Comprehensive analysis of microbiome biodiversity in popular date palm (Phoenix dactylifera L.) fruit varieties

• Published in: Scientific reports 2024-09, Vol.14 (1), p.20658-17, Article 20658
• Main Authors: Hamed, Khalid E., Alsaif, Abdullah N., Alhewairini, Saleh S., Sayyed, R. Z.
• Format: Article
• Language: English
• Subjects: 16S rDNA; 631/326; 631/449; Achromobacter; Air pollution; Allergies; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Biodiversity; Brucella; Cultivars; DNA, Ribosomal Spacer - genetics; Food contamination; Fruit - microbiology; Fruits; Fungi - classification; Fungi - genetics; Fungi - isolation & purification; Fungus; Health risks; Humanities and Social Sciences; Microbial contamination; Microbiological evaluation; Microbiomes; Microbiota; Microbiota - genetics; Microorganisms; Morphology; multidisciplinary; Nucleotide sequence; Nutritive value; Phoeniceae - genetics; Phoeniceae - microbiology; Phoenix dactylifera; Phylogeny; Ribosomal DNA; RNA, Ribosomal, 16S - genetics; rRNA 16S; Saudi Arabia; Science; Science (multidisciplinary); Sequence analysis; Spacer region; Stenotrophomonas
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-71249-x

Due to its nutritional value and health benefits, the date palm ( Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria , Fusarium , Curvilaria , Aspergillus , and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas , and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella , Achromobacter, and Stenotrophomonas , are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm ( P. d