Research in Microbial Ecology and Bioinformatics
Exploring the unseen majority
My passion is exploring the "unseen majority" – microbial communities with vast impacts on our world. I'm particularly interested in their metabolic interactions and their role in biogeochemical cycles. Additionally, I study how they influence eukaryotic evolution, especially animal gut microbiomes. I aim to understand their interactions with the environment and their broader implications in health and ecology.
Publications.
García-Saldaña, E. A., Cerqueda-García, D., Ibarra-Laclette, E., & Aluja, M. (2024). Insights into the differences related to the resistance mechanisms to the highly toxic fruit Hippomane mancinella (Malpighiales: Euphorbiaceae) between the larvae of the sister species Anastrepha acris and A. ludens (Diptera: Tephritidae) through comparative transcriptomics. Frontiers in Physiology, 15, 1263475. Link
Deng, Z., Sierra, J. M., Ferreira, A. L. M., Cerqueda-Garcia, D., Spanjers, H., & van Lier, J. B. (2023). Effect of operational parameters on the performance of an anaerobic sequencing batch reactor (AnSBR) treating protein-rich wastewater. Environmental Science and Ecotechnology, 100296. Link
Ramírez-Carrillo, E., G-Santoyo, I., López-Corona, O., Rojas-Ramos, O. A., Falcón, L. I., Gaona, O., Cerqueda-García, D. ... & Nieto, J. (2023). Similar connectivity of gut microbiota and brain activity networks is mediated by animal protein and lipid intake in children from a Mexican indigenous population. PLoS One, 18(6), e0281385. Link
Sánchez-Soto Jiménez, M. F., Cerqueda-García, D., Aguirre-Macedo, M., & García-Maldonado, J. Q. (2023). Spatiotemporal dynamics of benthic bacterial communities in the Perdido Fold Belt, Northwestern Gulf of Mexico. Frontiers in Marine Science, 10, 277. Link
Moran-Ramos, S., Cerqueda-García, D., López-Contreras, B., Larrieta-Carrasco, E., Villamil-Ramírez, H., Molina-Cruz, S., ... & Canizales-Quinteros, S. (2023). A metagenomic study identifies a Prevotella-copri enriched microbial profile associated with non-alcoholic steatohepatitis in subjects with obesity. Journal of Gastroenterology and Hepatology. Link
Aluja, M., Vázquez-Rosas-Landa, M., Cerqueda-García, D., Monribot-Villanueva, J. L., Altúzar-Molina, A., Ramírez-Vázquez, M., ... & Ibarra-Laclette, E. (2023). Assessment of the Molecular Responses of an Ancient Angiosperm against Atypical Insect Oviposition: The Case of Hass Avocados and the Tephritid Fly Anastrepha ludens. International Journal of Molecular Sciences, 24(3), 2060. Link
Rea, V. S. G., Sierra, J. D. M., El-Kalliny, A. S., Cerqueda-García, D., Lindeboom, R. E., Spanjers, H., & van Lier, J. B. (2023). Syntrophic acetate oxidation having a key role in thermophilic phenol conversion in anaerobic membrane bioreactor under saline conditions. Chemical Engineering Journal, 455, 140305. Link
Rea, V. S. G., Bueno, B. E., Sierra, J. D. M., Nair, A., Prieto, I. J. L., Cerqueda-García, D., ... & Spanjers, H. (2022). Chemical characterization and anaerobic treatment of bitumen fume condensate using a membrane bioreactor. Journal of Hazardous Materials, 130709. Link
Ochoa-Sánchez, M., Cerqueda-García, D., Moya, A., Ibarra-Laclette, E., Altúzar-Molina, A., Desgarennes, D., & Aluja, M. (2022). Bitter friends are not always toxic: The loss of acetic acid bacteria and the absence of Komagataeibacter in the gut microbiota of the polyphagous fly Anastrepha ludens could inhibit its development in Psidium guajava in contrast to A. striata and A. fraterculus that flourish in this host. Frontiers in microbiology, 13. Link
López-Montoya, P., Cerqueda-García, D., Rodríguez-Flores, M., López-Contreras, B., Villamil-Ramírez, H., Morán-Ramos, S., ... & Canizales-Quinteros, S. (2022). Association of Gut Microbiota with Atherogenic Dyslipidemia, and Its Impact on Serum Lipid Levels after Bariatric Surgery. Nutrients, 14(17), 3545. Link
Paredes-Trujillo, A., Mendoza-Carranza, M., Rodolfo, E., & Cerqueda-García, D. (2022). Comparative assessment of metazoans infestation of Nile tilapia (Oreochromis niloticus)(L.)(Perciformes: Cichlidae) in floating cages and ponds from Chiapas, Mexico. Veterinary Parasitology: Regional Studies and Reports, 34, 100757. Link
Carabantes, N., Cerqueda-García, D., García-Maldonado, J. Q., & Thomé, P. E. (2022). Changes in the bacterial community associated with experimental symbiont loss in the mucus layer of Cassiopea xamachana jellyfish. Frontiers in Marine Science, 762. Link
Wong-Villarreal, A., Méndez-Santiago, E. W., Gómez-Rodríguez, O., Aguilar-Marcelino, L., Cerqueda-García, D., García-Maldonado, J. Q., ... & Sanzón-Gómez, D. (2021). Nematicidal Activity of the Endophyte Serratia ureilytica against Nacobbus aberrans in Chili Plants (Capsicum annuum L.) and Identification of Genes Related to Biological Control. Plants, 10(12), 2655. Link
Rea, V. S. G., Egerland-Bueno, B., Cerqueda-García, D., Sierra, J. D. M., Spanjers, H., & van Lier, J. B. (2021). Degradation of p-cresol, resorcinol, and phenol in anaerobic membrane bioreactors under saline conditions. Chemical Engineering Journal, 132672. Link
Putzeys, S., Juárez-Fonseca, M., Valencia-Agami, S. S., Mendoza-Flores, A., Cerqueda-García, D., Aguilar-Trujillo, A. C., ... & Pech, D. (2021). Effects of a Light Crude Oil Spill on a Tropical Coastal Phytoplankton Community. Bulletin of Environmental Contamination and Toxicology, 1-9. Link
Ávila-López MB, García-Maldonado JQ, Estrada-Medina H, Hernández-Mena DI, Cerqueda-García D, Vidal-Martínez VM. (2021). First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti. PeerJ, 9:e11633. Link
Uribe-Flores, M. M., García-Cruz, U., Hernández-Nuñez, E., Cerqueda-García, D., Aguirre-Macedo, M. L., & García-Maldonado, J. Q. (2021). Assessing the Effect of Chemical Dispersant Nokomis 3-F4 on the Degradation of a Heavy Crude Oil in Water by a Marine Microbial Consortium. Bulletin of Environmental Contamination and Toxicology, 1-6. Link
Thome, P. E., Rivera-Ortega, J., Rodríguez-Villalobos, J. C., Cerqueda-García, D., Guzmán-Urieta, E. O., García-Maldonado, J. Q., ... & Jordán-Dahlgren, E. (2021). Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral Pseudodiploria strigosa. PeerJ, 9, e10695. Link
Sánchez-Soto, M. F., Cerqueda-García, D., Alcántara-Hernández, R. J., Falcón, L. I., Pech, D., Árcega-Cabrera, F., ... & García-Maldonado, J. Q. (2021). Assessing the diversity of benthic sulfate-reducing microorganisms in Northwestern Gulf of Mexico by illumina sequencing of dsrB gene. Microbial Ecology, 81(4), 908-921. Link
García Rea, V. S., Muñoz Sierra, J. D., Fonseca Aponte, L. M., Cerqueda-García, D., Spanjers, H., & Van Lier, J. B. (2020). Enhancing phenol conversion rates in saline anaerobic membrane bioreactor using acetate and butyrate as additional carbon and energy sources. Frontiers in Microbiology, 11, 2958. Link
González-Penagos, C. E., Zamora, J., Cerqueda-García, D., Amendola-Pimenta, M., Pérez-Vega, J. A., Hernández-Nuñez, E., & Rodríguez-Canul, R. (2020). Alterations in the gut microbiota of zebrafish (Danio rerio) in response to water-soluble crude oil components and its mixture with a chemical dispersant. Frontiers in Public Health, 8, 705. Link
Sanchez-Quinto, A., Cerqueda-García, D., Falcón, L. I., Gaona, O., Martinez, S., Nieto, J., & González-Santoyo, I. (2020). Gut Microbiome in Children from Indigenous and Urban Communities in Mexico: Different Subsistence Models Different Microbiomes. Microorganisms, 8(10), 1592. Link
Muñoz Sierra, J. D., Garcia Rea, V. S., Cerqueda-García, D., Spanjers, H., & Van Lier, J. (2020). Anaerobic conversion of saline phenol-containing wastewater under thermophilic conditions in a membrane bioreactor. Frontiers in Bioengineering and Biotechnology, 8, 1125. Link
Zamora-Briseño, J. A., Pereira-Santana, A., Reyes-Hernández, S. J., Cerqueda-García, D., Castaño, E., & Rodríguez-Zapata, L. C. (2020). Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges. Cell Stress and Chaperones. Link
Zamora-Briseño, J. A., Cerqueda-García, D., Hernández-Velázquez, I. M., Rivera-Bustamante, R., Huchín-Mian, J. P., Briones-Fourzán, P., ... & Rodríguez-Canul, R. (2020). Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1. Journal of Invertebrate Pathology, 107457. Link
Cerqueda-García, D., Améndola-Pimenta, M., Zamora-Briseño, J. A., González-Penagos, C. E., Árcega-Cabrera, F., Ceja-Moreno, V., & Rodríguez-Canul, R. (2020). Effects of chronic exposure to water accommodated fraction (WAF) of light crude oil on gut microbiota composition of the lined sole (Achirus lineatus). Marine Environmental Research, 105116. Link
Reyes-Hernández, S.J., Zamora-Briseño, J.A., Cerqueda-García, D. et al. (2020). Alterations in the sap-associated microbiota of Carica papaya in response to drought stress. Symbiosis 81, 93–100. Link
Améndola-Pimenta, M., Cerqueda-García, D., Zamora-Briseño, J. A., Couoh-Puga, D., Montero-Muñoz, J., Árcega-Cabrera, F., ... & Zapata-Pérez, O. (2020). Toxicity evaluation and microbiota response of the lined sole Achirus lineatus (Chordata: Achiridae) exposed to the light petroleum water-accommodated fraction (WAF). Journal of Toxicology and Environmental Health, Part A, 1-17. Link
Gaona, O, Cerqueda‐García, D, Moya, A, Neri‐Barrios, X, Falcón, LI. (2020). Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae. MicrobiologyOpen. 00:e1022. Link
Ramírez-Carrillo, E., Gaona, O., Nieto, J., Sánchez-Quinto, A., Cerqueda-García, D., Falcón, L. I., ... & González-Santoyo, I. (2020). Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression. Scientific Reports, 10 (1), 1-12. Link
Cerqueda-García, D., García-Maldonado, J. Q., Aguirre-Macedo, L., & García-Cruz, U. (2020). A succession of marine bacterial communities in batch reactor experiments during the degradation of five different petroleum types. Marine Pollution Bulletin, 150, 110775. Link
Gaona O., Cerqueda-García D., Falcón LI., Vázquez-Domínguez G., Valdespino-Castillo PM., Neri-Barrios C-X .(2019) Microbiota composition of the dorsal patch of reproductive male Leptonycteris yerbabuenae. PLoS ONE 14(12): e0226239. Link
Cadena, S., Aguirre-Macedo, M. L., Cerqueda-García, D., Cervantes, F. J., Herrera-Silveira, J. A., & García-Maldonado, J. Q. (2019). Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico. Estuarine, Coastal and Shelf Science, 106433. Link
Valencia-Agami SS., Cerqueda-García D., Putzeys S., Uribe-Flores MM., García-Cruz NU., Pech D., Herrera-Silveira J., Aguirre-Macedo ML., García-Maldonado JQ. (2019) Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale. Microorganisms. 7(10):441. Link
Cob-Calan NN., Chi-Uluac LA., Ortiz-Chi F., Cerqueda-García D., Navarrete-Vázquez G., Ruiz-Sánchez E., Hernández-Núñez E.. (2019). Molecular Docking and Dynamics Simulation of Protein β-Tubulin and Antifungal Cyclic Lipopeptides. Molecules. 24(18):3387. Link
Gaona, O., Gómez-Acata, E. S., Cerqueda-García, D., Neri-Barrios, C. X., & Falcón, L. I. (2019). Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae. PloS one, 14(7), e0219982. Link
Uribe‐Flores, M. M., Cerqueda‐García, D., Hernández‐Nuñez, E., Cadena, S., García‐Cruz, N. U., Trejo‐Hernández, M. R., ... & García‐Maldonado, J. Q. (2019). Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor. Journal of Applied Microbiology. Link
Sánchez-Soto Jiménez, M. F., Cerqueda-García, D., Montero-Muñoz, J. L., Aguirre-Macedo, M. L., & García-Maldonado, J. Q. (2018). Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. PeerJ, 6, e5583. doi:10.7717/peerj.5583. Link
Muñoz Sierra J., Wang W., Cerqueda-Garcia D., Oosterkamp M., Spanjers H., van Lier JB. (2018). Temperature susceptibility of a mesophilic anaerobic membrane bioreactor treating saline phenolic wastewater. Chemosphere. Link
Valdespino-Castillo, P. M., Cerqueda-García, D., Espinosa, A. C., Batista, S., Merino-Ibarra, M., Taş, N., ... & Falcón, L. I. (2018). Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments. FEMS Microbiology Ecology. Link
Valdespino-Castillo, P. M., Hu, P., Merino-Ibarra, M., López-Gómez, L. M., Cerqueda-García, D., Zayas, G. D., ... & Falcón, L. I. (2018). Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba. Frontiers in microbiology, 9, 510.Link
Cerqueda-García, D., & Falcón, L. I. (2016). Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources. Journal of bioinformatics and computational biology, 14(04), 1650020.Link
Cerqueda-García, D., & Falcón, L. I. (2016). La construcción del nicho y el concepto de holobionte, hacia la reestructuración de un paradigma. Revista mexicana de biodiversidad, 87(1), 239-241.Link
Beltrán, Y., Cerqueda-García, D., Taş, N., Thomé, P. E., Iglesias-Prieto, R., & Falcón, L. I. (2016). Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches. FEMS microbiology ecology, 92(1).Link
Cerqueda-García, D., Martínez-Castilla, L. P., Falcon, L. I., & Delaye, L. (2014). Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in ‘Chlorochromatium aggregatum’. The ISME journal, 8(5), 991.Link