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Pseudoflavonifractor capillosus ATCC 29799 (GenBank Accession Number for 16S rDNA gene: AY136666) is a member of the division Firmicutes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans, it represents, on average, ... 0.008% of all 16S rDNA sequences and 0.016% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 29799).

We have collected 8.2X coverage in plasmid end reads and 454 reads. We will be performing one round of automated sequence improvement (pre-finishing). 

Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xl sequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally, PCAP (Huang, et al, Genome Research, 13:2164, (2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads.

This sequenced strain is part of a comprehensive, sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine, the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled "Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)" (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf). These studies are supported by National Human Genome Research Institute.

Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. RNA genes were determined using tRNAscan-SE 1.23 or Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs.

For answers to your questions regarding this assembly or project, or any other GSC genome project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person.

Annotation was added to the contigs in July 2007, and the CDS comments were updated in January 2008.

This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC.
Product names were updated in August 2012  more

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