Metagenomic insights into the bacterial community diversity of Sengkubak (Pycnarrhena cauliflora (Miers.) Diels.) growth media

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Abstract Sengkubak (Pycnarrhena cauliflora (Miers.) Diels.) is highly valued among Malay and Dayak ethnic communities for its natural flavouring properties and potential bioactive compounds with anticancer properties. Host-microbe interactions play a crucial role in plant metabolism, potentially influencing the biosynthesis of these compounds. This study aimed to characterise the microbial diversity in the growth media of Sengkubak and investigate its potential relationship with monosodium glutamate (MSG) biosynthesis. Three potted Sengkubak seedlings were collected from Sintang Regency, West Kalimantan, Indonesia. The soil microbial community was analysed using full-length 16S ribosomal RNA (rRNA) sequencing with Oxford Nanopore Technology. Preprocessed reads were quality-checked and classified using the Centrifuge classifier with the NCBI 16S RefSeq database for Bacteria and Archaea. The analysis identified 5,547 OTUs with high microbial diversity indicated by Shannon’s index (6.77) and Simpson’s index (0.99). The predominant microbial orders in the soil included Hyphomicrobiales (28.09%), Bacillales (18.08%), Burkholderiales (12.33%), Rhodospirillales (5.28%), and Eubacteriales (4.30%). At the genus level, the most abundant taxa were Rhodoplanes (12.05%), Hyphomicrobium (9.07%), Bacillus (5.30%), Methyloligella (4.51%), and Clostridium (3.17%). The predominant species in Sengkubak growth media included Pradoshia eiseniae (5.07%), Vicinamibacter silvestris (4.51%), and Pseudolabrys taiwanensis (2.75%). Notably, members of the Rhodoplanes order play a key role in amino acid metabolism and polysaccharide degradation, essential processes in glutamate precursor biosynthesis. Bacillus contributes to enzymatic pathways for amino acid biosynthesis, while Clostridium facilitates organic matter decomposition, releasing substrates for glutamate formation. These findings establish a direct link between soil microbial composition and MSG biosynthesis potential, highlighting specific bacterial taxa that may enhance glutamate accumulation in Sengkubak. This research advances the understanding of soil-plant microbe interactions in natural flavor biosynthesis and opens new avenues for optimizing Sengkubak as a sustainable source of natural MSG for the food and agro-industrial sectors.