The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria

Abstract

Bulk production of medium-chain carboxylates (MCCs) with 6-12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0-5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that grows at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse β-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, <i>n</i>-butyrate, <i>n</i>-caproate, biomass, and H₂/CO₂ from hexoses. With only fructose as substrate (pH 5.5), the maximum <i>n</i>-caproate specificity (i.e., products <i>per</i> other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and <i>n</i>-butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and <i>n</i>-butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing <i>n</i>-caproate specificity from ∼92% at mildly acidic pH (pH 4.5-5.0) to ∼24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated <i>n</i>-caproic acid was ∼0.3 mM), the <i>n</i>-caproate selectivity (i.e., product <i>per</i> substrate fed) was 42.6 ± 19.0% higher compared to 7D4C2 cultures without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates <i>Caproicibacter fermentans</i> (99.5%) and <i>Caproiciproducens galactitolivorans</i> (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, <i>C. fermentans</i>, and <i>C. galactitolivorans</i> belong to the same genus of <i>Caproiciproducens</i>. Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as <i>Megasphaera</i> spp. In conclusion, <i>Caproiciproducens</i> spp., comprising strain 7D4C2, <i>C. fermentans</i>, <i>C. galactitolivorans</i>, and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. <i>Caproiciproducens</i> sp. 7D4C2 (DSM 110548) was studied here to understand <i>n</i>-caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into <i>n</i>-caproate.