Trends in Microbiome and Digital One Health

Student Poster Competition -Judging panel and winners

The poster competition was judged by the following panelist:

• Souhaila Al Khodor - Principal Investigator and Director, Maternal and Child Health Department, Sidra Medicine, Qatar
• Stefan Green - Associate Professor, RUSH Medical College, USA
• Dr Hosam Zowawi - Principle Investigator- King Saud bin Abdulaziz University for Health Sciences 

Poster competition winners were as the follows:

• The first prize winner was PhD Student Aaron Pantoja Angles, for his poster titled, " Microbes as Versatile Platforms for Targeted Delivery of Drugs"
  

Abstract:

Novel therapeutic strategies are harnessing the potential of microbes as platforms for the synthesis and delivery of biologicals. Microbes exhibit remarkable adaptability to harsh environmental conditions within the human body, making them ideal candidates for safeguarding and transporting functional cargoes. Additionally, their natural affinity for specific body tissues enhances the precision and efficacy of therapeutic release. However, ensuring safety in the human body is key to developing translational technologies for clinical applications. 

In this study, we present the development of a CRISPR-Cas12-based device capable of fragmenting the Escherichia coli genome, resulting in the generation of non-proliferative units. Chromosome-Shredded Cells (CS-Cells) retain their biosynthetic activity and exhibit programmed functionality as demonstrated by the expression of GFP. Moreover, we demonstrate CS-Cells' capacity to synthesize antimicrobial compounds, such as violacein, through the activation of genes from a complex biosynthetic pathway. 
Furthermore, we show our most recent efforts for refining and improving our mentioned technology. By generating Escherichia coli Nissle (EcN) CS-Cells, we now provide a compatible platform with enhanced therapeutic potential. To optimize the utilization of this microbial chassis, we leveraged state-of-the-art AI technologies for the identification of promising Anti-Cancer-Cell-Penetrating Peptides (ACCPPs). Our ongoing efforts are focused on evaluating the efficacy of these ACCPPs candidates for their production by EcN CS-Cells with the aim of developing a novel and effective approach to cancer treatment. 

These advances highlight the transformative potential of microbes as versatile and safe vehicles for the expression and delivery of therapeutics. By combining cutting-edge synthetic biology techniques with advanced AI-assisted peptide design, we pave the way for the development of innovative microbial-based therapies for various clinical applications.

• The second prize winner was PhD Student Lila Aldakheel, for her poster titled, “Detecting the Tiny Environmental Threat Using Raman Microscopy and Celebrating Nature's Plastic Fighters: Unveiling Microbial Plastic Degraders through Metagenomics"

Abstract:

Plastic production worldwide reached a staggering 390.7 million tones in 2021, with over 250,000 tones being dumped into the oceans. Due to the low rate of degradation, (micro)plastics remain in the ecosystem for long periods. There is currently a knowledge gap and growing interest in seeking green alternatives to mitigate marine plastic pollution, and fortunately, they may be susceptible to biodegradation by certain groups of microorganisms that live in the environment.  However, the process of degradation of synthetic polymers by microbes is not globally well developed.

The Red Sea coast of Saudi Arabia is home to unique marine ecosystems. Mangrove sediment contains diverse microbial communities and has been found to act as a long-term sink for microplastics. Here, we apply metagenomics and dilution to stimulation approaches to investigate the mechanisms of how microbial consortia degrades microplastics. Synthetic microplastic was used as the sole carbon source in the enrichment culture. Raman Scattering (SRS) microscopy technique was used to classify microplastics in environmental samples collected in different mangrove forests along the Red Sea. We estimate that our results will show several genes and microorganisms associated with the degradation of microplastics and open space for the mining of genes or enzymes involved in the degradation of complex polymers (hydrolases, laccase, etc.). There will be correlation between the abundance of these microplastics and these genes. We believe that our results will help to select consortia and build a framework to, in the future, engineer the microbial community and its metabolic activity to accelerate the degradation process.

• The third prize winner was PhD Student Faisal Alkhaldi, for his poster titled, “Direct Identification & Classification of Leishmania Species from Biopsy Samples by Oxford Nanopore Sequencing"

Abstract:

Results:
Initially, three multiplexed samples were sequenced on a singular MinION flow cell to assess the recovery potential of Leishmania reads from biopsy samples rich with human DNA. Employing our bioinformatic protocol, all three samples tested positive for Leishmania, with successful classification at the species level. Subsequently, the feasibility of ONT adaptive sampling technology for Leishmania read enrichment was examined. Data revealed that human read depletion offered greater benefits compared to Leishmania read enrichment. The final test assessed the capability of multiplexing an increased number of samples on one flow cell as a cost-cutting measure. A total of 15 Leishmania samples and one negative control were multiplexed on a singular MinION cell, resulting in 3Gbs overall throughput. Of the lot, 10 (or 66.6%) samples tested positive for Leishmania. Only a single low-confidence read was classified as Leishmania read in the negative control sample.

Conclusion:
Oxford Nanopore Sequencing presents a promising avenue for the direct identification and classification of Leishmania species from biopsy samples directly, avoiding the need for lengthy and labor-intensive culturing. This technology assures accuracy and also offers an efficient approach, especially when considering human DNA-rich samples. Our findings suggest that the method can be optimized for clinical scenarios, paving the way for more effective diagnostic procedures and subsequent patient care for Cutaneous Leishmaniasis.