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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Characterization of the Microbiome and Virulence and Resistance Genes in the Howler Monkey (Alouatta seniculus) in Colombian Andean Forests

by
Anyelo Florez
1,
Angie Patiño-Montoya
1,
Hernan Florez-Ríos
1,
Madelaine Piedrahita
1,
Juan Pablo Arias Marmolejo
1,
Néstor Roncancio-Duque
2,3,
Diana López-Alvarez
2 and
Andrés Castillo
1,*
1
Laboratorio TAO-Lab/OneHealth, CiBioFi, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali 760001, Colombia
2
Grupo de Investigación en Diversidad Biológica, Facultad de Ciencias Agropecuarias, Departamento de Ciencias Biológicas, Universidad Nacional de Colombia, Palmira 763531, Colombia
3
Instituto de Recursos Biológicos Alexander von Humboldt, Bogotá 111711, Colombia
*
Author to whom correspondence should be addressed.
Appl. Microbiol. 2025, 5(4), 129; https://doi.org/10.3390/applmicrobiol5040129
Submission received: 13 September 2025 / Revised: 5 November 2025 / Accepted: 5 November 2025 / Published: 11 November 2025
Review Reports Versions Notes

Abstract

The microbiome of howler monkeys is being studied as a potential indicator of forest health. This explorative research aimed to analyze the microbiome, antibiotic resistance genes, and virulence factors of the howler monkey (Alouatta seniculus) in two Colombian Andean forests. A total of six samples were collected from three monkeys in two different forests. The samples were processed and sequenced using 16S rRNA V3-V4 metabarcoding and shotgun metagenomics. No significant differences in microbial diversity were observed between locations. A total of 43 possible resistance genes were identified, 11 of which were associated with plasmids, while 66 virulence genes were detected. The bacterial genera with the highest number of resistance genes were Escherichia and Enterococcus, whereas Escherichia and Citrobacter exhibited the highest number of virulence factors. The bacteria were predominantly resistant to fluoroquinolones, macrolides and beta-lactams, while adherence was the dominant virulence mechanism. This exploratory study suggests that the locations provide similar habitats for howler monkeys and that the presence of resistance genes is primarily due to intrinsic bacterial resistance mechanisms and natural resistance in wild populations despite the environmental presence of bacterial genera with resistance genes and virulence factors. However, acquisition through interaction with domestic animals was not evaluated.
Keywords: antimicrobial resistance; howler monkey; metagenome; microbiome; primate; virulence factor antimicrobial resistance; howler monkey; metagenome; microbiome; primate; virulence factor

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MDPI and ACS Style

Florez, A.; Patiño-Montoya, A.; Florez-Ríos, H.; Piedrahita, M.; Marmolejo, J.P.A.; Roncancio-Duque, N.; López-Alvarez, D.; Castillo, A. Characterization of the Microbiome and Virulence and Resistance Genes in the Howler Monkey (Alouatta seniculus) in Colombian Andean Forests. Appl. Microbiol. 2025, 5, 129. https://doi.org/10.3390/applmicrobiol5040129

AMA Style

Florez A, Patiño-Montoya A, Florez-Ríos H, Piedrahita M, Marmolejo JPA, Roncancio-Duque N, López-Alvarez D, Castillo A. Characterization of the Microbiome and Virulence and Resistance Genes in the Howler Monkey (Alouatta seniculus) in Colombian Andean Forests. Applied Microbiology. 2025; 5(4):129. https://doi.org/10.3390/applmicrobiol5040129

Chicago/Turabian Style

Florez, Anyelo, Angie Patiño-Montoya, Hernan Florez-Ríos, Madelaine Piedrahita, Juan Pablo Arias Marmolejo, Néstor Roncancio-Duque, Diana López-Alvarez, and Andrés Castillo. 2025. "Characterization of the Microbiome and Virulence and Resistance Genes in the Howler Monkey (Alouatta seniculus) in Colombian Andean Forests" Applied Microbiology 5, no. 4: 129. https://doi.org/10.3390/applmicrobiol5040129

APA Style

Florez, A., Patiño-Montoya, A., Florez-Ríos, H., Piedrahita, M., Marmolejo, J. P. A., Roncancio-Duque, N., López-Alvarez, D., & Castillo, A. (2025). Characterization of the Microbiome and Virulence and Resistance Genes in the Howler Monkey (Alouatta seniculus) in Colombian Andean Forests. Applied Microbiology, 5(4), 129. https://doi.org/10.3390/applmicrobiol5040129

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