The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.

Here we performed metagenomic shotgun sequencing on fecal samples from 98 full-term Swedish infants (new born, 4-months and 12-months old) and their mothers; assembled gut microbial genomes and constructed reference gene catalogs from the cohort. We generated 1.52 Tb paired-end reads of high-quality sequences (average 3.99 Gb per sample). A gene catalog was constructed for each time point based on de novo assembly and metagenomic gene prediction; and functionally annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We also assembled a total of 4,356 microbial genomes (>0.9 MB) de novo; by binning assembled contigs according to abundance variations across samples. These de novo assembled genomes were complemented by 1,147 genomes from the National Center for Biotechnology Information (NCBI) Bacteria/Archaea genome database. All genomes were subsequently clustered into 690 unique metagenomic operational taxonomic units (MetaOTUs) that were equivalent to species-level classifications. Of these, 373 were annotated to species, the remaining 317 represent novel species related to known species. We constructed the metaOTUs profile by mapping reads to our metaOTUs sequences.

The May 2011 outbreak of an E. coli infection in Europe resulted in serious concerns about the potential appearance of a new deadly strain of bacteria, Escherichia coli O104:H4 TY-2482. In response to this situation, and immediately after the reports of deaths, the University Medical Centre Hamburg-Eppendorf and BGI-Shenzhen worked together to sequence the bacterium and assess its human health risk.

The bacteriums genome was first sequenced using Life Technologies; Ion Torrent sequencing platform. According to the results of the draft assembly, the estimated genome size of this new E. coli strain is about 5.2 Mb. Sequence analysis indicated this bacterium is an EHEC serotype O104 E. coli strain. Comparative analysis showed that this bacterium has 93% sequence similarity with the EAEC 55989 E. coli strain, which was isolated in the Central African Republic and known to cause serious diarrhea. This strain of E. coli, however, has also acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome. The acquisition of these genes may have occurred through horizontal gene transfer.

To maximize its utility to the research community and aid those fighting the epidemic, this genomic data was released into the public domain under a CC0 license.

To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to genomic data from the 2011 E. coli outbreak. This work is published from China.