PMID- 33584563 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20230919 IS - 1664-302X (Print) IS - 1664-302X (Electronic) IS - 1664-302X (Linking) VI - 11 DP - 2020 TI - 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. PG - 594524 LID - 10.3389/fmicb.2020.594524 [doi] LID - 594524 AB - 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 beta-oxidation (rBOX) genes to other bacteria. Strain 7D4C2 produces lactate, acetate, n-butyrate, n-caproate, biomass, and H(2)/CO(2) 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 approximately 92% at mildly acidic pH (pH 4.5-5.0) to approximately 24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated n-caproic acid was approximately 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. CI - Copyright (c) 2021 Esquivel-Elizondo, Bagci, Temovska, Jeon, Bessarab, Williams, Huson and Angenent. FAU - Esquivel-Elizondo, Sofia AU - Esquivel-Elizondo S AD - AG Angenent, Max Planck Institute for Developmental Biology, Max Planck Society (MPG), Tubingen, Germany. FAU - Bagci, Caner AU - Bagci C AD - Algorithms in Bioinformatics, Department of Computer Science, University of Tubingen, Tubingen, Germany. AD - International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, University of Tubingen, Tubingen, Germany. FAU - Temovska, Monika AU - Temovska M AD - Environmental Biotechnology Group, Center for Applied Geosciences, University of Tubingen, Tubingen, Germany. FAU - Jeon, Byoung Seung AU - Jeon BS AD - Environmental Biotechnology Group, Center for Applied Geosciences, University of Tubingen, Tubingen, Germany. FAU - Bessarab, Irina AU - Bessarab I AD - Integrative Analysis Unit, Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore. FAU - Williams, Rohan B H AU - Williams RBH AD - Integrative Analysis Unit, Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore. FAU - Huson, Daniel H AU - Huson DH AD - Algorithms in Bioinformatics, Department of Computer Science, University of Tubingen, Tubingen, Germany. AD - Integrative Analysis Unit, Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore. FAU - Angenent, Largus T AU - Angenent LT AD - AG Angenent, Max Planck Institute for Developmental Biology, Max Planck Society (MPG), Tubingen, Germany. AD - Environmental Biotechnology Group, Center for Applied Geosciences, University of Tubingen, Tubingen, Germany. LA - eng PT - Journal Article DEP - 20210114 PL - Switzerland TA - Front Microbiol JT - Frontiers in microbiology JID - 101548977 PMC - PMC7873966 OTO - NOTNLM OT - Caproiciproducens OT - chain elongation OT - chain-elongating bacteria OT - lactate OT - n-caproate OT - rBOX genes OT - reverse beta-oxidation OT - thiolase COIS- The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. EDAT- 2021/02/16 06:00 MHDA- 2021/02/16 06:01 PMCR- 2021/01/14 CRDT- 2021/02/15 06:08 PHST- 2020/08/13 00:00 [received] PHST- 2020/12/03 00:00 [accepted] PHST- 2021/02/15 06:08 [entrez] PHST- 2021/02/16 06:00 [pubmed] PHST- 2021/02/16 06:01 [medline] PHST- 2021/01/14 00:00 [pmc-release] AID - 10.3389/fmicb.2020.594524 [doi] PST - epublish SO - Front Microbiol. 2021 Jan 14;11:594524. doi: 10.3389/fmicb.2020.594524. eCollection 2020.