Sequence-Based Discovery of Novel Bacteria, Bradyrhizobium Enterica, in Cord Colitis Syndrome

Innate and therapy-induced states of immunosuppression are associated with a variety of potentially infectious idiopathic clinical syndromes. Using unbiased, next-generation sequencing, we investigated the metagenome of cord colitis syndrome (CCS), a recently described transplantation-associated colitis syndrome, in order to identify a candidate infectious trigger. Shotgun whole genome sequencing of DNA was performed followed by computational classification of reads. A large proportion of reads remained unmapped, suggesting the presence of a potentially novel organism. In order to investigate the source of these unmapped reads, de novo computational assembly of nonhuman reads was performed and yielded 98 contigs of > 2.5kb in length covering a total of 7.65Mb. Read coverage and GC content was similar for all of these contigs, suggesting they corresponded to a common organism. Phylogenetic analysis of this draft genome revealed that this organism was a novel species, which we have provisionally named Bradyrhizobium enterica. PCR confirmed the presence of B. enterica in three additional CCS patients and demonstrated absence of B. enterica in normal colon, colon cancer and graft-versus-host disease controls. In summary, we have demonstrated the assembly of a novel bacterial draft genome from human tissue specimens without isolation or culture of the organism. This organism, provisionally named B. enterica, is associated with CCS suggesting that it may function as an opportunistic human pathogen.