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:

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.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. and 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, pp.260-266.