Title:	Evaluation of propidium monoazide for 16S ribosomal RNA metabarcoding assessment of microbial communities in 60-day ripened raw goat milk cheese.
Authors:	FEITOZA, S. N. P. LIMA, L. A. de SARAIVA, C. A. S. DIAS, W. da S. MEDEIROS, A. B. A. de FERNANDES, A. C. de C. HEINEMANN, M. B. SOUZA, F. N. de FELISBERTO, N. R. de O. LEMOS, M. L. P. EGITO, A. S. do OLIVEIRA, C. J. B. de
Affiliation:	SINTIA NAIANNE PEREIRA FEITOZA, UNIVERSIDADE FEDERAL DA PARAÍBA; LAIORAYNE ARAÚJO DE LIMA, UNIVERSIDADE FEDERAL DA PARAÍBA; CARLA APARECIDA SOARES SARAIVA, UNIVERSIDADE FEDERAL DA PARAÍBA; WESLLA DA SILVA DIAS, UNIVERSIDADE FEDERAL DA PARAÍBA; ANA BEATRIZ AZEVEDO DE MEDEIROS, UNIVERSIDADE FEDERAL DA PARAÍBA; ARTUR CEZAR DE CARVALHO FERNANDES, UNIVERSIDADE FEDERAL DA PARAÍBA; MARCOS BRYAN HEINEMANN, UNIVERSIDADE DE SÃO PAULO; FERNANDO NOGUEIRA DE SOUZA; NIVEA REGINA DE OLIVEIRA FELISBERTO PERDIGAO, CNPC; MATEUS LACERDA PEREIRA LEMOS, UNIVERSIDADE FEDERAL DA PARAÍBA; ANTONIO SILVIO DO EGITO VASCONCELOS, CNPC; CELSO JOSÉ BRUNO DE OLIVEIRA, UNIVERSIDADE FEDERAL DA PARAÍBA.
Date Issued:	2026
Citation:	JDS Communications, v. 7, n. 2, p. 134-139, Mar. 2026.
Description:	Abstract: Cheese ripening is a complex microbial process marked by significant shifts in microbial composition. Considering that propidium monoazide (PMA) depletes DNA from nonviable cells, we hypothesized that PMA treatment of cheese samples could affect the microbiota characterization of 60-d-ripened raw goat curd cheese by 16S rRNA metabarcoding sequencing. After ripening, PMA-treated and nontreated (control) samples from the same cheese units were processed for DNA extraction, library preparation, and 16S rRNA metabarcoding sequencing on an Illumina MiSeq platform. Downstream bioinformatic analyses for microbial diversity assessment were performed using QIIME 2 and the phyloseq package in R. Statistical analyses included permutational multivariate analysis of variance (PERMANOVA), Wilcoxon tests, and linear discriminant analysis effect size (LEfSe). No significant differences were observed in either α or β diversity metrics between PMA-treated and nontreated samples. However, PMA treatment significantly reduced the abundance of farm environment–associated Dickeya and Pectobacteriaceae taxa in cheese samples, thus improving the accuracy of determining the cheese microbial structure using next-generation sequencing technologies. Further longitudinal studies focusing on different sampling periods during ripening, as well as other cheese types, may shed light on the potential benefits of using PMA for improving the accuracy of cheese microbial community characterization by next-generation sequencing. Summary: This study evaluated whether propidium monoazide (PMA) treatment affects the characterization of microbial communities in 60-day-ripened raw goat cheese using 16S ribosomal RNA (rRNA) metabarcoding. The PMA selectively depletes DNA from nonviable cells, potentially providing a more accurate representation of living microorganisms. Paired samples (PMA-treated and nontreated controls) from the same cheese units were analyzed using Illumina MiSeq sequencing, with downstream analyses performed in QIIME 2 and R. Results showed no significant differences in alpha or beta diversity metrics between treatments, indicating that PMA did not alter the overall microbial community structure. However, PMA treatment significantly reduced the abundance of farm environment-associated taxa, specifically Dickeya and Pectobacteriaceae, suggesting these organisms were predominantly nonviable with residual DNA persisting in the cheese matrix. This demonstrates that PMA pretreatment improves the accuracy of cheese microbiome characterization by filtering dead cell DNA from environmental contaminants, providing clearer insights into viable microbial communities during cheese ripening.
Thesagro:	Tecnologia de Alimento Caprino Maturação Microbiologia de Alimento Corante Qualidade
NAL Thesaurus:	Goat milk Goat cheese Raw milk Cheese ripening Food processing Food technology Milk quality Food quality
Keywords:	Queijo de cabra Seqüenciamento genético Genome sequencing Next generation sequencing
DOI:	https://doi.org/10.3168/jdsc.2025-0894
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Nota Técnica/Nota científica (CNPC)