What is biogasmicrobiome.com

Biogasmicrobiome.com is a repository related to the work performed in order to decipher the microbial community populating biogas reactors. Using next-generation shotgun sequencing, the obtained reads were assembled and the Genome Bins (GBs) were extracted using a two stage binning approach strategy.

In our first work, the extraction of 106 GBs from the biogas microbial community was achieved. Annotation of the identified genes and functional analysis of the species gave for the first time a clear understanding of the AD microbiome and allowed to establish a reference collection of biogas microbial genomes that will greatly simplify future genomic studies.

Background

Metagenomic assembly of shotgun reads generates huge number of scaffolds derived from different microbial genomes present in the community. Binning is the process of grouping scaffolds (or sequence reads) and assign them to the operational taxonomic units. The microbial genomes extracted from the binning procedure are frequently named "genome bins" to discriminate them from microbial genomes obtained from sequencing and assembly of bacterial clones.

From this project you can download the following:

Binning process v1

This link contains all the scripts that were used to perform the binning strategy

If you use this process please cite:

Stefano Campanaro, Laura Treu, Panagiotis G. Kougias, Davide De Francisci, Giorgio Valle, Irini Angelidaki., 2016. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnology for Biofuels 9:26, DOI:10.1186/s13068-016-0441-1. For full article press here

List of Biogas Genomes Fasta Format v1

This link contains as .gz file all the Genome Bins that were extracted with the binning process in Fasta format || The genomes are related to the work:

Campanaro, S., Treu, L., Kougias, P.G., Francisci, D., Valle, G. and Angelidaki, I., 2016. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnology for biofuels, 9(1), p.1.

List of Biogas Genomes Genbank Format v1

This link contains as .gz file all the Genome Bins that were extracted with the binning process in Genbank format || The genomes are related to the work:

Campanaro, S., Treu, L., Kougias, P.G., Francisci, D., Valle, G. and Angelidaki, I., 2016. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnology for biofuels, 9(1), p.1.

List of Biogas Genomes (SYMBIO project)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted for the SYMBIO project using the Binning process v1. The additional scripts used in this project can be downloaded by pressing here || The genomes are related to the work:

Treu, L., Kougias, P.G., Campanaro, S., Bassani, I., Angelidaki, I., 2016. Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes. Bioresource Technology, 216:260-6.

List of Biogas Genomes Genbank Format v1 (Denmark Biogas Plants)

This link contains as .gz file all the Genome Bins in Genbank format that were extracted using the binning process on reads obtained from 14 samples derived from Denmark Biogas Plants || The genomes are related to the work:

Campanaro, S., Treu, L., Kougias, P.G., Luo, G. and Angelidaki, I. Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants. (Submitted to Water Research)

List of Biogas Genomes Fasta Format v1 (Lignocellulose degradation process)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted using the binning process on reads obtained from samples derived from co-digestion of pig manure and silages || The genomes are related to the work:

Genome-centric metagenomics revealed the spatial distribution and the diverse metabolic functions of lignocellulose degrading uncultured bacteria. PG Kougias, S Campanaro, L Treu, P Tsapekos, A Armani, I Angelidaki. Applied and Environmental Microbiology, AEM. 01244-18.

List of Biogas Genomes Fasta Format v1 (Cheese whey degradation process)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted using the binning process on reads obtained from samples derived from degradation of cheese whey || The genomes are related to the work:

Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes. A Fontana, S Campanaro, L Treu, PG Kougias, F Cappa, L Morelli, Irini Angelidaki. Water research 134, 181-191

List of Biogas Genomes Fasta Format v1 (Saccharides degradation process)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted using the binning process on reads obtained from samples derived from degradation saccharides || The genomes are related to the work:

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics. X Zhu, S Campanaro, L Treu, PG Kougias, I Angelidaki. Water research 151, 271-279.

List of Biogas Genomes Fasta Format v1 (Carbon monoxide degradation process)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted using the binning process on reads obtained from samples derived from anaerobic granular sludge for CO conversion || The genomes are related to the work:

Anaerobic granular sludge for simultaneous biomethanation of synthetic wastewater and CO with focus on the identification of CO-converting microorganisms. Y Jing, S Campanaro, P Kougias, L Treu, I Angelidaki, S Zhang, G Luo. Water research 126, 19-28.

List of Biogas Genomes Fasta Format v1 (Global analysis of the biogas microbiome V1.0)

This link contains as .gz file all the Genome Bins in Fasta format that were extracted using the binning process on reads obtained from 134 samples collected from public databases || The genomes are related to the work:

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production. Campanaro S, Treu L, Rodriguez-Rd LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I. bioRxiv preprint. doi: https://doi.org/10.1101/680553