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Organism name:
Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505 (high GC Gram+)
Infraspecific name:
Strain: DSM 20438
Washington University Genome Sequencing Center
Assembly level:
Genome representation:
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000173435.1 (latest)
RefSeq assembly accession:
GCF_000173435.1 (latest)
RefSeq assembly and GenBank assembly identical:
WGS Project:

IDs: 215118 [UID] 215098 [GenBank] 215118 [RefSeq]

See Genome Information for Bifidobacterium pseudocatenulatum

There are 14 assemblies for this organism

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History (Show revision history)


Bifidobacterium pseudocatenulatum (GenBank Accession Number for 16S rDNA gene: M84785) is a member of the Actinobacteria division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und ... Zellkulturen GmbH (DSMZ) (DSM 20438).

This is a Newbler assembly (http://www.454.com/enabling-technology/the-software.asp) consisting of a one quarter plate 454 Titanium paired end library with a Q20 coverage of 50.7X. We have performed one round of automated sequence improvement (pre-finishing), along with manual improvement that includes breaking apart any mis-assembly, and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible.

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. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and 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.

This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC.  more

Global statistics

Total sequence length2,304,808
Total assembly gap length0
Number of contigs36
Contig N50570,758
Contig L502
Total number of chromosomes and plasmids0

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This assembly only contains unplaced WGS contigs. The WGS contigs can be viewed in the WGS Browser.

Download the full sequence report