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.

Characterization of Pseudomonas sp. NIBR-H-19, an Antimicrobial Secondary Metabolite Producer Isolated from the Gut of Korean Native Sea Roach, Ligia exotica

“…Besides the two antimicrobial peptides, enzymes which may be able to synthesize other bioactive peptides, such as arylpolyene, pyoverdin, and methanobactin, were also predicted in the isolated genome. However, these small peptides are considered to be involved in stress responses, such as metal (iron or copper) homeostasis and protection from oxidative stress [ 35 , 36 ].…”

Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants

“…Interestingly, Bombella species can protect the beehive from fungal pathogens [20]. Their genomes carry a gene encoding a polyketide synthase [21] that is thought to produce a yet unknown metabolite with antifungal activity. The biosynthetic gene cluster is not found in Oecophyllibacter [21] so a common ecological role cannot yet be established.…”

“…Their genomes carry a gene encoding a polyketide synthase [21] that is thought to produce a yet unknown metabolite with antifungal activity. The biosynthetic gene cluster is not found in Oecophyllibacter [21] so a common ecological role cannot yet be established. The description of further insect-associated Acetobacteraceae will help to shed light on their evolution, physiology and ecological function in the context of the insect host.…”

Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea

“…Additionally, they have a potentially broad range of agricultural applications, both as growth promoters for plants and as pest control, both of which have increased in popularity in recent years [1–5]. They are obligately aerobic Gram-stain-negative rods and belong to the acetous group of the family Acetobacteraceae , class Alphaproteobacteria [6–8]. They consist of 22 validly published genera (https://lpsn.dsmz.de/family/acetobacteraceae) [9].…”