Academic Work

• ORCID
• Google scholar
• ResearchGate
• Scopus

Sustainable Development Goals

Research interests

• Characterization of microbial communities in remediation systems
• Genomics and metagenomics in hypersaline environments
• Molecular microbiology in the cactus rhizosphere in semi-arid areas
• Microbial metagenomics in corals with white syndrome
• Diversity and structure of microbial communities in aquatic species

Profile

Doctor José Aguirre-Garrido is a Professor at the Universidad Autónoma Metropolitana (UAM) Lerma Campus, in the Department of Environmental Sciences. Due to his research experience and academic trajectory, Dr. Aguirre-Garrido is a National Researcher Level I of the National System of Researchers, appointment valid until December 31, 2021.

A total of 12 publications support his research work, with an h-index of 5 and 112 citations according to the Scopus database. He is co-author of 2 book chapters, has presented about 15 papers in international academic events, 20 papers in national congresses, and taught two bioinformatics courses, one at the Universidad Autónoma del Estado de México and the other at the Universidad Autónoma Metropolitana (UAM).

He has taught five courses on the conservation of marine ecosystems and environmental impact at the Lerma Campus within the framework of the agreement with the NGO Sea Shepherd. In the period from January 2014 to January 2015, he made a postdoctoral stay at the Zaidín Experimental Station dependent of the Spanish National Research Center, in the research group of Structure, Dynamics and Function of Rhizobacteria Genomes; during this stay he was related to the operation of the massive sequencing equipment of the center and the bioinformatics analysis of the projects assigned to the research group.

Professor Aguirre's main line of research is the characterization of microbial communities through traditional and molecular microbiology approaches in different environments.

Information provided by the academic staff

Research interests

Academic Work

On the following pages you can consult the research work:

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• ResearchGate

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• Scopus

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• ORCID

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Some examples of publications

Select the bibliographic reference to consult each publication:

Open Access	References	UN SDGs
OA	Hernández-Vázquez, A., Garcia-Arellano, H., González-Cervantes, R.M. and 4 more (...) (2026).Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes. Environmental Microbiology Reports,18(1)
OA	Michele, M.-P.I., Jaquelin, N.-B., Alicia, E.-L.M. and 6 more (...) (2026).Prevalence of Bacterial Sexually Transmitted Infections and Their Coinfections Among MSM in Mexico City. Microbiology Research,17(7)	3\|5
OA	De Sales-Millan, A., Reyes-Ferreira, P., González-Cervantes, R.M. and 6 more (...) (2026).Clinical Improvement and Taxonomic–Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder. Nutrients ,18(15)
	Alvarez-Moreno, B.B., González-Blanco, G., Hernández-Soto, L.M. and 3 more (...) (2026).Synergistic microalgae–bacteria interactions and gene dynamics in an intermittently aerated vertical fluidized reactor for C and N removal. Journal of Chemical Technology and Biotechnology,101(6) 1153-1161	6\|7\|9
OA	Avila-Andrade, A., Beristain-Cardoso, R., García-Mondragón, D. and 3 more (...) (2025).Biodegradation potential of thermophilic cellulolytic bacteria isolated from urban organic waste composting. Revista Mexicana de Ingeniera Quimica,24(3)	12
OA	Salinas-Velarde, I.D., Donaciano-Domínguez, J.M., Oros-Pantoja, R. and 6 more (...) (2025).Narrative Review: Gut Microbiota and Its Impact on α-syn Function in Parkinson's Disease. MicrobiologyOpen,14(6)
OA	Salinas-Virgen, L.I., de la Torre-Hernández, M.E., Aguirre-Garrido, J.F. and 2 more (...) (2024).Genotypic and Phenotypic Characterization of Pseudomonas atacamensis EMP42 a PGPR Strain Obtained from the Rhizosphere of Echinocactus platyacanthus (Sweet Barrel). Microorganisms,12(8)
OA	Martínez-Carrillo, B.E., De Sales-Millán, A., Aguirre-Garrido, J.F. and 3 more (...) (2024).Changes in the Composition and Diversity of the Intestinal Microbiota Associated with Carbohydrate Consumption in Type 2 Diabetes Mellitus Patients. International Journal of Molecular Sciences,25(22)	3
OA	González-García, S., Hamdan-Partida, A., Pérez-Ramos, J. and 3 more (...) (2024).Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus. Journal of Medical Microbiology,73(12)
OA	De Sales-Millán, A., Reyes-Ferreira, P., Aguirre-Garrido, J.F. and 3 more (...) (2024).Comprehensive Analysis of Gut Microbiota Composition and Functional Metabolism in Children with Autism Spectrum Disorder and Neurotypical Children: Implications for Sex-Based Differences and Metabolic Dysregulation. International Journal of Molecular Sciences,25(12)
OA	González, C.Y., Estrada, J.A., Oros-Pantoja, R. and 4 more (...) (2024).The Gut Microbiota Is Involved in the Regulation of Cognitive Flexibility in Adolescent BALB/c Mice Exposed to Chronic Physical Stress and a High-Fat Diet. Microorganisms,12(12)
OA	González-Velázquez, G., Aguirre-Garrido, J.F., Oros-Pantoja, R. and 4 more (...) (2024).Supplementation with inulin reverses cognitive flexibility alterations and modulates the gut microbiota in high-fat-fed mice. Frontiers in Behavioral Neuroscience,18
	López-Pérez, M., Aguirre-Garrido, J.F., Herrera-Zúñiga, L. and 1 more (...) (2024).Structure, expression regulation, and applications of fungal laccases, an interesting prospective in biotechnology. Studies in Natural Products Chemistry,80227-267
OA	Hernández-Soto, L.M., Martínez-Abarca, F., Ramírez-Saad, H. and 2 more (...) (2023).Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas. BMC Genomics,24(1)	6
OA	De Sales-Millán, A., Aguirre-Garrido, J.F., González-Cervantes, R.M. and 1 more (...) (2023).Microbiome–Gut–Mucosal–Immune–Brain Axis and Autism Spectrum Disorder (ASD): A Novel Proposal of the Role of the Gut Microbiome in ASD Aetiology. Behavioral Sciences,13(7)
OA	Cuetero-Martínez, Y., Monroy-Hermosillo, O., Aguirre-Garrido, J.F. and 2 more (...) (2023).Changes in the prokaryotic communities occurring along a two-stage anaerobic digestion system treating the organic fraction of solid waste. Journal of Hazardous Materials Advances,12	6\|11\|12
OA	Aguilar-Vilchis, R., Hernández-Rodríguez, I.A., González-Blanco, G. and 3 more (...) (2023).Characterization of sediments from the upper basin of the Lerma River, Mexico: Microbiome and biomethane potential. Revista Mexicana de Ingeniera Quimica,22(2)	6
	Cuetero-Martínez, Y., de los Cobos-Vasconcelos, D., Aguirre-Garrido, J.F. and 2 more (...) (2023).Next-generation Sequencing for Surveillance of Antimicrobial Resistance and Pathogenicity in Municipal Wastewater Treatment Plants. Current Medicinal Chemistry,30(1) 5-29	3\|6\|11
	Ramírez-Moreno, F.J., Gómez-Oliván, L.M., Islas-Flores, H. and 3 more (...) (2023).A comprehensive approach to how hospital effluents lead to oxidative stress and shift the gene expression in target organs of Danio rerio. Science of the Total Environment,887	6
	Cuetero-Martínez, Y., Flores-Ramírez, A., De los Cobos-Vasconcelos, D. and 3 more (...) (2023).Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment. Chemosphere,313	3\|6
	Cuetero-Martínez, Y., Villamizar-Ojeda, K.N., Hernández-Santiago, M.J. and 4 more (...) (2023).Removal of intI1, ARGs, and SARS-CoV-2 and changes in bacterial communities in four sewage treatment facilities. Science of the Total Environment,903	3\|6\|11
OA	Martínez-Carrillo, B.E., Mondragón-Velásquez, T., Ramírez-Durán, N. and 4 more (...) (2022).Changes in Metabolic Regulation and the Microbiota Composition after Supplementation with Different Fatty Acids in db/db Mice. International Journal of Food Science,2022
OA	Sánchez y Sánchez de la Barquera, B., Martínez Carrillo, B.E., Aguirre Garrido, J.F. and 4 more (...) (2022).Emerging Evidence on the Use of Probiotics and Prebiotics to Improve the Gut Microbiota of Older Adults with Frailty Syndrome: A Narrative Review. Journal of Nutrition, Health and Aging,26(10) 926-935
	Hernández-Rodríguez, I.A., González-Blanco, G., Aguirre-Garrido, J.F. and 1 more (...) (2022).An Intensified Hybrid Constructed Wetland for Polluted Channel Water Treatment. Water, Air, and Soil Pollution,233(3)	6
	Cienfuegos-Martínez, K., Monroy-Dosta, M.D.C., Hamdan-Partida, A. and 3 more (...) (2022).Effect of the probiotic Lactococcus lactis on the microbial composition in the water and the gut of freshwater prawn (Macrobrachium rosenbergii) cultivate in biofloc. Aquaculture Research,53(11) 3877-3889	14
OA	González-Blanco, G., Casas-Reyes, A., Velasco-Garduño, O. and 3 more (...) (2021).Simultaneous nitrification/denitrification and desulfurization of wastewater polluted with ammonium, COD and sulfide: effectiveness of a new up-flow vertical hybrid reactor. 3 Biotech,11(3)	6
OA	Escoto, J.A., Martínez-Carrillo, B.E., Ramírez-Durán, N. and 3 more (...) (2021).Chronic consumption of sweeteners in mice; effect on immune system and microbiota of small intestine. Biomedica,41(3) 1-61
	Guzmán-Mejía, F., Vega-Bautista, A., Molotla-Torres, D.E. and 2 more (...) (2021).Bovine lactoferrin as a Modulator of Neuroendocrine Components of Stress. Current Molecular Pharmacology,14(6) 1037-1045	3
	Aguirre-Garrido, J.F., Martínez-Abarca, F., Montiel-Lugo, D. and 2 more (...) (2020).Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample. International Microbiology,23(3) 467-474
OA	González-Blanco, G., Pérez-Pérez, V., Aguirre-Garrido, J.F. and 2 more (...) (2020).Kinetics and microbial structure of nitrogen cycle bacteria contained in the rhizosphere of natural wetland polluted with chromium. Revista Mexicana de Ingeniera Quimica,19(2) 543-553	6
OA	de la Torre-Hernández, M.E., Salinas-Virgen, L.I., Aguirre-Garrido, J.F. and 4 more (...) (2020).Composition, Structure, and PGPR Traits of the Rhizospheric Bacterial Communities Associated With Wild and Cultivated Echinocactus platyacanthus and Neobuxbaumia polylopha. Frontiers in Microbiology,11

Courses taught by the professor in recent trimesters

*Courses are conducted in spanish

Num.	Trim.	Course Name	Level
1	26P	Microbiología	Licenciatura
2	26P	Optativa Divisional de Ciencias Biológicas y de la Salud I	Licenciatura
3	26P	Seminario VI	Posgrado
4	26P	Temas Selectos de Biotecnología II	Posgrado
5	26P	Seminario I	Posgrado
6	26P	Trabajo de Investigación VI	Posgrado
7	26P	Temas Selectos I	Posgrado
8	26P	Trabajo Experimental IV	Posgrado
9	26P	Tópicos Selectos Interdisciplinarios VI	Licenciatura
10	26P	Bioinformática I	Posgrado
11	26P	Biología Molecular Genómica	Posgrado
12	26P	Seminario VI	Posgrado
13	26P	Trabajo de Redacción de Tesis I	Posgrado
14	26P	Trabajo de Redacción de Tesis III	Posgrado
15	26P	Trabajo de Investigación VI	Posgrado
16	26I	Microbiología y Ecología de Sistemas Acuáticos	Licenciatura
17	26I	Ecología Microbiana	Licenciatura
18	26I	Seminario V	Posgrado
19	26I	Seminario V	Posgrado
20	26I	Seminario VII	Posgrado
21	26I	Taller Optativo Interdivisional III	Licenciatura
22	26I	Tópicos Selectos Interdisciplinarios III	Licenciatura
23	26I	Trabajo de Investigación IX	Posgrado
24	26I	Trabajo de Investigación V	Posgrado
25	26I	Trabajo de Investigación V	Posgrado
26	26I	Trabajo de Redacción de Tesis II	Posgrado
27	26I	Temas Selectos Interdivisionales XIV	Licenciatura
28	26I	Biología Molecular	Posgrado
29	25O	Física	Licenciatura
30	25O	Análisis Económico	Licenciatura
31	25O	Análisis Económico	Licenciatura
32	25O	Ecotoxicología	Licenciatura
33	25O	Trabajo de Investigación IX	Posgrado
34	25O	Eje Integrador V: Practicas Profesionales	Licenciatura
35	25O	Instrumentos Remediales	Licenciatura
36	25O	Pedagogía y Didáctica Universitaria	Licenciatura
37	25O	Pedagogía y Didáctica Universitaria	Licenciatura
38	25O	Seminario IV	Posgrado
39	25O	Seminario IV	Posgrado
40	25O	Seminario VII	Posgrado
41	25O	Temas Selectos en Ciencias Naturales I	Licenciatura
42	25O	Temas Selectos en Ciencias Naturales II	Licenciatura
43	25O	Teoría de Juegos Evolutiva	Licenciatura
44	25O	Trabajo de Redacción de Tesis III	Posgrado
45	25O	Trabajo de Investigación IV	Posgrado
46	25O	Trabajo de Investigación IV	Posgrado
47	25O	Teoría de Juegos Evolutiva	Licenciatura
48	25P	Taller Optativo Interdivisional V	Licenciatura
49	25P	Seminario III	Posgrado
50	25P	Seminario III	Posgrado
51	25P	Seminario VII	Posgrado
52	25P	Taller Optativo Interdivisional II	Licenciatura
53	25P	Taller Optativo Interdivisional VIII	Licenciatura
54	25P	Trabajo de Redacción de Tesis II	Posgrado
55	25P	Trabajo de Investigación VIII	Posgrado
56	25P	Trabajo de Investigación IX	Posgrado
57	25P	Trabajo de Investigación III	Posgrado
58	25P	Tópicos Selectos Interdisciplinarios VI	Licenciatura
59	25P	Tópicos Selectos Interdisciplinarios IV	Licenciatura
60	25P	Taller Optativo Interdivisional VII	Licenciatura

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