Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS)
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Abstract. Estikomah SA, Suranto, Susilowati A, Masykuri M. 2024. Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS). Biodiversitas 25: 482-490. Cheese wastewater (whey) has a high content of organic substances, including lactose, protein, and fat. The lactose in whey wastewater can also be used as a bacterial growth medium. Bacterial community structure is an essential aspect of microbial water quality. The bacterial diversity data obtained can then be used to evaluate the existence of bacteria that might be useful for making microbiological products. This research employs Next Generation Sequencing (NGS) technology to determine the diversity and abundance of bacteria based on 16S rRNA gene amplicons for further processing of whey wastewater. The NGS-based technique overcomes the limitations of conventional bacterial culture techniques. The effectiveness and accuracy of microbial diversity analysis employing NGS technology are high. The research method includes the steps of sample preparation, DNA extraction using a ZymoBIOMICS DNA Microprep Kit (D4300), PCR amplification of the V3-V4 16S rRNA gene region, DNA sequencing, and a bioinformatics-statistical analysis. The results show that bacterial diversity in whey wastewater was found to have an average number of Operational Taxon Units (OTUs) of 259 tags. The metagenomics study of the microbial community in whey wastewater successfully detected the dominant genus of bacteria, which can benefit the management of whey wastewater. The presence of Lactobacillus and Acetobacter confirms that cheese whey wastewater exists in Yogyakarta Province. Acetobacter can oxidize ethanol to produce acetic acid, a pungent odor characteristic that causes environmental pollution. On the other hand, the presence of Lactobacillus and Acetobacter shows that whey wastewater can be reprocessed to produce fermented beverages, thereby improving their value and minimizing the impact of environmental pollution.
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REFERENCES
Alegría, A., González, R., Díaz, M., and Mayo, B. 2011. Assessment of microbial populations dynamics in a blue cheese by culturing and denaturing gradient gel electrophoresis. Curr. Microbiol. 62, 888–893. doi: 10.1007/s00284-010- 9799-7
Almeida, M., Hébert, A., Abraham, A. L., Rasmussen, S., Monnet, C., Pons, N., Delbès, C., Loux, V., Batto, J. M., Leonard, P., Kennedy, S., Ehrlich, S. D., Pop, M., Montel, M. C., Irlinger, F., & Renault, P. (2014). Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-1101
Ambarsari, H., Suryati, T., Akhadi, D. H., Herlina, S., Hanifah, I., Andriyani, R., ... & Suyanti, S. (2023). The effectiveness of coconut shell charcoal and activated carbon on deodorization of sludge from ice cream industry WWTP. In IOP Conference Series: Earth and Environmental Science (Vol. 1201, No. 1, p. 012016). IOP Publishing.
Belviso S, Giordano M, Dolci P, Zeppa G. 2009. In vitro cholesterol- lowering activity of Lactobacillus plantarum and Lactobacillus paracasei strains isolated from the Italian Castelmagno PDO cheese. Dairy Sci Technol 89: 169-176. DOI: 10.1051/dst/2009004.
Burlingame, G.A., Suffet, I.H., Khiari, D., Bruchet, A.L., 2004. Development of an odor wheel classification scheme for wastewater. Water. Sci. Technol. 49, 201e209.
Bokulich NA, Mills DA. 2013. Facility-specific “house” microbiome drives microbial landscapes ofartisan cheesemaking plants. Appl Environ Microbiol 79:5214–5223. http://dx.doi.org/10.1128/AEM.00934-13.
Bokulich NA, Mills DA. 2012. Next-generation approaches to the micro- bial ecology of food fermentations. BMB Rep 45:377–389. http://dx.doi .org/10.5483/BMBRep.2012.45.7.148.
Cheirsilp, B. dan Radchabut,S . 2011. Use of whey lactose from dairy industryfor economical kefiran production byLactobacillus kefiranofaciens in mixedcultures with yeasts. Elsevier, New Biotechnology 28
Chao A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian J Stat 11: 265-270.
Chao A, Hwang WH, Chen YC, Kuo CY. 2000. Estimating the number of shared species in two communities. Statistica Sinica 10: 227-246
Chen, X., Du, P., Mu, H., Bai, S., Song, Z., Liu, P., Li, F., Jing, H., Fang, L., Li, F., & Wang, R. (2022). Sensory Evaluation of Fuzzy Mathematics in Sticky Soup Food. Lecture Notes in Electrical Engineering, 800. https://doi.org/10.1007/978-981-16-5963-8_26
Cutone, A., Rosa, L., Ianiro, G., Lepanto, M. S., Bonaccorsi di Patti, M. C., Valenti, P., et al. (2020). Lactoferrin’s Anti-Cancer Properties: Safety, Selectivity, and Wide Range of Action. Biomolecules, 10(3):456.
Colwell RK. 2013. Statistical estimation of species richness and shared species from samples. EstimateS version 9.1
Da Silva Duarte, V., Carlot, M., Pakroo, S., Tarrah, A., Lombardi, A., Santiago, H., Corich, V., & Giacomini, A. 2020. Comparative evaluation of cheese whey microbial composition from four Italian cheese factories by viable counts and 16S rRNA gene amplicon sequencing. International Dairy Journal, 104, 104656. https://doi.org/10.1016/j.idairyj.2020.104656
Dullius, A., Inês, M., Fernanda, C., & Souza, V. De. 2018. Whey protein hydrolysates as a source of bioactive peptides for functional foods – Biotechnological facilitation of industrial scale-up. Journal of Functional Foods, 42(August 2017), 58–74. https://doi.org/10.1016/j.jff.2017.12.063
Edgar, R. C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10), 996–998. https://doi.org/10.1038/nmeth.2604
Fox PF, Guinee TP, Cogan TM, M. P. 2017. Whey and Whey Products. In M. Fundamentals of cheese science. Boston (Ed.), Whey and whey products. (pp. 755–69.). https://doi.org/10.1002/9780813804033.ch15
Gostelow, P., Parsons, S.A., Stuetz, R.M., 2001. Odour measurements for sewage treatment works. Water. Res. 35, 579e597.
Garner, E., Davis, B. C., Milligan, E., Blair, M. F., Keenum, I., Maile-Moskowitz, A., Pan, J., Gnegy, M., Liguori, K., Gupta, S., Prussin, A. J., Marr, L. C., Heath, L. S., Vikesland, P. J., Zhang, L., & Pruden, A. 2021. Next generation sequencing approaches to evaluate water and wastewater quality. Water Research, 194. https://doi.org/10.1016/j.watres.2021.116907
Guimarães, P. M. R., Teixeira, J. A., & Domingues, L. 2010. Fermentation of lactose to bio-ethanol by yeasts as part of integrated solutions for the valorisation of cheese whey. Biotechnology Advances, 28(3), 375–384. https://doi.org/10.1016/j.biotechadv.2010.02.002
Ji, Y., Park, S., Chung, Y., Kim, B., Park, H., Huang, E., Jeong, D., Jung, H. Y., Kim, B., Hyun, C. K., & Holzapfel, W. H. 2019. Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598-019-43092-y
Jiang, T., Wu, H., Yang, X., Li, Y., Zhang, Z., Chen, F., Zhao, L., & Zhang, C. (2020). Lactobacillus mucosae strain promoted by a high-fiber diet in genetic obese child alleviates lipid metabolism and modifies gut microbiota in apoe-/- mice on a western diet. Microorganisms, 8(8), 1–17. https://doi.org/10.3390/microorganisms8081225
Khan, S., Amin, N., Ansari, Z., & Majumder, D. R. 2015. Whey: Waste to health and wealth. International Journal of Current Mocrobiology and Applied Sciences, 2(2), 245–253.
Kumar M, Nagpal R, Hemalatha R, Yadav H, Marotta F.2016.Probiotics and prebiotics for promoting health: through gut micro- biota. Probiotics, prebiotics, and synbiotics. Bioact Foods Health Prom 897–908
Luongo, V., Policastro, G., Ghimire, A., Pirozzi, F., & Fabbricino, M. (2019). Repeatedbatch fermentation of cheese whey for semi-continuous lactic acid production using mixed cultures at uncontrolled pH. Sustainability., 11(12), 3330
Lusk, T. S., Ottesen, A. R., White, J. R., Allard, M. W., Brown, E. W., & Kase, J. A. 2012. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology. BMC Microbiology, 12(1), 1. https://doi.org/10.1186/1471-2180-12-254
Mazorra-Manzano, M. A., Robles-Porchas, G. R., Martínez-Porchas, M., Ramírez-Suárez, J. C., García-Sifuentes, C. O., Torres-Llanez, M. J., González-Córdova, A. F., Hernández-Mendoza, A., & Vallejo-Cordoba, B. 2022. Bacterial Diversity and Dynamics during Spontaneous Cheese Whey Fermentation at Different Temperatures. Fermentation, 8(7). https://doi.org/10.3390/fermentation8070342
Nalepa, B., Ciesielski, S., & Aljewicz, M. 2020. The microbiota of edam cheeses determined by cultivation and high-throughput sequencing of the 16S rRNA amplicon. Applied Sciences (Switzerland), 10(12), 1–12. https://doi.org/10.3390/APP10124063
Nagarajan, D., Nandini, A., Dong, C. D., Lee, D. J., & Chang, J. S. 2020. Lactic acid production from renewable feedstocks using poly(vinyl alcohol)-immobilized Lactobacillus plantarum 23. Industrial and Engineering Chemistry Research, 59(39), 17156–17164
Nguyen, H. T., Gu, M., Werlinger, P., Cho, J. H., Cheng, J., & Suh, J. W. 2022. Lactobacillus sakei MJM60958 as a Potential Probiotic Alleviated Non-Alcoholic Fatty Liver Disease in Mice Fed a High-Fat Diet by Modulating Lipid Metabolism, Inflammation, and Gut Microbiota. International Journal of Molecular Sciences, 23(21). https://doi.org/10.3390/ijms232113436
Odum, E.P. 1993. Dasar-dasar Ekologi. Terjemahan Tjahjono Samingan. Edisi Ketiga. Yogyakarta: Gadjah Mada University Press
Olszewska-Widdrat, A., Alexandri, M., Lopez-G ´ omez, ´ J. P., Schneider, R., & Venus, J. 2020. Batch and continuous lactic acid fermentation based on a multi-substrate approach. Microorganisms, 8(7), 1084.
Palaniveloo, K., Amran, M. A., Norhashim, N. A., Mohamad-Fauzi, N., Peng-Hui, F., Hui-Wen, L., Kai-Lin, Y., Jiale, L., Chian-Yee, M. G., Jing-Yi, L., Gunasekaran, B., & Razak, S. A. 2020. Food waste composting and microbial community structure profiling. Processes, 8(6), 1–30. https://doi.org/10.3390/pr8060723
Quigley, L., O’Sullivan, O., Beresford, T. P., Ross, R. P., Fitzgerald, G. F., & Cotter, P. D. 2012. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Applied & Environmental Microbiology, 78(16), 5717–5723.
Rama, G. R., Kuhn, D., Beux, S., Maciel, M. J., & Volken de Souza, C. F.2019. Potential applications of dairy whey for the production of lactic acid bacteria cultures. International Dairy Journal, 98, 25–37. https://doi.org/10.1016/j.idairyj.2019.06.012
Sahoo, T. K., & Jayaraman, G. 2019. Co-culture of Lactobacillus delbrueckii and engineered Lactococcus lactis enhances stoichiometric yield of d-lactic acid from whey permeate. Applied Microbiology and Biotechnology, 103(14), 5653–5662.
Seaby RMH, Henderson PA. 2007. SDR-IV Help: Measuring and Understanding Biodiversity. Pisces Conservation Ltd., Hampshire.
Shen, Y., Jiang, B., Zhang, C., Wu, Q., Li, L., & Jiang, P. 2023. Combined Inhibition of the TGF-?1/Smad Pathway by Prevotella copri and Lactobacillus murinus to Reduce Inflammation and Fibrosis in Primary Sclerosing Cholangitis. International Journal of Molecular Sciences, 24(13), 11010. https://doi.org/10.3390/ijms241311010
Shannon, C. E., & Weaver, W. (1949). The mathematical theory of communication., (The University of Illinois Press: Urbana, IL, USA).
Simamora, C. J. K., Solihin, D. D., & Lestari, Y. (2016). Culturable and unculturable actinomycetes associated with the sponge Neofibularia from Bira Island, Indonesia. Malaysian Journal of Microbiology, 12(3), 211–220. https://doi.org/10.21161/mjm.77015
Sun, L., Müller, B., Schnürer, A., 2013. Biogas production from wheat straw : community structure of cellulose- degrading bacteria. Energy. Sustain. Soc. 3, 1–11. https://doi.org/10.1186/2192-0567-3-15
Taranto, M. P., Medici, M., Perdigon, G., Ruiz Holgado, A. P., & Font de Valdez, G. 2000. Effect of Lactobacillus reuteri on the prevention of hypercholesterolemia in mice. Journal of Dairy Science, 83(3), 401–403. https://doi.org/10.3168/jds.S0022-0302(00)74895-8
Wang, Y., Guo, J., & Huang, A. (2018). Study on bacterial diversity in traditional sour whey of Yunnan province. Journal of Food Processing and Preservation, 42(3), 1–9. https://doi.org/10.1111/jfpp.13553
Watanabe Y, Nagayama K, Tamai Y. 2008. Expression of Glycerol 3- Phosphate Dehydrogenase Gene (CvGPDI) in salt-tolerant yeast Candida versatilis is stimulated by high concentrations of NaCl. Yeast 25: 107-116.
Weschenfelder, S., Paim, M. P., Gerhardt, C., Carvalho, H. H. C., & Wiest, J. M. 2018. Antibacterial activity of different formulations of cheese and whey produced with kefir grains. Revista Ciencia Agronomica, 49(3), 443–449. https://doi.org/10.5935/1806-6690.20180050
Yeluri Jonnala, B. R., McSweeney, P. L. H., Sheehan, J. J., & Cotter, P. D. 2018. Sequencing of the cheese microbiome and its relevance to industry. Frontiers in Microbiology, 9(MAY). https://doi.org/10.3389/fmicb.2018.01020
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