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INTRODUCTION
dietary recommendations to individual needs. It recognizes that each person is unique, with
distinct physiological, genetic, and lifestyle factors that influence their nutritional requirements.
This personalized approach aims to navigate the intricate landscape of individual dietary needs,
acknowledging that a one-size-fits-all approach to nutrition may not be effective for everyone.
In the pursuit of precision nutrition, various factors are taken into account, such as genetics,
metabolism, body composition, medical history, and lifestyle choices. Advances in technology,
including genetic testing and other biomarker assessments, play a crucial role in gathering
The fundamental principle of precision nutrition is to move beyond generic dietary guidelines
and instead focus on tailoring nutritional advice to address the specific needs and goals of each
individual. Lopez-Miranda J, Williams C, Lairon D. (2007 This approach recognizes that what
works for one person may not work for another, even if they share similar demographics.
individuals themselves to gather comprehensive data and design a personalized roadmap for
optimal nutrition. This may include identifying specific nutrient deficiencies, understanding
individual responses to certain foods, and considering lifestyle factors that impact dietary
choices.
The ultimate goal of precision nutrition is to enhance overall health, support weight
management, optimize athletic performance, and mitigate the risk of chronic diseases. Ordovas
JM, Corella D. (2004) By embracing this individualized approach, individuals can make
informed choices about their nutrition, leading to more sustainable and effective results.
Dietary information is also collected independent of genetics, as a feature in its own right.
management Zeevi D, Korem T, Zmora N, et al. (2015). In some cases, not only dietary features
in the long term but also the content of an individual meal and the timing features of the meal
(e.g., timing of the meal, time elapsed since the previous meal, etc.) are required to be known.
This is the case in research investigating postprandial meal responses, where the composition of
an individual meal in relation to its postprandial effect is relevant to know. Meal timing features
are relevant due to their impact on health. Metabolomics is an increasingly popular field that
quantifies the presence of small molecules in a sample with high accuracy using sophisticated
techniques such as nuclear magnetic resonance and mass spectrometry Rodgers GP, Collins FS.
(2020). As the field of metabolomics develops further and these techniques become more
frequently used, metabolomics will have a role to play in precision nutrition such as by
traditional methods (i.e., not assessed from a metabolomics perspective) is currently more
commonly seen and represents features in the group of clinical biochemical parameters. Included
here are common clinical measures such as blood-sugar, hormonal levels, blood counts, and
other parameters deemed to be relevant for a given precision nutrition intervention. other
precision nutrition features are the microbiome, due to its emerging role in health and
relationship with nutritional intake Ordovas JM, Ferguson LR, Tai ES, Mathers JC (2018);
activity parameters (PA amount and intensity, sedentary behavior, and energy expenditure (EE)),
due to their established interaction with health and disease; anthropometric features, such as
height, weight, body mass index (BMI), etc.; and personal features, which includes information
about individuals that can have an impact on model outcome such age, medical information and
Nutrition is a fundamental pillar of health, and diet is the modifiable factor that exerts the
greatest impact on human health and wellbeing (1). Dietary recommendations have traditionally
requirements and responses mimic the average response observed in study populations (2). The
improved our understanding of how factors such as genetic, microbiome, and metabolic
signatures, may predict whether what we eat supports or harms our health and to what degree
Studies in the field of nutritional genomics have unveiled associations between genetic factors
and metabolic responses to food, nutrient requirements, dietary preferences, and disease
outcomes. Advances in this and other areas of precision nutrition have added new dimensions
that help explain the variability in responses observed in otherwise well-controlled trials of diet
and nutrients. In particular, promising research results support the predictive potential of
assessments of the gut microbiome and metabolome—among other factors—and showcase the
As we bring new perspectives to the multiple dimensions of food and health, we are also
overcoming some of the barriers created by previous reductionistic thinking about nutrition. It is
in this context that precision nutrition is driving the scientific journey toward a more
personalized, predictive, and integrative systems approach to understanding how nature and
Precision nutrition can be considered as occurring at three levels: (1) conventional nutrition
based on general guidelines for population groups by age, gender and social determinants; (2)
individualized nutrition that adds phenotypic information about the person's current nutritional
status (e.g. anthropometry, biochemical and metabolic analysis, physical activity, among others),
and (3) genotype-directed nutrition based on rare or common gene variation Gibney MJ, Walsh
MC (2013). The ultimate goal is to integrate such sources of information to ensure that health-
care professionals, including dietitians, physicians, pharmacists and genetic counselors, know
sufficient concepts about nutrigenetics and nutrigenomics to decide on the most appropriate level
of care to achieve a precision nutrition which integrates phenotypical and genotypical issues as
well as social, environmental and metabolic factors Juma S, Imrham V, Vijayagopal P, Prasad C
(2014).
Precision nutrition is founded upon the concept of biological variability between individuals in
response to nutrition Ordovas JM, Ferguson LR, Tai ES, Mathers JC (2018). Thus, if the
variables responsible for causing this variation and their effect on a desired outcome variable can
be known, the outcome variable can be predicted, and this can be translated into nutrition advice.
What, then, are these variables? The answer to this question depends on the desired outcome
variable. There is no set of fixed variables that will provide any given output. Instead, features
thought to be of importance to predicting the outcome are selected on a per situation basis. In
some cases, this can reach to large numbers of individual features. however, they can be
separated into groups, here referred to as precision nutrition elements. one common precision
nutrition element is genetics. genetics is understood as a reason for many obvious examples of
variation, such as eye color and hair color, and this is extended to response to nutrition. indeed,
in some circumstances such as pku, genetics is an extremely relevant feature for precision
nutrition approaches. there is also some known relationships between genetics and weight
management, lactose (as in the case of lactose intolerance), metabolic syndrome , and more.
however, unlike with eye and hair color, what has become clear is that genetics can rarely
explain nutritional response entirely. in some cases, the genetic contribution is virtually absent,
as berry et al. witnessed when predicting postprandial triglycerides. another relevant factor is not
only genes alone but also their interaction with nutritional intake, termed nutrigenomics. genetic
variation impacts metabolism of dietary components, but also dietary components regulate gene
expression and signaling. failing to account for this interaction will naturally lead to
collected in precision nutrition approaches. gene-diet interactions for various chronic conditions
are known and as more continue to be discovered, precision nutrition approaches considering
LITERATURE REVIEW
Suboptimal diet and nutritional imbalance are well established as contributors to the global
burden of non-communicable diseases with a high incidence worldwide (Roth et al., 2018).
Globally, in 2017, an estimated 11 million deaths were attributable to dietary risk factors, with
more than half of these deaths associated with high sodium intake (Afshin et al., 2019). National
dietary guidelines designed to influence consumers’ nutritional behavior and dietary patterns
have had minimal impact (Kalmpourtzidou, Eilander, & Talsma, 2020). Thus, health targets, as
well as environmental targets, highlight the need for integrated population efforts to prioritize
food-based guidelines that shift diets towards high intake of whole grains, fruit and vegetables,
nuts and seeds and legumes (Springmann et al., 2020). However, the “one-size-fits-all” nature of
national and international dietary guidelines does not account for the diverse biological and
sociocultural factors that drive human conduct (Herforth et al., 2019). Human variability is wide-
ranging, and can include genetic, phenotypic, and physiological determinants, medical history,
and lifestyle practices, such as dietary habits and physical activity, as well as sociocultural and
socioeconomic factors, such as the food environment, gastronomy, and educational attainment
(Ordovas, Ferguson, Tai, & Mathers, 2018). This range of potential dietary influences has led to
the emergence of personalized and precision nutrition investigations to improve dietary patterns
(Ordovas et al., 2018), which are now central pillars of many national and international nutrition
research priorities and position statements (Ferguson et al., 2016; Kohlmeier et al., 2016).
The connections between nutrition and wellbeing are numerous and wide-ranging, concerning
individualized interventions to improve population and planetary health, the measurement and
assessment has been routinely performed to identify and treat undernutrition, however efforts are
now increasingly focused on quantifying the contributing factors to overnutrition and obesity
(Martínez-González et al., 2021). Indeed, the concept of personalized nutrition has been a long-
standing endeavor, which was first alluded to by the ancient Greeks, including Hippocrates
(“your food is the base of your health), and Galen ("personal attitudes and unique responses to
food”), and has since evolved to include nutriomics and the development of global tools to
The ultimate goal of personalized and precision nutrition is to preserve or ameliorate health and
wellbeing using dietary interventions, products or services that leveraging human variability
(Ferguson et al., 2016; Ordovas et al., 2018). However, there is no international consensus on the
definition of these terms, and terminology varies depending on the country, health field and
scope of the research question (Bush et al., 2020). For example, the terms precision public health
and precision health have been coined to consider the needs of digital health interventions and
data-driven public health systems to prevent non-communicable diseases (Canfell et al., 2022),
as well as the social determinants of health inequity (Olstad & McIntyre, 2019) when designing
precision nutrition approaches. For the purpose of this review, personalized nutrition will be
and other relevant information are used to design tailored nutritional advice and support for each
individual (Jinnette et al., 2021). In turn, the overarching term of precision nutrition is defined as
a methodology to integrate genetic, metabolic and environmental information at scale, which can
2018).
Systems biology has been responsible for some of the most important developments in the
the complexity of biological systems that starts from the understanding that the networks that
form the whole of living organisms are more than the sum of their parts. It is collaborative,
physics and others – to predict how these systems change over time and under varying
conditions, and to develop solutions to the world’s most pressing health and environmental
This ability to design predictive, multiscale models enables our scientists to discover new
biomarkers for disease, stratify patients based on unique genetic profiles, and target drugs and
other treatments. Systems biology, ultimately, creates the potential for entirely new kinds of
(McMahon et a; 2014).
Because systems biology requires constant attention to a very complex, very human social
experiment, ISB fosters the kind of financial, social and psychological environment in which the
world’s best scientists, technologists, engineers and mathematicians can collaborate and do their
best work.
A fundamental tenet of systems biology is that solving challenging biological problems always
requires the development of new technologies in order to explore new dimensions of data space
(Valleé Marcotte, 2016). New data types require novel analytical tools. This virtuous cycle of
physicists, physicians and others can come together in teams to tackle grand challenges. This is
ISB. And this describes what we call the “innovation engine” (depicted below) that drives our
always emphasize how our lab groups are intentionally and necessarily cross-disciplinary. One
of our labs, for example, includes molecular biologists, microbiologists, geneticists, engineers,
oceanographers, and even an astrophysicist (Ouellette, 2014). The complexity of biology in this
age of “big data” requires diverse teams in order to tackle such vast amounts of data and to make
sense of it all. New technologies that crunch data faster and more efficiently also permit
shareable insights more quickly. Our interdisciplinary teams have contributed notable advances
cancers.
levels. Social networks have transformed communications in the 21st Century, democratizing
our platforms for communications. At ISB we are also concerned with networks (Rudkowska,
2015). One of the tenets of systems biology we often refer to is the “Network of Networks.” On a
biological level, our bodies are made up of many networks that are integrated at and
communicating on multiple scales. From our genome to the molecules and cells that makeup the
organs in our bodies all the way out to ourselves in our world: we are fundamentally a network
of networks. Systems biology looks at these networks across scales to integrate behaviors at
different levels, to formulate hypotheses for biological function and to provide spatial and
temporal insights into dynamical biological changes. It is not enough to understand only one part
of a system when studying the complexity of biology. Therefore the framework of the “Network
of Networks” provides meaningful insight into understanding how systems biology’s approach is
different, more integrated and more capable of analyzing and predicting state transitions in
biological systems.
Whether we explicitly recognize it or not, multiscale phenomena are part of our daily lives. We
organize our time in days, months and years, as a result of the multiscale dynamics of the solar
system. Our society is organized in a hierarchical structure, from towns to states, countries and
continents. The human body is a complex machine, with many little parts that work by
themselves or with other parts to perform specific functions (Tremblay et al, 2015). Organelles
inside each cell in our bodies interact with one another to maintain a healthy functioning cell that
moves, differentiates and dies. These subcellular organelles and their processes govern each
cell’s signalling mechanism to interact with its neighboring cells, and form multi-cellular
systems called tissues (e.g. epithelial tissue, muscular tissue). Two or more types of tissues work
together to form an organ that performs a specific task (e.g. mouth, stomach, liver). Two or more
organs work together to form organ systems, such as the digestive system and the nervous
system, that perform more complex tasks. All these organ systems interact with each other to
enable a healthy functioning organism. Traditional approaches to modeling real world systems
focus on a single scale that imparts a limited understanding of the system. The pace at which
biotechnology has grown has enabled us to collect large volumes of data capturing behavior at
multiple scales of a biological system. Genetic as well as environmental alterations to the DNA,
expression levels of RNAs, expression of genes and synthesis of proteins – all this is measurable
now within a matter of days at a rapidly declining cost. So, it is really up to scientists and data
analysts to make use of this variety of data types and build integrative models that enable a
comprehensive understanding of the system under study. Multiscale models do just that. By
integrating models at different scales and allowing flow of information between them, multiscale
models describe a system in its entirety, and as such, are intrinsic to the principles of systems
With the completion of human genome sequencing and entering the-Omics area, the new term
“Nutritional Genomics” tends to replace the former “nutrient-gene interactions” (Rasinpera et al,
2004). It has been demonstrated that numerous genetic polymorphisms can influence protein
structure function. The Nutritional genomic area includes two parts: first Nutrigenomics that is
the study of interaction between dietary components and the genome, and the regulating changes
in proteins and other metabolism; second Nutrigenetics that identify the response to dietary
demonstrated that DNA metabolism and repair depend on a wide range of dietary factors that act
as cofactors or substrates in metabolic pathway, but much less is known about the impact of
cofactors and/or micronutrients deficiency or excess on the fidelity of DNA replication and
repair (3). Although the nutrients can influence the development of a particular phenotype, the
response to a specific nutrient that determined by the individual genotype has also to be
study and evaluate disease mechanisms and phenotypes. Omics data include, but are not limited
metabolites, proteins, microbial taxa, genes, or transcripts. For simplicity, we refer to these
molecules or entities as “analytes” throughout this work. Multi-omics data may also include
descriptors from multiple timepoints in one or more omic modalities, phenotype information
such as case/control labels, and relevant clinical variables such as age and sex. Collectively,
these data provide holistic insights into disease-driven biological pathway dysregulation, which
in turn provides preliminary evidence to drive the identification of new targets or intervention
strategies (Giner et al, 2001). While the utility of assessing multi-omics data is clear, the
integration of metabolomic data with other omic data poses significant computational challenges
that range from the need for developing statistical methods that are appropriately adapted to
multi-omics integration, to the need for providing comprehensive open-source resources that
provide validated relationships between omics types, biological pathways, and diseases. Multi-
omics integration typically follows the general workflow depicted in Figure 2.4.
Fig 2.4: The metabolome in the context of other omics data types and broad approaches
Ongoing efforts to support the integrative analysis of multi-omics data include the development
computational methods comprise novel metrics or novel applications of metrics that describe the
relationship between multiple omic data. These include univariate and multivariate analyses,
correlation networks, and traditional machine learning and deep learning techniques. A tool is an
implementation of a method with proven utility, many of which are designed to be user-friendly
software. Tools are often downloadable as an executable file or stored in a public code
repository. A series of methods and tools can be combined into workflows to perform an
analysis. Supported analyses could span the conversion of raw data (e.g., direct output from
instruments or a matrix of un-normalized metabolite and gene levels) to interpretable data that
explain a biological system under study. Workflows are particularly useful for conducting
repetitive tasks, and typically provide default parameters that are globally applicable, hence
MetaboAnalyst, XCMS, mixomics, miodin, and many others reviewed elsewhere (Goni et al,
2015). These workflows are particularly useful for end users that may not have a strong data
analysis or computational background and are invaluable for outputting reproducible results.
Ideally, methods, tools, and workflows provide up-to-date, publicly available datasets that can be
used as an input for testing and benchmarking, allowing users to readily evaluate the utility of
Many high-level analytical concepts are employed across workflows and data modalities.
Understanding the general steps taken by many workflows is crucial to compare the different
resources available for performing these tasks. Starting with raw data, prior to analysis, the data
quality of each omic data must be carefully assessed to ensure that measurements are
reproducible. This step typically requires a comparison of analyte measurements across technical
replicates using metrics such as standard deviation or the coefficient of variation. Samples should
also be evaluated, making sure that the overall distribution of analyte measurements is consistent
across samples. We note that identification of potential outliers (analytes or samples) is critical,
as some analytical models for multi-omics analyses (e.g., Principal Components Analysis and
Student’s t-test) could be strongly affected by the presence of outliers (Rukh et al, 2013). Other
preprocessing steps may include normalization to account for differences in experimental effects
such as differences in amounts of starting material and batch effects. Data are then typically
transformed so that they follow a Gaussian or “Normal” distribution, which is commonly used
for statistical analyses. Importantly, as some analyses will not work on missing data, missing
values can be imputed. We note that the imputation method used can affect downstream analysis
results, and thus imputation is still an active area of research (Olsen et al, 2016). Finally, noting
that the range of values may differ between omic modalities, appropriate scaling (e.g., to a
standard deviation of 1, z-scores) within and across omic datasets is critical for ensuring that
each omic modality contributes to the analyses and that the effect of one omic modality does not
dominate all analyses performed. Special scaling considerations should also be taken for time-
series data.
After preprocessing, omics data can be integrated in multiple ways. One can analyze or model
each omic modality separately and then integrate results (a posteriori integration) or one can
integrate data for all omic modalities before any statistical or computational modeling (a priori
differently. For example, scaling analyte measurements appropriately within each omic modality
is particularly critical when applying a priori integration. Additionally, the sample origin of the
multi-omics datasets dictates which integration approach can be used. For example, a priori
integration requires the measurements to be collected in the same biospecimens (tissue, blood,
etc.) or individuals to allow measurements to be matched to the same sample, while a posteriori
integration does not. When the analysis is performed on the same individual but different
biospecimens, e.g., genomic data from blood and metabolomic data from urine, we note that it is
not possible to evaluate direct relationships between genes and metabolites and how they may
relate to phenotype. However, it is feasible to evaluate whether one omic modality (e.g.,
metabolites) could act as a biomarker for what is occurring at another level (e.g., genome), or
one omic modality can be used to corroborate findings (e.g., biological pathways) uncovered in
Recognizing that other reviews provide a comprehensive list of available methods, software,
and/or workflows (Brunkwall et al, 2016), we instead focus on providing concepts and
considerations that are useful when choosing a method or tool appropriate for one’s desired data
types and analyses. As such, we discuss existing guidelines in data curation and tool
development and describe the building blocks that are used for developing computational tools
and workflows, namely unsupervised clustering approaches to assess data quality or separation
by sample type, approaches for modeling co-regulations between multiple omic modalities,
methods), and methods that provide a biological, chemical, and/or disease context to multi-omics
data (e.g., pathway analysis). We provide a summary illustration of these approaches in Figure
2.5.
Fig 2.5: Analysis techniques on a dataset with n samples and d analytes in two classes.
Further, the review focuses on open-source resources, and we reference example research
projects that make use of these resources in the context of metabolomic and other omic data,
denoting whether and to what extent the data used is publicly available.
Dietary assessment is an evaluation of food and nutrient intake and dietary pattern of an
individual or individuals in the household or population group over time. It is one of the four
comprehensively.
The other three are anthropometrics, biochemical parameters and clinical examination (Gibson,
2005). Dietary assessment methods are usually categorized according to the nature of the method
used as shown in Figure 1. Indirect methods utilize secondary data for assessing diets, while
direct methods collect primary dietary data from individuals. Prospective and retrospective
methods refer to the time food consumption is recorded. Prospective methods involve recording
the diet when the foods are being consumed; retrospective methods are based on a recall of food
(types and amounts of food consumed). The latter allows estimation of an individual’s food,
energy and nutrient intakes. Selection of an appropriate method for dietary assessment depends
on the purposes of the study, which may be to measure food consumption, nutrient intake or
eating habits.
expenditure) to estimate food available for consumption at the national and household levels.
Firstly, we will look at the Food Balance Sheet (FBS) 4, which provides food consumption
information at national level: food consumption is estimated from the point of view of food
supply.
Secondly, we will discuss about the Household Consumption and Expenditure Survey (HCES),
which provide food consumption information at household level: food consumption is estimated
from the point of view of food demand. Neither of the two methods directly obtain primary
dietary data from individuals to evaluate dietary intake or food consumption on an individual
basis. Indirect methods are useful for identifying trends in food availability and consumption
Direct methods using individual-based dietary assessment can be classified into two groups, as
described in Figure 2.6. Retrospective methods measure food intake from the past. These
methods include 24-hour recall, food frequency questionnaires (FFQ), and dietary history.
These methods include food records and the duplicate meal method. Estimates obtained from
direct methods are used to identify trends in food consumption, food and nutrient intakes, eating
patterns, and to evaluate diet–disease associations. Information provided by such methods can
also be used to calculate relevant food-based indicators for monitoring and evaluation purposes.
This section will describe dietary assessment methods used in individualbased surveys, and
analyse their application, focusing mainly on low resource settings, and will also cover the issues
Fig 2.6: Overview of dietary assessment methods to estimate food and nutrient
CONCLUSION
complex landscape of individual dietary needs. By acknowledging and embracing the unique
biological, genetic, and lifestyle factors that influence how individuals respond to food, precision
nutrition offers a more tailored and effective way to optimize health outcomes. The emphasis on
importance of treating each person as a distinct entity with specific nutritional requirements.
This approach is not only about addressing existing health concerns but also preventing future
issues and promoting overall well-being. The adaptability and flexibility inherent in precision
nutrition recognize that dietary needs are dynamic and may change over time, requiring
individuals working together, highlights the importance of a team approach in developing and
strategies.
As precision nutrition continues to evolve, fueled by ongoing research and technological
requirements further. This dynamic field has the potential to revolutionize how we approach
nutrition, moving away from one-size-fits-all recommendations to strategies that truly align with
individual dietary needs, providing a pathway to optimize health, prevent diseases, and foster
RECOMMENDATION
analyze genetic and biomarker data, and provide personalized dietary recommendations
Take an active role in understanding your own health and nutritional needs. Stay
informed about the latest research and advancements in precision nutrition. This
knowledge empowers you to make informed decisions and actively participate in the
Regularly monitor your progress and be open to adjusting your nutrition plan as needed.
Lifestyle, health status, and dietary needs may change over time, and ongoing assessment
allows for timely adjustments to optimize the effectiveness of your precision nutrition
approach
Understand that achieving optimal results with precision nutrition takes time. Be patient
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