Periodic Reporting for period 2 - MICAfrica (Towards a North-African Consortium of the Human Microbiome (NACHM) through strengthening the Capacities in Microbiome Analysis for Human Diseases at University of Sfax)
Berichtszeitraum: 2022-04-01 bis 2023-12-31
The analysis of the human microbiome is a research area of great interest regarding its role in human health. Disruption of the microbial community constitutes a major risk factor for many chronic diseases.
Numerous initiatives were launched to take advantage of high-throughput technologies to characterize the human microbiome and to explore the relationship between dysbiosis and diseases and to provide response to the need to standardize methods and protocols. Despite these increasing number of European and international initiatives, very few studies have been carried out in North Africa (NA). With the 3 years of the MICAfrica project, USFAX and its staff will have the strong potential to be a leading force in the region for future NA collaborative microbiome projects. So, the MICAfrica project aims to: increase USFAX staff capacities in (i) using standardized metagenomic approaches for analyzing the human microbiome (ii) using functional metagenomics strategy to identify microbial effectors that affect the host response in microbiome-associated diseases (iii) setting-up and then coordinating “the North African Human Microbiome Consortium” (NAHMC). This will be achieved through implementation of a set of activities focusing on conferences, lab course, internships, networking activities and also communication and dissemination activities.
Conclusion of the action :
Despite the Covid crisis whish took place during the first period of the project and affected the implementation of activities, the consortium has succeeded after the 3 years of project to reach the main objectives through the implementation of almost the activities:
- First, after the implementation of capacity-building activities, the researchers from USFAX (ER and ESR) acquired strong competencies in using metagenomic approaches for human microbiome studies and studying the microbiota- host interplay in diseases. This has been materialised by performing research activities and publishing many scientific articles in open access journals. This contributed to raise the visibility of USFAX and the H-index of its scientists staff.
- Secondly, during the second period of the project, USFAX created in collaboration with North African partners the NACHM during a meeting organised with the objective to implement collaborative activities focusing on the development of the NA database and on the development of collaborative projects to characterise the human microbiota in NA populations and its variation regarding environmental and geographical factors.
- Thirdly, many activities of dissemination and exploitation have been organised and contributed to promote the project outcomes and to raise the awareness of the general public of the importance of the microbiome-based personalized medicine.
- Finally, all the activities implemented during the three years of MICAfrica project contributed to stimulate scientific excellence and to reinforce the capacity of the USFAX to develop new successful proposals and to coordinate EU projects
Numerous initiatives were launched to take advantage of high-throughput technologies to characterize the human microbiome and to explore the relationship between dysbiosis and diseases and to provide response to the need to standardize methods and protocols. Despite these increasing number of European and international initiatives, very few studies have been carried out in North Africa (NA). With the 3 years of the MICAfrica project, USFAX and its staff will have the strong potential to be a leading force in the region for future NA collaborative microbiome projects. So, the MICAfrica project aims to: increase USFAX staff capacities in (i) using standardized metagenomic approaches for analyzing the human microbiome (ii) using functional metagenomics strategy to identify microbial effectors that affect the host response in microbiome-associated diseases (iii) setting-up and then coordinating “the North African Human Microbiome Consortium” (NAHMC). This will be achieved through implementation of a set of activities focusing on conferences, lab course, internships, networking activities and also communication and dissemination activities.
Conclusion of the action :
Despite the Covid crisis whish took place during the first period of the project and affected the implementation of activities, the consortium has succeeded after the 3 years of project to reach the main objectives through the implementation of almost the activities:
- First, after the implementation of capacity-building activities, the researchers from USFAX (ER and ESR) acquired strong competencies in using metagenomic approaches for human microbiome studies and studying the microbiota- host interplay in diseases. This has been materialised by performing research activities and publishing many scientific articles in open access journals. This contributed to raise the visibility of USFAX and the H-index of its scientists staff.
- Secondly, during the second period of the project, USFAX created in collaboration with North African partners the NACHM during a meeting organised with the objective to implement collaborative activities focusing on the development of the NA database and on the development of collaborative projects to characterise the human microbiota in NA populations and its variation regarding environmental and geographical factors.
- Thirdly, many activities of dissemination and exploitation have been organised and contributed to promote the project outcomes and to raise the awareness of the general public of the importance of the microbiome-based personalized medicine.
- Finally, all the activities implemented during the three years of MICAfrica project contributed to stimulate scientific excellence and to reinforce the capacity of the USFAX to develop new successful proposals and to coordinate EU projects
During the 3 years of the project the consortium have made great efforts to implement the project activities planned in the Action despite the fact that unforseen risks have occured during the two reporting periods:
- During the first reporting period (RP1), the majority of activities planned in the action were accomplished, but regarding the covid crisis, many of them were performed remotely.
After the KoM (M1), the MICAfrica consortium organized many conferences. The first one was organized in March 2021 in the frame of WP1 and has been a considerable contribution to the theoretical training of young researchers of USFAX in metagenomics. As a part of WP2 a second conference on “Microbiota-Host Interplay” was organized on May 2021 to initiate ER and ESR from USFAX to functional metagenomics.
Many online meetings and webinars were also organized in the frame of WP1 dealing the Linux operating system in metagenomic analysis. They were followed by a lab course during 4 days at USFAX with the participation of 23 ESR, ER and technicians who were trained in the metagenomic approach, since sampling to sequencing by NGS.
Internships in the IHUMI involving 4 ESRs and 8 ERs were then performed in order to initiate them to bioinformatic tools (Spades, Blastn,Prokka, etc...)
- During RP2, the consortium implemented the expected activities and those related to RP1 whish have been postponed regarding the covid crisis. Thus, a workshop on functional metagenomics has been organised at USFAX in April 2022 (M16); it was followed by intrneships involving ERs and ESRs from USFAX at INRAE and UNIFI (M17-M22) to be trained in functional metagfenomics, culturomics and metabolomics. Also two conferences for dissemination have been organised at USFAX on 2022 and 2023. The scientific activity has also focused on research and publication of scientifi articles.
The main activity during RP2 was the creation in collaboration with NA partners of the NACHM during a meeting organised at USFAX in July 2022 (M19); during this meeting a consortium agreement has been prepared, validated and signed and an action plan has been prepared. After that, USFAX coordinated the implementation of three workshops at NA coutries (Morocco, Algeria and Egypt) and many online meetings to assess the progress of the NA database development whish has been the main objective of the creation of NACHM (M25-M34).
Many communication and dissemination activities were performed using different tools of communication to promote the project outcomes and to raise the awareness of the general public of the importance of the microbiome-based personalized medicine.
- During the first reporting period (RP1), the majority of activities planned in the action were accomplished, but regarding the covid crisis, many of them were performed remotely.
After the KoM (M1), the MICAfrica consortium organized many conferences. The first one was organized in March 2021 in the frame of WP1 and has been a considerable contribution to the theoretical training of young researchers of USFAX in metagenomics. As a part of WP2 a second conference on “Microbiota-Host Interplay” was organized on May 2021 to initiate ER and ESR from USFAX to functional metagenomics.
Many online meetings and webinars were also organized in the frame of WP1 dealing the Linux operating system in metagenomic analysis. They were followed by a lab course during 4 days at USFAX with the participation of 23 ESR, ER and technicians who were trained in the metagenomic approach, since sampling to sequencing by NGS.
Internships in the IHUMI involving 4 ESRs and 8 ERs were then performed in order to initiate them to bioinformatic tools (Spades, Blastn,Prokka, etc...)
- During RP2, the consortium implemented the expected activities and those related to RP1 whish have been postponed regarding the covid crisis. Thus, a workshop on functional metagenomics has been organised at USFAX in April 2022 (M16); it was followed by intrneships involving ERs and ESRs from USFAX at INRAE and UNIFI (M17-M22) to be trained in functional metagfenomics, culturomics and metabolomics. Also two conferences for dissemination have been organised at USFAX on 2022 and 2023. The scientific activity has also focused on research and publication of scientifi articles.
The main activity during RP2 was the creation in collaboration with NA partners of the NACHM during a meeting organised at USFAX in July 2022 (M19); during this meeting a consortium agreement has been prepared, validated and signed and an action plan has been prepared. After that, USFAX coordinated the implementation of three workshops at NA coutries (Morocco, Algeria and Egypt) and many online meetings to assess the progress of the NA database development whish has been the main objective of the creation of NACHM (M25-M34).
Many communication and dissemination activities were performed using different tools of communication to promote the project outcomes and to raise the awareness of the general public of the importance of the microbiome-based personalized medicine.
Through the MICAfrica activities during the three years of the project, the expected results until focus mainly on the acquisition by the staff of USFAX of knowledge and skills in the field of human microbiome studies and data analysis, using standardized protocols allowing to:
- Strengthen the capacity of Sfax University and its scientific and medical staff in the management of human diseases related to microbe variations.
- Increase the USFAX's research excellence and visibility and enhancement of USFAX’s staff capacity in research support activities
- Enhance the reputation, attractiveness and networking USFAX channels through the creation and coordination of the NAHMC that has several missions, such us setting-up a database on human microbiome in the NA region
- Improve the USFAX ability to compete successfully for competitive research funding opportunities (increased number of EU projects coordinated par USFAX)
Throught the implementation of research activities performed during the duration of the project and through the developed of more collaborative research in the field of human microbiome after the end of the project, MICAfrica project will have more socio-economic impact via the generation of new knowledge and results about the relationship between microbiome and diseases such as diabetes, obesity, inflammatory bowel disease, colorectal cancer, etc... and via the implementation of new tools for diagnosis and disease prevention; this will contribute to promoting the personalised medecine and to gradually reducing the incidence and the burden of many chronic diseases in NA and beyond and finally the cost of the public health care services. This also will contribute to the increase of the quality of life in the society and well being.
- Strengthen the capacity of Sfax University and its scientific and medical staff in the management of human diseases related to microbe variations.
- Increase the USFAX's research excellence and visibility and enhancement of USFAX’s staff capacity in research support activities
- Enhance the reputation, attractiveness and networking USFAX channels through the creation and coordination of the NAHMC that has several missions, such us setting-up a database on human microbiome in the NA region
- Improve the USFAX ability to compete successfully for competitive research funding opportunities (increased number of EU projects coordinated par USFAX)
Throught the implementation of research activities performed during the duration of the project and through the developed of more collaborative research in the field of human microbiome after the end of the project, MICAfrica project will have more socio-economic impact via the generation of new knowledge and results about the relationship between microbiome and diseases such as diabetes, obesity, inflammatory bowel disease, colorectal cancer, etc... and via the implementation of new tools for diagnosis and disease prevention; this will contribute to promoting the personalised medecine and to gradually reducing the incidence and the burden of many chronic diseases in NA and beyond and finally the cost of the public health care services. This also will contribute to the increase of the quality of life in the society and well being.