Meili, C. H., A. L. Jones, A. X. Arreola, J. Habel, C. J. Pratt, R. A. Hanafy, Y. Wang, A. S. Yassin, M. A. Tag ElDein, C. D. Moon, et al., "Patterns and determinants of the global herbivorous mycobiome.", Nature communications, vol. 14, issue 1, pp. 3798, 2023. Abstract

Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

Attia, H., S. A. Elbanna, R. A. Khattab, M. A. Farag, A. S. Yassin, and R. K. Aziz, "Integrating Microbiome Analysis, Metabolomics, Bioinformatics, and Histopathology to Elucidate the Protective Effects of Pomegranate Juice against Benzo-alpha-pyrene-Induced Colon Pathologies", International Journal of Molecular Sciences, vol. 24, issue 13, 2023. Abstract

Polycyclic aromatic hydrocarbons, e.g., benzo[a]pyrene (BaP), are common dietary pollutants with potential carcinogenic activity, while polyphenols are potential chemopreventive antioxidants. Although several health benefits are attributed to polyphenol-rich pomegranate, little is known about its interaction with BaP. This study integrates histochemical, microbiomic, and metabolomic approaches to investigate the protective effects of pomegranate juice from BaP-induced pathologies. To this end, 48 Sprague–Dawley rats received, for four weeks, either pomegranate, BaP, both, or neither (n = 12 rats per group). Whereas histochemical examination of the colon indicated tissue damage marked by mucin depletion in BaP-fed animals, which was partially restored by administration of pomegranate juice, the fecal microbiome and metabolome retained their resilience, except for key changes related to pomegranate and BaP biotransformation. Meanwhile, dramatic microbiome restructuring and metabolome shift were observed as a consequence of the elapsed time (age factor). Additionally, the analysis allowed a thorough examination of fecal microbiome–metabolome associations, which delineated six microbiome clusters (marked by a differential abundance of Lactobacillaceae and Prevotellaceae, Rumincococcaceae, and Erysipelotrichaceae) and two major metabolome clusters (a sugar- and amino-acids-dominated metabotype vs. a cluster of fatty acids and hydrocarbons), with sugar alcohols maintaining a unique signature. In conclusion, using paired comparisons to minimize inter-individual animal variations allowed the dissection of temporal vs. treatment-derived variations. Microbiome–metabolome association clusters may be further exploited for metabotype prediction and gut-health biomarker discovery.

Rabea, S., A. S. Yassin, A. F. Mohammed, M. M. Salem-Bekhit, F. K. Alanazi, E. A. Esmail, N. A. Moneib, and A. G. M. Hashem, "Immunological characterization of the chemically prepared ghosts of Salmonella Typhimurium as a vaccine candidate", BMC Veterinary Research, vol. 18, issue 1: BioMed Central, pp. 1-11, 2022. Abstract
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Tag ElDein, M. A., A. S. Yassin, O. El-Tayeb, and M. O. N. A. T. KASHEF, "Chlorhexidine leads to the evolution of antibiotic-resistant Pseudomonas aeruginosa", European Journal of Clinical Microbiology & Infectious Diseases, vol. 40, issue 11: Springer Berlin Heidelberg, pp. 2349-2361, 2021. Abstract
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NAGY, M. E. N. N. A., A. H. Zaki, A. S. Yassin, H. A. L. A. S. H. SALAM, and M. Raslan, COMPARATIVE EVALUATION OF DIFFERENT GARLIC EXTRACTS AGAINST ANTIBIOTIC RESISTANT BACTERIA, , pp. 121 - 133, 2021. Abstract
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ElKenawy, N. M., N. H. Youssef, R. K. Aziz, M. A. Amin, and A. S. Yassin, Draft genome sequence of a prodigiosin-hyperproducing Serratia marcescens strain isolated from Cairo, Egypt, , vol. 11, issue 10: Oxford University Press, pp. jkab284, 2021. Abstract
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Ayoub, E. A., C. F. Shafik, A. M. Gaynor, E. W. Mohareb, M. A. Amin, A. S. Yassin, S. El-Refaey, M. Genedy, and A. Kandeel, "A molecular investigative approach to an outbreak of acute hemorrhagic conjunctivitis in Egypt, October 2010", Virology journal, vol. 10, no. 1: BioMed Central, pp. 1–9, 2013. Abstract
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Shafik, C. F., E. W. Mohareb, A. S. Yassin, M. A. Amin, A. Elkholy, H. El-Karaksy, and F. G. Youssef, "Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age", BMC Infectious Diseases, vol. 12, no. 1: BioMed Central, pp. 1–8, 2012. Abstract
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Agrawal, R. K., M. R. Sharma, A. Yassin, I. Lahiri, and others, "Structure and function of organellar ribosomes as revealed by cryo-EM", Ribosomes: Springer, Vienna, pp. 83–96, 2011. Abstract
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Lu, Z., T. R. Shaikh, D. Barnard, X. Meng, H. Mohamed, A. Yassin, C. A. Mannella, R. K. Agrawal, T. - M. Lu, and T. Wagenknecht, "Monolithic microfluidic mixing–spraying devices for time-resolved cryo-electron microscopy", Journal of structural biology, vol. 168, no. 3: Academic Press, pp. 388–395, 2009. Abstract
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