Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites

Abstract

Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.

Keywords: Acetobacteraceae; Biosynthesis; Phylogeny; Specialized metabolites.

Fig. 1

GC content vs genome size plot and phylogenomic tree for Acetobacteraceae type strains a GC content and genome size plot grouping the type strains from each genus under the same symbol. The strains Azospirillum lipoferum 59b^T and Skermanella aerolata KACC 11604^T are used as outgroups for the family Acetobacteraceae. The plot reveals three groups of bacteria with some degree of overlap, globally differentiated as mostly acidophilic, mostly acetous, and acetous species often associated with insects. b Phylogenomic tree inferred from 50 housekeeping protein sequences showing the two different groups of the family Acetobacteraceae. The topology of the tree is supported by both Bayesian and maximum likelihood inference methods. Distinct clades (based on monophyly and a shorter branch length distance) were proposed particularly for the acetous group. The species organization into clades is detailed in Supplementary Table 2

Fig. 2

Presence of biosynthetic gene clusters (BGCs) in the two groups of the family Acetobacteraceae. a The number of BGCs per genome was plotted for each type strain, organized according to the taxonomic classification into acetous and acidophilic species. b BGCs for the biosynthesis of different metabolite classes were plotted for each type strain and were organized according to the taxonomic classification into acetous and acidophilic species. The numbers inside the boxplots are the calculated mean values

Fig. 3

Phylogenomic analysis of the family Acetobacteraceae and their biosynthetic gene clusters (BGCs) as detected using antiSMASH. a Phylogenomic tree based on 50 housekeeping protein sequences. b Type and number of BCGs in the genomes of each type species. c Total number of BCGs with at least one core gene detected using antiSMASH. The subgroups were classified according to the class or pathway of the metabolite as follows: A = terpenoid, B = aryl polyene, C = ribosomally synthesized and post-translationally modified peptide, D = ectoine, E = lactone, F = siderophore, G = type-1 polyketide, H = type-3 polyketide, I = hybrid polyketide/non-ribosomal peptide, J = non-ribosomal peptide, K = other specialized metabolites

Fig. 4

Type-1 polyketide synthase biosynthetic gene cluster in Acetobacteraceae. a Unrooted tree based on type-1 PKS showing the differentiation into four groups labelled α, β, γ and δ which correlate with certain taxonomic clades. Organization of the biosynthetic gene clusters for the type-1 PKS from the groups α b β c γ d and δ e showing the probable annotation of certain genes according to antiSMASH and blast analysis