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

Brettin, Thomas S.

Bruce, David

Copeland, Alex

Dalin, Eileen

Davenport, Karen Walston

de Vos, Willem M.

Detter, John C.

Glavina del Rio, Tijana

Goodwin, Lynne

Han, Shunsheng

Hauser, Loren

Kant, Ravi

Kyrpides, Nikolaos

Land, Miriam L.

Lapidus, Alla

Larimer, Frank W.

Lucas, Susan

Ovchinnikova, Galina

Palva, Airi

Pitluck, Sam

Richardson, P. Paul

Sims, David

Smidt, Hauke

Tice, Hope

van Passel, Mark W. J.

Zoetendal, Erwin G.

PubMed

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.
          </jats:p

Mark W. J. van Passel

Ravi Kant

Airi Palva

Susan Lucas

Alex Copeland

Alla Lapidus

Tijana Glavina del Rio

Eileen Dalin

Hope Tice

David Bruce

Lynne Goodwin

Sam Pitluck

Karen Walston Davenport

David Sims

Thomas S. Brettin

John C. Detter

Shunsheng Han

Frank W. Larimer

Miriam L. Land

Loren Hauser

Nikolaos Kyrpides

Galina Ovchinnikova

P. Paul Richardson

Willem M. de Vos

Hauke Smidt

Erwin G. Zoetendal

Crossref

Journal of Bacteriology

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

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 trac

Passel, M.W.J., van

Vos, W.M., de

Smidt, H.

Zoetendal, E.G.

Wageningen Yield 

JOURNAL OF BACTERIOLOGY, May 2011, p. 2373–2374 Vol. 193, No. 9
0021-9193/11/$12.00 doi:10.1128/JB.00271-11
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic
Bacterium from the Phylum Lentisphaerae, Isolated from the
Human Gastrointestinal Tract
Mark W. J. van Passel,1 Ravi Kant,2 Airi Palva,2 Susan Lucas,3,4 Alex Copeland,3,5 Alla Lapidus,3,5†
Tijana Glavina del Rio,3,5 Eileen Dalin,3,5‡ Hope Tice,3,5 David Bruce,6 Lynne Goodwin,6
Sam Pitluck,3,5 Karen Walston Davenport,6 David Sims,7 Thomas S. Brettin,8 John C. Detter,6
Shunsheng Han,6 Frank W. Larimer,8 Miriam L. Land,8 Loren Hauser,8 Nikolaos Kyrpides,3,5
Galina Ovchinnikova,3,5 P. Paul Richardson,3,5 Willem M. de Vos,1,2
Hauke Smidt,1 and Erwin G. Zoetendal1*
Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands1; Department of Veterinary Biosciences, Faculty of
Veterinary Medicine, FIN-00014 University of Helsinki, Finland2; DOE Joint Genome Institute, Walnut Creek, California 945983;
Lawrence Livermore National Laboratory, Livermore, California 945504; Lawrence Berkeley National Laboratory,
Berkeley, California 947205; Los Alamos National Laboratory, Los Alamos, New Mexico 875456;
HudsonAlpha Genome Sequencing Center, Huntsville, Alabama 358067;
Biosciences Division, Oak Ridge National Laboratory,
Oak Ridge, Tennessee 378318
Received 25 February 2011/Accepted 28 February 2011
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.
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 bac-
terium 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 sec-
ond 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 assem-
bled 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 pseu-
doreads. Quality scores were assigned based on Newbler con-
sensus q-scores with modifications to account for overlap re-
dundancy and adjust inflated q-scores. A hybrid 454/Sanger
assembly was made using the Phrap assembler. Possible mis-
assemblies 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, fol-
lowed by a round of manual curation with the GenePRIMP
pipeline (8). Noncoding genes and other miscellaneous fea-
tures 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 repre-
sentatives from the PVC superphylum, including the human
gut isolate Akkermansia muciniphila (11), a relatively large
* Corresponding author. Mailing address: Laboratory of Microbiol-
ogy, University of Wageningen, Dreijenplein 10, 6703 HB Wagenin-
gen, Netherlands. Phone: 31 317 483111. Fax: 31 317 483829. E-mail:
Erwin.Zoetendal@wur.nl.
† Present address: Fox Chase Cancer Center, Philadelphia, PA.
‡ Present address: Synthetic Genomics, La Jolla, CA 92037.
 Published ahead of print on 11 March 2011.
2373
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 acces-
sion numbers ABDE02000001 to ABDE02000027.
M.W.J.V.P. is funded by the Netherlands Organization for Scientific
Research (NWO) via a VENI grant. R.K. was supported by the Center
of Excellence in Microbial Food Safety Research (MiFoSa), Academy
of Finland.
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English

A human gut microbial gene catalogue established by metagenomic sequencing.

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae.

Highthroughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57:1605–1615. 2374

Improved prediction of signal peptides:

Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum,

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Prodigal: prokaryotic gene recognition and translation initiation site identification.

Rfam: an RNA family database.

RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res.

The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One 6:316876.

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.

Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces.

Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastrointestinal tract

van Passel, M.W.J.

de Vos, W.M.

NARCIS 

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3133096

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

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

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