Genome sequence and description of Bacteroides timonensis sp. nov

Abstract

Bacteroides timonensis strain AP1(T) (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.

Keywords: Bacteroides timonensis; culturomics; genome; taxono-genomics.

Figure 1

Phylogenetic tree highlighting the position of Bacteroides timonensis strain AP1^T relative to other type strains within the Bacteroides genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained from 500 replicates. Prevotella melaninogenica was used as outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Figure 2

Gram staining of B. timonensis strain AP1^T

Figure 3

Transmission electron microscopy of B. timonensis strain AP1^T, made using a Morgani 268D (Philips) at an operating voltage of 60kV.The scale bar represents 200 nm

Figure 4

Reference mass spectrum from B. timonensis strain AP1^T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5

Gel view comparing B. timonensis strain AP1^T to other Bacteroides species. The gel view displays the raw spectra of loaded spectrum files as a pseudo-electrophoretic gel. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a grey scale scheme code. The grey scale bar on the right y-axis indicate the relation between the shade of grey a peak is displayed with and the peak intensity in arbitrary units. Displayed species are detailed in the left column.

Figure 6

Graphical circular map of the chromosome. From the outside in: open reading frames oriented in the forward (colored by COG categories) direction, open reading frames oriented in the reverse (colored by COG categories) direction, RNA operon (red), and tRNAs (green), GC content plot, and GC skew (purple: negative values, olive: positive values)..

Figure 7

Distribution of predicted genes of B. timonensis and 9 other Bacteroides species into COG categories. B. uni = B. uniformis, B. fin = B. finegoldii, B. hel = B. helcogenes, B. sal = B. salanitronis, B. the = B. thetaiotaomicron, B. vul = B. vulgatus, B. fra = B. fragilis, B. cel = B. cellulosilyticus, B. int = B. intestinalis, B. tim = B. timonensis.