Esquivel-Elizondo Sofia, Bağcı Caner, Temovska Monika, Jeon Byoung Seung, Bessarab Irina, Williams Rohan B H, Huson Daniel H, Angenent Largus T
AG Angenent, Max Planck Institute for Developmental Biology, Max Planck Society (MPG), Tübingen, Germany.
Algorithms in Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.
Front Microbiol. 2021 Jan 14;11:594524. doi: 10.3389/fmicb.2020.594524. eCollection 2020.
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, -butyrate, -caproate, biomass, and H/CO from hexoses. With only fructose as substrate (pH 5.5), the maximum -caproate specificity (i.e., products other carboxylates produced) was 60.9 ± 1.5%. However, this was considerably higher at 83.1 ± 0.44% when both fructose and -butyrate (electron acceptor) were combined as a substrate. A comparison of 7D4C2 cultures with fructose and -butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing -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 -caproic acid was ∼0.3 mM), the -caproate selectivity (i.e., product 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 (99.5%) and (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, , and belong to the same genus of . 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 spp. In conclusion, spp., comprising strain 7D4C2, , , and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. sp. 7D4C2 (DSM 110548) was studied here to understand -caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into -caproate.
批量生产含6至12个碳原子的中链羧酸盐（MCCs）对生物技术具有重大意义。开放式培养（如反应器微生物群落）已被用于在生物反应器中生成MCCs。当需要在线MCC提取和防止产物抑制时，生物反应器已在轻度酸性pH（5.0 - 5.5）下运行。然而，典型的链延长细菌在中性pH值下生长最佳。在此，我们分离出一种能在轻度酸性pH下生长的链延长细菌（菌株7D4C2）。我们研究了其代谢，并将其全基因组和反向β - 氧化（rBOX）基因与其他细菌进行了比较。菌株7D4C2从己糖产生乳酸、乙酸、丁酸、己酸、生物质和H₂/CO₂。仅以果糖为底物（pH 5.5）时，最大己酸特异性（即产物/其他产生的羧酸盐）为60.9 ± 1.5%。然而，当果糖和丁酸（电子受体）作为底物组合时，这一比例显著更高，为83.1 ± 0.44%。将含果糖和丁酸的7D4C2培养物在pH值从4.5增加到9.0的条件下进行比较，结果显示己酸特异性从轻度酸性pH（pH 4.5 - 5.0）下的约92%降至碱性pH（pH 9.0）下的约24%。此外，当从肉汤中提取羧酸盐（未解离的己酸约为0.3 mM）时，与未提取的7D4C2培养物相比，己酸选择性（即产物/进料底物）高42.6 ± 19.0%。基于16S rRNA基因序列，菌株7D4C2与分离株（99.5%）和（94.7%）关系最为密切，这两种分离株也是能够产生乳酸的链延长细菌。全基因组分析表明，菌株7D4C2、和属于同一属。它们的rBOX基因保守且彼此相邻，形成一个基因簇，这与其他链延长细菌如 spp. 不同。总之，包括菌株7D4C2、、和几个未分类菌株的 spp. 是编码高度保守的rBOX基因簇的链延长细菌。在此对 sp. 7D4C2（DSM 110548）进行了研究，以更好地了解微生物群落中轻度酸性pH条件下己酸的产生情况，并且它还具有作为纯培养生产菌株将糖转化为己酸的额外潜力。
