Acknowledgement
This work was supported by the Natural Science Foundation of China (31770090), Sichuan Science and Technology Support Program (2021YJ0022), and the Open-foundation project of CAS Key Laboratory of Environmental and Applied Microbiology (KLCAS-2017-01).
References
- Brodowski F, Duber A, Zagrodnik R, Oleskowicz-Popiel P. 2020. Co-production of hydrogen and caproate for an effective bioprocessing of waste. Bioresour. Technol. 318: 123895. https://doi.org/10.1016/j.biortech.2020.123895
- Roghair M, Liu Y, Adiatma JC, Weusthuis RA, Bruins ME, Buisman CJN, et al. 2018. Effect of n-Caproate concentration on chain elongation and competing processes. ACS Sustain Chem. Eng. 6: 7499-7506. https://doi.org/10.1021/acssuschemeng.8b00200
- Nzeteu CO, Trego AC, Abram F, O'Flaherty V. 2018. Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system. Biotechnol. Biofuels 11: 108. https://doi.org/10.1186/s13068-018-1101-4
- Roghair M, Liu Y, Strik D, Weusthuis RA, Bruins ME, Buisman CJN. 2018. Development of an effective chain elongation process from acidified food waste and ethanol into n-Caproate. Front. Bioeng. Biotechnol. 6: 50. https://doi.org/10.3389/fbioe.2018.00050
- Yang PX, Leng L, Tan GYA, Dong CY, Leu SY, Chen WH, et al. 2018. Upgrading lignocellulosic ethanol for caproate production via chain elongation fermentation. Int. Biodeter. Biodegr. 135: 103-109. https://doi.org/10.1016/j.ibiod.2018.09.011
- Spirito CM, Richter H, Rabaey K, Stams AJ, Angenent LT. 2014. Chain elongation in anaerobic reactor microbiomes to recover resources from waste. Curr. Opin. Biotechnol. 27: 115-122. https://doi.org/10.1016/j.copbio.2014.01.003
- Seedorf H, Fricke WF, Veith B, Bruggemann H, Liesegang H, Strittimatter A, et al. 2008. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. USA 105: 2128-2133. https://doi.org/10.1073/pnas.0711093105
- Steinbusch KJJ, Hamelers HVM, Plugge CM, Buisman CJN. 2011. Biological formation of caproate and caprylate from acetate: fuel and chemical production from low grade biomass. Energy Environ. Sci. 4: 216-224. https://doi.org/10.1039/C0EE00282H
- Chen WS, Ye Y, Steinbusch KJJ, Strik DPBTB, Buisman CJN. 2016. Methanol as an alternative electron donor in chain elongation for butyrate and caproate formation. Biomass Bioenerg. 93: 201-208. https://doi.org/10.1016/j.biombioe.2016.07.008
- Kenealy WR, Waselefsky DM. 1985. Studies on the substrate range of Clostridium-Kluyveri - the use of propanol and succinate. Arch. Microbiol. 141: 187-194. https://doi.org/10.1007/BF00408056
- Jeon BS, Kim BC, Um Y, Sang BI. 2010. Production of hexanoic acid from ᴅ-galactitol by a newly isolated Clostridium sp. BS-1. Appl. Microbiol. Biotechnol. 88: 1161-1167. https://doi.org/10.1007/s00253-010-2827-5
- Kucek LA, Nguyen M, Angenent LT. 2016. Conversion of l-lactate into n-caproate by a continuously fed reactor microbiome. Water Res. 93: 163-171. https://doi.org/10.1016/j.watres.2016.02.018
- Zhu X, Tao Y, Liang C, Li X, Wei N, Zhang W, et al. 2015. The synthesis of n-caproate from lactate: a new efficient process for medium-chain carboxylates production. Sci. Rep. 5: 14360. https://doi.org/10.1038/srep14360
- Zhu X, Zhou Y, Wang Y, Wu T, Li X, Li D, et al. 2017. Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6. Biotechnol. Biofuels 10: 102. https://doi.org/10.1186/s13068-017-0788-y
- Wang H, Li X, Wang Y, Tao Y, Lu S, Zhu X, et al. 2018. Improvement of n-caproic acid production with Ruminococcaceae bacterium CPB6: selection of electron acceptors and carbon sources and optimization of the culture medium. Microb. Cell Fact. 17: 99. https://doi.org/10.1186/s12934-018-0946-3
- Tao Y, Zhu XY, Wang H, Wang Y, Li XZ, Jin H, et al. 2017. Complete genome sequence of Ruminococcaceae bacterium CPB6: A newly isolated culture for efficient n-caproic acid production from lactate. J. Biotechnol. 259: 91-94. https://doi.org/10.1016/j.jbiotec.2017.07.036
- Sedlar K, Koscova P, Vasylkivska M, Branska B, Kolek J, Kupkova K, et al. 2018. Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq. BMC Genomics. 19: 415. https://doi.org/10.1186/s12864-018-4805-8
- Zararsiz G, Goksuluk D, Korkmaz S, Eldem V, Zararsiz GE, Duru IP, et al. 2017. A comprehensive simulation study on classification of RNA-Seq data. PLoS One 12: e0182507. https://doi.org/10.1371/journal.pone.0182507
- Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ. 2008. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat. Methods 5: 679-682. https://doi.org/10.1038/nmeth.1230
- Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. 2010. The sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38: 1767-1771. https://doi.org/10.1093/nar/gkp1137
- Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359. https://doi.org/10.1038/nmeth.1923
- Patro R, Mount SM, Kingsford C. 2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat. Biotechnol. 32: 462-U174. https://doi.org/10.1038/nbt.2862
- Kirk DG, Palonen E, Korkeala H, Lindstrom M. 2014. Evaluation of normalization reference genes for RT-qPCR analysis of spo0A and four sporulation sigma factor genes in Clostridium botulinum Group I strain ATCC 3502. Anaerobe 26: 14-19. https://doi.org/10.1016/j.anaerobe.2013.12.003
- Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15: 550. https://doi.org/10.1186/s13059-014-0550-8
- Riederer A, Takasuka TE, Makino S, Stevenson DM, Bukhman YV, Elsen NL, et al. 2011. Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose. Appl. Environ. Microbiol. 77: 1243-1253. https://doi.org/10.1128/AEM.02008-10
- Rogatzki MJ, Ferguson BS, Goodwin ML, Gladden LB. 2015. Lactate is always the end product of glycolysis. Front. Neurosci. 9: 22. https://doi.org/10.3389/fnins.2015.00022
- Weghoff MC, Bertsch J, Muller V. 2015. A novel mode of lactate metabolism in strictly anaerobic bacteria. Environ. Microbiol. 17: 670-677. https://doi.org/10.1111/1462-2920.12493
- Skory CD. 2000. Isolation and expression of lactate dehydrogenase genes from Rhizopus oryzae. Appl. Environ. Microbiol. 66: 2343-2348. https://doi.org/10.1128/AEM.66.6.2343-2348.2000
- Schoelmerich MC, Katsyv A, Sung W, Mijic V, Wiechmann A, Kottenhahn P, et al. 2018. Regulation of lactate metabolism in the acetogenic bacterium Acetobacterium woodii. Environ. Microbiol. 20: 4587-4595. https://doi.org/10.1111/1462-2920.14412
- Yang Q, Wei C, Guo S, Liu J, Tao Y. 2020. Cloning and characterization of a L-lactate dehydrogenase gene from Ruminococcaceae bacterium CPB6. World J. Microbiol. Biotechnol. 36: 182. https://doi.org/10.1007/s11274-020-02958-4
- Lee J, Jang YS, Han MJ, Kim JY, Lee SY. 2016. Deciphering Clostridium tyrobutyricum Metabolism based on the whole-genome sequence and proteome analyses. mBio 7: e00743-16.
- Yang Q, Guo S, Lu Q, Tao Y, Zheng D, Zhou Q, et al. 2021. Butyryl/Caproyl-CoA:Acetate CoA-transferase: cloning, expression and characterization of the key enzyme involved in medium-chain fatty acid biosynthesis. Biosci. Rep. 41: BSR20211135. https://doi.org/10.1042/BSR20211135
- Sauer U, Santangelo JD, Treuner A, Buchholz M, Durre P. 1995. Sigma factor and sporulation genes in Clostridium. FEMS Microbiol. Rev. 17: 331-340. https://doi.org/10.1016/0168-6445(95)00005-W
- Woods DR, Jones DT. 1986. Physiological responses of Bacteroides and Clostridium strains to environmental stress factors. Adv. Microb. Physiol. 28: 1-64.
- Wang Y, Li XZ, Blaschek HP. 2013. Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq. Biotechnol. Biofuels 6: 138. https://doi.org/10.1186/1754-6834-6-138
- Hollenstein K, Dawson RJ, Locher KP. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17: 412-418. https://doi.org/10.1016/j.sbi.2007.07.003
- Cui J, Davidson AL. 2011. ABC solute importers in bacteria. Essays Biochem. 50: 85-99. https://doi.org/10.1042/bse0500085
- Qin J, Wang X, Wang L, Zhu B, Zhang X, Yao Q, et al. 2015. Comparative transcriptome analysis reveals different molecular mechanisms of Bacillus coagulans 2-6 response to sodium lactate and calcium lactate during lactic acid production. PLoS One 10: e0124316. https://doi.org/10.1371/journal.pone.0124316
- Zhu Z, Yang J, Yang P, Wu Z, Zhang J, Du G. 2019. Enhanced acid-stress tolerance in Lactococcus lactis NZ9000 by overexpression of ABC transporters. Microb. Cell Fact. 18: 136. https://doi.org/10.1186/s12934-019-1188-8
- Jones PM, George AM. 2004. The ABC transporter structure and mechanism: perspectives on recent research. Cell Mol. Life Sci. 61: 682-699. https://doi.org/10.1007/s00018-003-3336-9
- Jason G. McCoy, Elena J. Levin, Zhou M. 2015. Structural insight into the PTS sugar transporter EIIC. Biochim. Biophys. Acta 1850: 577-585. https://doi.org/10.1016/j.bbagen.2014.03.013
- Nguyen TX, Yen MR, Barabote RD, Saier MH, Jr. 2006. Topological predictions for integral membrane permeases of the phosphoenolpyruvate:sugar phosphotransferase system. J. Mol. Microbiol. Biotechnol. 11: 345-360. https://doi.org/10.1159/000095636
- Nikaido H, Hall JA. 1998. Overview of bacterial ABC transporters. Methods Enzymol. 292: 3-20. https://doi.org/10.1016/S0076-6879(98)92003-1