Table_1_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.XLSX
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, n-butyrate, n-caproate, biomass, and H2/CO2 from hexoses. With only fructose as substrate (pH 5.5), the maximum n-caproate specificity (i.e., products per other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and n-butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and n-butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing n-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 n-caproic acid was ∼0.3 mM), the n-caproate selectivity (i.e., product per 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 Caproicibacter fermentans (99.5%) and Caproiciproducens galactitolivorans (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, C. fermentans, and C. galactitolivorans belong to the same genus of Caproiciproducens. 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 Megasphaera spp. In conclusion, Caproiciproducens spp., comprising strain 7D4C2, C. fermentans, C. galactitolivorans, and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. Caproiciproducens sp. 7D4C2 (DSM 110548) was studied here to understand n-caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into n-caproate.
History
References
- https://doi.org//10.2166/wst.2013.549
- https://doi.org//10.1039/c2ee22101b
- https://doi.org//10.1021/es302352c
- https://doi.org//10.1021/acs.est.5b04847
- https://doi.org//10.1038/nmeth.3176
- https://doi.org//10.1016/j.watres.2020.116396
- https://doi.org//10.1093/bioinformatics/btz848
- https://doi.org//10.1016/j.watres.2019.115215
- https://doi.org//10.2174/157489112801619728
- https://doi.org//10.1039/C8GC01759J
- https://doi.org//10.1093/nar/gkh340
- https://doi.org//10.1101/2020.07.19.210914
- https://doi.org//10.1099/ijsem.0.004283
- https://doi.org//10.1021/acs.est.5b00238
- https://doi.org//10.1111/j.1096-0031.2008.00217.x
- https://doi.org//10.1021/acs.est.7b02014
- https://doi.org//10.1039/c3gc41554f
- https://doi.org//10.1093/molbev/msx148
- https://doi.org//10.1093/nar/gky1085
- https://doi.org//10.1093/bioinformatics/14.1.68
- https://doi.org//10.1186/s13062-018-0208-7
- https://doi.org//10.1186/s13068-016-0549-3
- https://doi.org//10.1007/s00253-010-2827-5
- https://doi.org//10.1016/j.enzmictec.2013.02.008
- https://doi.org//10.1007/BF00169952
- https://doi.org//10.1099/ijsem.0.000665
- https://doi.org//10.3389/fmicb.2020.00724
- https://doi.org//10.1016/j.watres.2016.02.018
- https://doi.org//10.1039/c6ee01487a
- https://doi.org//10.1099/ijs.0.059816-0
- https://doi.org//10.1016/0141-0229(81)90087-9
- https://doi.org//10.1093/bioinformatics/bty191
- https://doi.org//10.1099/00221287-133-12-3557
- https://doi.org//10.1099/ijs.0.64717-0
- https://doi.org//10.3390/microorganisms8121970
- https://doi.org//10.1128/aem.55.6.1570-1573.1989
- https://doi.org//10.1186/1471-2105-14-60
- https://doi.org//10.1007/s00203-013-0888-4
- https://doi.org//10.1186/1944-3277-9-2
- https://doi.org//10.1099/00207713-26-2-238
- https://doi.org//10.1016/j.biortech.2017.08.132
- https://doi.org//10.1038/nbt.4229
- https://doi.org//10.1101/gr.186072.114
- https://doi.org//10.1089/cmb.2009.0179
- https://doi.org//10.1128/JB.01688-14
- https://doi.org//10.1128/genomeA.00985-1
- https://doi.org//10.1073/pnas.0906412106
- https://doi.org//10.1093/bioinformatics/btv681
- https://doi.org//10.1002/(sici)1097-4660(199707)69:3<383::aid-jctb723>3.0.co;2-h
- https://doi.org//10.1128/JB.01217-10
- https://doi.org//10.1128/mBio.03235-19
- https://doi.org//10.1111/j.1365-2672.1992.tb04990.x
- https://doi.org//10.1093/bioinformatics/btu153
- https://doi.org//10.1021/acs.est.8b03856
- https://doi.org//10.1016/j.copbio.2014.01.003
- https://doi.org//10.1093/bioinformatics/btu033
- https://doi.org//10.1093/nar/gkw569
- https://doi.org//10.1101/gr.214270.116
- https://doi.org//10.1186/s12934-018-0946-3
- https://doi.org//10.1371/journal.pcbi.1005595
- https://doi.org//10.1039/c5cc01897h
- https://doi.org//10.1016/j.joule.2017.11.008
- https://doi.org//10.1038/nrmicro3330
- https://doi.org//10.1186/s13068-017-0788-y