Research in Microbial Ecology and Bioinformatics

Publications.

1. Aluja, M., Cerqueda-García, D., Altúzar-Molina, A., Guillén, L., Acosta-Velasco, E., Conde-Alarcón, J., & Moya, A. (2024). Geographic variation and core microbiota composition of Anastrepha ludens (Diptera: Tephritidae) infesting a single host across latitudinal and altitudinal gradients. PeerJ, 12, e18555. Link 

2. Zamudio-Flores, J., Cerqueda, D., Phillips-Farfán, B., Rangel, S. G., Salinas-García, A. F., Meléndez-Herrera, E., ... & Lajud, N. (2024). Environmental enrichment-induced cognitive recovery after a moderate pediatric traumatic brain injury is associated with the gut microbiota and neuroinflammation. Experimental Neurology, 115109. Link 

3. van Tussenbroek, B. I., Monroy-Velázquez, L. V., Rodríguez, D., Suescún-Bolívar, L. P., Thomé, P. E., Cerqueda-García, D., ... & Escalante-Mancera, J. E. (2024). Monitoring drift and associated biodiversity of nearshore rafts of holopelagic Sargassum spp. in the Mexican Caribbean. Aquatic Botany, 195, 103792. Link 

4. Espinosa-Zaragoza, S., Domínguez-Liévano, A., Gómez-Gutiérrez, J. A., Wong-Villarreal, A., Aguilar-Marcelino, L., Cerqueda-García, D., ... & Sachman-Ruíz, B. (2024). In vitro Acaricidal Activity of Serratia Ureilytica Against the Dust Mite Tyrophagus Putrescentiae and Identification of Genes Related to Biocontrol. Current Microbiology, 81(7), 199. Link 

5. Arjona-Cambranes, K. A., Olvera-Novoa, M. A., Cerqueda-García, D., Arjona-Torres, M. G., Aguirre-Macedo, M. L., Vidal-Martínez, V. M., & García-Maldonado, J. Q. (2024). Characterization of microbiota and histology of cultured sea cucumber Isostichopus badionotus juveniles during an outbreak of skin ulceration syndrome. Plos one, 19(5), e0303480. Link 

6. Valencia‐Agami, S. S., Cerqueda‐García, D., Gamboa‐Muñoz, A. M., Aguirre‐Macedo, M. L., & García‐Maldonado, J. Q. (2024). Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon‐degrading microorganisms. Environmental Microbiology Reports, 16(3), e13264. Link 

7. Cadena, S., Cerqueda-García, D., Uribe-Flores, M. M., & Ramírez, S. I. (2024). Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms. Extremophiles, 28(2), 25. Link 

8. 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 

9. 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 

10. 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 

11. 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 

12. 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 

13. 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 

14. 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 

15. 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 

16. 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 

17. 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 

18. 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 

19. 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 

20. 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 

21. 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 

22. 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 

23. 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 

24. 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 

25. 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

26. 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 

27. 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

28. 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

29. 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 

30. 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 

31. 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

32. 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 

33. 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

34. 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

35. 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 

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. 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