Periodic Reporting for period 1 - BIOMA (Bacteriocins Impact on Obesity and MicrobiotA)
Okres sprawozdawczy: 2022-02-01 do 2024-01-31
There is a strengthening link between the gut microbiota with complex metabolic conditions like obesity. In the present world scenario, obesity has almost attained the level of a pandemic and is progressing at a rapid rate. More than 500 million people across the world live with the stigma of this disease, which shows the severity of its incidence and the challenges confronting health practitioners. Since the gut microbiota is an environmental regulator of fat storage and adiposity, alterations of the gut microbiota composition has been implicated as a contributory factor in obesity-related metabolic dysregulation. This has been reported in both animal and human studies, where the microbiota is characterized by reduced diversity.
Bacteriocins are antimicrobial peptides produced by bacteria of many genera that can have a narrow or broad spectrum of activity. Many producer strains are generally regarded as safe (GRAS) or have qualitative presumption of safety (QPS). Unlike broad spectrum antibiotics that can significantly impact microbiota composition, bacteriocins are often very specific and can kill target organisms without causing collateral damage to host bacterial populations. There is sound evidence suggesting that bacteriocin-producing bacteria can be used to modify the gut microbiota, which makes bacteriocins and bacteriocin-producer strains an interesting strategy to prevent or treat diseases like obesity, which is associated with changes in the microbiota.
The aim of BIOMA was to study the impact of different bacteriocin-producing strains on the composition of the gut microbiota and on metabolic function, to determine if they can be suitable as a possible therapeutic intervention to impact on obesity. This project provided rigorous experimental results on how bacteriocin production can effectively inhibit specific target populations and their impact on other gut microbes. By using bacteriocin-producing strains (Bac+) and their corresponding bacteriocin-negative mutants (Bac-), it was possible to assess the effect of bacteriocin production on human gut-derived microbial communities.
While the gut microbiota is a realistic target for addressing obesity-related metabolic dysfunction, it has been suggested that the specificity of the antimicrobial agent employed may be critical. Some narrow spectrum bacteriocins are reported to have the potential to modulate gut health by elimination of specific pathogens. On the other hand, though broad spectrum bacteriocins can have a detrimental effect on the resident intestinal populations, they have exhibited promise with respect to their ability to improve metabolic health. Based on this, we selected a set of bacteriocins from different classes, subclasses and spectrum range. We proposed to work with bacteriocin-producing strains instead of the pure peptide for two main reasons; 1) bacteriocin-producing organisms provide a mean of delivering bacteriocins in the anaerobic environment of the gut and 2) the use of bacteriocin-producing cultures in functional foods is more cost effective than using pure peptide and is subject to less regulatory control.
The main output from BIOMA was a panel of isogenic L. lactis strains that effectively produce bacteriocins from different classes and spectrum of activity and their corresponding non-producing controls. These strains have valuable potential to be used in both food and pharmaceutical industries as microbiome-editing tool.
We assessed the behaviour of gut-derived communities over time and experimentally evaluated how the system is impacted by different bacteriocin producers. We established that the composition of the community changes in response to the presence of either broad- or narrow-spectrum bacteriocin producers and confirmed that there are significant off-target effects. These effects were analysed considering the inter-species interactions, providing a comprehensive insight into the possible mechanisms by which bacterial communities can be shaped by bacteriocins (published in Front. Microbiol; 2023).
Bacteriocins are antimicrobial peptides produced by bacteria of many genera that can have a narrow or broad spectrum of activity. Many producer strains are generally regarded as safe (GRAS) or have qualitative presumption of safety (QPS). Unlike broad spectrum antibiotics that can significantly impact microbiota composition, bacteriocins are often very specific and can kill target organisms without causing collateral damage to host bacterial populations. There is sound evidence suggesting that bacteriocin-producing bacteria can be used to modify the gut microbiota, which makes bacteriocins and bacteriocin-producer strains an interesting strategy to prevent or treat diseases like obesity, which is associated with changes in the microbiota.
The aim of BIOMA was to study the impact of different bacteriocin-producing strains on the composition of the gut microbiota and on metabolic function, to determine if they can be suitable as a possible therapeutic intervention to impact on obesity. This project provided rigorous experimental results on how bacteriocin production can effectively inhibit specific target populations and their impact on other gut microbes. By using bacteriocin-producing strains (Bac+) and their corresponding bacteriocin-negative mutants (Bac-), it was possible to assess the effect of bacteriocin production on human gut-derived microbial communities.
While the gut microbiota is a realistic target for addressing obesity-related metabolic dysfunction, it has been suggested that the specificity of the antimicrobial agent employed may be critical. Some narrow spectrum bacteriocins are reported to have the potential to modulate gut health by elimination of specific pathogens. On the other hand, though broad spectrum bacteriocins can have a detrimental effect on the resident intestinal populations, they have exhibited promise with respect to their ability to improve metabolic health. Based on this, we selected a set of bacteriocins from different classes, subclasses and spectrum range. We proposed to work with bacteriocin-producing strains instead of the pure peptide for two main reasons; 1) bacteriocin-producing organisms provide a mean of delivering bacteriocins in the anaerobic environment of the gut and 2) the use of bacteriocin-producing cultures in functional foods is more cost effective than using pure peptide and is subject to less regulatory control.
The main output from BIOMA was a panel of isogenic L. lactis strains that effectively produce bacteriocins from different classes and spectrum of activity and their corresponding non-producing controls. These strains have valuable potential to be used in both food and pharmaceutical industries as microbiome-editing tool.
We assessed the behaviour of gut-derived communities over time and experimentally evaluated how the system is impacted by different bacteriocin producers. We established that the composition of the community changes in response to the presence of either broad- or narrow-spectrum bacteriocin producers and confirmed that there are significant off-target effects. These effects were analysed considering the inter-species interactions, providing a comprehensive insight into the possible mechanisms by which bacterial communities can be shaped by bacteriocins (published in Front. Microbiol; 2023).
BIOMA conducted experiments through two complementary in vitro approaches.
a) Simplified Intestinal HUman MIcrobiota (SIHUMI). SIHUMI is a bacterial consortium consisting of seven fully sequenced and diverse human gut species that can be cultured in anaerobic conditions and for which the growth of each strain can be individually tracked (as genome copy number over time) with specific primers by quantitative real time PCR (qPCR). Although this model was not included in the original proposal, it enabled us to ensure bacteriocins were effectively delivered and functional in a dynamic gut-derived community under anaerobic conditions as a prior step to fermentation studies.
b) Fermentation systems (fermenters) mimicking the distal colon. We used mini-fermentation bioreactors (MicroMatrix™ , Applikon Biotechnology) to monitor the effect of the Bac+ and Bac- strains on microbial populations in the human faecal environment. Fermenters allowed the direct analysis over time of the microbial community structure under different experimental conditions, relying on the taxonomic assignment of 16S rRNA gene sequences.
Results from BIOMA project were disseminated in multiple conferences (FEBS, AMP, ISAPP, FEMS, Probiota) and published as an original article in the Journal Frontiers in Microbiology under the title “Impact of Bacteriocin-Producing Strains on Bacterial Community Composition in a Simplified Human Intestinal Microbiota”.
Our research was also extensively communicated through APC Education and Public Engagement (EPE) Team following a communication plan for broad public audiences. We actively participated in Outreach events organized by APC including APC microbiome day, APC Budding Biologists, APC Food is Funky. Furthermore, our project was selected for the MSCA Falling Walls (Paris, 2022) and the first EU TalentON (Leiden, 2022) to showcase our research to multiple types of audiences (academic, investors, and general public). In 2022 the BIOMA project Instagram account was released to share videos and infographics related to the project, both in English and Spanish.
a) Simplified Intestinal HUman MIcrobiota (SIHUMI). SIHUMI is a bacterial consortium consisting of seven fully sequenced and diverse human gut species that can be cultured in anaerobic conditions and for which the growth of each strain can be individually tracked (as genome copy number over time) with specific primers by quantitative real time PCR (qPCR). Although this model was not included in the original proposal, it enabled us to ensure bacteriocins were effectively delivered and functional in a dynamic gut-derived community under anaerobic conditions as a prior step to fermentation studies.
b) Fermentation systems (fermenters) mimicking the distal colon. We used mini-fermentation bioreactors (MicroMatrix™ , Applikon Biotechnology) to monitor the effect of the Bac+ and Bac- strains on microbial populations in the human faecal environment. Fermenters allowed the direct analysis over time of the microbial community structure under different experimental conditions, relying on the taxonomic assignment of 16S rRNA gene sequences.
Results from BIOMA project were disseminated in multiple conferences (FEBS, AMP, ISAPP, FEMS, Probiota) and published as an original article in the Journal Frontiers in Microbiology under the title “Impact of Bacteriocin-Producing Strains on Bacterial Community Composition in a Simplified Human Intestinal Microbiota”.
Our research was also extensively communicated through APC Education and Public Engagement (EPE) Team following a communication plan for broad public audiences. We actively participated in Outreach events organized by APC including APC microbiome day, APC Budding Biologists, APC Food is Funky. Furthermore, our project was selected for the MSCA Falling Walls (Paris, 2022) and the first EU TalentON (Leiden, 2022) to showcase our research to multiple types of audiences (academic, investors, and general public). In 2022 the BIOMA project Instagram account was released to share videos and infographics related to the project, both in English and Spanish.
This project has provided a comprehensive insight into the impact of bacteriocin production in a gut polymicrobial community context. We have revealed that both broad- and narrow-spectrum bacteriocin producers exert significant effects on both targeted and non-targeted strains, considering antagonistic interactions among community members competing within the niche. By using simplified systems of human gut species, we could overcome the multifactorial complexity of the gut microbiome, providing reproducible results in a controlled experimental setting to uncover possible mechanisms by which bacteriocin-producing strains might shape human gut microbial communities.
From a clinical perspective, the under-utilization of bacteriocins can be ascribed to a lack of awareness of their potential as precision modulators of the microbiome. The results from this project represent a step toward a more extensive use of bacteriocins in the food and pharmaceutical industries. They provide a clear and deep understanding of how bacteriocins can influence the gut microbiome in a predictable and beneficial manner.
From a clinical perspective, the under-utilization of bacteriocins can be ascribed to a lack of awareness of their potential as precision modulators of the microbiome. The results from this project represent a step toward a more extensive use of bacteriocins in the food and pharmaceutical industries. They provide a clear and deep understanding of how bacteriocins can influence the gut microbiome in a predictable and beneficial manner.