Challenges and perspectives of quantitative microbiome profiling in food fermentations

References

• Ackerman, C. M., C. Myhrvold, S. G. Thakku, C. A. Freije, H. C. Metsky, D. K. Yang, S. H. Ye, C. K. Boehm, T. S. F. Kosoko-Thoroddsen, J. Kehe, et al. 2020. Massively multiplexed nucleic acid detection with Cas13. Nature 582 (7811):277–82. doi: 10.1038/s41586-020-2279-8.
   PubMed Web of Science ®Google Scholar
• Ahmed, A., J. V. Rushworth, N. A. Hirst, and P. A. Millner. 2014. Biosensors for whole-cell bacterial detection. Clinical Microbiology Reviews 27 (3):631–46. doi: 10.1128/cmr.00120-13.
   PubMed Web of Science ®Google Scholar
• Anderson, D. L., M. E. Pollock, and D. L. F. Brower. 1965. Morphology of Mycoplasma laidlawii type A. I. comparison of electron microscopic counts with colony-forming units. Journal of Bacteriology 90 (6):1764–7. doi: 10.1128/jb.90.6.1764-1767.1965.
   PubMed Web of Science ®Google Scholar
• Andorrà, I., M. Berradre, A. Mas, B. Esteve-Zarzoso, and J. M. Guillamón. 2012. Effect of mixed culture fermentations on yeast populations and aroma profile. Lwt 49 (1):8–13. doi: 10.1016/j.lwt.2012.04.008.
   Web of Science ®Google Scholar
• Angelakis, E., M. Million, M. Henry, and D. Raoult. 2011. Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry. Journal of Food Science 76 (8):M568–M572. doi: 10.1111/j.1750-3841.2011.02369.x.
   PubMed Web of Science ®Google Scholar
• Auty, M. A. E., G. E. Gardiner, S. J. McBrearty, E. O. O’Sullivan, D. M. Mulvihill, J. K. Collins, G. F. Fitzgerald, C. Stanton, and R. P. Ross. 2001. Direct in situ viability assessment of bacteria in probiotic dairy products using viability staining in conjunction with confocal scanning laser microscopy. Applied and Environmental Microbiology 67 (1):420–5. doi: 10.1128/aem.67.1.420-425.2001.
   PubMed Web of Science ®Google Scholar
• Baek, H., S. Kim, W. Min, S. Kang, S. Shim, N. S. Han, and J. Seo. 2021. A species-specific qPCR method for enumeration of Lactobacillus sanfranciscensis, Lactobacillus brevis, and Lactobacillus curvatus during cocultivation in sourdough. Food Analytical Methods 14 (4):750–60. doi: 10.1007/s12161-020-01920-2.
   Web of Science ®Google Scholar
• Bakken, L. R. 1985. Separation and purification of bacteria from soil. Applied and Environmental Microbiology 49 (6):1482–7. doi: 10.1128/aem.49.6.1482-1487.1985.
   PubMed Web of Science ®Google Scholar
• Ban, S., L. Chen, S. Fu, Q. Wu, and Y. Xu. 2022. Modelling and predicting population of core fungi through processing parameters in spontaneous starter (Daqu) fermentation. International Journal of Food Microbiology 363:109493. doi: 10.1016/j.ijfoodmicro.2021.109493.
   PubMed Web of Science ®Google Scholar
• Barlow, J. T., S. R. Bogatyrev, and R. F. Ismagilov. 2020. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nature Communications 11 (1):2590. doi: 10.1038/s41467-020-16224-6.
   PubMed Web of Science ®Google Scholar
• Bartle, L., J. G. Mitchell, and J. S. Paterson. 2021. Evaluating the cytometric detection and enumeration of the wine bacterium, Oenococcus oeni. Cytometry. Part A: The Journal of the International Society for Analytical Cytology 99 (4):399–406. doi: 10.1002/cyto.a.24258.
   PubMed Web of Science ®Google Scholar
• Behera, S. S., A. F. El Sheikha, R. Hammami, and A. Kumar. 2020. Traditionally fermented pickles: How the microbial diversity associated with their nutritional and health benefits? Journal of Functional Foods 70:103971. doi: 10.1016/j.jff.2020.103971.
   Web of Science ®Google Scholar
• Bernáldez, V., J. J. Córdoba, M. Rodríguez, M. Cordero, L. Polo, and A. Rodríguez. 2013. Effect of Penicillium nalgiovense as protective culture in processing of dry-fermented sausage salchichón. Food Control. 32 (1):69–76. doi: 10.1016/j.foodcont.2012.11.018.
   Web of Science ®Google Scholar
• Bernáldez, V., A. Rodríguez, J. Delgado, L. Sánchez-Montero, and J. J. Córdoba. 2018. Gene expression analysis as a method to predict OTA accumulation in dry-cured meat products. Food Analytical Methods 11 (9):2463–71. doi: 10.1007/s12161-018-1231-0.
   Web of Science ®Google Scholar
• Bertani, G., A. Levante, C. Lazzi, B. Bottari, M. Gatti, and E. Neviani. 2020. Dynamics of a natural bacterial community under technological and environmental pressures: The case of natural whey starter for Parmigiano Reggiano cheese. Food Research International (Ottawa, Ont.) 129:108860. doi: 10.1016/j.foodres.2019.108860.
   PubMed Web of Science ®Google Scholar
• Blaiotta, G., D. Ercolini, G. Mauriello, G. Salzano, and F. Villani. 2004. Rapid and reliable identification of Staphylococcus equorum by a species-specific PCR assay targeting the sodA gene. Systematic and Applied Microbiology 27 (6):696–702. doi: 10.1078/0723202042369901.
   PubMed Web of Science ®Google Scholar
• Blasche, S., Y. Kim, R. A. T. Mars, D. Machado, M. Maansson, E. Kafkia, A. Milanese, G. Zeller, B. Teusink, J. Nielsen, et al. 2021. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology 6 (2):196–208. doi: 10.1038/s41564-020-00816-5.
   PubMed Web of Science ®Google Scholar
• Bogatyrev, S. R., J. C. Rolando, and R. F. Ismagilov. 2020. Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine. Microbiome 8 (1):19. doi: 10.1186/s40168-020-0785-4.
   PubMed Web of Science ®Google Scholar
• Bracquart, P. 1981. An agar medium for the differential enumeration of Streptococcus thermophilus and Lactobacillus bulgaricus in yoghurt. Journal of Applied Bacteriology 51 (2):303–5. doi: 10.1111/j.1365-2672.1981.tb01246.x.
   Google Scholar
• Bubeck, A. M., L. Preiss, A. Jung, E. Dörner, D. Podlesny, M. Kulis, C. Maddox, C. Arze, C. Zörb, N. Merkt, et al. 2020. Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection. Scientific Reports 10 (1):13828. doi: 10.1038/s41598-020-70535-8.
   PubMed Web of Science ®Google Scholar
• Callahan, B. J., P. J. McMurdie, M. J. Rosen, A. W. Han, A. J. A. Johnson, and S. P. Holmes. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13 (7):581–3. doi: 10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Chang, H., J. S. Haudenshield, C. R. Bowen, and G. L. Hartman. 2017. Metagenome-wide association study and machine learning prediction of bulk soil microbiome and crop productivity. Frontiers in Microbiology 8:519. doi: 10.3389/fmicb.2017.00519.
   PubMed Web of Science ®Google Scholar
• Chen, H., S. Wang, and M. Chen. 2008. Microbiological study of lactic acid bacteria in kefir grains by culture-dependent and culture-independent methods. Food Microbiology 25 (3):492–501. doi: 10.1016/j.fm.2008.01.003.
   PubMed Web of Science ®Google Scholar
• Chen, J, and Y. Zhu. 2013. Solid state fermentation for foods and beverages. 1st ed. Boca Raton: CRC Press. doi: 10.1201/b16054.
   Google Scholar
• Cocolin, L., M. Manzano, D. Aggio, C. Cantoni, and G. Comi. 2001. A novel polymerase chain reaction (PCR) - denaturing gradient gel electrophoresis (DGGE) for the identification of Micrococcaceae strains involved in meat fermentations. Its application to naturally fermented Italian sausages. Meat Science 58 (1):59–64. doi: 10.1016/S0309-1740(00)00131-5.
   PubMed Web of Science ®Google Scholar
• Davies, D. 2012. Cell separations by flow cytometry. Methods in Molecular Biology (Clifton, N.J.) 878:185–99. doi: 10.1007/978-1-61779-854-2_12.
   PubMedGoogle Scholar
• Deshmukh, R. A., K. Joshi, S. Bhand, and U. Roy. 2016. Recent developments in detection and enumeration of waterborne bacteria: A retrospective minireview. MicrobiologyOpen 5 (6):901–22. doi: 10.1002/mbo3.383.
   PubMed Web of Science ®Google Scholar
• Ding, X., C. Wu, J. Huang, and R. Zhou. 2015. Interphase microbial community characteristics in the fermentation cellar of Chinese Luzhou-flavor liquor determined by PLFA and DGGE profiles. Food Research International 72:16–24. doi: 10.1016/j.foodres.2015.03.018.
   Web of Science ®Google Scholar
• Dreier, M., H. Berthoud, N. Shani, D. Wechsler, and P. Junier. 2021. Development of a high-throughput microfluidic qPCR system for the quantitative determination of quality-relevant bacteria in cheese. Frontiers in Microbiology 11:619166. doi: 10.3389/fmicb.2020.619166.
   PubMed Web of Science ®Google Scholar
• Du, H., X. Wang, Y. Zhang, and Y. Xu. 2019. Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter. International Journal of Food Microbiology 297:32–40. doi: 10.1016/j.ijfoodmicro.2019.02.020.
   PubMed Web of Science ®Google Scholar
• Du, R., S. Wang, Q. Wu, and Y. Xu. 2022. LSQP-DB: A species-specific quantitative PCR primer database for 307 Lactobacillaceae species. Systems Microbiology and Biomanufacturing. doi: 10.1007/s43393-022-00128-1.
   Google Scholar
• Du, R., Q. Wu, and Y. Xu. 2020a. Chinese liquor fermentation: Identification of key flavor-producing Lactobacillus spp. by quantitative profiling with indigenous internal standards. Applied and Environmental Microbiology 86 (12):e00456–20. doi: 10.1128/AEM.00456-20.
   PubMed Web of Science ®Google Scholar
• Du, R., Q. Wu, and Y. Xu. 2020b. Distribution of Lactobacillus sp. in Chinese liquor fermentation system from different producing location by three-step fluorescent quantitative PCR. Microbiology China 47 (1):1–12. doi: 10.13344/j.microbiol.china.190150.
   Google Scholar
• Dugat-Bony, E., L. Garnier, J. Denonfoux, S. Ferreira, A.-S. Sarthou, P. Bonnarme, and F. Irlinger. 2016. Highlighting the microbial diversity of 12 French cheese varieties. International Journal of Food Microbiology 238:265–73. doi: 10.1016/j.ijfoodmicro.2016.09.026.
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. 2016. UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv. doi: 10.1101/081257.
   Google Scholar
• Fernández-Pérez, R., C. T. Rodríguez, and F. Ruiz-Larrea. 2019. Fluorescence microscopy to monitor wine malolactic fermentation. Food Chemistry 274:228–33. doi: 10.1016/j.foodchem.2018.08.088.
   PubMed Web of Science ®Google Scholar
• Fonseca, S., A. Cachaldora, M. Gómez, I. Franco, and J. Carballo. 2013. Monitoring the bacterial population dynamics during the ripening of Galician chorizo, a traditional dry fermented Spanish sausage. Food Microbiology 33 (1):77–84. doi: 10.1016/j.fm.2012.08.015.
   PubMed Web of Science ®Google Scholar
• Galazzo, G. N., B. J. van Best, K. Benedikter, L. Janssen, C. Bervoets, M. Driessen, M. Oomen, P. H. Lucchesi, H. van Eijck, E. F. Becker, et al. 2020. How to count our microbes? The effect of different quantitative microbiome profiling approaches. Frontiers in Cellular and Infection Microbiology 10:403. doi: 10.3389/fcimb.2020.00403.
   PubMed Web of Science ®Google Scholar
• Gänzle, M, and V. Ripari. 2016. Composition and function of sourdough microbiota: From ecological theory to bread quality. International Journal of Food Microbiology 239:19–25. doi: 10.1016/j.ijfoodmicro.2016.05.004.
   PubMed Web of Science ®Google Scholar
• Garofalo, C., G. Silvestri, L. Aquilanti, and F. Clementi. 2008. PCR-DGGE analysis of lactic acid bacteria and yeast dynamics during the production processes of three varieties of Panettone. Journal of Applied Microbiology 105 (1):243–54. doi: 10.1111/j.1365-2672.2008.03768.x.
   PubMed Web of Science ®Google Scholar
• Gómez-Rojo, E. M., L. Romero-Santacreu, I. Jaime, and J. Rovira. 2015. A novel real-time PCR assay for the specific identification and quantification of Weissella viridescens in blood sausages. International Journal of Food Microbiology 215:16–24. doi: 10.1016/j.ijfoodmicro.2015.08.002.
   PubMed Web of Science ®Google Scholar
• Gong, H., Q. Du, S. Xie, W. Hu, M. A. Akram, Q. Hou, L. Dong, Y. Sun, A. Manan, Y. Deng, et al. 2021. Soil microbial DNA concentration is a powerful indicator for estimating soil microbial biomass C and N across arid and semi-arid regions in northern China. Applied Soil Ecology 160:103869. doi: 10.1016/j.apsoil.2020.103869.
   Web of Science ®Google Scholar
• Gong, S., P. Fei, A. Ali, X. Cai, W. Xue, W. Jiang, and L. Guo. 2020. Effect of milk types on the attributes of a glutinous rice wine-fermented yogurt-like product. Journal of Dairy Science 103 (1):220–7. doi: 10.3168/jds.2019-17091.
   PubMed Web of Science ®Google Scholar
• Green, H. C, and K. G. Field. 2012. Sensitive detection of sample interference in environmental qPCR. Water Research 46 (10):3251–60. doi: 10.1016/j.watres.2012.03.041.
   PubMed Web of Science ®Google Scholar
• Guan, Q., W. Zheng, T. Huang, Y. Xiao, Z. Liu, Z. Peng, D. Gong, M. Xie, and T. Xiong. 2020. Comparison of microbial communities and physiochemical characteristics of two traditionally fermented vegetables. Food Research International (Ottawa, Ont.) 128:108755. doi: 10.1016/j.foodres.2019.108755.
   PubMed Web of Science ®Google Scholar
• Hammes, F., M. Berney, Y. Wang, M. Vital, O. Köster, and T. Egli. 2008. Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Research 42 (1-2):269–77. doi: 10.1016/j.watres.2007.07.009.
   PubMed Web of Science ®Google Scholar
• Hammes, F., F. Goldschmidt, M. Vital, Y. Wang, and T. Egli. 2010. Measurement and interpretation of microbial adenosine tri-phosphate (ATP) in aquatic environments. Water Research 44 (13):3915–23. doi: 10.1016/j.watres.2010.04.015.
   PubMed Web of Science ®Google Scholar
• Haque, Z. U., E. Kucukoner, and K. J. Aryana. 1997. Aging-induced changes in populations of Lactococci, Lactobacilli, and aerobic microorganisms in low-fat and full-fat cheddar cheese. Journal of Food Protection 60 (9):1095–8. doi: 10.4315/0362-028x-60.9.1095.
   PubMed Web of Science ®Google Scholar
• He, S., L. Ding, K. Xu, J. Geng, and H. Ren. 2016. Effect of low temperature on highly unsaturated fatty acid biosynthesis in activated sludge. Bioresource Technology 211:494–501. doi: 10.1016/j.biortech.2016.03.069.
   PubMed Web of Science ®Google Scholar
• He, S., X. Hong, T. Huang, W. Zhang, Y. Zhou, L. Wu, and X. Yan. 2017. Rapid quantification of live/dead lactic acid bacteria in probiotic products using high-sensitivity flow cytometry. Methods and Applications in Fluorescence 5 (2):024002. doi: 10.1088/2050-6120/aa64e4.
   PubMed Web of Science ®Google Scholar
• Hill, G. T., N. A. Mitkowski, L. Aldrich-Wolfe, L. R. Emele, D. D. Jurkonie, A. Ficke, S. Maldonado-Ramirez, S. T. Lynch, and E. B. Nelson. 2000. Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology 15 (1):25–36. doi: 10.1016/S0929-1393(00)00069-X.
   Web of Science ®Google Scholar
• Hu, Y., Y. Dun, S. Li, B. Fu, X. Xiong, N. Peng, Y. Liang, and S. Zhao. 2017. Changes in microbial community during fermentation of high-temperature Daqu used in the production of Chinese ‘Baiyunbian’ liquor. Journal of the Institute of Brewing 123 (4):594–9. doi: 10.1002/jib.455.
   Web of Science ®Google Scholar
• Huang, Z., Y. Shen, X. Huang, M. Qiao, R. K. He, and L. Song. 2021. Microbial diversity of representative traditional fermented sausages in different regions of China. Journal of Applied Microbiology 130 (1):133–41. doi: 10.1111/jam.14648.
   PubMed Web of Science ®Google Scholar
• Ipek, D, and N. N. D. Zorba. 2018. Microbial load of white cheese process lines after CIP and COP: A case study in Turkey. Lwt-Food Science and Technology 90:505–12. doi: 10.1016/j.lwt.2017.12.062.
   Web of Science ®Google Scholar
• Jeong, J., K. Yun, S. Mun, W.-H. Chung, S.-Y. Choi, Y-d Nam, M. Y. Lim, C. P. Hong, C. Park, Y. J. Ahn, et al. 2021. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Scientific Reports 11 (1):1727– doi: 10.1038/s41598-020-80826-9.
   PubMed Web of Science ®Google Scholar
• Jiang, S., Y. Yu, R. Gao, H. Wang, J. Zhang, R. Li, X. Long, Q. Shen, W. Chen, and F. Cai. 2019. High-throughput absolute quantification sequencing reveals the effect of different fertilizer applications on bacterial community in a tomato cultivated coastal saline soil. The Science of the Total Environment 687:601–9. doi: 10.1016/j.scitotenv.2019.06.105.
   PubMed Web of Science ®Google Scholar
• Jin, G., Y. Zhu, and Y. Xu. 2017. Mystery behind Chinese liquor fermentation. Trends in Food Science & Technology 63:18–28. doi: 10.1016/j.tifs.2017.02.016.
   Web of Science ®Google Scholar
• Jin, J. S., R. Yamamoto, T. Takeuchi, G. W. Cui, E. Miyauchi, N. Hojo, K. Ikuta, H. Ohno, and K. Shiroguchi. 2022. High-throughput identification and quantification of single bacterial cells in the microbiota. Nature Communications 13 (1):863. doi: 10.1038/s41467-022-28426-1.
   PubMed Web of Science ®Google Scholar
• Johannes, J. R., E. Nelson, M. Bibbo, and D. H. Bagley. 2010. Voided urine fluorescence in situ hybridization testing for upper tract urothelial carcinoma surveillance. The Journal of Urology 184 (3):879–82. doi: 10.1016/j.juro.2010.05.023.
   PubMed Web of Science ®Google Scholar
• Johnson, J. S., D. J. Spakowicz, B. Y. Hong, L. M. Petersen, P. Demkowicz, L. Chen, S. R. Leopold, B. M. Hanson, H. O. Agresta, M. Gerstein, et al. 2019. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications 10 (1):5029. doi: 10.1038/s41467-019-13036-1.
   PubMed Web of Science ®Google Scholar
• Kang, J., J. Hong, Y. Gao, Y. Yang, M. Chen, X. Yi, and X. Gao. 2019. Analysis of bacterial diversity during fermentation of naturally fermented vegetables in Shanxi. Food Science, China 40 (10):106–11. doi: 10.7506/spkx1002-6630-20180615-306.
   Google Scholar
• Kántor, A., M. Kluz, C. Puchalski, M. Terentjeva, and M. Kačániová. 2016. Identification of lactic acid bacteria isolated from wine using real-time PCR. Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes 51 (1):52–6. doi: 10.1080/03601234.2015.1080497.
   PubMed Web of Science ®Google Scholar
• Kim, D., J. Chon, H. Kim, and K. Seo. 2015. Modulation of intestinal microbiota in mice by kefir administration. Food Science and Biotechnology 24 (4):1397–403. doi: 10.1007/s10068-015-0179-8.
   Web of Science ®Google Scholar
• Kim, D., I. Kang, D. Jeong, H. Kim, H. Kim, S. Lee, K. Song, and K. Seo. 2016. Development of rapid and highly specific TaqMan probe-based real-time PCR assay for the identification and enumeration of Lactobacillus kefiri in kefir milk. International Dairy Journal 61:18–21. doi: 10.1016/j.idairyj.2016.03.007.
   Web of Science ®Google Scholar
• Kim, S., J. K. Im, S. Yun, H. Koh, D. Kang, T. Kwon, and H. Kim. 2020. Large-scale species-specific microbial identification by fluorescence in situ hybridization. Biophysical Journal 118 (3):464A. doi: 10.1016/j.bpj.2019.11.2578.
   PubMed Web of Science ®Google Scholar
• Klanicova, B., I. Slana, H. Vondruskova, M. Kaevska, and I. Pavlik. 2011. Real-time quantitative PCR detection of Mycobacterium avium subspecies in meat products. Journal of Food Protection 74 (4):636–40. doi: 10.4315/0362-028x.Jfp-10-332.
   PubMed Web of Science ®Google Scholar
• Knight, R., A. Vrbanac, B. C. Taylor, A. Aksenov, C. Callewaert, J. Debelius, A. Gonzalez, T. Kosciolek, L. I. McCall, D. McDonald, et al. 2018. Best practices for analysing microbiomes. Nature Reviews. Microbiology 16 (7):410–22. doi: 10.1038/s41579-018-0029-9.
   PubMed Web of Science ®Google Scholar
• Learbuch, K. L. G., H. Smidt, and P. W. J. J. van der Wielen. 2021. Influence of pipe materials on the microbial community in unchlorinated drinking water and biofilm. Water Research 194:116922. doi: 10.1016/j.watres.2021.116922.
   PubMed Web of Science ®Google Scholar
• Lee, B., H. Yi, Y. Moon, and S. Oh. 2018. Development of a functional mixed-starter culture for kefir fermentation. Journal of Milk Science and Biotechnology 36 (3):178–85. doi: 10.22424/jmsb.2018.36.3.178.
   Google Scholar
• Leite, A. M. O., B. Mayo, C. Rachid, R. S. Peixoto, J. T. Silva, V. M. F. Paschoalin, and S. Delgado. 2012. Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis. Food Microbiology 31 (2):215–21. doi: 10.1016/j.fm.2012.03.011.
   PubMed Web of Science ®Google Scholar
• Lewis, W. H., G. Tahon, P. Geesink, D. Z. Sousa, and T. J. G. Ettema. 2021. Innovations to culturing the uncultured microbial majority. Nature Reviews. Microbiology 19 (4):225–40. doi: 10.1038/s41579-020-00458-8.
   PubMed Web of Science ®Google Scholar
• Li, R., M. Lin, S. Guo, S. Yang, X. Han, M. Ren, Y. Song, L. Du, Y. You, J. Zhan, et al. 2021. A fundamental landscape of fungal biogeographical patterns across the main Chinese wine-producing regions and the dominating shaping factors. Food Research International (Ottawa, Ont.) 150 (Pt A):110736. doi: 10.1016/j.foodres.2021.110736.
   PubMedGoogle Scholar
• Li, S., P. Li, X. Liu, L. Luo, and W. Lin. 2016. Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar. Applied Microbiology and Biotechnology 100 (10):4395–411. doi: 10.1007/s00253-016-7284-3.
   PubMed Web of Science ®Google Scholar
• Liang, F., S. Ban, H. Huang, F. Che, Q. Wu, and Y. Xu. 2022. Predicting the effect of climatic factors on diversity of flavor compounds in Daqu fermentation. LWT 169:113984. doi: 10.1016/j.lwt.2022.113984.
   Web of Science ®Google Scholar
• Liang, H., L. Yin, Y. Zhang, C. Chang, and W. Zhang. 2018. Dynamics and diversity of a microbial community during the fermentation of industrialized Qingcai paocai, a traditional Chinese fermented vegetable food, as assessed by Illumina MiSeq sequencing, DGGE and qPCR assay. Annals of Microbiology 68 (2):111–22. doi: 10.1007/s13213-017-1321-z.
   Web of Science ®Google Scholar
• Liang, H., A. Zhang, Z. Wu, S. Cheng, W. Yu, and W. Zhang. 2016a. Microbial community characteristics in industrial matured Chinese paocai, a fermented vegetable food, from different factories. Food Science and Technology Research 22 (5):595–604. doi: 10.3136/fstr.22.595.
   Web of Science ®Google Scholar
• Liang, H., A. Zhang, Z. Wu, C. Liu, and W. Zhang. 2016b. Characterization of microbial community during the fermentation of Chinese homemade paocai, a traditional fermented vegetable food. Food Science and Technology Research 22 (4):467–75. doi: 10.3136/fstr.22.467.
   Web of Science ®Google Scholar
• Lin, L., R. Du, Y. Wang, Q. Wu, and Y. Xu. 2022. Regulation of auxotrophic lactobacilli growth by amino acid cross-feeding interaction. International Journal of Food Microbiology 377:109769. doi: 10.1016/j.ijfoodmicro.2022.109769.
   PubMed Web of Science ®Google Scholar
• Lin, Y., S. Gifford, H. Ducklow, O. Schofield, and N. Cassar. 2019. Towards quantitative microbiome community profiling using internal standards. Applied and Environmental Microbiology 85 (5):e02634–18. doi: 10.1128/AEM.02634-18.
   PubMed Web of Science ®Google Scholar
• Liu, C., S. Feng, Q. Wu, H. Huang, Z. Chen, S. Li, and Y. Xu. 2019a. Raw material regulates flavor formation via driving microbiota in Chinese liquor fermentation. Frontiers in Microbiology 10:1520. doi: 10.3389/fmicb.2019.01520.
   PubMed Web of Science ®Google Scholar
• Liu, D., J. L. Legras, P. Zhang, D. Chen, and K. Howell. 2021. Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine. International Journal of Food Microbiology 338:108983. doi: 10.1016/j.ijfoodmicro.2020.108983.
   PubMed Web of Science ®Google Scholar
• Liu, D, and C. Tong. 2017. Bacterial community diversity of traditional fermented vegetables in China. Lwt 86:40–8. doi: 10.1016/j.lwt.2017.07.040.
   Web of Science ®Google Scholar
• Liu, L., X. Chen, L. Hao, G. Zhang, Z. Jin, C. Li, Y. Yang, J. Rao, and B. Chen. 2020a. Traditional fermented soybean products: Processing, flavor formation, nutritional and biological activities. Critical Reviews in Food Science and Nutrition 62 (7):1971–89. doi: 10.1080/10408398.2020.1848792.
   PubMed Web of Science ®Google Scholar
• Liu, L., X. She, X. Chen, Y. Qian, Y. Tao, Y. Li, S. Guo, W. Xiang, G. Liu, and Y. Rao. 2020b. Microbiota succession and chemical composition involved in the radish fermentation process in different containers. Frontiers in Microbiology 11:445. doi: 10.3389/fmicb.2020.00445.
   PubMed Web of Science ®Google Scholar
• Liu, Y., P. Le, S. J. Lim, L. Ma, S. Sarkar, Z. Han, S. J. Murphy, F. Kosari, G. Vasmatzis, J. C. Cheville, et al. 2018. Enhanced mRNA FISH with compact quantum dots. Nature Communications 9 (1):4461. doi: 10.1038/s41467-018-06740-x.
   PubMedGoogle Scholar
• Liu, Y., S. Rousseaux, R. Tourdot-Maréchal, M. Sadoudi, R. Gougeon, P. Schmitt-Kopplin, and H. Alexandre. 2017. Wine microbiome: A dynamic world of microbial interactions. Critical Reviews in Food Science and Nutrition 57 (4):856–73. doi: 10.1080/10408398.2014.983591.
   PubMed Web of Science ®Google Scholar
• Liu, Z., J. Li, B. Wei, T. Huang, Y. Xiao, Z. Peng, M. Xie, and T. Xiong. 2019b. Bacterial community and composition in Jiang-shui and Suan-cai revealed by high-throughput sequencing of 16S rRNA. International Journal of Food Microbiology 306:108271. doi: 10.1016/j.ijfoodmicro.2019.108271.
   PubMed Web of Science ®Google Scholar
• Lozano-Ojalvo, D., A. Rodríguez, M. Cordero, V. Bernáldez, M. Reyes-Prieto, and J. J. Córdoba. 2015. Characterisation and detection of spoilage mould responsible for black spot in dry-cured fermented sausages. Meat Science 100:283–90. doi: 10.1016/j.meatsci.2014.10.003.
   PubMed Web of Science ®Google Scholar
• Lv, X.-C., R.-B. Jia, J.-H. Chen, W.-B. Zhou, Y. Li, B.-X. Xu, Y.-T. Liang, B. Liu, S.-J. Chen, Y.-T. Tian, et al. 2017a. Development of reverse transcription quantitative real-time PCR (RT-qPCR) assays for monitoring Saccharomycopsis fibuligera, Rhizopus oryzae, and Monascus purpureus during the traditional brewing of Hong Qu glutinous rice wine. Food Analytical Methods 10 (1):161–71. doi: 10.1007/s12161-016-0565-8.
   Web of Science ®Google Scholar
• Ma, T., D. Xiao, and X. Xing. 2020. MetaBMF: A scalable binning algorithm for large-scale reference-free metagenomic studies. Bioinformatics (Oxford, England) 36 (2):356–63. doi: 10.1093/bioinformatics/btz577.
   PubMed Web of Science ®Google Scholar
• Martín-Garcia, A., M. Riu-Aumatell, and E. López-Tamames. 2021. Influence of process parameters on sourdough microbiota, physical properties and sensory profile. Food Reviews International 1–15. doi: 10.1080/87559129.2021.1906698.
   Web of Science ®Google Scholar
• Martineau, F., F. J. Picard, D. Ke, S. Paradis, P. H. Roy, M. Ouellette, and M. G. Bergeron. 2001. Development of a PCR assay for identification of staphylococci at genus and species levels. Journal of Clinical Microbiology 39 (7):2541–7. doi: 10.1128/jcm.39.7.2541-2547.2001.
   PubMed Web of Science ®Google Scholar
• Mataragas, M., F. Rovetto, A. Bellio, V. Alessandria, K. Rantsiou, L. Decastelli, and L. Cocolin. 2015. Differential gene expression profiling of Listeria monocytogenes in Cacciatore and Felino salami to reveal potential stress resistance biomarkers. Food Microbiology 46:408–17. doi: 10.1016/j.fm.2014.09.003.
   PubMed Web of Science ®Google Scholar
• Meng, X., Q. Wu, L. Wang, D. Wang, L. Chen, and Y. Xu. 2015. Improving flavor metabolism of Saccharomyces cerevisiae by mixed culture with Bacillus licheniformis for Chinese Maotai-flavor liquor making. Journal of Industrial Microbiology & Biotechnology 42 (12):1601–8. doi: 10.1007/s10295-015-1647-0.
   PubMed Web of Science ®Google Scholar
• Mesa, M. M., M. Macías, D. Cantero, and F. Barja. 2003. Use of the direct epifluorescent filter technique for the enumeration of viable and total acetic acid bacteria from vinegar fermentation. Journal of Fluorescence 13 (3):261–5. doi: 10.1023/A:1025094017265.
   Web of Science ®Google Scholar
• Miller, D. M., E. G. Dudley, and R. F. Roberts. 2012. Technical note: Development of a quantitative PCR method for monitoring strain dynamics during yogurt manufacture. Journal of Dairy Science 95 (9):4868–72. doi: 10.3168/jds.2012-5445.
   PubMed Web of Science ®Google Scholar
• Moh, L. G., P. T. Etienne, and K. Jules-Roger. 2021. Seasonal diversity of lactic acid bacteria in artisanal yoghurt and their antibiotic susceptibility pattern. International Journal of Food Science 2021:6674644. doi: 10.1155/2021/6674644.
   PubMedGoogle Scholar
• Monica, S., E. Bancalari, V. Castellone, J. Rijkx, S. Wirth, A. Jahns, and B. Bottari. 2021. ATP bioluminescence for rapid and selective detection of bacteria and yeasts in wine. Applied Sciences 11 (11):4953. doi: 10.3390/app11114953.
   Google Scholar
• M. d Mendonca., J. F. F. d O. Vieira, I. Fonseca, J. B. Ribeiro, E. F. Arcuri, M. d F. Borges, C. A. Vieira Borges, J. F. O. D. Sa, and M. F. Martins. 2019. Detection of viable Salmonella Typhimurium and Staphylococcus aureus in coalho cheese by real-time PCR. Food Science and Technology 39 (suppl 2):690–6. doi: 10.1590/fst.29318.
   Google Scholar
• Moter, A, and U. B. Gobel. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiological Methods 41 (2):85–112. doi: 10.1016/S0167-7012(00)00152-4.
   PubMed Web of Science ®Google Scholar
• Murugesan, S., M. P. Reyes-Mata, K. Nirmalkar, A. Chavez-Carbajal, J. I. Juárez-Hernández, R. E. Torres-Gómez, A. Piña-Escobedo, O. Maya, C. Hoyo-Vadillo, E. G. Ramos-Ramírez, et al. 2018. Profiling of bacterial and fungal communities of Mexican cheeses by high throughput DNA sequencing. Food Research International (Ottawa, Ont.) 113:371–81. doi: 10.1016/j.foodres.2018.07.023.
   PubMed Web of Science ®Google Scholar
• Muyzer, G, and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73 (1):127–41. 10.1023/a:1000669317571.
   PubMed Web of Science ®Google Scholar
• Muyzer, G., E. C. d Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel ­electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59 (3):695–700. doi: 10.1128/aem.59.3.695-700.1993.
   PubMed Web of Science ®Google Scholar
• Nalepa, B., S. Ciesielski, and M. Aljewicz. 2020. The microbiota of Edam cheeses determined by cultivation and high-throughput sequencing of the 16S rRNA amplicon. Applied Sciences 10 (12):4063. doi: 10.3390/app10124063.
   Google Scholar
• Nam, J. H., Y. S. Cho, B. Rackerby, L. Goddik, and S. H. Park. 2021. Shifts of microbiota during cheese production: Impact on production and quality. Applied Microbiology and Biotechnology 105 (6):2307–18. doi: 10.1007/s00253-021-11201-5.
   PubMed Web of Science ®Google Scholar
• Nejati, F., S. Junne, J. Kurreck, and P. Neubauer. 2020. Quantification of major bacteria and yeast species in Kefir consortia by multiplex TaqMan qPCR. Frontiers in Microbiology 11:1291. doi: 10.3389/fmicb.2020.01291.
   PubMed Web of Science ®Google Scholar
• Nickelson, R.II, J. Hosch, and L. E. Wyatt. 1975. A direct microscopic count procedure for the rapid estimation of bacterial numbers on green-headless shrimp. Journal of Milk and Food Technology 38 (2):76–7. doi: 10.4315/0022-2747-38.2.76.
   Web of Science ®Google Scholar
• Novitsky, J. A. 1987. Microbial growth rates and biomass production in a marine sediment: Evidence for a very active but mostly nongrowing community. Applied and Environmental Microbiology 53 (10):2368–72. doi: 10.1128/aem.53.10.2368-2372.1987.
   PubMed Web of Science ®Google Scholar
• Nunes de Lima, A., R. Magalhães, F. M. Campos, and J. A. Couto. 2021. Survival and metabolism of hydroxycinnamic acids by Dekkera bruxellensis in monovarietal wines. Food Microbiology 93:103617. doi: 10.1016/j.fm.2020.103617.
   PubMed Web of Science ®Google Scholar
• Pega, J., G. I. Denoya, M. L. Castells, S. Sarquis, G. F. Aranibar, S. R. Vaudagna, and M. Nanni. 2018. Effect of high-pressure processing on quality and microbiological properties of a fermented beverage manufactured from sweet whey throughout refrigerated storage. Food and Bioprocess Technology 11 (6):1101–10. doi: 10.1007/s11947-018-2078-5.
   Web of Science ®Google Scholar
• Pega, J., S. Rizzo, L. Rossetti, C. D. Perez, G. Diaz, A. M. Descalzo, and M. Nanni. 2017. Impact of extracellular nucleic acids from lactic acid bacteria on qPCR and RT-qPCR results in dairy matrices: Implications for defining molecular markers of cell integrity. Lwt 80:416–22. doi: 10.1016/j.lwt.2017.03.010.
   Web of Science ®Google Scholar
• Pérez-Díaz, I. M., J. S. Hayes, E. Medina, A. M. Webber, N. Butz, A. N. Dickey, Z. J. Lu, and M. A. Azcarate-Peril. 2019. Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl. Food Microbiology 77:10–20. doi: 10.1016/j.fm.2018.08.003.
   PubMed Web of Science ®Google Scholar
• Pontonio, E., R. D. Cagno, J. Mahony, A. Lanera, M. De Angelis, D. van Sinderen, and M. Gobbetti. 2017. Sourdough authentication: Quantitative PCR to detect the lactic acid bacterial microbiota in breads. Scientific Reports 7 (1):624. doi: 10.1038/s41598-017-00549-2.
   PubMedGoogle Scholar
• Quan, P. L., M. Sauzade, and E. Brouzes. 2018. dPCR: A technology review. Sensors 18 (4):1271. doi: 10.3390/s18041271.
   PubMed Web of Science ®Google Scholar
• Rantsiou, K., V. Alessandria, R. Urso, P. Dolci, and L. Cocolin. 2008. Detection, quantification and vitality of Listeria monocytogenes in food as detennined by quantitative PCR. International Journal of Food Microbiology 121 (1):99–105. doi: 10.1016/j.ijfoodmicro.2007.11.006.
   PubMed Web of Science ®Google Scholar
• Rao, C., K. Z. Coyte, W. Bainter, R. S. Geha, C. R. Martin, and S. Rakoff-Nahoum. 2021. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature 591 (7851):633–8. doi: 10.1038/s41586-021-03241-8.
   PubMed Web of Science ®Google Scholar
• Ren, Y., Y. Yang, D. Zhang, D. Wang, H. Zhang, and W. Liu. 2017. Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet. Food Biotechnology 31 (1):1–19. doi: 10.1080/08905436.2016.1269290.
   Web of Science ®Google Scholar
• Rodríguez, A., Á. Medina, J. J. Córdoba, and N. Magan. 2014. The influence of salt (NaCl) on ochratoxin A biosynthetic genes, growth and ochratoxin A production by three strains of Penicillium nordicum on a dry-cured ham-based medium. International Journal of Food Microbiology 178:113–9. doi: 10.1016/j.ijfoodmicro.2014.03.007.
   PubMed Web of Science ®Google Scholar
• Seinige, D., C. Krischek, G. Klein, C. Kehrenberg, and D. W. Schaffner. 2014. Comparative analysis and limitations of ethidium monoazide and propidium monoazide treatments for the differentiation of ­viable and nonviable Campylobacter cells. Applied and Environmental Microbiology 80 (7):2186–92. doi: 10.1128/AEM.03962-13.
   PubMed Web of Science ®Google Scholar
• Serpaggi, V., F. Remize, A. Sequeira-Le Grand, and H. Alexandre. 2010. Specific identification and quantification of the spoilage microorganism Brettanomyces in wine by flow cytometry: A useful tool for winemakers. Cytometry. Part A: The Journal of the International Society for Analytical Cytology 77 (6):497–9. doi: 10.1002/cyto.a.20861.
   PubMedGoogle Scholar
• Settanni, L., P. Barbaccia, A. Bonanno, M. Ponte, R. D. Gerlando, E. Franciosi, A. D. Grigoli, and R. Gaglio. 2020. Evolution of indigenous starter microorganisms and physicochemical parameters in spontaneously fermented beef, horse, wild boar and pork salamis produced under controlled conditions. Food Microbiology 87:103385. doi: 10.1016/j.fm.2019.103385.
   PubMed Web of Science ®Google Scholar
• Settanni, L., G. Ventimiglia, A. Alfonzo, O. Corona, A. Miceli, and G. Moschetti. 2013. An integrated technological approach to the selection of lactic acid bacteria of flour origin for sourdough production. Food Research International 54 (2):1569–78. doi: 10.1016/j.foodres.2013.10.017.
   Web of Science ®Google Scholar
• Shen, F., W. Du, J. E. Kreutz, A. Fok, and R. F. Ismagilov. 2010. Digital PCR on a SlipChip. Lab on a Chip 10 (20):2666–72. doi: 10.1039/C004521G.
   PubMed Web of Science ®Google Scholar
• Shen, T., J. Liu, Q. Wu, and Y. Xu. 2020. Increasing 2-furfurylthiol content in Chinese sesame-flavored Baijiu via inoculating the producer of precursor L-cysteine in Baijiu fermentation. Food Research International (Ottawa, Ont.) 138 (Pt A):109757. doi: 10.1016/j.foodres.2020.109757.
   PubMedGoogle Scholar
• Smets, W., J. W. Leff, M. A. Bradford, R. L. McCulley, S. Lebeer, and N. Fierer. 2016. A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing. Soil Biology and Biochemistry 96:145–51. doi: 10.1016/j.soilbio.2016.02.003.
   Web of Science ®Google Scholar
• Soares-Santos, V., I. Pardo, and S. Ferrer. 2018. Improved detection and enumeration of yeasts in wine by Cells-qPCR. Lwt 90:90–7. doi: 10.1016/j.lwt.2017.12.007.
   Web of Science ®Google Scholar
• Stämmler, F., J. Gläsner, A. Hiergeist, E. Holler, D. Weber, P. J. Oefner, A. Gessner, and R. Spang. 2016. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome 4 (1):28. doi: 10.1186/s40168-016-0175-0.
   PubMedGoogle Scholar
• Stevenson, D. M., R. E. Muck, K. J. Shinners, and P. J. Weimer. 2006. Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover. Applied Microbiology and Biotechnology 71 (3):329–38. doi: 10.1007/s00253-005-0170-z.
   PubMed Web of Science ®Google Scholar
• Suh, S. H, and M. K. Kim. 2021. Microbial communities related to sensory characteristics of commercial drinkable yogurt products in Korea. Innovative Food Science & Emerging Technologies 67:102565. doi: 10.1016/j.ifset.2020.102565.
   Web of Science ®Google Scholar
• Takahashi, N., Y. Moriya, Y. Takatsu, N. Kaneta, Y. Tomimatsu, M. Yanagisawa, Y. Tsujimoto, and H. Kamikado. 2018. Rapid test for coliforms in milk and yogurt using automatic ATP measurement system. Japanese Journal of Food Microbiology 35 (4):179–86. doi: 10.5803/jsfm.35.179.
   Google Scholar
• Tamang, J. P., P. D. Cotter, A. Endo, N. S. Han, R. Kort, S. Q. Liu, B. Mayo, N. Westerik, and R. Hutkins. 2020. Fermented foods in a global age: East meets West. Comprehensive Reviews in Food Science and Food Safety 19 (1):184–217. doi: 10.1111/1541-4337.12520.
   PubMed Web of Science ®Google Scholar
• Tasara, T, and R. Stephan. 2007. Evaluation of housekeeping genes in Listeria monocytogenes as potential internal control references for normalizing mRNA expression levels in stress adaptation models using real-time PCR. FEMS Microbiology Letters 269 (2):265–72. doi: 10.1111/j.1574-6968.2007.00633.x.
   PubMed Web of Science ®Google Scholar
• Tessonnière, H., S. Vidal, L. Barnavon, H. Alexandre, and F. Remize. 2009. Design and performance testing of a real-time PCR assay for sensitive and reliable direct quantification of Brettanomyces in wine. International Journal of Food Microbiology 129 (3):237–43. doi: 10.1016/j.ijfoodmicro.2008.11.027.
   PubMed Web of Science ®Google Scholar
• Tkacz, A., M. Hortala, and P. S. Poole. 2018. Absolute quantitation of microbiota abundance in environmental samples. Microbiome 6 (1):110. doi: 10.1186/s40168-018-0491-7.
   PubMedGoogle Scholar
• Tofalo, R., M. Schirone, A. Corsetti, and G. Suzzi. 2012. Detection of Brettanomyces spp. in red wines using real-time PCR. Journal of Food Science 77 (9):M545–M549. doi: 10.1111/j.1750-3841.2012.02871.x.
   PubMed Web of Science ®Google Scholar
• Tourlousse, D. M., S. Yoshiike, A. Ohashi, S. Matsukura, N. Noda, and Y. Sekiguchi. 2017. Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing. Nucleic Acids Research 45 (4):e23. doi: 10.1093/nar/gkw984.
   PubMed Web of Science ®Google Scholar
• Vandeputte, D., G. Kathagen, K. D’hoe, S. Vieira-Silva, M. Valles-Colomer, J. Sabino, J. Wang, R. Y. Tito, L. De Commer, Y. Darzi, et al. 2017. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551 (7681):507–11. doi: 10.1038/nature24460.
   PubMed Web of Science ®Google Scholar
• Velusamy, V., K. Arshak, O. Korostynska, K. Oliwa, and C. Adley. 2010. An overview of foodborne pathogen detection: In the perspective of biosensors. Biotechnology Advances 28 (2):232–54. 10.1016/j.biotechadv.2009.12.004.
   PubMed Web of Science ®Google Scholar
• Vero, L., d E. Gala, M. Gullo, L. Solieri, S. Landi, and P. Giudici. 2006. Application of denaturing gradient gel electrophoresis (DGGE) analysis to evaluate acetic acid bacteria in traditional balsamic vinegar. Food Microbiology 23 (8):809–13. doi: 10.1016/j.fm.2006.01.006.
   PubMed Web of Science ®Google Scholar
• Veum, K. S., T. Lorenz, and R. J. Kremer. 2019. Phospholipid fatty acid profiles of soils under variable handling and storage conditions. Agronomy Journal 111 (3):1090–6. doi: 10.2134/agronj2018.09.0628.
   Web of Science ®Google Scholar
• Vieira-Silva, S., J. Sabino, M. Valles-Colomer, G. Falony, G. Kathagen, C. Caenepeel, I. Cleynen, S. van der Merwe, S. Vermeire, and J. Raes. 2019. Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses. Nature Microbiology 4 (11):1826–31. doi: 10.1038/s41564-019-0483-9.
   PubMed Web of Science ®Google Scholar
• Walsh, A. M., G. Macori, K. N. Kilcawley, and P. D. Cotter. 2020. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nature Food 1 (8):500–10. doi: 10.1038/s43016-020-0129-3.
   PubMedGoogle Scholar
• Wang, F., Y. Jiang, and C. LiN. 1995. Lipid and cholesterol oxidation in Chinese-style sausage using vacuum and modified atmosphere packaging. Meat Science 40 (1):93–101. doi: 10.1016/0309-1740(94)00020-8.
   PubMed Web of Science ®Google Scholar
• Wang, S., Q. Wu, Y. Han, R. Du, X. Wang, Y. Nie, X. Du, and Y. Xu. 2021a. Gradient internal standard method for absolute quantification of microbial amplicon sequencing data. mSystems 6 (1):e00964–20. doi: 10.1128/mSystems.00964-20.
   PubMed Web of Science ®Google Scholar
• Wang, S., Q. Wu, Y. Nie, J. Wu, and Y. Xu. 2019. Construction of synthetic microbiota for reproducible flavor compound metabolism in Chinese light-aroma-type liquor produced by solid-state fermentation. Applied and Environmental Microbiology 85 (10):e03090–18. doi: 10.1128/AEM.03090-18.
   PubMed Web of Science ®Google Scholar
• Wang, S., W. Xiong, Y. Wang, Y. Nie, Q. Wu, Y. Xu, and S. Geisen. 2020. Temperature-induced annual variation in microbial community changes and resulting metabolome shifts in a controlled ­fermentation system. mSystems 5 (4):e00555–20. doi: 10.1128/mSystems.00555-20.
   PubMed Web of Science ®Google Scholar
• Wang, X., J. Xiao, Y. Jia, Y. Pan, and Y. Wang. 2018a. Lactobacillus kefiranofaciens, the sole dominant and stable bacterial species, exhibits distinct morphotypes upon colonization in Tibetan kefir grains. Heliyon 4 (6):e00649. doi: 10.1016/j.heliyon.2018.e00649.
   PubMed Web of Science ®Google Scholar
• Wang, X., Y. Zhang, H. Ren, and Y. Zhan. 2018b. Comparison of bacterial diversity profiles and microbial safety assessment of salami, Chinese dry-cured sausage and Chinese smoked-cured sausage by high-throughput sequencing. LWT 90:108–15. doi: 10.1016/j.lwt.2017.12.011.
   Web of Science ®Google Scholar
• Wang, Y., B. Li, Y. Liu, X. Huang, N. Zhang, Y. Yang, Z. Xiao, Q. Yu, S. Chen, L. He, et al. 2021b. Investigation of diverse bacteria encoding histidine decarboxylase gene in Sichuan-style sausages by culture-dependent techniques, polymerase chain reaction-denaturing gradient gel electrophoresis, and high-throughput sequencing. LWT 139:110566. doi: 10.1016/j.lwt.2020.110566.
   Web of Science ®Google Scholar
• Wang, Y. M., X. J. Wang, T. R. Pan, B. Q. Li, and J. R. Chu. 2021c. Label-free single-cell isolation enabled by microfluidic impact printing and real-time cellular recognition. Lab on a Chip 21 (19):3695–706. doi: 10.1039/d1lc00326g.
   PubMed Web of Science ®Google Scholar
• Wei, Y., Y. Ye, M. Ji, S. Peng, F. Qin, W. Guo, and H. H. Ngo. 2021. Microbial analysis for the ammonium removal from landfill leachate in an aerobic granular sludge sequencing batch reactor. Bioresource Technology 324:124639. doi: 10.1016/j.biortech.2020.124639.
   PubMed Web of Science ®Google Scholar
• Welch, N. L., M. Zhu, C. Hua, J. Weller, M. E. Mirhashemi, T. G. Nguyen, S. Mantena, M. R. Bauer, B. M. Shaw, C. M. Ackerman, et al. 2022. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nature Medicine 28 (5):1083–94. 10.1038/s41591-022-01734-. 1.
   PubMed Web of Science ®Google Scholar
• Wu, C., Z. Qin, J. Huang, and R. Zhou. 2014a. Characterization of microbial community in Daqu by PLFA method. Food Science and Technology Research 20 (1):147–54. doi: 10.3136/fstr.20.147.
   Web of Science ®Google Scholar
• Wu, C., J. Zheng, J. Huang, and R. Zhou. 2014b. Reduced nitrite and biogenic amine concentrations and improved flavor components of Chinese sauerkraut via co-culture of Lactobacillus plantarum and Zygosaccharomyces rouxii. Annals of Microbiology 64 (2):847–57. doi: 10.1007/s13213-013-0724-8.
   Web of Science ®Google Scholar
• Wu, Q., Y. Zhu, C. Fang, R. H. Wijffels, and Y. Xu. 2021. Can we control microbiota in spontaneous food fermentation? – Chinese liquor as a case example. Trends in Food Science & Technology 110:321–31. doi: 10.1016/j.tifs.2021.02.011.
   Web of Science ®Google Scholar
• Wu, Z., S. Wang, Q. Zhang, J. Hao, Y. Lin, J. Zhang, and A. Li. 2020. Assessing the intestinal bacterial community of farmed Nile tilapia (Oreochromis niloticus) by high-throughput absolute abundance quantification. Aquaculture 529:735688. doi: 10.1016/j.aquaculture.2020.735688.
   Web of Science ®Google Scholar
• Xiang, X., F. Li, Q. Ye, Y. Shang, M. Chen, J. Zhang, B. Zhou, H. Suo, Y. Ding, and Q. Wu. 2022. High-throughput microfluidic strategy based on RAA-CRISPR/Cas13a dual signal amplification for accurate identification of pathogenic Listeria. Sensors and Actuators B: Chemical 358:131517. doi: 10.1016/j.snb.2022.131517.
   Web of Science ®Google Scholar
• Xiao, Y., T. Huang, C. Huang, J. Hardie, Z. Peng, M. Xie, and T. Xiong. 2020. The microbial communities and flavour compounds of Jiangxi yancai, Sichuan paocai and Dongbei suancai: Three major types of traditional Chinese fermented vegetables. LWT 121:108865. doi: 10.1016/j.lwt.2019.108865.
   Web of Science ®Google Scholar
• Xing, X., J. Ma, Z. Fu, Y. Zhao, Z. Ai, and B. Suo. 2020. Diversity of bacterial communities in traditional sourdough derived from three terrain conditions (mountain, plain and basin) in Henan Province, China. Food Research International (Ottawa, Ont.) 133:109139. doi: 10.1016/j.foodres.2020.109139.
   PubMed Web of Science ®Google Scholar
• Xiong, T., J. Chen, T. Huang, M. Xie, Y. Xiao, C. Liu, and Z. Peng. 2019. Fast evaluation by quantitative PCR of microbial diversity and safety of Chinese paocai inoculated with Lactobacillus plantarum NCU116 as the culture starter. LWT 101:201–6. doi: 10.1016/j.lwt.2018.11.001.
   Web of Science ®Google Scholar
• Xiong, Z., Y. Li, Y. Xiang, Y. Xia, H. Zhang, S. Wang, and L. Ai. 2020. Short communication: Dynamic changes in bacterial diversity during the production of powdered infant formula by PCR-DGGE and high -throughput sequencing. Journal of Dairy Science 103 (7):5972–7. doi: 10.3168/jds.2019-18064.
   PubMed Web of Science ®Google Scholar
• Xue, T., Y. Lu, H. Yang, X. Hu, K. Zhang, Y. Ren, C. Wu, X. Xia, R. Deng, and Y. Wang. 2022. Isothermal RNA amplification for the detection of viable pathogenic bacteria to estimate the Salmonella virulence for causing enteritis. Journal of Agricultural and Food Chemistry 70 (5):1670–8. doi: 10.1021/acs.jafc.1c07182.
   PubMed Web of Science ®Google Scholar
• Yan, T., J. Zhu, T. Jiang, K. Chen, and S. Fang. 2018. Isolation and optimization on spore-forming conditions of Bacillus coagulans. Microbiology China 45 (2):238–49. doi: 10.13344/j.microbiol.china.170224.
   Google Scholar
• Yang, L., W. Fan, and Y. Xu. 2020. Metaproteomics insights into traditional fermented foods and beverages. Comprehensive Reviews in Food Science and Food Safety 19 (5):2506–29. doi: 10.1111/1541-4337.12601.
   PubMed Web of Science ®Google Scholar
• Yang, L., J. Lou, H. Wang, L. Wu, and J. Xu. 2018. Use of an improved high-throughput absolute abundance quantification method to characterize soil bacterial community and dynamics. The Science of the Total Environment 633:360–71. doi: 10.1016/j.scitotenv.2018.03.201.
   PubMed Web of Science ®Google Scholar
• Yang, Z.-W., Y. Men, J. Zhang, Z.-H. Liu, J.-Y. Luo, Y.-H. Wang, W.-J. Li, and Q. Xie. 2021. Evaluation of sample preservation approaches for better insect microbiome research according to next-generation and third-generation sequencing. Microbial Ecology 82 (4):971–80. doi: 10.1007/s00248-021-01727-6.
   PubMed Web of Science ®Google Scholar
• Yao, H., S. Y. Lu, B. A. Williams, B. M. Flanagan, M. J. Gidley, and D. Mikkelsen. 2022. Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro. Food Hydrocolloids 127:107422. doi: 10.1016/j.foodhyd.2021.107422.
   Web of Science ®Google Scholar
• Young, A. P., D. J. Jackson, and R. C. Wyeth. 2020. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 8:e8806. doi: 10.7717/peerj.8806.
   PubMed Web of Science ®Google Scholar
• Yulandi, A., A. Suwanto, D. E. Waturangi, and A. T. Wahyudi. 2020. Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh. BMC Research Notes 13 (1):562. doi: 10.1186/s13104-020-05406-6.
   PubMed Web of Science ®Google Scholar
• Yun, J., F. Zhao, W. Zhang, H. Yan, F. Zhao, and D. Ai. 2019. Monitoring the microbial community succession and diversity of Liangzhou fumigated vinegar during solid-state fermentation with next-generation sequencing. Annals of Microbiology 69 (3):279–89. doi: 10.1007/s13213-018-1418-z.
   Web of Science ®Google Scholar
• Zhang, H., L. Wang, Y. Tan, H. Wang, F. Yang, L. Chen, F. Hao, X. Lv, H. Du, and Y. Xu. 2021. Effect of Pichia on shaping the fermentation microbial community of sauce-flavor Baijiu. International Journal of Food Microbiology 336:108898. doi: 10.1016/j.ijfoodmicro.2020.108898.
   PubMed Web of Science ®Google Scholar
• Zhang, J., L. Wang, L. Shi, X. Chen, M. Liang, and L. Zhao. 2020. Development and application of a real-time loop-mediated isothermal amplification method for quantification of Acetobacter aceti in red wine. FEMS Microbiology Letters 367 (19):fnaa152. doi: 10.1093/femsle/fnaa152.
   PubMed Web of Science ®Google Scholar
• Zhi, N., K. Zong, J. Yang, J. Yao, and Z. Wei. 2016. Microbial diversity of yogurt depth detected by Illumina Miseq platform. Science & Technology of Food Industry 37 (24):78–82. doi: 10.13386/j.issn1002-0306.2016.24.007.
   Google Scholar