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 FNS  Vol.12 No.1 , January 2021
Bacterial Community Diversity of Fermented Pepper in Brazzaville Revealed by Illumina Miseq of 16S rRNA Gene
Abstract: Fermented foods play an important role in the daily life and diet of the populations in Congo. Among these fermented foods, there is Pilipili or fermented pepper which is consumed without prior cooking. The microorganisms present are eaten alive. Few studies have been carried out on these microorganisms which may have beneficial effects on health. This study aimed to investing taxonomic diversity of bacterial communities in 3 samples of fermented peppers produced in 3 distinct areas of Brazzaville. To do this investigation, Illumina Miseq sequencing of 16S rRNA gene was used. The results showed that the number of identified operational taxonomic units (OTUs) ranged from 156 to 392. All OTUs belong to the domain of Bacteria and could be categorized into 21 Phyla, 36 Classes, 58 Orders, 100 Families and 171 genera. Firmicutes and Proteobacteria were the main dominant phyla of the total phyla present with a relative abundance of 89.12% and 8.08%, respectly. At the class level, Bacili were dominant in EB1 (99.50%), EB3 (85.32%) and EB2 (42.29%) while Clostridia in EB2 (40.10%). Lactobacillus, Clostridium sensu stricto and Frutobacillus were the dominant genera in the sample EB1, EB2 and EB3, respectively. The hierarchical classification showed that the samples EB1 and EB2 form the same group and EB3 is unique. Principal component analysis showed that the younger EB3 and EB2 samples were more diverse than the older EB1 sample. This study is a first in Congo on the diversity of fermented pepper using Illumina Miseq. It has shown that this food is very diverse and can be a source for the isolation of bacteria with biotechnological potential.
Cite this paper: Lembella Boumba, A. , Lebonguy, A. , Goma-Tchimbakala, J. , Eckzehel Nzaou, S. , Limingi Polo, C. and Moukala, M. (2021) Bacterial Community Diversity of Fermented Pepper in Brazzaville Revealed by Illumina Miseq of 16S rRNA Gene. Food and Nutrition Sciences, 12, 37-53. doi: 10.4236/fns.2021.121004.
References

[1]   Kouassi kouassi, C. and Koffi-nevry, R. (2012) Evaluation de la connaissance et utilisation des variétés de piment (capsicum) cultivées en c?te d’ivoire. International Journal of Biological and Chemical Science, 6, 175-185.
https://doi.org/10.4314/ijbcs.v6i1.16

[2]   Dagnoko, S., Yaro-Diarisso, N., Sanogo, P.N., Adetula, O., Dolo-Nantoumé, A., Gamby-Touré, K., Traoré-Théra, A., Katilé, S. and Diallo-Ba, D. (2013) Overview of Pepper (Capsicum spp.) Breeding in West Africa. African Journal of Agricultural Research, 8, 1108-1114.
https://doi.org/10.5897/AJAR2012.1758

[3]   Kouassi kouassi, C., Koffi-nevry, R., Yao, L.G., Nanga, Z.Y., Koussémon, M., Kablan, T. and Kouassi, K.A. (2012) Profiles of Bioactive Compounds of Some Pepper Fruit (Capsicum L.) Varieties Grown in C?te D’ivoire. Innovative Romanian Food Biotechnology, 11, 23-31.

[4]   Tano, K., Koffi-Nevry, R., Koussémon, M. and Oulé, M.K. (2008) The Effects of Different Storage Temperatures on the Quality of Fresh Bell Pepper (Capsicum annum L.). Agricultural Journal, 3, 157-162.

[5]   Mokemiabeka, N.S., Kayath, C.A., Nguimbi, E., Lébonguy, A.A., Eboungabeka, A.G.M., Mendosa, D.R., Kéléké, S., Kobawila, S.C. and Botteaux, A. (2016) Microbiological and Biochemical Assessment of Crushed Red Pepper from Capsicum frutescens Preserved in Jars and Manufactured in Local Markets in Republic of Congo. International Journal of Biotechnology Research, 4, 1-10.

[6]   Louémbé, D., Kobawila, S.C., Bouanga-Kalou, G. and Kéléké, S. (2003) Etude microbiologique des feuillesfermentées de manioc: Ntobambodi. Tropicultura, 21, 106-111.

[7]   Tamang, J.P., Shin, D.H., Jung, S.J. and Chae, S.W. (2016) Functional Properties of Microorganisms in Fermented Foods. Frontiers in Microbiology, 7, 578.
https://doi.org/10.3389/fmicb.2016.00578

[8]   Garbowska, M., Berthold-Pluta, A. and Stasiak-Rozanska, L. (2015) Microbiological Quality of Selected Spices and Herbs Including the Presence of Cronobacter spp. Food Microbiology, 49, 1-5.
https://doi.org/10.1016/j.fm.2015.01.004

[9]   Vegas, C., Zavaleta, A.I. and Zarzoso, B. (2018) Optimization of Fermentation Process Conditions for Chili Pepper (Capsicum frutescens) Fruit Using Response Surface Methodology. Agronomia Colombiana, 36, 89-97.
https://doi.org/10.15446/agron.colomb.v36n1.69164

[10]   Nuraida, L. (2015) A Review: Health Promoting Lactic Acid Bacteria in Traditional Indonesian Fermented Foods. Food Science and Human Wellness, 4, 47-55.
https://doi.org/10.1016/j.fshw.2015.06.001

[11]   Moutou-Tchitoula, D.P., Nguimbi, E., Giusti-Miller, S., Mora, P., Kobawila, S.C. and Miambi, E. (2018) Assessment of Dominant Bacterial Strains Isolated from Ntoba Mbodi, an Indigenous African Alkaline-Fermented Food, and Their Potential Enzyme Activities. African Journal of Microbiology Research, 12, 779-787.
https://doi.org/10.5897/AJMR2018.8875

[12]   Anila, K., Kunzes, A. and Bhalla, T.C. (2016) In Vitro Cholesterol Assimilation and Functional Enzymatic Activities of Putative Probiotic Lactobacillus sp. ?solated from Fermented Foods/Beverages of North West India. Journal of Nutrition and Food Sciences, 6, 2.
https://doi.org/10.4172/2155-9600.1000467

[13]   Iranmanesh, M., Ezzatpanah, H. and Mojgani, N. (2014) Antibacterial Activity and Cholesterol Assimilation of Lactic Acid Bacteria Isolated from Traditional Iranian Dairy Products. LWT—Food Science and Technology, 58, 355-359.
https://doi.org/10.1016/j.lwt.2013.10.005

[14]   Dortu, C. and Thonart, P. (2009) Les bactéries lactiques: Caractéristiques et intérêts pour la bioconservation des produits alimentaires. Biotechnologie Agronomie Société et Environnement, 13, 143-154.

[15]   Kayath, C.A., Nguimbi, E., Goma-Tchimbakala, J., Mamonékéné, V., Lebonguy, A.A. and Ahombo, G. (2016) Towards the Understanding of Fermented Food Biotechnology in Congo Brazzaville. Advance Journal of Food Science and Technology, 12, 593-602.
https://doi.org/10.19026/ajfst.12.3317

[16]   Louémbé, D., Keléké, S., Kobawila, S.C. and Nzounzi, J.P. (2003) Bactéries lactiques de la pate fermentée de ma?s au Congo. Tropicultura, 21, 3-9.

[17]   Miambi, E., Guyot, J.P. and Ampe, F. (2003) Identification, Isolation and Quantification of Representative Bacteria from Fermented Cassava Dough Using an Integrated Approach of Culture Dependent and Culture-Independent Methods. International Journal of Food Microbiology, 82, 111-120.
https://doi.org/10.1016/S0168-1605(02)00256-8

[18]   Hugenholtz, P. (2002) Exploring Prokaryotic Diversity in the Genomic Era. Genome Biology, 3, REVIEWS0003.
https://doi.org/10.1186/gb-2002-3-2-reviews0003

[19]   Zhang, J., Kobert, K., Flouri, T. and Stamatakis, A. (2014) PEAR a Fast and Accurate Illumina Paired-End reAd mergeR. Bioinformatics, 30, 614-620.
https://doi.org/10.1093/bioinformatics/btt593

[20]   Schmieder, R. and Edwards, R. (2011) Quality Control and Preprocessing of Metagenomic Datasets. Bioinformatics, 27, 863-864.
https://doi.org/10.1093/bioinformatics/btr026

[21]   Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. and Knight, R. (2011) UCHIME Improves Sensitivity and Speed of Chimera Detection. Bioinformatics, 27, 2194-2200.
https://doi.org/10.1093/bioinformatics/btr381

[22]   Edgar, R.C. (2010) Search and Clustering Orders of Magnitude Faster than BLAST. Bioinformatics, 26, 2460-2461.
https://doi.org/10.1093/bioinformatics/btq461

[23]   Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pe?a, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge , B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J. and Knight, R. (2010) QIIME Allows Analysis of High-Throughput Community Sequencing Data. Nature Methods, 7, 335-336.
https://doi.org/10.1038/nmeth.f.303

[24]   Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lasniewski, R.A., Oakley, B.B., Park, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Talliger, G.G., Van Horn, D.J. and Weber, C.F. (2009) Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology, 75, 7537-7541.
https://doi.org/10.1128/AEM.01541-09

[25]   Cao, J., Yang, J., Hou, Q., Xu, H., Zheng, Y., Zhang, H. and Zhang, L. (2017) Assessment of Bacterial Profiles in Aged, Home-Made Sichuan Paocai Brine with Varying Titratable Acidity by PacBio SMRT Sequencing Technology. Food Control, 78, 14-23.
https://doi.org/10.1016/j.foodcont.2017.02.006

[26]   Ter Braak, C.J.F. and S?milauer, P. (2003) Canoco 4. Cambridge University Press, Cambridge, 242 p.

[27]   Liu, D.Q. and Tong, C. (2017) Bacterial Community Diversity of Traditional Fermented Vegetables in China. LWT—Food Science and Technology, 86, 40-48.
https://doi.org/10.1016/j.lwt.2017.07.040

[28]   Zhang, J., Wang, X., Huo, D., Li, W., Hu, Q., Xu, C., Liu, S. and Li, C. (2016) Metagenomic Approach Reveals Microbial Diversity and Predictive Microbial Metabolic Pathways in Yucha, a Traditional Li Fermented Food. Scientific Reports, 6, Article No. 32524.
https://doi.org/10.1038/srep32524

[29]   Serra, J.L., Moura, F.G., de Melo Pereira, G.V., Soccol, C.R., Rogeza, H. and Darneta, S. (2019) Determination of the Microbial Community in Amazonian Cocoa Bean Fermentation by Illumina-Based Metagenomic Sequencing. LWT—Food Science and Technology, 106, 229-239.
https://doi.org/10.1016/j.lwt.2019.02.038

[30]   Li, H., Li, Z., Qu, J. and Wang, J. (2017) Bacterial Diversity in Traditional Jiaozi and Sourdough Revealed by High-Throughput Sequencing of 16S rRNA Amplicons. Food Science and Technology, 81, 319-325.
https://doi.org/10.1016/j.lwt.2017.04.007

[31]   Jiménez, E., Yépez, A., Pérez-Cataluňa, A., Vásquez, E.R., Dávila, D.Z., Vignolo, G. and Aznar, R. (2018) Exploring Diversity and Biotechnological Potential of Lactic Acid Bacteria from Tocosh—Traditional Peruvian Fermented Potatoes—By High Throughput Sequencing (HTS) and Culturing. LWT—Food Science and Technology, 87, 567-574.
https://doi.org/10.1016/j.lwt.2017.09.033

[32]   Liu, Z., Penga, Z., Huanga, T., Xiaoa, Y., Li, J., Xie, M. and Xiong, T. (2019) Comparison of Bacterial Diversity in Traditionally Homemade Paocai and Chinese Spicy Cabbage. Food Microbiology, 83, 141-149.
https://doi.org/10.1016/j.fm.2019.02.012

[33]   Nam, Y.D., Yi, S.H. and Lim, S.I. (2012) Bacterial Diversity of Cheonggukjang, a Traditional Korean Fermented Food, Analyzed by Barcoded Pyrosequencing. Food Control, 28, 135-142.
https://doi.org/10.1016/j.foodcont.2012.04.028

[34]   Park, E.J., Chun, J., Cha, C.J., Park, W.S., Jeon, C.O. and Bae, J.W. (2012) Bacterial Community Analysis during Fermentation of Ten Representative Kinds of Kimchi with Barcoded Pyrosequencing. Food Microbiology, 30, 197-204.
https://doi.org/10.1016/j.fm.2011.10.011

[35]   Phewpana, A., Phuwaprisirisanb, P., Takahashic, H., Ohshimac, C., Lopetcharatd, K., Techaruvichite, P. and Keeratipibulf, S. (2020) Microbial Diversity during Processing of Thai Traditional Fermented Shrimp Paste, Determined by Next Generation Sequencing. LWT—Food Science and Technology, 122, 108-989.
https://doi.org/10.1016/j.lwt.2019.108989

[36]   Jung, W.Y., Jung, J.Y., Lee, H.J. and Jeon, C.O. (2016) Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste. Frontiers in Microbiology, 7, 827.
https://doi.org/10.3389/fmicb.2016.00827

[37]   Wang, X., Du, H. and Xu, Y. (2017) Source Tracking of Prokaryotic Communities in Fermented Grain of Chinese Strong-Flavor Liquor. International Journal of Food Microbiology, 244, 27-35.
https://doi.org/10.1016/j.ijfoodmicro.2016.12.018

[38]   Chai, L.J., Lu, Z.M., Zhang, X.J., Ma, J., Xu, P.X., Qian, W., Xiao, C., Wang, S.T., Shen, C.H., Shi, J.S. and Xu, Z.H. (2019) Zooming in on Butyrate-Producing Clostridial Consortia in the Fermented Grains of Baijiu via Gene Sequence-Guided Microbial Isolation. Frontiers in Microbiology, 10, 1397.
https://doi.org/10.3389/fmicb.2019.01397

[39]   Liu, X., Zhoua, M., Jiaxina, C., Luoc, Y., Yed, F., Jiaoe, S., Huc, X., Zhang, J. and Lüa, X. (2018) Bacterial Diversity in Traditional Sourdough from Different Regions in China. LWT—Food Science and Technology, 96, 251-259.
https://doi.org/10.1016/j.lwt.2018.05.023

[40]   Ennadir, J., Hassikou, R., Al Askari, G., Arahou, M., Bouazza, F., Amallah, L., Amine, S.A. and Khedid, K. (2014) Caractérisation phénotypique et génotypique des bactéries lactiques isolées des farines de blé d’origine marocaine (Phenotypic and Genotypic Characterization of Lactic Acid Bacteria Isolated from Wheat Flour from Morocco). Journal of Materials and Environmental Science, 5, 1125-1132.

[41]   Snauwaert, I., Papalexandratou, Z., De Vuys, L. and Vandamme, P. (2013) Characterization of Strains of Weissella fabalis sp. nov. and Fructobacillus tropaeoli from Spontaneous Cocoa Bean Fermentations. International Journal of Systematic and Evolutionary Microbiology, 63, 1709-1716.
https://doi.org/10.1099/ijs.0.040311-0

[42]   Liang, H., Yin, L., Zhang, Y., Chang, C. and Zhang, W. (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, 111-122.
https://doi.org/10.1007/s13213-017-1321-z

 
 
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