Metagenomic analysis of bacterial diversity in pigeon pea after soaking in water
https://doi.org/10.22146/ijbiotech.94293 Yuni Sine(1), Donny Widianto(2), Yekti Asih Purwestri(3), Byong Hoon Lee(4), Widodo Widodo(5*)
(1) The Graduate School of Biotechnology, Universitas Gadjah Mada, Jl Teknika Utara Barek, Yogyakarta 55281, Indonesia
(2) The Graduate School of Biotechnology, Universitas Gadjah Mada, Jl Teknika Utara Barek, Yogyakarta 55281, Indonesia; Department of Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Jl Flora Bulaksumur, Yogyakarta 55281, Indonesia
(3) The Graduate School of Biotechnology, Universitas Gadjah Mada, Jl Teknika Utara Barek, Yogyakarta 55281, Indonesia; Laboratory of Biochemistry, Faculty of Biology, Universitas Gadjah Mada, Jl Teknika Selatan, Sekip Utara, Yogyakarta 55281, Indonesia
(4) Departments of Microbiology/Immunology and Food Science, McGill University, Montreal, QC, Canada H3A 2B4
(5) The Graduate School of Biotechnology, Universitas Gadjah Mada, Jl Teknika Utara Barek, Yogyakarta 55281, Indonesia; Faculty of Animal Science, Universitas Gadjah Mada, Jl Fauna 3 Bulaksumur, Yogyakarta 55281, Indonesia
(*) Corresponding Author
Abstract
This study investigated the diversity of bacterial community in the samples of pigeon pea (Cajanus cajan L. Millsp.) soaked in water for 12 h and 24 h. The detection of certain bacterial species in the samples that can be isolated and potentially be used as starter cultures in the development of pigeon pea‐based functional foods is the importance of this study. For bacterial identification, the V1–V9 regions on the 16S ribosomal RNA gene were amplified using 27F and 1492R primers under specific polymerase chain reaction conditions. Genomic DNA (130 ng) was sequenced on the R9.4 flow cell by Oxford Nanopore Technologies using a GridION sequencer. Library preparations were conducted using a Native Barcoding Kit 24 V14 (SQK‐NBD114.24). Primary data were acquired using MinKNOW version 22.05.7. A total of 13 bacterial families and 89 genera were identified in the pigeon pea sample soaked for 12 h, and 26 families and 90 genera were identified in the pigeon pea soaked for 24 h. The values of five diversity indices showed that the sample soaked in water for 24 h had richer bacterial abundance and diversity than for 12 h. Shannon and Simpson values revealed the higher bacterial diversity in the samples collected at 24 h than in those collected at 12 h. Species observation and abundance‐based coverage estimators (ACE) values demonstrated that the samples collected at 24 h harbored higher bac‐ terial richness than those collected at 12 h. Bacterial communities during soaking of the pigeon pea were dominated by the family Enterobacteriaceae and genus Enterobacter. The presence of bacterial genera like Lacticaseibacillus, Lentilactobacillus, and Secundilactobacillus is interesting because of their importance as starter cultures for fermented plant‐based milk products
Keywords
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through metagenomics. Fermentation 9(1):41.
doi:10.3390/fermentation9010041.
Fang RS, Dong YC, Chen F, Chen QH. 2015. Bacterial diversity analysis during the fermentation processing of traditional Chinese yellow rice wine revealed by 16S rDNA 454 pyrosequencing. J. Food Sci. 80(10):2265–2271. doi:10.1111/17503841.13018.
Fredrikson M, Andlid T, Haikara A, Sandberg AS. 2002. Phytate degradation by microorganisms in synthetic media and pea flour. J. Appl. Microbiol. 93(2):197– 204. doi:10.1046/j.13652672.2002.01676.x.
Gan RY, Li HB, Gunaratne A, Sui ZQ, Corke H. 2017. Effects of fermented edible seeds and their products on human health: Bioactive components and bioactivities. Compr. Rev. Food Sci. Food Saf. 16(3):489–531. doi:10.1111/15414337.12257.
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Hickisch A, Beer R, Vogel RF, Toelstede S. 2016. Influence of lupinbased milk alternative heat treatment and exopolysaccharideproducing lactic acid bacteria on the physical characteristics of lupinbased yogurt alternatives. Food Res. Int. 84:180–188. doi:10.1016/j.foodres.2016.03.037.
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Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: Rapid and sensitive classification of metagenomic sequences. Genome Res. 26(12):1721–1729. doi:10.1101/gr.210641.116.
Kim M, Chun J. 2005. Bacterial community structure in kimchi, a Korean fermented vegetablefood, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103(1):91–96.doi:10.1016/j.ijfoodmicro.2004.11.030.
Li Z, Rui J, Li X, Li J, Dong L, Huang Q, Huang C, Wang Z, Li L, Xuan P, Tang Y, Chen F. 2017. Bacterial community succession and metabolite changes during doubanjiangmeju fermentation, a Chinese traditional fermented broad bean (Vicia faba L.) paste. Food Chem. 218:534–542.doi:10.1016/j.foodchem.2016.09.104.Liu L, Chen X, Hao L, Zhang G, Jin Z, Li C, YangY, Rao J, Chen B. 2022. Traditional fermented soybean products: processing, flavor formation, nutritional and biological activities. Crit. Rev. Food Sci. Nutr. 62(7):1971–1989. doi:10.1080/10408398.2020.1848792.
Luo YY, Guo Y, Hu XY, Liu WH, Liu BQ, Yang J, Tu ZC, Huang YH. 2023. Flavor improvement of fermented soybean foods by cofermentation with Bacillus velezensis and Lactiplantibacillus plantarum. LWT 186:115257. doi:10.1016/j.lwt.2023.115257.
Ma H, Wang L, Yu H, Wang W, Wu G, Qin G, Tan Z, Wang Y, Pang H. 2022. Proteaseproducing lactic acid bacteria with antibacterial properties and their potential use in soybean meal fermentation. Chem. Biol. Technol. Agric. 9(1):40. doi:10.1186/s4053802200303 5.
Maesen LVD. 1985. Cajanus DC. and Atylosia W. & A. (Leguminosae), volume 854. Wageningen: Wa
DOI: https://doi.org/10.22146/ijbiotech.94293
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