Team:Thessaly/Implementation
Overview
Our work in implementation has been focused on the user perception of our toolkit, user safety
and data management. We have integrated expert advice, governmental regulations and our own
considerations in this process. We aim to develop an easy-to-use toolkit, with an efficient
user interface, accounting for every probable outcome. Our main concerns are:
We recognize that challenges still exist that need to be solved for our product.
- Safety by design
- Recognizing target groups for potential market entry
- Establishing the basis of real-time measurements for users
- Constructing a framework for analyzing our environmental impact
We recognize that challenges still exist that need to be solved for our product.
Introduction
AMALTHEA is a holistic and sustainable approach, aiming to tackle gut dysbiosis both in humans
and animals. Its aim is to offer a proposal for evaluating the state of the gut microflora,
transmitting and storing the evaluation data and alleviating the dysbiosis derived symptoms in
a data-driven manner. AMALTHEA’s purpose is to detect, evaluate and ameliorate GI-related
disturbances, giving us results that are also visible in many areas including animal welfare and
human mental health. The implementation of our project mainly comprises the three following tools:
AMALTHEA travels through the GI tract taking site specific measurements. The results of those measurements are digitized, analyzed and assessed by experts which lead to further examinations that, in turn, can verify or exclude the existence of GI-related disorders.
We designed AMALTHEA by combining biological and electronic components, analog and digital.
The biological part of the system consists of genetically engineered bacteria confined in a tank inside the capsule. These bacteria communicate with the external environment via a semipermeable membrane that allows the SCFAs’ passing from the gut lumen to the bacteria’s tank. When the bacteria sense the SCFAs’ concentration, they produce a proportional output, which alters the electric potential in the bacterial medium. This potential is measured using electrodes and transmitted wirelessly as a signal to a mobile device, which translates and analyzes the signal.
- AMALTHEA: a bioelectronic capsule that serves as an non-invasive evaluation tool for the functional status of the gut microbiome
- e-AMALTHEA: a mobile application that receives the data from the gut’s functional evaluation
- CERAS: a living bio-therapeutic synbiotic supplement that produces a metabolite of major importance for gut health, supplemented through a dairy product.
AMALTHEA
Capsule Design
Short Chain Fatty Acids (SCFAs) are products of the gut microflora and reflect the balance between
different microbial populations, as well as the metabolic capacity of the beneficial commensal
microbiota. For that reason, we utilized SCFAs as a biomarker, the concentration levels of which we
measure with AMALTHEA, a bioelectronic capsule.
Figure 1: The 3D design of the capsule showcasing the outer cell and the inner components.
AMALTHEA travels through the GI tract taking site specific measurements. The results of those measurements are digitized, analyzed and assessed by experts which lead to further examinations that, in turn, can verify or exclude the existence of GI-related disorders.
We designed AMALTHEA by combining biological and electronic components, analog and digital.
The biological part of the system consists of genetically engineered bacteria confined in a tank inside the capsule. These bacteria communicate with the external environment via a semipermeable membrane that allows the SCFAs’ passing from the gut lumen to the bacteria’s tank. When the bacteria sense the SCFAs’ concentration, they produce a proportional output, which alters the electric potential in the bacterial medium. This potential is measured using electrodes and transmitted wirelessly as a signal to a mobile device, which translates and analyzes the signal.
- Non-invasiveness
Non-invasiveness can be a very appealing characteristic for patients that are not willing to go through examinations like colonoscopy, especially for prevention purposes. - Site specificity
Site-specific measurements allow the localization of maximum SCFAs production in the GI-tract, hence increasing the quality and specificity of the measurements. - Dynamic sampling
The data transmission and reception are simultaneous with the detection of the concentration changes in SCFAs levels in the gut, thus achieving real-time measurements. - Paradigm for the development of analogous devices
It can work as a model for the development of similar devices that are based on different kinds of indicators/biomarkers, this way covering a very broad spectrum of physiological phenomena that can be detected, characterised or quantified. - Research tool
It can serve as a research tool, providing quality data that can be correlated with environmental factors and underlying diseases, both for humans and animals. - Patients suffering from GI disorders
- Individuals with high prevalence for a GI disorder
- Gut Microbiome and Nutrition Researchers
- Stock farmers and owners of domesticated animals
- General Public
- A nutritional supplement in an existing food (not just a dietary supplement)
- The probiotic colonization in the gut makes it sustainable and requires consumption in limited quantities weekly
- This “superfood” is already integrated in the consumer’s diet and possesses a high nutritional value
- Consumers are more familiar with yogurts containing bacteria/probiotics
- Affordable for reasonable price
- Site specificity
By the protection of the alginate beads, the probiotic strains are pH-derived release in a specific site in the colon, appropriate to mass produce SCFAs in large quantities. - Sustainability
Through the colonization of the patient’s gut, our probiotic strains stay inside the host’s body is prolonged, maximizing the production of SCFAs in a long-term way. - Patient-Friendly
Alginate beads are well documented to be a IBD-friendly prebiotic that can become food for several strains in our microbial community. Thus, not only are we elevating the levels of SCFAs in the gut but also provide high nutritional value feed for the patient’s fragile gut. - Safe
Being able to control the time spent on the gut flora, we can account for probable errors and stop potential mutations before they allow our strain to become dominant. - Patients suffering from GI disorders
Replenishing the lost levels of SCFAs can help metabolic active populations sustain dysbiosis, alleviate symptoms and halt the disease’s progression to a manageable level. - Individuals with high prevalence for a GI disorder
Accompanied with a proper diet that ensures the probiotics survivability, people at high risk of developing symptomatology related to GI disorders strengthen their microbial community’s populations and metabolic capabilities. - Domestic Animals and Livestock
Production animals can receive our probiotic strains in different administration methods based on their digestive system morphology. Those can be administered regardless of the capsule’s result as a feed additive due to the immuno-protective and neurotrophic nature of SCFAs. On domesticated animals, the probiotics can be administered in a similar way as other commercial animal probiotics.
For more information check our Animal Welfare Page. - General Public
Our product, CERAS, is suitable for a large portion of the general public, only excluding a small group with special nutrition demands due to age or gut-related diseases/medication.
To ensure safe usage by the users, we have documented a comprehensive guide for the CERAS’ use. - Cumate:This is a completely controlled system that is activated upon external administration which is distributed along with CERAS, in order to end the probiotic’s colonization.
- Tryptophan System:The second kill switch is a system based on the amino acid tryptophan, which suppresses cell death. When the bacteria exit the host’s body, the tryptophan that naturally occured in the gut environment is missing, hence allowing a toxin to be produced and the bacteria to die.
- Standardization: the nature of the gut microbiome morphology indicates that everyone has a different microbial community structure, with different nutritional needs and so on. Determining accurate measurement levels and appropriate procedure timing must be determined experimentally in small-scale clinical trials.
- Precision: We should consider how to improve precision. We should investigate how a particular dietary pattern may give us false positive results, determine the proper time periods for use and provide a framework for how many readings would be necessary to get a proper idea of the levels.
- Acceptance of GMO: The way we convey our message should be cautiously thought out, as we have seen that a proper explanation of the modifications of the bacterial strains, the electric parts and its purpose are necessary to receive approval and acceptance from the general public.
- Price of our toolkit: Even though our estimations regarding the financial burden of a user indicate that it will not be high, we should take into consideration several factors such as competitors, willingness for consumers to pay and the business plan.
- Badal, V. D., Wright, D., Katsis, Y., Kim, H.-C., Swafford, A. D., Knight, R., & Hsu, C.-N. (2019). Challenges in the construction of knowledge bases for human microbiome-disease associations. Microbiome, 7(1). doi:10.1186/s40168-019-0742-2
- Cummings, J. H., Pomare, E. W., Branch, W. J., Naylor, C. P., & Macfarlane, G. T. (1987). Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut, 28(10), 1221–1227. https://doi.org/10.1136/gut.28.10.1221
- Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018). Current understanding of the human microbiome. Nature medicine, 24(4), 392–400.https://www.google.com/url?q=https://doi.org/10.1038/nm.4517
Innovation
We designed the capsule, aspiring to innovating in the following topics:
End Users
Although suffering from a GI disorder such as Crohn's Disease or Irritable Bowel Syndrome present a chronic issue for the patient, our toolkit helps in testing treatment efficacy, finding the correct dietary pattern and managing to halt symptoms at mild levels.
Due to the multifactorial nature of those diseases, people with a genetic predisposal, age or a highly unhealthy lifestyle are recommended to receive capsule measurements.
SCFA concentrations in the gut are often derived from dead subjects or are estimated by stool samples, but not very accurately. Our toolkit can help researchers retrieve data and help them unravel the metabolic network of the gut microbiome.
Except for humans, AMALTHEA can also be used for the evaluation of the gut microbiome in domesticated and production animals, since SCFAs have been shown to be good indicators in animal models, too. Our device can be implemented in animals, especially for research purposes, since the study of animal gut microbiome is still at its infancy.
For more information check our Animal Welfare Page.
Considering that the device is destined mainly for prevention purposes, it can be used by
anyone as a way to explore their microbial capacity and of course, pure curiosity of the
unknown!
Aiming to ensure safe and responsible usage of the capsule, we have developed distinct comprehensive guides that are destined to be utilized by users and experts, respectively.
The Auxotrophy based kill switch limits the cells’ life span to a short time frame, enough for them to complete the examination but not proliferate in the environment after exiting the user’s body.
The Arabinose-based kill switch utilises a compartment in which a substance (arabinose) that is able to kill the bacteria is confined. If a rupture in the capsule occurs, a sensitive mechanism mixes the arabinose with the bacteria, leading to their immediate death.
For more detailed documentation, visit our Safety Page.
More specifically, the data transmitted are presented in a diagram that correlates the SCFAs concentration with time. That, of course, is the main functionality of our application, yet we also developed many independent features which address a user’s needs, an expert’s demands for data that describe a patient’s health status and a researcher’s need for a database with a statistically significant sample (Cummings J. H. 1987).
e-AMALTHEA also provides a set of questionnaires that collect information related to the user’s symptoms, dietary habits and general lifestyle in order for an expert to evaluate their somatic and mental health. The results acquired, if combined with the user’s answers to the daily questionnaires, can lead to conclusions about the correlation between the gut microbiome’s state and diet or mental disorders.
For more information visit our Application page.
Why choose yogurt ?
After our discussion with Olympos, one of the biggest dairy companies in Greece and Europe, yoghurt production this year reached 100.000 tons/year, making yoghurt one of the most selected dairy products with high demand. So engineering an already widely-spread product ensures production sustainability and financial affordability.
Through our discussion with experts, we took into consideration the ideal growth environment and the condition in which a bacterial population must reside. Thus, the engineered probiotic strains are encapsulated by alginate, a linear carbohydrate prebiotic that protects our strains from the yoghurt’s and stomach’s acidic conditions.
Aiming to ensure safe and responsible usage of the capsule, we have developed distinct comprehensive guides that are destined to be utilized by users and experts, respectively.
user's guide
expert's guide
Safety
We designed two distinct biological mechanisms to ensure cell death in case any bacteria
escape the capsule:
The Auxotrophy based kill switch limits the cells’ life span to a short time frame, enough for them to complete the examination but not proliferate in the environment after exiting the user’s body.
The Arabinose-based kill switch utilises a compartment in which a substance (arabinose) that is able to kill the bacteria is confined. If a rupture in the capsule occurs, a sensitive mechanism mixes the arabinose with the bacteria, leading to their immediate death.
For more detailed documentation, visit our Safety Page.
Industrialization
Given the complexity of the capsule (especially the engineered bacteria’s sensitivity), the
whole device should be assembled strictly by pharmaceutical companies that possess both the
required equipment and the expertise. At this point, we need to underline the fact that the
most delicate part of our device is the biological one, and for the aforementioned reasons a
pharmaceutical company can be assigned the task of preparing and loading the bacterial cultures
in the capsule’s tank. On the other hand, the electronic parts will not stand in the way of the
whole process, due to their ease of assembly and their affordability; thus, no third-party
manufacturer is required in the overall system’s mass production. This way, we ensure
environmental containment and safety for the manufacturers themselves and at the same time we
reduce the possibility of error, which rises with respect to the number of intermediaries. Right
after manufacturing, the capsule is distributed under strict conditions, (especially temperature
ones) to clinics and pharmacies.
Figure 2: : The course of the capsule’s manufacturing and distribution, until utilization by the end user.
e-AMALTHEA
Application Design
To support our capsule and allow data analysis and visualization, we developed e-Amalthea, a
mobile app that receives, visualizes and stores the data transmitted by the capsule’s hardware.
Figure 3: a)The login interface of the app. (left), b)The μV versus time diagram that represents the results of the examination from the capsule.(right)
More specifically, the data transmitted are presented in a diagram that correlates the SCFAs concentration with time. That, of course, is the main functionality of our application, yet we also developed many independent features which address a user’s needs, an expert’s demands for data that describe a patient’s health status and a researcher’s need for a database with a statistically significant sample (Cummings J. H. 1987).
Figure 4: The concentrations of SCFAs in different parts of the gastrointestinal tract.
Figure 5: The concentrations of SCFAs in different blood samples.
e-AMALTHEA also provides a set of questionnaires that collect information related to the user’s symptoms, dietary habits and general lifestyle in order for an expert to evaluate their somatic and mental health. The results acquired, if combined with the user’s answers to the daily questionnaires, can lead to conclusions about the correlation between the gut microbiome’s state and diet or mental disorders.
Figure 6: Overview of the app’s different features. From left to right: μV versus time diagram, representing the results from the capsule, dietary patterns customized to the user’s needs by a dietitian, chat between the user and the experts.
Lastly, the collected information can be used for research purposes, since there is a lack of
experimental data retrieved directly from the gut concerning the microbiome’s state
(Gilbert J.A., 2018),(Badal, V. D., 2019). This way, the application’s interface can serve as
a portal to a database that can offer anonymized data to the academic community for research
purposes.
Interface
Experts can register in the application, access the patients’ data, evaluate them and provide
feedback, synchronously or asynchronously, thus achieving a holistic approach to the user’s
needs. But who are those experts? Given the fact that the principle reason for downloading the
application is the evaluation of the data by gastroenterologists, these doctors are definitely
part of this multidisciplinary team. Since the alleviation of the potential symptoms identified
by gastroenterologists is promoted through a personalised dietary pattern, the participation of
a (clinical) dietitian is vital. Finally, taking into consideration the close interaction between
gut and mental state, and through our extensive research and conversations with experts on Mental
Health[c], we concluded on encompassing psychologists and psychiatrists as experts on our
retrograde approach: Fighting GI disorders from the starting point of diagnosed or speculated
mental diseases.
Figure 7: The gastroenterologists can evaluate the patient’s results and comment on them.
A gastroenterologist retrieves data from the functional evaluation of the microbiome (if the
user has used the capsule) and the user’s answers to the offered questionnaires.
Afterwards, they provide advice and consult the user through the application’s interactive
interface.
Figure 8: The dietitian can provide a personalized dietary pattern based on the user’s data.
A nutritionist retrieves data from the user’s answers to the questionnaire’s questions that
are related to their diet, their body’s response to different foods and the characteristics of
their feces (from the provided stool chart). Consequently, they provide dietary advice
through the application’s interactive interface, possibly leading to a personalized dietary
pattern that fits the user’s needs and preferences.
Figure 9: The experts have the ability to communicate with the user both synchronously and asynchronously.
A psychologist or a psychiatrist retrieves data from the user’s answers to questions related to their
gut health and mental state and provides feedback by utilizing the application’s interactive interface.
Data Management
As in all components of AMALTHEA, we considered data security very seriously in our application’s
development process, too. We protect our user’s data on many levels: first and foremost, e-AMALTHEA
strictly follows the GDPR regulations, and, additionally, we connect it with a hybrid database that
combines the advantages of a cloud and a conventional database. Knowing the importance of data
anonymization, we also ensured that the data is encrypted with standard algorithms the cloud database
provides, so that no user can be linked or correlated to their sensitive information such as SSN, TIN,
medical results etc.
For more information visit our Application page.
CERAS
Design
Even though SCFAs can be used as an indicator for gut dysbiosis, the replenishment of those bacterial
metabolites in the gut can halt the problem’s progression, giving time to the microbial community to
recover. Our synbiotic supplement aims to administrare large quantities of SCFAs in a site specific
manner in the user’s gut.
Personalisation and Administration
In our effort to ensure maximum administration efficacy of our synbiotic product as well as
providing something
financially and scientifically friendly to every user, we chose that our administration method could be
the stir yoghurt.
Why choose yogurt ?
Figure 10: Diary production in industries.
After our discussion with Olympos, one of the biggest dairy companies in Greece and Europe, yoghurt production this year reached 100.000 tons/year, making yoghurt one of the most selected dairy products with high demand. So engineering an already widely-spread product ensures production sustainability and financial affordability.
Through our discussion with experts, we took into consideration the ideal growth environment and the condition in which a bacterial population must reside. Thus, the engineered probiotic strains are encapsulated by alginate, a linear carbohydrate prebiotic that protects our strains from the yoghurt’s and stomach’s acidic conditions.
Next Generation
End Users
user's guide
Safety
We have designed a live biotherapeutic that, except for being genetically engineered, it also
colonizes the patient’s gut, prolonging its stay inside the host’s body. It becomes obvious
that the need for a carefully planned biosafety strategy to ensure safety for the user as well
as environmental containment, is of vital importance. For that reason, we have designed two
distinct kill switches that control the cells’ death inside and outside the consumer’s body:
Manufacturing
We add our probiotic in the yoghurt in the late stages of its production, separately from the
bacteria that conduct its fermentation. After achieving the desired composition and bacterial
load, the yoghurt gets sealed and stored at low temperatures so that we preserve the probiotic’s
viability and capacity for the SCFAs’ production. The probiotic’s lifespan is approximately two
months, a period long enough for the product’s distribution and its stay on the pharmacy’s shelf.
The CERAS’ package, except for the yoghurt itself, also includes the proper amount of cumate for
the colonisation termination and a detailed guideline for the product’s safe consumption.
Implementation Challenges
References