Research Article Comparative Investigation of the Diabetic Foot Ulcer Microbiome
by Amr TM Saeb1,2, Hamsa T Tayeb3,4*, Abdulmohsen Alqasabi5, Samir Ouizi6, Majed S Nassar7, Assim Alfadda1,2,8,9, Udaya Raja GK10, Balavenkatesh Mani10, Mohammed S Alsuabeyl7
1Strategic Center for Diabetes Research, College of Medicine, King Saud University, Saudi Arabia
2King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
3Saudi Human Genome Project, King Abdulaziz City for Science and Technology (KACST), Riyadh, KSA
4Genetics Department, King Faisal Specialist Hospital and Research Center, Riyadh, KSA.
5Organ Transplant Center, King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh, KSA
6University Diabetes Center, King Saud University, KSA
7Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, KSA
8Obesity Research Center, College of Medicine, King Saud University
9Department of Internal Medicine, College of Medicine, King Saud University, KSA
10Integrated Gulf Biosystems, Riyadh, KSA
*Corresponding author: Hamsa T. Tayeb, Genetics Department, King Faisal Specialist Hospital and Research Center, Riyadh, KSA.
Received Date: 22 September 2025
Accepted Date: 07 October 2025
Published Date: 10 October 2025
Citation: Saeb ATM, Tayeb HT, Alqasabi A, Ouizi S, Nassar MS, et al. (2025) Comparative Investigation of the Diabetic Foot Ulcer Microbiome. Infect Dis Diag Treat 9: 279. https://doi.org/10.29011/2577-1515.100279
Abstract
Background: Many factors may affect wound healing in Diabetic foot ulcer, namely, microbial density, microorganisms, microbial synergy, the host immune response, and infected tissue quality. Methodology: This study used a cross-sectional design. We assessed 38 Subjects with DFUs, 23 neuroischaimic, and 15 neuropathic, for microbiota colonizing the DFU utilizing traditional cultures and 16S gene sequencing methods. All the relevant clinical factors were collected. Wound swabs were collected for both traditional microbiological analysis, direct swab (DSM), and cultured (CM) microbiome analysis. DNA isolation, and 16SrRNA hypervariable regions were amplified. Bioinformatics analysis was performed using IonReporter Software, statistical analysis, and diversity indices were computed with vegan R-package. Results: The traditional microbiological method was able to detect a maximum of one or two pathogens, and, in some cases, no pathogen was detected. The total number of the observed species was 176. The number of identified species was higher in the cultured microbiome (155) than the direct swab microbiome (136). Diversity analysis indicated that biological diversity is higher in the cultured microbiome compared with the DSM. The Shannon H index was 2.75 for the cultured microbiome and 2.63 for DSM. We observed some differences in the major bacterial taxa amongst neuroischaimic and neuropathic DFU microbiomes. Conclusions: cultured microbiome is superior to both the traditional method and direct swab microbiome. The Neuroischaimic group showed higher values for the tested diversity indices than the Neuroischaimic group. Neither Cluster Analysis nor Principal Component Analysis showed apparent clustering amongst the two types of ulcers.
Keywords: Diabetic foot ulcer (DFU); Diabetes complications; 16SrRNA; Next-generation sequencing; Emerging pathogens; Operational taxonomic units (OUTs); Biological diversity; Microbiome
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