The Construction of Reference Gene and Genome Catalogs of Chinese Liquor

The workflow for constructing the Moutai Microbiome Catalog is provided in the following figure:

Schematic for constructing the Moutai microbiome catalog and the key results. (A) Taxonomic structure analysis of the fermented grain microbiome. This module includes biomarker analysis, network analysis, community assembly process, and Mantel test analysis. (B) Functional and taxonomic annotation for the gene catalog. The number and percentage of genes were calculated by annotations analyses against the mainstream functional databases (Swiss-Prot, UniRef50, TrEMBL, eggNOG, KEGG, COG, GO, EC, CAZy, and CARD). (C) Genome profile and biosynthetic gene clusters (BGCs) as examined by the analytical pipeline. This module includes BGC prediction and annotation, the species-level clustering of MAGs, and the taxonomical and functional annotation for MAGs. In the whole figure, the green rectangles show the main results, the blue parallelograms represent the analytic procedures, and the software applied for each analytic procedure is shown in purple text. Yellow cylinders represent the databases used for MTFGC analysis.

Software

The name, version, and availability of the software for constructing the Moutai Microbiome Catalog are provided as below:

Reagent or resources	Version	Identifier	Source
Software and algorithms
Trimmomatic	v0.38	https://github.com/usadellab/trimmomatic	https://doi.org/10.1093/bioinformatics/btu170
MetaPhlAn2	v2.6.0	https://github.com/biobakery/metaphlan2	https://doi.org/10.1038/nmeth.3589
MEGAHIT	v1.1.2	https://github.com/voutcn/megahit	https://doi.org/10.1093/bioinformatics/btv033
FastNC2	v2	https://github.com/wqssf102/fastnc2	https://doi.org/10.1073/pnas.202532111
QUAST	v5.0.2	https://github.com/ablab/quast	https://doi.org/10.1093/bioinformatics/btt086
MetaWRAP	v1.2.2	https://github.com/bxlab/metawrap	https://doi.org/10.1186/s40168-018-0541-1
CheckM	v1.0.18	https://github.com/tribe29/checkmk	https://doi.org/10.1101/gr.186072.114
Prodigal	v2.6.3	https://github.com/hyattpd/prodigal	https://doi.org/10.1186/1471-2105-11-119
Prokka	v1.14.5	https://github.com/tseemann/prokka	https://doi.org/10.1093/bioinformatics/btu153
MMseqs2	v4.8.1	https://github.com/soedinglab/mmseqs2	https://doi.org/10.1093/bioinformatics/btq003
KofamScan	v1.3.0	https://github.com/rotheconrad/keggdecoder-binder	https://doi.org/10.1093/bioinformatics/btz859
DIAMOND	v2.0.14.152	https://github.com/python-diamond/diamond	https://doi.org/10.1038/nmeth.3176
DeepARG	v1.0.2	https://github.com/deeparg/deeparg	https://doi.org/10.1186/s40168-018-0401-z
eggNOG-mapper	v2.1.6	https://github.com/eggnogdb/eggnog-mapper	https://doi.org/10.1093/molbev/msab293
antiSMASH	v6.0.0	https://github.com/antismash/antismash	https://doi.org/10.1093/nar/gkab335
BiG-SCAPE	v1.1.5	https://github.com/medema-group/big-scape	https://doi.org/10.1038/s41589-019-0400-9
dRep	v3.4.0	https://github.com/mrolm/drep	https://doi.org/10.1038/ismej.2017.126
GTDB-tk	v2.1.1	https://gtdb.ecogenomic.org/downloads	https://doi.org/10.1093/bioinformatics/btac672
Rosetta2	v2.0	https://github.com/h33p/docker-rosetta2	https://doi.org/10.1006/jmbi.1997.0959

Database

The name, description, and availability of the databases for constructing the Moutai Microbiome Catalog are provided as below:

Databases	Identifier	Source
eggNOG	http://eggnog5.embl.de/#/app/downloads	https://doi.org/10.1093/nar/gky1085
KEGG	http://kobas.cbi.pku.edu.cn/kobas3/download/	https://doi.org/10.1093/nar/gkaa970
COG	http://www.ncbi.nlm.nih.gov/cog/	http://oi.org/10.1093/nar/gkaa1018
GO	http://geneontology.org/	http://oi.org/10.1093/nar/gky1055
CAZyDB	http://www.cazy.org/	https://doi.org/10.1093/nar/gkn663
EC	https://enzyme.expasy.org/index.html	http://oi.org/10.1093/nar/28.1.304
CARD	https://card.mcmaster.ca/download	https://doi.org/10.1093/nar/gkz935
GTDB	https://gtdb.ecogenomic.org/downloads	https://doi.org/10.1093/bioinformatics/btac672
Swiss-Prot	https://www.uniprot.org/	https://doi.org/10.1093/nar/gkac1052
TrEMBL	https://www.uniprot.org/	https://doi.org/10.1093/nar/gkac1052
UniRef50	https://www.uniprot.org/	https://doi.org/10.1093/bioinformatics/btm098
Pfam	http://pfam-legacy.xfam.org/	https://doi.org/10.1093/nar/gkaa913

Data availability

The raw metagenomic data could be assessed at the GSA database (https://ngdc.cncb.ac.cn/gsub/) with ProjectID: PRJCA018633 for fermented grain samples and PRJCA018634 for starter samples. The data used for constructing MTFGC could be assessed in the National Genomics Data Center (NGDC) database (https://ngdc.cncb.ac.cn/) with BioProject ID: PRJCA018633. The raw data of MTFGC could be assessed with accession ID: CRA014449 and CRA012433 for raw data, GWHERCQ00000000 and GWHERDV00000000 for MAGs (MTFGC-Genome), as well as GWHERDA00000000 and GWHERDZ00000000 for nonredundant genes (MTFGC-Gene). The data used for constructing MTC could be assessed in the NGDC database with BioProject ID: PRJCA018633 and PRJCA018634. The raw data of MTC could be assessed with accession ID: CRA012433 and CRA012434 for raw data, GWHERDW00000000 for MAGs (MTC-Genome), and GWHERDX00000000 for nonredundant genes (MTC-Gene).

Code availability

The bioinformatics analysis of Moutai Microbiome in R is provided in "scripts/".

The test data are provided under the directory "data/".

The result is provided in the directory "Figures/".

To use them, please download the whole package and run in the R.

For more details, please refer to https://github.com/zhuxue1002/Moutai-Catalog/