Macrogenomic next-generation sequencing of microbial community diversity and functional genes in Dermatophagoides farinae

doi:10.12140/j.issn.1000-7423.2025.03.014

Abstract

Abstract:

Objective To investigate the composition, structure and function of the microbial community in Dermatophagoides farinae and to analyze characteristics of their functional genes. Methods Total DNA was extracted from D. farinae and paired-end library was constructed, and metagenomic next-generation sequencing (mNGS) was performed following bridging PCR assay. The obtained gene sequences aligned with BLAST program in the non-redundant protein sequence (NR), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG), the Kyoto Encyclopedia of Genes and Genomes (KEGG), the Carbohydrate Activating Enzymes (CAZY) and the Comprehensive Antibiotic Resistance (CARD) databases. The diversity of microbial genes was analyzed in D. farinae with observed species index, Ace index, Chao1 index, Shannon diversity index, Simpson’s diversity index and coverage index. Results mNGS results of D. farinae yielded (1.18 to 1.29) × 10⁷ bases. Following sequence assembly, there were 34 527 overlapping groups, with an N50 value of 25 005, and the mean length of overlapping groups was 11 509. The top 20 most abundant species were annotated to 73 phyla, 430 genera, and 689 species, and bacteria was the predominant microorganism in D. farina (80.9%), followed viruses (5.5%) and fungi (1.2%) in D. farinae. Within the bacterial community, Proteobacteria (97.8%) and Firmicutes (0.8%) were dominant phyla, with Bartonella (59.0%) and unclassified Alphaproteobacteria (11.0%) as dominant genera. Within the fungal community, Microsporidia (66.6%) and Ascomycota (19.6%) were dominant phyla, with Pancytospora (41.4%) and Saccharomyces (12.2%) as dominant genera. In the viral community, Cressdnaviricota (96.2%) and Uroviricota (2.6%) were dominant phyla, with Orbivirus (96.2%) as the dominant genus. α diversity analysis showed a good repeatability of D. farinae samples. Protein sequence annotation results in the EggNOG database showed that bacteria and fungi were annotated to 23 and 22 functional categories, respectively, with the percentage of genes associated with translation/ribosome structure and biogenesis (bacteria, 15.3%; fungi, 27.4%). KEGG annotation results showed that cofactor- and vitamin metabolism-related genes were dominant in bacteria (10.5), and genes associated with folding, sorting, and degradation were more pronounced in fungi (12.0%). CAZY annotations showed that 98.3% of bacterial genes were matched to 65 distinct CAZY families, with glycosyltransferases as the dominant CAZY family member (57.6%), and only 0.4% of fungal genes were annotated to 12 CAZY families, with glycosyltransferases as the primary CAZY family member (87.7%). CARD annotations showed that 99.1% of bacterial genes were annotated to 17 diverse antibiotic resistance genes, with multidrug resistance genes exhibiting the highest prevalence (39.5%), and 0.3% of fungal genes were annotated to 5 antibiotic resistance genes, with tetracycline resistance genes (41.6%) and multidrug resistance genes (39.7%) as the two most common genes. Conclusion The microbial community within D. farinae exhibits a significant complexity and diversity, and the gene functions and metabolic pathways vary between bacteria and fungi.

Key words: Dermatophagoides farinae, Metagenomic next-generation sequencing, Microbial community, Functional gene

CLC Number:

R384.429

YANG Yawen, HONG Yujie, QIAN Gege, LING Min, WANG Zixuan, YU Hui, SUN Huaiyu, TAO Xianglin, LI Minjie, SUN Entao. Macrogenomic next-generation sequencing of microbial community diversity and functional genes in Dermatophagoides farinae[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2025, 43(3): 395-402.

Figures/Tables 5

References 34

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