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. 2016 Jan 29:10:142-50.
doi: 10.1016/j.nmni.2016.01.013. eCollection 2016 Mar.

Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5

A H Togo  1 , S Khelaifia  1 , J-C Lagier  1 , A Caputo  1 , C Robert  1 , P-E Fournier  1 , M Maraninchi  2 , R Valero  3 , D Raoult  4 , M Million  1
Affiliations

Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5

A H Togo et al. New Microbes New Infect. .

Expression of concern in

Abstract

Paenibacillus ihumii sp. nov. strain AT5 (= CSUR 1981 = DSM 100664) is the type strain of P. ihumii. This bacterium was isolated from a stool sample from a morbidly obese French patient using the culturomics approach. The genome of this Gram-negative, facultative anaerobic, motile and spore-forming bacillus is 5 924 686 bp long. Genomic analysis identified 253 (5%) of 3812 genes as ORFans and at least 2599 (50.03%) of 5194 orthologous proteins not shared with the closest phylogenetic species.

Keywords: Culturomics; Paenibacillus ihumii sp. nov.; genome; taxonogenomics.

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Figures

Fig. 1
Fig. 1
Gram staining of Paenibacillus ihumii strain AT5.
Fig. 2
Fig. 2
Transmission electron microscopy of Paenibacillus ihumii strain AT5 using Tecnai G20 (FEI Company) at operating voltage of 60 kV. Scale bar = 500 nm.
Fig. 3
Fig. 3
MALDI-TOF reference mass spectrum from Paenibacillus ihumii strain AT5. MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Fig. 4
Fig. 4
Phylogenetic tree highlighting position of Paenibacillus ihumii strain AT5 relative to other close species. Sequences are recovered using nucleotide blast against 16S rRNA Database of Silva ‘All-Species Living Tree’ project (LTPs119). Sequences were aligned using muscle and phylogenetic inferences obtained using approximately maximum likelihood method within Fast Tree software. Numbers at nodes are support local values computed using Shimodaira-Hasegawa test. Corresponding GenBank accession numbers for 16S rRNA genes are indicated at right of strains in tree.
Fig. 5
Fig. 5
Gel view comparing Paenibacillus ihumii strain AT5 to other species. Gel view displays raw spectra of loaded spectrum files arranged in pseudo-gel-like look. x-axis records m/z value. Left y-axis displays running spectrum number originating from subsequent spectra loading. Peak intensity is expressed by greyscale scheme code. The right y-axis indicates the peak intensity according to the colour of this peak, in arbitrary units. Displayed species are indicated on left.
Fig. 6
Fig. 6
Circular graphical map of genome. From outside to centre: Contigs (red/grey), COGs category of genes on forward strand (three circles), genes on forward strand (blue circle), genes on reverse strand (red circle), COGs category on reverse strand (three circles), G + C content. COGs, Clusters of Orthologous Groups database.
Fig. 7
Fig. 7
Distribution of functional classes of predicted genes according to clusters of orthologous groups of proteins.
See this image and copyright information in PMC

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