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Fermentation trip: amazing microbes, amazing metabolisms

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Abstract

Fermentation has been applied to many areas of human life, including industrial production, sewage treatment, and environment management. By understanding the process and mechanism of fermentation, more comprehensive and profound cognition of the fermentation may be established to lay a foundation for our further research. In this review, we present a brief summary of recent research about fermentation and microorganisms in different territories, including foods, environment, and human health. According to the growth characteristics of different stages of microorganisms, we introduced a series of metabolic changes, fermentation mechanism, and regulation methods and how the enzymes were transported out of the cell. With further understanding and utilization of microorganisms, food can produce better flavor, nutrition, and functional metabolites through fermentation. Fermentation is also used in other industries, such as wastewater and garbage disposal, environment, and soil management. The human gut flora, in particular, has begun to receive more attention. The profound influence of microorganism on human health cannot to be underestimated. It has become a hot research area in recent years. We can get the metabolites we want by controlling the rate of fermentation and regulate the direction of fermentation. As one of the important components of modern biotechnology, fermentation engineering has been widely used in areas including food, pharmaceutical, energy, chemical industries, and environmental protection. The development of genetic engineering has brought new vitality to fermentation engineering. The application of modernization, automation and artificial intelligence technology also opens up new space for fermentation engineering. In addition, research on the understanding and regulation of metabolic mechanism has further developed the fermentation function of microorganisms.

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References

  • Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J (2014) The placenta harbors a unique microbiome. Sci Transl Med 6(237):237ra265

    Google Scholar 

  • Abdelmohsen UR, Grkovic T, Balasubramanian S, Kamel MS, Quinn RJ, Hentschel U (2015) Elicitation of secondary metabolism in actinomycetes. Biotechnol Adv 33(6):798–811

    CAS  PubMed  Google Scholar 

  • Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI (2017) Optimization of lag phase shapes the evolution of a bacterial enzyme. Nat Ecol Evol 1(6):149

    PubMed  PubMed Central  Google Scholar 

  • Agostoni, C. V. (2010). "Scientific opinion on the substantiation of health claims related to live yoghurt cultures and improved lactose digestion (ID 1143, 2976) pursuant to Article 13(1) of Regulation (EC) No 1924/2006." EFSA J 8(10): n/a-n/a

  • Allison SD, Vitousek PM (2005) Responses of extracellular enzymes to simple and complex nutrient inputs. Soil Biol Biochem 37(5):937–944

    CAS  Google Scholar 

  • Althuri, A., A. D. Chintagunta, K. C. Sherpa and R. Banerjee (2018). "Simultaneous saccharification and fermentation of lignocellulosic biomass."

    Google Scholar 

  • Alugongo GM, Xiao JX, Chung YH, Dong SZ, Li SL, Yoon I, Wu ZH, Cao ZJ (2017) Effects of Saccharomyces cerevisiae fermentation products on dairy calves: performance and health. J Dairy Sci 100(2):1189–1199

    CAS  PubMed  Google Scholar 

  • Amin FR, Khalid H, Zhang H, Rahman SU, Zhang R, Liu G, Chen C (2017) Pretreatment methods of lignocellulosic biomass for anaerobic digestion. AMB Express 7(1):72

    PubMed  PubMed Central  Google Scholar 

  • Ash C (2017) Light, fat, and commensals. Science 357(6354):882.883–882.882

    Google Scholar 

  • Awate B, Steidl RJ, Hamlischer T, Reguera G (2017) Stimulation of electro-fermentation in single-chamber microbial electrolysis cells driven by genetically engineered anode biofilms. J Power Sources

  • Bassis CM, Erbdownward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, Beck JM, Curtis JL, Huffnagle GB (2015) Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. Mbio 6(2):e00037

    PubMed  PubMed Central  Google Scholar 

  • Belda I, Ruiz J, Estebanfernández A, Navascués E, Marquina D, Santos A, Morenoarribas MV (2017) Microbial contribution to wine aroma and its intended use for wine quality improvement. Molecules 22(2):189

    PubMed Central  Google Scholar 

  • Bérdy J (2005) Bioactive microbial metabolites. J Antibiotics 58(1):1–26

    Google Scholar 

  • Beyersmann PG, Tomasch J, Son K, Stocker R, Göker M, Wagnerdöbler I, Simon M, Brinkhoff T (2017) Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens. Sci Rep 7(1)

  • Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM (2016) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351(6275):aad3311

    PubMed  Google Scholar 

  • Boukouris AE, Zervopoulos SD, Michelakis ED (2016) Metabolic enzymes moonlighting in the nucleus: metabolic regulation of gene transcription. Trends Biochem Sci 41(8):712–730

    CAS  PubMed  Google Scholar 

  • Cabrol L, Marone A, Tapia-Venegas E, Steyer JP, Ruiz-Filippi G, Trably E (2017) Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function. FEMS Microbiol Rev 41(2):158

    CAS  PubMed  Google Scholar 

  • Canada, H. (2009). Accepted claims about the nature of probiotic microorganisms in food

    Google Scholar 

  • Castro RJSD, Ohara A, Nishide TG, Bagagli MP, Dias FFG, Sato HH (2015) A versatile system based on substrate formulation using agroindustrial wastes for protease production by Aspergillus niger under solid state fermentation. Biocatal Agric Biotechnol 4(4):678–684

    Google Scholar 

  • Charbonneau MR, O'Donnell D, Blanton LV, Totten SM, Davis JC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR (2016) Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition. Cell 164(5):859

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Sheng J, Tao J, Stevens J, Feng X, Na W (2016) Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae. Biotechnol Biofuels 9(1):9

    PubMed  PubMed Central  Google Scholar 

  • Chen G, Chen C, Lei Z (2017) Meta-omics insights in the microbial community profiling and functional characterization of fermented foods. Trends Food Sci Technol 65:23–31

    CAS  Google Scholar 

  • Cheng Y, Wang L, Faustorilla V, Megharaj M, Naidu R, Chen Z (2017) Integrated electrochemical treatment systems for facilitating the bioremediation of oil spill contaminated soil. Chemosphere 175:294–299

    CAS  PubMed  Google Scholar 

  • Consortium THMP (2012) A framework for human microbiome research. Nature 486(7402):215

    Google Scholar 

  • Daâssi D, Zouarimechichi H, Frikha F, Rodríguezcouto S, Nasri M, Mechichi T (2016) Sawdust waste as a low-cost support-substrate for laccases production and adsorbent for azo dyes decolorization. J Environ Health Sci Eng 14(1):1–12

    PubMed  PubMed Central  Google Scholar 

  • Desnoues E, Baldazzi V, Génard M, Mauroux JB, Lambert P, Confolent C, Quilot-Turion B (2016) Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development. J Exp Bot 67(11):3419–3431

    CAS  PubMed  PubMed Central  Google Scholar 

  • Desvaux M, Hébraud M, Talon R, Henderson IR (2009) Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 17(4):139

    CAS  PubMed  Google Scholar 

  • Deutsch (2000) History of modern biotechnology I—Springer. Springer, Berlin

    Google Scholar 

  • Devadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, Bäckhed F, Mithieux G (2014) Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits. Cell 156(1-2):84

    CAS  Google Scholar 

  • Doron S, Snydman DR (2015) Risk and safety of probiotics. Clin Infect Dis 60(suppl_2):S129

    PubMed  PubMed Central  Google Scholar 

  • Dragana G, Milica C, Wen WX, Filomena N, Jasna R (2016) Exploring the secretomes of microbes and microbial communities using filamentous phage display. Front Microbiol 7(58):429

    Google Scholar 

  • Economou A (2002) Bacterial secretome: the assembly manual and operating instructions (review). Membr Biochem 19(3):159–169

    CAS  Google Scholar 

  • Elfahri KR, Vasiljevic T, Yeager T, Donkor ON (2016) Anti-colon cancer and antioxidant activities of bovine skim milk fermented by selected Lactobacillus helveticus strains. J Dairy Sci 99(1):31–40

    CAS  PubMed  Google Scholar 

  • Enes D, Toker OS, Zeki DM, Yilmaz MT, Nevruz Berna TS, Osman S, Hasan C (2016) Development of a fermented ice-cream as influenced by in situ exopolysaccharide production: Rheological, molecular, microstructural and sensory characterization. Carbohydr Polym 136:427–440

    Google Scholar 

  • Eran ET, Shira OB, Julie V, Ke X, Shaul P, Tasneem B, Ishay BZ, Bassler BL, Avigdor E (2016) Social evolution selects for redundancy in bacterial quorum sensing. PLoS Biol 14(2):e1002386

    Google Scholar 

  • Eren KB, Laleman I, Yalnızoğlu T, Kuru L, Teughels W (2017) The influence of a Bifidobacterium animalis probiotic on gingival health: a randomized controlled clinical trial. J Periodontol 88(11):1

    Google Scholar 

  • Fessard A, Kapoor A, Patche J, Assemat S, Hoarau M, Bourdon E, Bahorun T, Remize F (2017) Lactic Fermentation as an Efficient Tool to Enhance the Antioxidant Activity of Tropical Fruit Juices and Teas. Microorganisms 5(2):23

    PubMed Central  Google Scholar 

  • Fleet GH (2003) Yeast interactions and wine flavour. Int J Food Microbiol 86(1–2):11–22

    CAS  PubMed  Google Scholar 

  • Fountain JC, Bajaj P, Nayak SN, Yang L, Pandey MK, Kumar V, Jayale AS, Chitikineni A, Lee RD, Kemerait RC (2016) Responses of Aspergillus flavus to oxidative stress are related to fungal development regulator, antioxidant enzyme, and secondary metabolite biosynthetic gene expression. Front Microbiol 7

  • Fox PF (1993) Cheese: chemistry, physics and microbiology. Volume 1. General aspects. Springer, US

    Google Scholar 

  • Francis MB, Sorg JA (2016) Detecting cortex fragments during bacterial spore germination. J Visual Exp Jove 2016(112)

  • Ghosh A, Baltekin Ö, Wäneskog M, Elkhalifa D, Hammarlöf DL, Elf J, Koskiniemi S (2018) Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations. EMBO J 37(9):e98026

    PubMed  PubMed Central  Google Scholar 

  • Gomez d AM, Ganalvonarburg SC, Fuhrer T, Rupp S, Uchimura Y, Li H, Steinert A, Heikenwalder M, Hapfelmeier S, Sauer U (2016) The maternal microbiota drives early postnatal innate immune development. Science 351(6279):1296

    Google Scholar 

  • Gonzalez-Gonzalez C, Gibson T, Jauregi P (2013) Novel probiotic-fermented milk with angiotensin I-converting enzyme inhibitory peptides produced by Bifidobacterium bifidum MF 20/5. Int J Food Microbiol 167(2):131–137

    CAS  PubMed  Google Scholar 

  • Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8(1):15–25

    CAS  PubMed  PubMed Central  Google Scholar 

  • Huang L (2016) Mathematical modeling and validation of growth of Salmonella Enteritidis and background microorganisms in potato salad—one-step kinetic analysis and model development ☆. Food Control 68:69–76

    Google Scholar 

  • Incharoensakdi A, Velmurugan R (2016) Proper ultrasound treatment increases ethanol production from simultaneous saccharification and fermentation of sugarcane bagasse. RSC Adv 6(94)

  • Jafarnejad S, Djafarian K, Fazeli MR, Yekaninejad MS, Rostamian A, Keshavarz SA (2017) Effects of a multispecies probiotic supplement on bone health in osteopenic postmenopausal women: a randomized, double-blind, controlled trial. J Am Coll Nutr 36(2):1–10

    Google Scholar 

  • Joyce SA, Gahan CG (2014) The gut microbiota and the metabolic health of the host. Curr Opin Gastroenterol 30(2):120–127

    CAS  PubMed  Google Scholar 

  • Khalesi S, Bellissimo N, Vandelanotte C, Williams S, Stanley D, Irwin C (2018) A review of probiotic supplementation in healthy adults: helpful or hype? Eur J Clin Nutr 1

  • Kim BJ, Jung HK, Jeong YS, Yang SJ, Hong JH (2016) Effect of microencapsulated Bacillus subtilis strain CBD2-fermented grain on loperamide-induced constipation in mice. Appl Biol Chem 59(3):1–12

    Google Scholar 

  • Kim EB, Jin GD, Lee JY, Choi YJ (2016) Genomic features and niche-adaptation of enterococcus faecium strains from Korean soybean-fermented foods. PLoS One 11(4):e0153279

    PubMed  PubMed Central  Google Scholar 

  • Knight and Rob (2015). "Follow your gut."

    Google Scholar 

  • Kubistova L, Dvoracek L, Tkadlec J, Melter O, Licha I (2017) Environmental stress affects the formation of Staphylococcus aureus persisters tolerant to antibiotics. Microb Drug Resist 24(5)

    CAS  PubMed  Google Scholar 

  • Larsen N, Boye M, Siegumfeldt H, Jakobsen M (2006) Differential expression of proteins and genes in the lag phase of Lactococcus lactis subsp. lactis grown in synthetic medium and reconstituted skim milk. Appl Environ Microbiol 72(2):1173

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leitão AL, Costa MC, Enguita FJ (2017) Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites. J Biotechnol 241:50–60

    PubMed  Google Scholar 

  • Li X, Song C, Xiong L, Chen X, Huang C, Lin X, Chen X, Ma L (2017) Microbial conversion of wastewater from butanol fermentation to microbial oil and biomass by oleaginous yeasts. Environ Prog Sustain Energy

  • Linares JF, Gustafsson I, Baquero F, Martinez JL (2006) Antibiotics as intermicrobial signaling agents instead of weapons. Proc Natl Acad Sci U S A 103(51):19484–19489

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Rousseaux S, Tourdotmaréchal R, Sadoudi M, Gougeon R, Schmittkopplin P, Alexandre H (2015) Wine microbiome, a dynamic world of microbial interactions. CRC Crit Rev Food Technol 57(4):856–873

    Google Scholar 

  • Liu H, Chen D, Zhang R, Hang X, Rong L, Shen Q (2016) Amino acids hydrolyzed from animal carcasses are a good additive for the production of bio-organic fertilizer. Front Microbiol 7(e6669)

  • Louis P, Scott KP, Duncan SH, Flint HJ (2007) Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol 102(5):1197–1208

    CAS  PubMed  Google Scholar 

  • Luo L, Meng H, Gu JD (2017) Microbial extracellular enzymes in biogeochemical cycling of ecosystems. J Environ Manag 197:539–549

    CAS  Google Scholar 

  • Makino S, Sato A, Goto A, Nakamura M, Ogawa M, Chiba Y, Hemmi J, Kano H, Takeda K, Okumura K (2016) Enhanced natural killer cell activation by exopolysaccharides derived from yogurt fermented with Lactobacillus delbrueckii ssp. bulgaricus OLL1073R-1. J Dairy Sci 99(2):915

    CAS  PubMed  Google Scholar 

  • Manzanares W, Lemieux M, Langlois PL, Wischmeyer PE (2016) Probiotic and synbiotic therapy in critical illness: a systematic review and meta-analysis. Crit Care 20(1):262

    PubMed Central  Google Scholar 

  • Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A (2017) Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol 44:94

    CAS  PubMed  Google Scholar 

  • Mares JH, Gramacho KP, Santos EC, Santiago ADS, Santana JO, Sousa AOD, Alvim FC, Pirovani CP (2017) Proteomic analysis during of spore germination of Moniliophthora perniciosa, the causal agent of witches’ broom disease in cacao. BMC Microbiol 17(1):176

    PubMed  PubMed Central  Google Scholar 

  • Marmann A, Aly AH, Lin W, Wang B, Proksch P (2014) Co-cultivation—a powerful emerging tool for enhancing the chemical diversity of microorganisms. Mar Drugs 12(2):1043–1065

    PubMed  PubMed Central  Google Scholar 

  • Meijnikman AS, Gerdes VE, Nieuwdorp M, Herrema H (2018) Evaluating causality of gut microbiota in obesity and diabetes in humans. Endocr Rev 39(2):133

    PubMed  Google Scholar 

  • Mendes GDO, AntoniaGalvez MV, Vassilev N (2017) Fermentation liquid containing microbially solubilized P significantly improved plant growth and P uptake in both soil and soilless experiments. Appl Soil Ecol 117-118:208–211

    Google Scholar 

  • Miquel S, Martín R, Rossi O, Bermúdezhumarán LG, Chatel JM, Sokol H, Thomas M, Wells JM, Langella P (2013) Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 16(3):255–261

    CAS  PubMed  Google Scholar 

  • Mohapatra S, Sarkar B, Samantaray DP, Daware A, Maity S, Pattnaik S, Bhattacharjee S (2017) Bioconversion of fish solid waste into PHB using Bacillus subtilis based submerged fermentation process. Environ Technol 1

  • Morenogámez S, Sorg RA, Domenech A, Kjos M, Weissing FJ, Doorn GSV, Veening JW (2016) Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence. Nat Commun 8(1):854

    Google Scholar 

  • Morita M, Naito Y, Niki E, Yoshikawa T (2017) Antioxidant action of fermented grain food supplement: Scavenging of peroxyl radicals and inhibition of plasma lipid oxidation induced by multiple oxidants. Food Chem 237:574–580

    CAS  PubMed  Google Scholar 

  • Moscoviz R, Toledo-Alarcón J, Trably E, Bernet N (2016) Electro-fermentation: how to drive fermentation using electrochemical systems. Trends Biotechnol 34(11):856–865

    CAS  PubMed  Google Scholar 

  • Mukherjee S, Hooper L (2015) Antimicrobial defense of the intestine. Immunity 42(1):28

    CAS  PubMed  Google Scholar 

  • Müller G, Kalyani DC, Horn SJ (2016) LPMOs in cellulase mixtures affect fermentation strategies for lactic acid production from lignocellulosic biomass. Biotechnol Bioeng

  • Murali N, Fernandez S, Ahring BK (2017) Fermentation of wet-exploded corn stover for the production of volatile fatty acids. Bioresour Technol 227:197

    CAS  PubMed  Google Scholar 

  • Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA (2015) Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 6(299):299

    PubMed  PubMed Central  Google Scholar 

  • Ohata M, Uchida S, Zhou L, Arihara K (2016) Antioxidant activity of fermented meat sauce and isolation of an associated antioxidant peptide. Food Chem 194:1034–1039

    CAS  PubMed  Google Scholar 

  • Ojha KS, Kerry JP, Alvarez C, Walsh D, Tiwari BK (2016) Effect of high intensity ultrasound on the fermentation profile of Lactobacillus sakei in a meat model system. Ultrason Sonochem 31:539–545

    CAS  PubMed  Google Scholar 

  • Ojha KS, Mason TJ, O'Donnell CP, Kerry JP, Tiwari BK (2017) Ultrasound technology for food fermentation applications. Ultrason Sonochem 34:410–417

    CAS  PubMed  Google Scholar 

  • Olson CA, Vuong HE, Yano JM, Liang QY, Nusbaum DJ, Hsiao EY (2018) The gut microbiota mediates the anti-seizure effects of the ketogenic diet. Cell 173(7)

  • Park S, Bae JH (2016) Fermented food intake is associated with a reduced likelihood of atopic dermatitis in an adult population (Korean National Health and Nutrition Examination Survey 2012-2013). Nutr Res 36(2):125

    CAS  PubMed  Google Scholar 

  • Patrignani F, Siroli L, Serrazanetti DI, Braschi G, Betoret E, Reinheimer JA, Lanciotti R (2017) Microencapsulation of functional strains by high pressure homogenization for a potential use in fermented milk. Food Res Int 97:250

    CAS  PubMed  Google Scholar 

  • Pendse, M. and L. V. Hooper (2016). "Immunology: mum’s microbes boost baby’s immunity: the microorganisms that colonize pregnant mice have been shown to prime the innate immune system in newborn offspring, preparing them for life in association with microbes." Nat Int Wkly J Sci 533: págs 42–42

  • Pessione E, Cirrincione S (2016) Bioactive molecules released in food by lactic acid bacteria: encrypted peptides and biogenic amines. Front Microbiol 7(2393):876

    PubMed  PubMed Central  Google Scholar 

  • Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U (2017) Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow. Cell Systems 5(4):345–357 e346

    CAS  PubMed  PubMed Central  Google Scholar 

  • Porter NT, Martens EC (2017) The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol

  • Pot B, Hill C, Merenstein DJ, Guarner F, Gibson GR, Reid G, Flint HJ, Morelli L, Sanders ME, Calder PC (2014) Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11(8):506

    PubMed  Google Scholar 

  • Prats C, López D, Giró A, Ferrer J, Valls J (2006) Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase. J Theor Biol 241(4):939–953

    PubMed  Google Scholar 

  • Reen FJ, Romano S, Dobson ADW, O’Gara F (2015) The sound of silence: activating silent biosynthetic gene clusters in marine microorganisms. Mar Drugs 13(8):4754–4783

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rivera VM, Wang X, Wardwell S, Courage NL, Volchuk A, Keenan T, Holt DA, Gilman M, Orci L, Jr CF (2000) Regulation of protein secretion through controlled aggregation in the endoplasmic reticulum. Science 287(5454):826

    CAS  PubMed  Google Scholar 

  • Robinson TP, Aboaba OO, Kaloti A, Ocio MJ, Baranyi J, Mackey BM (2001) The effect of inoculum size on the lag phase of Listeria monocytogenes. Int J Food Microbiol 70(1–2):163–173

    CAS  PubMed  Google Scholar 

  • Rodrigues KL, Araújo TH, Schneedorf JM, Ferreira CDS, Moraes GDOI, Coimbra RS, Rodrigues MR (2016) A novel beer fermented by kefir enhances anti-inflammatory and anti-ulcerogenic activities found isolated in its constituents. J Funct Foods 21:58–69

    CAS  Google Scholar 

  • Rokana N, Singh R, Mallappa RH, Batish VK, Grover S (2016) Modulation of intestinal barrier function to ameliorate Salmonella infection in mice by oral administration of fermented milks produced with Lactobacillus plantarum MTCC 5690 - a probiotic strain of Indian gut origin. J Med Microbiol 65(12):1482

    PubMed  Google Scholar 

  • Romero D, Traxler MF, López D, Kolter R (2011) Antibiotics as signal molecules. Chem Rev 111(9):5492–5505

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rosa DD, Mms D, Grześkowiak ŁM, Reis SA, Conceição LL, Mdcg P (2017) Milk kefir: nutritional, microbiological and health benefits. Nutr Res Rev 30(1):82

    CAS  PubMed  Google Scholar 

  • Sánchez S, Chávez A, Forero A, Garcíahuante Y, Romero A, Sánchez M, Rocha D, Sánchez B, Avalos M, Guzmántrampe S (2010) Carbon source regulation of antibiotic production. J Antibiot 63(8):442

    Google Scholar 

  • Sasano Y, Watanabe D, Ukibe K, Inai T, Ohtsu I, Shimoi H, Takagi H (2017) Overexpression of the yeast transcription activator Msn2 confers furfural resistance and increases the initial fermentation rate in ethanol production. Eurointervention Journal of Europcr in Collaboration with the Working Group on Interventional Cardiology of the European Society of Cardiology 13(Z):Z51

    Google Scholar 

  • Savaiano DA (2014) Lactose digestion from yogurt: mechanism and relevance. Am J Clin Nutr 99(5 Suppl):1251S

    CAS  PubMed  Google Scholar 

  • Schievano A, Pepã© ST, Vanbroekhoven K, De WH, Puig S, Andersen SJ, Rabaey K, Pant D (2016) Electro-fermentation—merging electrochemistry with fermentation in industrial applications. Trends Biotechnol 34(11):866–878

    CAS  PubMed  Google Scholar 

  • Setlow P (2003) Spore germination. Curr Opin Microbiol 6(6):550–556

    CAS  PubMed  Google Scholar 

  • Shank EA, Kolter R (2009) New developments in microbial interspecies signaling. Curr Opin Microbiol 12(2):205

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shen Y, Gao J, Li L (2017) Municipal wastewater treatment via co-immobilized microalgal-bacterial symbiosis: microorganism growth and nutrients removal. Bioresour Technol 243:905–913

    CAS  PubMed  Google Scholar 

  • Shibata K, Obase K, Itoh K, Amemiya T (2018) The effects of starvation and acidification on lag phase duration of surviving yeast cells. J Biotechnol

  • Singh D, Lee S, Lee CH (2017) Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages. Trends Food Sci Technol 61:103–115

    CAS  Google Scholar 

  • Song Y, Fu G, Dong H, Li J, Du Y, Zhang D (2017) High-efficiency secretion of β-mannanase in Bacillus subtilis through protein synthesis and secretion optimization. J Agric Food Chem 65(12):2540–2548

    CAS  PubMed  Google Scholar 

  • Sun S, Zhang H, Lu S, Lai C, Liu H, Zhu H (2016) The metabolic flux regulation of Klebsiella pneumoniae based on quorum sensing system. Sci Rep 6:38725

    CAS  PubMed  PubMed Central  Google Scholar 

  • Swinnen IA, Bernaerts K, Dens EJ, Geeraerd AH, Van Impe JF (2004) Predictive modelling of the microbial lag phase: a review. Int J Food Microbiol 94(2):137–159

    CAS  PubMed  Google Scholar 

  • Tancredi DJ (2017) Global health: probiotic prevents infections in newborns. Nature 548(7668):404

    CAS  PubMed  Google Scholar 

  • Thomas-White K, Brady M, Wolfe AJ, Mueller ER (2016) The bladder is not sterile: history and current discoveries on the urinary microbiome. Curr Bladder Dysfunct Rep 11(1):18

    PubMed  PubMed Central  Google Scholar 

  • Tjalsma H, Bolhuis A, Jongbloed JD, Bron S, van Dijl JM (2000) Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biol Rev 64(3):515

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tjalsma H, Antelmann H, Jongbloed JDH, Braun PG, Darmon E, Dorenbos R, Dubois J-YF, Westers H, Zanen G, Quax WJ (2004) Proteomics of protein secretion by Bacillus subtilis: separating the “secrets” of the secretome. Microbiol Mol Biol Rev 68(2):207

    CAS  PubMed  PubMed Central  Google Scholar 

  • Von HG (1998) Life and death of a signal peptide. Nature 396(6707):111–113

    Google Scholar 

  • Von Heijne G (1990) The signal peptide. J Membr Biol 115(3):195–201

    Google Scholar 

  • Vrieze A, Nood EV, Holleman F, Salojärvi J, Kootte RS, Bartelsman JFWM, Dallinga-Thie GM, Ackermans MT, Serlie MJ, Oozeer R (2012) Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143(4):913–916

    CAS  PubMed  Google Scholar 

  • Wang Y, Kuang Z, Yu X, Ruhn KA, Kubo M, Hooper LV (2017) The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science 357(6354):912

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xafenias N, Kmezik C, Mapelli V (2017) Enhancement of anaerobic lysine production in Corynebacterium glutamicum electrofermentations. Bioelectrochemistry 117:40–47

    CAS  PubMed  Google Scholar 

  • Xiao JX, Alugongo GM, Chung R, Dong SZ, Li SL, Yoon I, Wu ZH, Cao ZJ (2016) Effects of Saccharomyces cerevisiae fermentation products on dairy calves: ruminal fermentation, gastrointestinal morphology, and microbial community. J Dairy Sci 99(7):5401

    CAS  PubMed  Google Scholar 

  • Xu Y, Sun B, Fan G, Teng C, Xiong K, Zhu Y, Li J, Li X (2017) The brewing process and microbial diversity of strong flavour Chinese spirits: a review. J Inst Brew 123(1)

    CAS  Google Scholar 

  • Yazid NA, Barrena R, Komilis D, Sánchez A (2017) Solid-state fermentation as a novel paradigm for organic waste valorization: a review. Sustainability 9(2):224

    Google Scholar 

  • Yu X-W, Sun W-H, Wang Y-Z, Xu Y (2017) Identification of novel factors enhancing recombinant protein production in multi-copy Komagataella phaffii based on transcriptomic analysis of overexpression effects. Sci Rep 7(1):16249

    PubMed  PubMed Central  Google Scholar 

  • Zakharchenko, A., N. Guz, A. M. Laradji, E. Katz and S. Minko (2017). "Magnetic field remotely controlled selective biocatalysis."

    Google Scholar 

  • Zhang LH (2016) Studies on secondary metabolites produced by co-cultures of marine-derived microorganisms. Journal of the Graduates Sun Yat-Sen University (Natural Sciences, Medicine)

  • Zhao L (2013) The gut microbiota and obesity: from correlation to causality. Nat Rev Microbiol 11(9):639

    CAS  PubMed  Google Scholar 

  • Zhao CJ, Schieber A, Gänzle MG (2016) Formation of taste-active amino acids, amino acid derivatives and peptides in food fermentations—a review. Food Res Int 89(Pt 1):39–47

    CAS  PubMed  Google Scholar 

  • Zhao HM, Guo XN, Zhu KX (2017) Impact of solid state fermentation on nutritional, physical and flavor properties of wheat bran. Food Chem 217:28

    CAS  PubMed  Google Scholar 

  • Zulkawi N, Ng KH, Zamberi R, Yeap SK, Jaganath IB, Satharasinghe D, Yong CY, Jamaluddin AB, Tan SW, Wan YH (2017) The in vivo hepato-recovery effects of the polyphenol-rich fermented food Xeniji™ on ethanol-induced liver damage. RSC Adv 7(61):38287–38299

    CAS  Google Scholar 

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Funding

This study was funded by the Scientific Research Promotion Fund for the National Natural Science Foundation of China (No. 31572467), the Scientific Research Promotion Fund for the Talents of Jiangsu University (No. 1291330009), and the National Nature Science Foundation of China (No. 31802140).

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Authors and Affiliations

  1. School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China

    Rong Feng & Keping Chen

  2. Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang, Jiangsu Province, China

    Liang Chen & Keping Chen

Authors
  1. Rong Feng
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  2. Liang Chen
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  3. Keping Chen
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Correspondence to Keping Chen.

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The authors declare that they have no conflict of interest.

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Feng, R., Chen, L. & Chen, K. Fermentation trip: amazing microbes, amazing metabolisms. Ann Microbiol 68, 717–729 (2018). https://doi.org/10.1007/s13213-018-1384-5

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