An imbalanced respiratory microbiota has been observed in pneumonia which caused high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue which will significantly advance our understanding of host-microbiota interactions.
In this study, we collected 334 respiratory microbial samples from 171 healthy children and 76 pneumonia children. The established respiratory microbial gene catalogue (RMGC) comprised 2.25 million non-redundant microbial genes covering 90.52% prevalent genes. The core microbial species in the oropharynx (OP) of the healthy children mainly comprised Prevotella and Streptococcus. The OP microbial diversity and gene number in children with Mycoplasma pneumoniae pneumonia (MPP) decreased compared to that in healthy children, and the concurrence network of OP microbiota in patients is featured by Staphylococcus spp. and M. pneumoniae.Functional orthologues, which are associated with the metabolism of various lipids, membrane transport and signal transduction, accumulated in the OP microbiome of sick children. Several antibiotics-resistance genes (ARGs) and virulence-factor genes (VFGs) were identified in M. pneumoniae as well as other 13 microbial draft genomes, which were reconstructed via metagenomic data. Though the common macrolides/beta-lactam-resistance genes were not identified in assembled M. pneumoniae genome, a SNP mutation (A2063G) related with macrolides resistance was identified in 23S rRNA gene.
This study will facilitate exploring unknown microbial components and host-microbiota interaction in respiratory microbiome studies as well as render further insights into the microbial aetiology of MPP.

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.