Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic Bacterium from the Phylum Lentisphaerae, Isolated from the Human Gastrointestinal Tract

Abstract

Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract.

TEXT

The gastrointestinal (GI) tract is inhabited by a complex mixture of bacteria, which perform various functions that are beneficial to the host (13). Although numerous bacteria in the GI tract have yet to be cultivated, metagenomic analyses have unraveled much of the microbiome's genetic complexity (9). Still, validation of the actual capacities of microbes requires pure strains and, if possible, their genome sequences. Here, we represent the genome sequence of Victivallis vadensis ATCC BAA-548.

V. vadensis is a Gram-negative, nonmotile, strictly anaerobic coccus-shaped bacterium isolated from human feces (12). It is only capable of growth on a range of sugars in basal media, either as broth or semisolid (0.75%) agar, and does not grow on regular agar plates. V. vadensis was the first isolate from the phylum Lentisphaerae. Currently, this phylum holds only two orders, the Victivallales and the Lentisphaerales, with the latter order represented by the Gram-negative aerobic marine bacterium Lentisphaera araneosa (2, 10). Both V. vadensis and L. araneosa produce extracellular slime.

The phylum Lentisphaerae is most closely related to the deep-branching Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum. The V. vadensis genome is only the second from the Lentisphaerae, which may help to illustrate the lack of known diversity within this phylum.

The genome of Victivallis vadensis was sequenced using a combination of Sanger (2.5-kb pUC, 8-kb pMCL, and fosmids) and 454 sequencing (GS FLX). All general aspects of library construction and sequencing can be found at the JGI website (http://www.jgi.doe.gov/). Pyrosequencing reads were assembled using the Newbler assembler, version 1.1.02.15 (Roche). Large Newbler contigs were broken into 5,854 overlapping fragments of 1,000 bp and entered into assembly as pseudoreads. Quality scores were assigned based on Newbler consensus q-scores with modifications to account for overlap redundancy and adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the Phrap assembler. Possible misassemblies were corrected and gaps between contigs were closed by editing in Consed or by custom primer walks from subclones or PCR products.

Genes were identified using Prodigal (4) as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation with the GenePRIMP pipeline (8). Noncoding genes and other miscellaneous features were predicted using tRNAscan-SE (7), RNAMMer (6), Rfam (3), TMHMM (5), and signalP (1).

The unclosed draft genome has 4,577,257 bases comprising 3,541 predicted protein-coding sequences (CDS) and a GC content of 59.5%. There are three predicted copies of the 5S but only one each of the 16S and 23S rRNA genes. A total of 48 predicted tRNAs were identified. A putative function could be predicted for 2,031 CDS (57.4%). Similar to other representatives from the PVC superphylum, including the human gut isolate Akkermansia muciniphila (11), a relatively large number of genes containing signal peptides were found (877 CDS, 24.8%).

Nucleotide sequence accession number.

The draft genome sequence of V. vadensis is available in GenBank under accession numbers ABDE02000001 to ABDE02000027.