Optimization of fermentation parameters for the valorization of tomato pomace into biomass to produce single cell protein using Saccharomyces cerevisiae

Abstract

Tomato pomace, a byproduct of tomato processing industry, can be utilized through fermentation to produce single cell protein (SCP). In this study, fermentation parameters were optimized in a 3-L bioreactor using a full factorial design (FFD), to which a second order polynomial regression model was subsequently fitted to locate the optimum via response surface analysis. While pH, temperature, agitation speed and airflow rate were held constant, the effects of solid load, inoculum volume, and fermentation period were analyzed using a 3 × 3 × 5 experimental design. The resulting biomass was harvested, and its protein content was analyzed. Optimal conditions were identified as a 10.35% solid load and a 2.07% inoculum volume over a 5-day fermentation period. Under these optimized conditions, the model-predicted dry cell weight of 6.92 g/L was validated experimentally at 6.25 g/L, with protein content of 38.40%. These results demonstrate the effective valorization of tomato industry waste into a high value protein resource through optimized bioprocessing.

Graphical abstract

Keywords

Fermentation / Bioprocessing / Tomato pomace / Single cell protein / Optimization / Full factorial design / Second-order polynomial resgression

References

[1] Akgun AS, Mentes D, Oztop MH. Valorization of tomato pomace to use it as a substrate in the fermentation. Acta Hort, 2025, 1445: 295-302

[2] Alancay MM, Lobo MO, Quinzio CM, Iturriaga LB. Extraction and physicochemical characterization of pectin from tomato processing waste. J Food Meas Charact, 2017, 11(4): 2119-2130

[3] Aljurf BN, Cutroneo S, Bugatti K, Barlas B, Bashir AKH, Sahin S, Oztop HM, Tedeschi T. Tomato pomace as a sustainable protein source: Comprehensive characterization of proteins extracted by conventional alkaline, microwave, and ultrasound-assisted methods. Food Hydrocolloids, 2026, 176: 112565

[4] Allison BJ, Cádiz JC, Karuna N, Jeoh T, Simmons CW. The Effect of Ionic Liquid Pretreatment on the Bioconversion of Tomato Processing Waste to Fermentable Sugars and Biogas. Appl Biochem Biotechnol, 2016, 179(7): 1227-1247

[5] Anderson A, Van Der Mijnsbrugge A, Cameleyre X, Gorret N. From yeast screening for suitability as single cell protein to fed-batch cultures. Biotechnol Lett. 2024

[6] Arabani AA, Hosseini F, Abbaspour F, Anarjan N. The effects of ultrasound pretreatment processes on oil extraction from tomato wastes. Int J Biosci, 2015, 4(4): 8-15

[7] Bajić B, Vučurović D, Vasić Đ, Jevtić-Mučibabić R, Dodić S. Biotechnological Production of Sustainable Microbial Proteins from Agro-Industrial Residues and By-Products. Foods, 2022, 12(1): 107

[8] Baker PW, Preskett D, Krienke D, Runager KS, Hastrup ACS, Charlton A. Pre-processing Waste Tomatoes into Separated Streams with the Intention of Recovering Protein: Towards an Integrated Fruit and Vegetable Biorefinery Approach to Waste Minimization. Waste Biomass Valoriz, 2022, 1383463-3473

[9] Bruggeman FJ, Teusink B, Steuer R. Trade-offs between the instantaneous growth rate and long‐term fitness: Consequences for microbial physiology and predictive computational models. BioEssays, 2023, 45(10): 2300015

[10] Concha-Meyer A, Palomo I, Plaza A, Gadioli Tarone A, Junior MRM, Sáyago-Ayerdi SG, Fuentes E. Platelet Anti-Aggregant Activity and Bioactive Compounds of Ultrasound-Assisted Extracts from Whole and Seedless Tomato Pomace. Foods, 2020, 9111564

[11] Da Silva AS, Espinheira RP, Teixeira RSS, De Souza MF, Ferreira-Leitão V, Bon EPS. Constraints and advances in high-solids enzymatic hydrolysis of lignocellulosic biomass: A critical review. Biotechnol Biofuels, 2020, 13158

[12] Dunuweera AN, Nikagolla DN, Ranganathan K. Fruit Waste Substrates to Produce Single-Cell Proteins as Alternative Human Food Supplements and Animal Feeds Using Baker’s Yeast (Saccharomyces cerevisiae). J Food Qual, 2021, 20211-6

[13] Eslami E, Carpentieri S, Pataro G, Ferrari G. A Comprehensive Overview of Tomato Processing By-Product Valorization by Conventional Methods versus Emerging Technologies. Foods, 2022, 12(1): 166

[14] Grassino AN, Brnčić M, Vikić-Topić D, Roca S, Dent M, Brnčić SR. Ultrasound assisted extraction and characterization of pectin from tomato waste. Food Chem, 2016, 19893-100

[15] Güneşer O, Demirkol A, Karagül Yüceer Y, Özmen Toğay S, İşleten Hoşoğlu M, Elibol M. Bioflavour production from tomato and pepper pomaces by Kluyveromyces marxianus and Debaryomyces hansenii. Bioprocess Biosyst Eng, 2015, 38(6): 1143-1155

[16] Hijosa-Valsero M, Garita-Cambronero J, Paniagua-García AI, Díez-Antolínez R. Tomato Waste from Processing Industries as a Feedstock for Biofuel Production. Bioenergy Res, 2019, 12(4): 1000-1011

[17] Hülsen T, Hsieh K, Lu Y, Tait S, Batstone DJ. Simultaneous treatment and single cell protein production from agri-industrial wastewaters using purple phototrophic bacteria or microalgae – A comparison. Bioresour Technol, 2018, 254214-223

[18] Jaafar RA, Rahman ARBA, Mahmod NZC, Vasudevan R. Proximate Analysis of Dragon Fruit (Hylecereus polyhizus). Am J Appl Sci, 2009, 6(7): 1341-1346

[19] Jalasutram V, Kataram S, Gandu B, Anupoju GR. Single cell protein production from digested and undigested poultry litter by Candida utilis: Optimization of process parameters using response surface methodology. Clean Technol Environ Policy, 2013, 15(2): 265-273

[20] Kehili M, Schmidt LM, Reynolds W, Zammel A, Zetzl C, Smirnova I, Allouche N, Sayadi S. Biorefinery cascade processing for creating added value on tomato industrial by-products from Tunisia. Biotechnol Biofuels, 2016, 9(1): 261

[21] Kehili M, Kammlott M, Choura S, Zammel A, Zetzl C, Smirnova I, Allouche N, Sayadi S. Supercritical CO 2 extraction and antioxidant activity of lycopene and β-carotene-enriched oleoresin from tomato (Lycopersicum esculentum L.) peels by-product of a Tunisian industry. Food Bioprod Process, 2017, 102340-349

[22] Kim J-H, Block DE, Mills DA. Simultaneous consumption of pentose and hexose sugars: An optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol, 2010, 88(5): 1077-1085

[23] Kılmanoğlu H, Hoşoğlu Mİ, Güneşer O, Yüceer YK. Optimization of pretreatment and enzymatic hydrolysis conditions of tomato pomace for production of alcohols and esters by Kluyveromyces marxianus. LWT, 2021, 138110728

[24] Kottelat J, Freeland B, Dabros M. Novel Strategy for the Calorimetry-Based Control of Fed-Batch Cultivations of Saccharomyces cerevisiae. Processes, 2021, 9(4): 723

[25] Koukoumaki DI, Tsouko E, Papanikolaou S, Ioannou Z, Diamantopoulou P, Sarris D. Recent advances in the production of single cell protein from renewable resources and applications. Carbon Resour Convers, 2024, 72100195

[26] Lisichkov K, Kuvendziev S, Lisichkov B (2011) Isolation of tomato seed oil from tomato waste by application of supercritical fluid CO₂ extraction. Qual Life (Banja Luka) - APEIRON. https://doi.org/10.7251/QOL1101005L

[27] Lu Z, Wang J, Gao R, Ye F, Zhao G. Sustainable valorisation of tomato pomace: A comprehensive review. Trends Food Sci Technol, 2019, 86172-187

[28] Matassa S, Batstone DJ, Hülsen T, Schnoor J, Verstraete W. Can Direct Conversion of Used Nitrogen to New Feed and Protein Help Feed the World?. Environ Sci Technol, 2015, 49(9): 5247-5254

[29] Mazi BG (2010) Evaluating Microemulsions for Purification of Beta-Galactosidase from Kluyveromyces lactis [Middle East Technical University]. http://etd.lib.metu.edu.tr/upload/12612692/index.pdf

[30] Mazzoleni S, Landi C, Cartenì F, De Alteriis E, Giannino F, Paciello L, Parascandola P. A novel process-based model of microbial growth: Self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures. Microb Cell Fact, 2015, 14(1): 109

[31] Miller GL. Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar. Anal Chem, 1959, 313426-428

[32] Moreno AD, González-Fernández C, Ballesteros M, Tomás-Pejó E. Insoluble solids at high concentrations repress yeast’s response against stress and increase intracellular ROS levels. Sci Rep, 2019, 9(1): 12236

[33] Morning Star (2024) Post Season Global Tomato Crop Update. https://www.morningstarco.com/2024-post-season-global-tomato-crop-update/ (accessed 20 January 2026).

[34] Mujdalipah S, Putri ML. Utilization of pineapple peel and rice washing water to produce single cell proteins using Saccharomyces cerevisiae. IOP Conf Series: Earth Environ Sci, 2020, 4721012029

[35] Olivares-Marin IK, González-Hernández JC, Regalado-Gonzalez C, Madrigal-Perez LA (2018) Saccharomyces cerevisiae exponential growth kinetics in batch culture to analyze respiratory and fermentative metabolism. J Visualized Experiments. https://doi.org/10.3791/58192

[36] Øverland M, Skrede A. Yeast derived from lignocellulosic biomass as a sustainable feed resource for use in aquaculture. J Sci Food Agric, 2017, 973733-742

[37] Paniagua-García AI, Garita-Cambronero J, González-Rojo S, Díez-Antolínez R. Optimization of lactic acid production from apple and tomato pomaces by thermotolerant bacteria. J Environ Manage, 2024, 366121806

[38] Pereira PR, Freitas CS, Paschoalin VMF. Saccharomyces cerevisiae biomass as a source of next-generation food preservatives: Evaluating potential proteins as a source of antimicrobial peptides. Compr Rev Food Sci Food Saf, 2021, 20(5): 4450-4479

[39] Pillaca-Pullo OS, Lopes M, Bautista‐Cruz A, Estela‐Escalante W. From coffee waste to nutritional gold: Bioreactor cultivation of single‐cell protein from Candida sorboxylosa. J Chem Technol Biotechnol, 2025, 100(2): 360-368

[40] Pirozzi A, Ferrari G, Donsì F. Cellulose Isolation from Tomato Pomace Pretreated by High-Pressure Homogenization. Foods, 2022, 11(3): 266

[41] Rajput SD, Pandey N, Sahu K. A comprehensive report on valorization of waste to single cell protein: Strategies, challenges, and future prospects. Environ Sci Pollut Res, 2024, 311826378-26414

[42] Razzaq ZU, Khan MKI, Maan AA, Rahman SU. Characterization of single cell protein from Saccharomyces cerevisiae for nutritional, functional and antioxidant properties. J Food Meas Charact, 2020, 14(5): 2520-2528

[43] Sakarika M, Kerckhof F-M, Van Peteghem L, Pereira A, Van Den Bossche T, Bouwmeester R, Gabriels R, Van Haver D, Ulčar B, Martens L, Impens F, Boon N, Ganigué R, Rabaey K. The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microb Cell Fact, 2023, 22(1): 254

[44] Salafia F, Ferracane A, Tropea A. Pineapple Waste Cell Wall Sugar Fermentation by Saccharomyces cerevisiae for Second Generation Bioethanol Production. Fermentation, 2022, 83100

[45] Saravanan K, Rajendran M, Kathirvel P. Utilization of Water Hyacinth (Eichhornia crassipes) as a Feasible Substrate for the Production of Single Cell Protein Using Saccharomyces cerevisiae (Baker’s Yeast). Waste Biomass Valoriz, 2023, 14124231-4242

[46] Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res, 2023, 276127478

[47] Simões A, Coelhoso IM, Alves VD, Brazinha C. Recovery and Purification of Cutin from Tomato By-Products for Application in Hydrophobic Films. Membranes, 2023, 13(3): 261

[48] Simutis R, Lübbert A. Bioreactor control improves bioprocess performance. Biotechnol J, 2015, 1081115-1130

[49] Singh J, Dwivedi B, Kumar V. Optimization of Solid-State Fermentation Conditions for Enhancing the Nutrition Contents in Tomato Pomace Using RSM. J Institution Eng (India): Ser A, 2024, 105(2): 409-418

[50] Tang C, Martín C, Jönsson LJ. Effects of aeration of softwood pretreatment liquid on inhibitors and fermentability using Saccharomyces cerevisiae yeast. Biotechnol Biofuels Bioprod, 2025, 18(1): 103

[51] Tedeschi G, Benitez JJ, Ceseracciu L, Dastmalchi K, Itin B, Stark RE, Heredia A, Athanassiou A, Heredia-Guerrero JA. Sustainable Fabrication of Plant Cuticle-Like Packaging Films from Tomato Pomace Agro-Waste, Beeswax, and Alginate. ACS Sustain Chem Eng, 2018, 61114955-14966

[52] Tropea A, Ferracane A, Albergamo A, Potortì AG, Turco L, Di Bella G. Single Cell Protein Production through Multi Food-Waste Substrate Fermentation. Fermentation, 2022, 8(3): 91

[53] Ubeyitogullari A, Ciftci ON. Enhancing the bioaccessibility of lycopene from tomato processing byproducts via supercritical carbon dioxide extraction. Curr Res Food Sci, 2022, 5553-563

[54] Verbelen PJ, Saerens SMG, Van Mulders SE, Delvaux F, Delvaux FR. The role of oxygen in yeast metabolism during high cell density brewery fermentations. Appl Microbiol Biotechnol, 2009, 82(6): 1143-1156

[55] Verhagen KJA, Pardijs IH, Van Klaveren HM, Wahl SA. A Dive Into Yeast’s Sugar Diet—Comparing the Metabolic Response of Glucose, Fructose, Sucrose, and Maltose Under Dynamic Feast/Famine Conditions. Biotechnol Bioeng, 2025, 122(4): 1035-1050

[56] Wortel MT, Noor E, Ferris M, Bruggeman FJ, Liebermeister W. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. PLoS Comput Biol, 2018, 14(2): e1006010

[57] Yang R, Chen Z, Hu P, Zhang S, Luo G. Two-stage fermentation enhanced single-cell protein production by Yarrowia lipolytica from food waste. Bioresour Technol, 2022, 361127677

[58] Yang Y-Q, Li X, Wang Z-Z, Huang X-Y, Zeng D-W, Zhao X-Q, Liu Z-Q, Zhang F-L. Single cell protein production of co-culture Kodamaea ohmeri and Lactococcus lactis in corn straw hydrolysate. Bioresour Technol, 2025, 433132649

[59] Zhang X, Zhang H, Wang R, Zhang Z, Yan X, Zhang J. Bioconversion of Baijiu Huangshui for single cell protein using Saccharomyces cerevisiae: A study on influence of carbon metabolic pathways. J Environ Manage, 2025, 393127077

[60] Zhang P, He Z, Li H, Jiang Z. Resurrection and characterization of ancestral xylose transporters enhance the capability of xylose uptake in the mixed sugar co-fermentation of Recombinant Saccharomyces cerevisiae. Bioresources Bioprocess, 2026, 1311

[61] Zhao S, Zhang D. A parametric study of supercritical carbon dioxide extraction of oil from Moringa oleifera seeds using a response surface methodology. Sep Purif Technol, 2013, 1139-17

Funding

European Union’s Horizon 2020-PRIMA Section I Program(2232)

RIGHTS & PERMISSIONS

The Author(s)