WELCOME
TO THE CSIR MICROBIOME MAPPING INITIATIVE
In collaboration with the Sydney Brenner Institute for Molecular
Bioscience, Wits University
This project is
based on the investigation of the human microbiome in the South African
population and using this information to quantify/describe the specific
microbiomes present in South Africans. The overall aim of this project is to set
up the necessary infrastructure to create a national digital platform for the
analysis of the human microbiomes present and develop health models for
predicting health outcomes and solutions.
COMMUNICATIONS
Next Gen Health launches CSIR Microbiome Mapping Initiative
The Next Generation Health cluster is
piloting a CSIR Microbiome Mapping Initiative (CMMI) to set up the
infrastructure necessary for establishing a national microbiome profiling
platform.
According to the project leader: Dr
Jerolen Naidoo, “This project will involve capturing a snapshot of the gut microbial
diversity to characterize the baseline profile in the average South African
community at the CSIR.”
“The microbiome refers to all the genetic material
of the community of 100 trillion microorganisms living inside your gut! This
community is really important in several fundamental bodily processes and is
influenced by diet, lifestyle, genetics and more that we aim to uncover with
your help!”
Why is this study so important?
“In 2019, South Africa was named the
world’s unhealthiest country according to the Indigo Wellness Index. This may
reflect the epidemiological transition to a more urbanized society, which has
major implications in the development of various pathologies such as diabetes and
cancer, due to simultaneous increases in sedentary lifestyles and changes in
dietary habits,” Jerolen says.
“An imbalanced microbiome (i.e.
dysbiosis) has been shown to influence therapeutic outcomes in cancer treatment
and the susceptibility to infectious disease such as HIV and TB. Further
investigation would aid in understanding how these changes in healthy gut
microbiome profiles in the SA population affects health and reveal future
significant implications in personalized medicine,” he adds.
The success of this project depends on your help
“By providing a small stool sample, you will be giving us access to
this vast community of microorganisms. We will link this gut community profile
to the information you provide us through a questionnaire about your diet, demographics
and lifestyle, and generate a report about the profile and potential links to
these factors.”
RECRUITMENT DRIVE
To learn more about the gut microbiome and CSIR Microbiome Mapping
Initiative please watch this video:
https://www.youtube.com/watch?v=WfH9-DfCGqY
TO VOLUNTEER AS A CITIZEN SCIENTIST PLEASE
FOLLOW THIS LINK:
https://redcap.link/cmmi.csir.co.za [For CSIR Pretoria employees only]
INFORMATION AND RESOURCES
Quick facts on the gut
microbiome:
v All the genetic material of this community of bacteria, fungi, viruses and protozoa, is referred to as the MICROBIOME.
v The most abundant living material which scientists suggest is a “SECOND GENOME” or WHOLE human organ!
v It is established at birth and increases in abundance of microorganisms into adulthood.
v It plays a role in disease susceptibility throughout life and is known to be involved in several fundamental bodily processes.
v Such processes include metabolizing food, breaking down drugs and toxins, and protection from infections.
v Several studies have shown its influence in numerous pathologies such as the onset of diabetes, obesity, mental and neurological disorders (e.g. depression, Parkinson’s disease), cancer and the efficacy of treatments and the long-term severity of COVID-19.
v Significant factors such as an innutritious DIET, poor ENVIRONMENT or LIFESTYLE, or the use of ANTIBIOTICS can cause an imbalanced gut microbiome and can have major impacts on human health.
OVERVIEW
OF THE PROJECT
The CSIR Microbiome
Mapping Initiative is about understanding our gut microbiome and how our
everyday choices and environment impacts it. The microbiome refers to the
community of 10-100 trillion bacteria, viruses, fungi and protozoa living
inside your gut! This community of microorganisms is really important to
several fundamental aspects of our physiology and health, and can be influenced
by factors like age, diet, antibiotic use and more. We aim to investigate this
with your help.
A number of recent
scientific breakthroughs have shown us how factors like poor diet and lifestyle
choices can cause an imbalanced gut microbiome, leading to poor health outcomes
and increased risk for the onset of certain diseases. This project will involve
capturing a snapshot of gut microbial diversity to characterise the baseline
profile in the average South African community as represented at the CSIR.
In doing so, we hope
to gain greater insights into how an individual’s gut microbiome may be
indicative of different health outcomes and risks in South Africa.
In order to do so, we
require your help. By providing a small stool sample, you will be joining a
global citizen science community where individuals across the world are making
similar contributions to microbiome profiling efforts in their respective
countries. We will ultimately link the gut community profiles to the
anthropological information provided to us through a questionnaire about you,
your diet and lifestyle. All of this information will help pioneer microbiome
research in South Africa.
You will also get an exciting report about your individual gut profile
and be able to see how your profile compared to other anonymised profiles in
the study.
SAMPLE COLLECTION:
The DNA/RNA Shield™ Fecal Collection kit provides the materials and instructions for collecting and stabilizing microbial DNA from a stool sample. The kit includes gloves, the collection tube, a toilet hammock and an instruction leaflet.
SAMPLE COLLECTION DEMONSTRATION
Please follow this link and navigate to under Product Video:
THIS PROJECT HAS WITS
HREC AND CSIR REC APPROVAL
FAQS
v
What are
microbiomes?
A complex ecosystem that simultaneously
exists as bacteria, viruses, fungi and bacteriophages, which interact with each
other and their environment (e.g. air, water, soil, different sites of the
human body). The collective microbial genes from this community of
microorganisms is referred to as the "microbiome".
v How different are gut microbiomes from
genes? What role does each play in the human body and which would say one
should consider when thinking “overall health?”
Genes are
the basic unit of heredity in biology (i.e. a single gene is a “code”). The
central dogma of biology describes the blueprint of genes being DNA
(deoxyribose nucleic acid), which is transcribed to an intermediate called RNA
(ribose nucleic acid), and is finally translated into protein. Proteins include
essential compounds and are
required for the structure, function, and regulation of the body's cells,
tissues, and organs. The gut microbiome is composed of millions of various
microbial organisms made up of trillions of genes (i.e. numerous codes) that
are translated into different proteins. These proteins interact with the human
host and ultimately have differing essential roles in human biology.
The gut microbiome contains almost 100-fold
more unique microbial genes than the human genome. The significance of this has
led to a trend in research to describe the gut microbiota as a whole human
“organ”. The gut microbiome composition is unique to an individual, established
in early life and – due to their interaction with the host – plays a role in
disease susceptibility throughout life.
v
What is
the relationship between gut microbiome, health, the environment, lifestyle and
geo-spatiality?
The early colonization of the gut to form a
“core” microbiome profile is influenced by several factors including genetics,
the mode of delivery, diet, gestational age, environment and antibiotic
administration. These factors influence the functioning of the gut microbiome,
especially bacteria and its role in several protective mechanisms against
harmful pathogens as a process for maintaining control over the resident
microbes. As well as various functions involved in nutrition, modulating host
immune responses, maintaining health and metabolic homeostasis.
Research has shown that a more diverse gut
microbiome is associated with healthy or improved health outcomes. In contrast,
the loss of diversity is associated with the susceptibility or the onset of
specific disease, dependent on the microbial species affected by the decrease
in abundance. The environment has arguably the most significant impact on the
gut microbiome and drives the overall diversity profile. Environmental impacts
include things humans are exposed to, such as what they eat, how physically
active they are, or how long they are exposed to car fumes in traffic etc.
These factors all contribute to an individual’s unique microbiome profile.
v
So, if
the gut microbiome is influenced by geo-spatiality, environment etc and all
this has an influence on the kind of disease one is susceptible to and how one
responds to treatment, would it be fair to conclude that, there are certain
diseases that are more prevalent in developing countries than in developed
countries because of this?
The conclusions that individuals are more
susceptible to certain diseases and respond differently to treatment depending
on their environment is accurate. A study found that within six to nine months,
immigrants to the United States from Thailand experienced a striking
westernization of their gut microbiome accompanied by increased risk of
obesity, attributed in part to adopting a US diet. Their relocation lead to a
myriad of short-term gut microbiome responses, including disruption to the gut
microbiome immediately after arrival, expansion of opportunistic pathogens, gut
disruption several months after arrival, and stability of microbiome diversity.
Genetically unrelated individuals residing in close proximity (i.e. in the same
household) are more likely to exhibit similar microbiome profiles than
genetically related individuals residing in different locations (i.e. in
different households and as far as different continents), highlighting that
microbiome diversity has very little to do with ethnicity.
v
What
causes one’s microbiome profile to change with age?
Research has shown that the gut microbiome is
established and seeded in utero, and
the subsequent mode of delivery and early infant feeding practices continue the
diversification of the microbial profile. As the infant diet is changed to more
solid foods and environmental exposures increase, the dynamic nature of the
diversifying gut microbiome becomes more stable, and a “core” microbiome is
formed after approximately three years of life. This core gut microbiome
profile generally remains stable throughout life, however it also features a
variable profile, which can be affected and changed by acute environmental
exposures such as a temporary change in diet or location. This variable gut
microbiome profile can see an increase/decrease in microbial diversity, but the
core microbiome remains constant. However, a long term change in these factors
(e.g. adopting a vegetarian diet) can cause a more drastic change in the
variable and the core microbiome, which can have subsequent effects on overall
health over time. The use of antibiotics also causes drastic changes in the gut
microbiome by essentially causing a reset of the profile, which can then be
stably reformed into the profile the individual previously had if their
lifestyle remains consistent.
v
Why is it
important to have a much broader and deeper understanding of South Africa’s
potentially diverse profile? What is it at stake if we don’t understand the diversity
of these profiles?
South Africa is composed of a variety of
individuals of culturally diverse and demographic groups, each with lifestyles,
diets and social practices that would inevitably influence their gut microbial
profiles. In 2019 South Africa was named the world’s unhealthiest country
according to the Indigo Wellness Index, which tracks several criteria including
blood glucose, obesity, depression and exercise. This may reflect the
epidemiological transition to a more urbanized society which has major
implications in the development of various pathologies such as diabetes,
cardiovascular disease and cancer, due to simultaneous increases in sedentary
lifestyles and changes in dietary habits. Microbiome variations and
perturbations (i.e. dysbiosis) have been shown to influence therapeutic
outcomes. A study on cancer treatment using cyclophosphamide – one of the most
prescribed medications at public hospitals in South Africa which is used as a
chemotherapy and to suppress the immune system – has shown that its efficacy is
significantly dependent on the individuals gut health. The susceptibility to
infectious disease largely affecting SA such as HIV and TB is also impacted by
gut microbiome profiles and health. Further investigation would aid in understanding
how these changes in healthy gut microbiome profiles in the SA population
affects health and reveal future significant implications in personalized
medicine.
v
With
Africa and South Africa riddled with disease, how does the development of a
microbiome digital platform solve some of our health problems in the country?
A digital
platform would serve as a novel health metric that would assist in the work
towards the reduction and eradication of the rise of non-communicable diseases.
This platform would answer questions such as those pertaining to the general
health of the South African population, and ideally be used as an early warning
system for the onset of disease. Due to the dynamic and malleable nature of the
microbiome, it can respond early to the potential susceptibility to disease as
opposed to late outcomes of diagnosis. Therefore, this platform would be used
as an early intervention system to prevent disease before it becomes too
serious.
v
I
understand that you will be having a Microbiome Mapping Initiative for internal
staff members. What will this initiative entail?
The CSIR Microbiome Mapping Initiative (CMMI)
is essentially a pilot project that has been set up within the Next Generation
Health Cluster. The endpoint aim of this project is to set up the
infrastructure and technical information necessary for establishing a national
microbiome profiling platform. This project will involve capturing a snapshot
of the microbial diversity to enable us to understand what the baseline profile
looks like in the average South African community at the CSIR. We also aim to
seek out how this baseline relates to various different factors previously
mentioned e.g. diet, environment and lifestyle practices, and how this compares
to international studies (Human Microbiome Project, American Gut Project). The
information from the CMMI would set up the foundation for the generation of
this knowledge and a digital platform.
v
Why are
you choosing to use faecal samples, is there no other method we can consider?
In order to be in line with the international
standards of microbiome research, we will collect stool as a proxy for the
human gut microbiome. Faecal collection is a convenient method to examine the
gut microbiome because it is relatively non-invasive and ensures easy
rapid collection by the participants at home and preservation of faecal sample
microbial profiles.
v
Once, you
have collected the samples, how will you use the information collected? What
role will this data collection process assist in the development of this
platform?
Large
sets of microbial sequencing data will be generated from the samples collected,
along with a vast amount of anthropological and environmental data. The big
data generated will be used to characterize what the baseline microbiome
profile looks like, and how it is affected by differences in the information
collected about the individual’s lifestyle and environment. Ultimately, statistical models will be
applied to identify associated features between the collected datasets and be
used to train an artificial neural network. This will serve as the basis of a
predictive model for disease risk linked to particular lifestyle practices or
exposure to harmful environmental pollutants by using the microbiome as the
input layer. The role of this data collection will subsequently assist in the
development of the platform.
v
NextGen
Health has collaborated with Smart Places on this project, what expertise will
Smart Places be contributing towards this project?
Environmental modelling will be undertaken by
the CSIR Air Quality group at Smart Places. Geolocation data supplied for “work” and
“home” will be utilized to associate a participant's profile (through postal
codes provided) with specific water quality, air quality and meteorological
data collected. This group will contribute to the project by providing
climate models, which will be used to generate Air quality (AQ) metrics. Importantly, AQ measurements of ambient
air pollutants known to modulate the human microbiome, such as particulate
matter, ozone, sulphur dioxide, nitric oxide and nitric dioxide will be
collected. Accompanying this will be meteorological measurements such as
ambient temperature, rainfall, wind speed and wind direction, which are all
factors that can affect the distribution of these air pollutants.
v
Bringing
the AI element to the project is IBM, how does the AI element brought by IBM
make this platform more novel?
Machine learning and AI development will
enable the application of mathematical modelling to real-world applications
including health based AI development. Since the project will produce large
datasets, it is important to be able to pry out what information is relevant in
terms of the microbiome and health, and collaboration with IBM will bring about
a multidisciplinary approach in making sense of these datasets and the
development of the platform.
v
How will
a technology platform like this revolutionise the public and private sector?
How will it add value in different applications?
The
development of a precision medicine based platform with an early detection
strategy has the enormous potential to revolutionise healthcare in South
Africa. This would shift the
emphasis in medicine from reaction to prevention, predict susceptibility to disease and improve
disease detection. It would enable the customization of disease-prevention strategies to a region or
an individual, depending on the resources available. The ideal of pre-empting disease progression could be
realized, with the prescription of more effective drugs whilst avoiding prescribing drugs with predictable
side effects. This would inevitably reduce the time, cost, and failure rate of treatment regimens by eliminating the trial-and-error
inefficiencies that increase health care costs and undermine patient care.
v
Those
interested in being a part of the Mapping Initiative, What is the process for
signing up to be a volunteer? Take us through the process.
We will
be rolling out a recruitment drive by creating online awareness for the project
through collaboration with the CSIR communications team. This will involve
written information about the CMMI and visual recruitment presentations.
Individuals above 18 years old of all genders and ethnic groups employed by the
CSIR will be invited to join. Interested individuals will be invited to sign up
via email and provide informed consent through an electronic database, and will
then be redirected fill out and submit an anthropological survey (available in
English, isiZulu and Afrikaans). This survey will serve to explain why a
microbiome profile is unique to the participant. They will then be provided
with a sample collection kit from the Knowledge Commons building for an easy
collection of stool at a single time point in the privacy of their homes. These
kits come with an instruction manual and a link to online support. These
samples will be anonymised by assigning an identifier then processed. Microbial
DNA will be extracted and sequenced, which will tell us all the different types
of bacteria present within the individuals gut and at what ratios. This
sequencing data will be analysed in conjunction with the anthropological and
environmental data, and associations will be identified to assist in explaining
what drives the changes in the gut microbiome.
v How will an individual benefit from
volunteering for this Microbiome Mapping Initiative?
Once
the study analyses is concluded, participants will receive a report detailing
their microbiome composition and how their sample relates to other individuals
on the CSIR campus e.g. an individual with a vegetarian diet will see where
their sample composition lies in comparison to an individual that consumes
meat.
v How could microbiome profile data
potentially help with the issue of COVID-19 and vaccine response?
The data
from this project is relevant to the respiratory virus infection because
perturbations in the gut microbiota relate to the lung-gut axis. Although,
corona virus primarily causes lung infection through binding of ACE2 receptors
present on the alveolar epithelial cells, it was recently reported that
coronavirus RNA was found in the stool of infected patients. The intestinal
epithelial cells, particularly the enterocytes of the small intestine, also
express ACE2 receptors and thus the gut microbiota plays a role in influencing
lung diseases and a normal microbiome profile may be altered. Numerous
individuals diagnosed with COVID-19 have also been shown to experience
gastrointestinal issues related to the interaction of this virus with the ACE2
receptors in the gut. Exposure to COVID-19 and diagnosis will be addressed in
the study, and this may enable an additional investigation of COVID-19 severity
of susceptibility and vaccine treatment response.
FOR MORE
INFORMATION PLEASE CONTACT:
Official project communications: cmmi@csir.co.za
CSIR PI:
Dr. Jerolen Naidoo | jnaidoo@csir.co.za
CSIR/Wits PhD student researcher:
Claudine Nkera-Gutabara | cnkeragutabara@csir.co.za