Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness

Abstract

The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.

Keywords: Arcobacter; Bacterial genomes; Genomics; Gram negative; Virulence genes.

Fig. 1

Analysis of gene clusters presence-absence in the Arcobacter species. The figure shows genomes characteristics of the Arcobacter species sorted for gene cluster presence and absence (species order). The strain isolation sources and the different species groups are displayed (presence/absence of bars; 1/0). Strains included in “clinical” were involved in clinical onset. The “num of contributing genomes” indicates the number of genomes where a gene cluster is present. The core genes are shown in the section indicated with the asterisk (*). The bars indicates difference information about the genomes. The bars above the names of the species, in addition to indicating the source of isolation, carry information regarding the genomes. The gray bars indicate the genome size (1.54–3.19 Mb), blue bars indicate completion percentages, dark brown bars indicate the number of gene clusters while light brown bars indicate the number of singleton gene clusters. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

Dendrograms of Arcobacter species. The trees have been computed from different input sequences. The dendrogram in panel A was produced on amino acidic sequences from Prokka analyzed with bcgTree (107 core sequences). The scale bar and numbers represent the number of amino acid substitutions per site. The dendrogram B represents the maximum likelihood estimation obtained on 16S rRNA sequences (10.000 bootstraps). The species have been marked with different colors according to the group. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Pangenome analysis of the Arcobacter species. The histogram (A) shows the percentages of the different persistent OGs and gene pathway families. The panel B shows the presence of multiple genes copies (blue = present, red = absent). Most of the multiple copies are in the right part of the graph in correspondence of the genomic portion related to core and shell genome. The bar chart (C) shows the percentage of COGs classes with standard deviations. The groups shown are: group 1 (G1), group S (G1S), group 2–5 together (G2-5) and all groups excluding the subgroup S (G2-5 and G1 w/o S). The asterisks (*) indicates differences statistically significant (p-value < 0.05) between G1 compared to G2-5 (dark red asterisks) and G1S compared to G2-5 and G1 w/o S (red asterisks). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

Genomes Annotated Pathway. The histogram shows the pathway modules with at least 80% of completeness in at least one genome (MicrobeAnnotator).

Fig. 5

PVGs presence-absence dendrogram. The figure shows the dendrogram produced on the presence-absence binary matrix of ten genes currently considered virulence-related. The tree (Jaccard, Neighbor-joining) shows bootstrap value (10.000) while the different colors near species names indicate the species belonging group. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)