp PowerFecal Pro DNA Kit NovaSeq 6000

Amino acid Bacterial genes Biosynthetic Carbohydrate Enzyme Gene clusters Genome Hybridization Ligation Nucleotide Strain Trees

Corresponding Organization : Food Industry Research and Development Institute

Other organizations : Taiwan Livestock Research Institute, Council of Agriculture, National Institute of Technology and Evaluation, Ministry of Health and Welfare, National Sun Yat-sen University, National Pingtung University of Science and Technology

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Variable analysis

independent variables

Oxford Nanopore Technologies (ONT) sequencing
Illumina NovaSeq 6000 sequencing
Flye version 2.8.3 for genome assembly
Racon v1.4.22 for genome polishing
Minimap2 v2.17 for Illumina read alignment
DDBJ Fast Annotation and Submission Tool for genome annotation
Digital DNA–DNA hybridization (dDDH), amino acid identity (AAI), and average nucleotide identity (ANI) calculations
Phylogenomic tree construction using up-to-date bacterial core genes pipeline and EDGAR platform
Functional assignment using 3ggNOG 4.5 database and carbohydrate-active enzyme (CAZy) database
Pangenome analysis using OrthoVenn2 webserver
Prediction of biosynthetic gene clusters using AntiSMASH software (v. 6.0)

dependent variables

Genomic DNA extracted from the KD337-16^T strain

control variables

QIAamp PowerFecal Pro DNA Kit (Qiagen, Hilden, Germany) for genomic DNA extraction
SQK-LSK109 Ligation Sequencing Kit on a PromethION Flow Cell (R9.4.1) for ONT sequencing

Annotations

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