PMC4831113_01
Phylogenetic tree showing the position of Haemophilus massiliensis strain FF7T relative to the most closely related type strains other type strains (type = T) within the genus Haemophilus. The GenBank accession numbers for 16S rRNA genes are indicated in parentheses. An asterisk marks strains that have a genome sequence in the NCBI database. Sequences were aligned using MUSCLE, and a phylogenetic tree inferred using the Maximum Likelihood method with Kimura 2-parameter model using the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. Only bootstrap values equal to or greater than 70 % are displayed. The scale bar represents a rate of substitution per site of 1 %. Escherichia coli strain ATCC 11775T was used as outgroup
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Fig1
Strain FF7T exhibited a 94.8 % 16S rRNA sequence identity with Haemophilus parasuis strain ATCC 19417T (GenBank accession number AY362909), the phylogenetically-closest bacterial species with a validly published name (Fig. 1). FF7T was incremented in our database (Additional file 3: Figure S1). Finally, the gel view showed that all members of the genus Haemophilus for which spectra were available in the database could be discriminated (Additional file 4: Figure S2). In addition, in this last figure, Haemophilusmassiliensis shared 2,021, 1,956, 2,020, 1,717, 1,977, 1,610, 1,980, 2,010, 2,390, and 2,123 orthologous genes with H. parasuis,
Morphology of Haemophilus massiliensis sp. nov. strain FF7T. a: Gram staining. b: Transmission electron microscopy. The scale bar represents 500 nm
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Fig2
Gram staining showed rod-shaped Gram-negative bacilli that were not motile and unable to form spores (Fig. 2). In electron microscopy, cells had a mean length of 2.6 mum (range 2.0-3.2 mum) and width of 0.35 mum (range 0.2-0.5 mum) (Fig. 2). FF7T was incremented in our database (Additional file 3: Figure S1). Finally, the gel view showed that all members of the genus Haemophilus for which spectra were available in the database could be discriminated (Additional file 4: Figure S2). In addition, in this last figure, Haemophilusmassiliensis shared 2,021, 1,956, 2,020, 1,717, 1,977, 1,610, 1,980, 2,010, 2,390, and 2,123 orthologous genes with H. parasuis,
Graphical circular map of the Haemophilus massiliensis strain FF7T chromosome. From the outside in, the outer two circles show open reading frames oriented in the forward (colored by COG categories) and reverse (colored by COG categories) directions, respectively. The third circle marks the tRNA genes (green). The fourth circle shows the G + C% content plot. The inner-most circle shows GC skew, purple indicating negative values whereas olive for positive values
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Fig3
Table 3 and Fig. 3.
Distribution of functional classes of predicted genes in the genomes from Haemophilus massiliensis (HM) strain FF7T, H. parasuis (HPA) strain ATCC 19417T, Aggregatibacter segnis (AE) strain ATCC 33393T, H. aegyptius (HA) strain ATCC 11116T, H. ducreyi (HD) strain CIP 54.2, H. haemolyticus (HH) strain ATCC 33390T, H. influenzae (HI) strain ATCC 33391T, H. parahaemolyticus (HP), H. parainfluenzae (HPI) strain ATCC 10014T, H. pittmaniae (HPT) strain HK 85T, and H. sputorum (HS) strain CCUG 13788T chromosomes according to the clusters of orthologous groups of proteins
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Fig4
The distribution of genes into COGs functional categories is presented in Table 4 and Fig. 4. The distribution of genes into COGs categories was similar for most of the compared species (Fig. 4). However, H. influenzae and H. aegyptius were over-represented for category N (cell motility), and H. ducreyi was under-represented for category W (extracellular structures) (Fig. 4). Haemophilus massiliensis is larger than those of H. parasuis,H. influenzae,A. segnis, H. sputorum, H. aegyptius,H. parainfluenzae, H. haemolyticus, H. ducreyi, and H. parahaemolyticus (2,319, 2,299, 1,765, 1,956, 2,072, 2,020, 2,068, 2,056, 1,717, and 1,980, respectively) but smaller than that of H. pittmaniae (2,390). However the distribution of genes into COG categories was similar in all compared genomes as shown in Fig. 4.