Advances in Nutrition 14 (2023) 1–11

journal homepage: www.journals.elsevier.com/advances-in-nutrition

Perspective

Perspective: Multiomics and Machine Learning Help Unleash the

Alternative Food Potential of Microalgae
Mohamed Helmy 1, 2, Hosam Elhalis 3, Yan Liu 4, Yvonne Chow 3, Kumar Selvarajoo 1, 3, 5, 6, *
1
Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; 2 Department of Computer Science, Lakehead
University, Ontario, Canada; 3 Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR),
Singapore, Singapore; 4 Institute of Sustainability for Chemistry, Energy and Environment (ISCE2), Agency for Science, Technology and Research
(A*STAR), Singapore, Singapore; 5 Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore,
Singapore; 6 School of Biological Sciences, Nanyang Technological University, Singapore

A B S T R A C T

Food security has become a pressing issue in the modern world. The ever-increasing world population, ongoing COVID-19 pandemic, and
political conflicts together with climate change issues make the problem very challenging. Therefore, fundamental changes to the current
food system and new sources of alternative food are required. Recently, the exploration of alternative food sources has been supported by
numerous governmental and research organizations, as well as by small and large commercial ventures. Microalgae are gaining momentum
as an effective source of alternative laboratory-based nutritional proteins as they are easy to grow under variable environmental conditions,
with the added advantage of absorbing carbon dioxide. Despite their attractiveness, the utilization of microalgae faces several practical
limitations. Here, we discuss both the potential and challenges of microalgae in food sustainability and their possible long-term contribution
to the circular economy of converting food waste into feed via modern methods. We also argue that systems biology and artificial intel-
ligence can play a role in overcoming some of the challenges and limitations; through data-guided metabolic flux optimization, and by
systematically increasing the growth of the microalgae strains without negative outcomes, such as toxicity. This requires microalgae da-
tabases rich in omics data and further developments on its mining and analytics methods.

Keywords: microalgae, omics, machine learning, alternative proteins, systems biology

Statements of significance
Microalgae can be a promising platform for alternative protein production. However, there are several challenges related to cultivation costs,
protein extraction, and processing, as well as taste and sensory properties. The employment of modern omics techniques, artificial intelligence
(AI), and advanced data analytics can help unleash the full potential of microalgae in alternative protein production.

current climate changes affecting large parts of the world with

Introduction
severe drought and floods, together with recurrent pandemics
and the ongoing Russia-Ukraine conflict, the food security
The world is currently facing food security and cost inflation
problem severely manifests itself with added challenges in the
challenges, where millions of people are struggling for physical
food supply chain and reduced food production over the coming
and economic access to sufficient, safe, and nutritious food [1].
seasons. Moreover, the recent volatility in oil prices also adds
By 2050, it is estimated that the world will have ~10 billion
immense stress to common people worldwide, notably in the
people to feed [2]. In times of exceptional events, such as the

Abbreviations: AI, artificial intelligence; DE, differentially expressed; DW, dry weight; IAA, indispensable amino acids; KEGG, Kyoto Encyclopaedia of Genes and
Genomes; ML, machine learning; PCA, principal component analysis; TAG, triacylglycerol.
* Corresponding author. E-mail address: kumar_selvarajoo@bii.a-star.edu.sg (K. Selvarajoo).

https://doi.org/10.1016/j.advnut.2022.11.002
Received 22 April 2022; Received in revised form 31 October 2022; Accepted 9 November 2022; Available online 23 December 2022
2161-8313/© 2022 The Author(s). Published by Elsevier Inc. on behalf of American Society for Nutrition. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

developing world, as the overall cost of food is significantly There already are several examples of single-cell organisms
increasing [3]. Collectively, these issues pose an unprecedented being included in human diets either as food or ingredients (e.g.,
threat, as current agricultural approaches and food distribution mushrooms and yeast). Fungi, such as Fusarium venenatum which
systems are both unable to cover the current need and cope with grows on carbohydrate substrates, eliminating the need for an
the increased nutritional demands for the future [4]. exogenous protein input, produces mycoproteins that are used as
Proteins, which are vital components of food, are getting meat and chicken analogs, and are available in markets of many
more traction recently as any forthcoming food output should be countries [23]. Bacteria, which are a very rich source of protein,
nutritional. The current major source of protein is plant-based, have long been included in human diets, mainly for fermenting
and increasing its production to match the demand with tradi- food and as probiotic drinks [24,25]. However, the high contents
tional agricultural approaches is highly resource-intensive with of nucleic acids in bacteria, which can be harmful, require
an overall negative environmental impact [5]. The production of further technological development for neutralization [20].
animal-based proteins, on top of concerns regarding animal Microalgae-based protein products can be classified into 5
welfare and healthy diets, is also a burden to agricultural land groups based on their protein content and the degree of purifi-
use and water resources and, thus, increases greenhouse gas cation. A whole-cell protein levels range from 60% to 89% with
emissions [6]. The current food production system accounts for ~40%–50% comprising of protein components, protein con-
between 20% and 30% of the total environmental impact and for centrates, isolates, hydrolysates, and bioactive peptides [26].
almost 30% of global greenhouse gas emissions [5]. Therefore, The microaglae protein components are characterized by their
there is an urgent need for a transformation in the food system slightly denatured protein state compared with other types
that supports its availability, accessibility, affordability, and because of their preserved intact rigid cell wall and membranes
desirability [7]. during processing; however, it has been reported to be poorly
Novel plant-based and laboratory-grown meat protein alter- digestible [27]. To produce protein concentrates and isolates, the
natives have recently been developed [8,9]. Several plant-based host-cell protein is subjected to several steps of extraction and
products are successfully commercialized, and the first purification using chemicals and heat. Subsequently, the
laboratory-grown meat product has recently been approved by extracted protein is subjected to enzymatic degradation into
the authorities in Singapore [10]. Although this is a positive new smaller peptides to form protein hydrolysates and bioactive
direction toward the alternative food initiative, especially peptides that correlate with positive contributions to human
imminent in current food challenges [3], such novel food prod- physiology functions [26,28].
ucts usually involve additives, genetic modifications, or syn-
thetic modifications that may improve the product safety and Microalgae as Potential Biofactory Platform
quality; however, they do not yet meet the increasing consumer Various microorganisms, including bacteria, mushrooms,
demand for healthy, vegan, or natural food products [11–13]. yeasts, and microalgae, have been explored as sources for
Furthermore, although plant proteins are typically insufficient in alternative proteins [20,29]. Microalgae form a diverse group
essential amino acids compared to animal proteins, containing ~200,000 species of photosynthetic and heterotro-
laboratory-grown meat faces religious and cultural challenges phic microorganisms with morphological, physiological, and
[14]. A new solution is needed to provide protein without genetic diversity [30] (Table 1). Some microalgae species such as
causing climate change, deforestation, and depletion of water Arthrospira platensis, Spirulina maxima, Chlorella vulgaris, and
resources. Chlorella pyrenoidosa contain up to 70% of the dry cell weight
(DCW) as protein [31]. Such high protein concentration exceeds
Alternative Proteins from Single-Cell Organisms the protein levels found in many fungi including several Asper-
Compared with plant or meat proteins, producing protein gillus, Fusarium, and Saccharomyces species that were reported to
from single-cell organisms is thought to be a good alternative for have concentrations ranging from 40% to 50% (DCW) [32,33]
several reasons: 1) they require less water; 2) wastewater can be and are comparable with some types of bacteria [34]. In addi-
recycled within the process; 3) they need little land area; 4) they tion, microalgae have less nucleic acid and their amino acid
are less harmful to the environment with minimal contribution profile is closer to conventional protein sources such as eggs and
to climate change (as they have a smaller net carbon footprint, oyster larvae [35,36]. Yet, they differ widely in terms of cellular
through releasing oxygen and sequestrating carbon dioxide); 5) composition and metabolic characteristics [24].
unlike plants, they do not require herbicides, fertilizers, or an- In response to external conditions, microalgae synthesize
tibiotics; 6) they can be cultured on non-agricultural land; and 7) different metabolites (primary and secondary), many of which
their positive impact on human health is highlighted as many of are of significant health, nutritional, and industrial value [37].
these organisms are already used as supplements for human or in Some microalgae can produce compounds with anticarcino-
traditional medications [15–19]. genic, anti-inflammatory, immunomodulatory, antimicrobial,
Therefore, single-cell organisms, such as bacteria, yeasts, or antioxidative, antihypertensive, and anticoagulant activities
algae, might be promising sources of alternative proteins [20]. [38]. They can also produce environmentally friendly agricul-
They were reported to have high protein concentration and tural compounds such as plant biostimulants [39]. In addition,
contain amounts of indispensable amino acids (IAAs) that are microalgae are known to grow effectively using CO2 as a carbon
important for health, growth, and pregnancy, and they are usu- source, making them play significant roles in carbon capture
ally obtained from meat-based proteins or plant alternatives while producing alternative proteins for food production. On
[21]. Additionally, the amount of protein in some of these or- scaling up efforts, they are promising for environmental and
ganisms was shown to be relatively similar to oilseed plants, and sustainable biomanufacturing. Therefore, microalgae present a
they can be mass-produced using standard bioreactors [22]. promising platform for pharmaceutical and industrial

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M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

TABLE 1
Microalgae classification and examples of some key metabolites
Class Species Metabolite Biological activities
Cyanophyceae (blue-green algae) Arthrospira platensis c-phycocyanin Antitumor, antioxidant, antibacterial, anti-
Arthrospira maxima inflammatory, hepatoprotective
Chlorophyceae (green algae) Chlorella sp. β-1,3-glucan-peptides Immune-stimulating, antioxidant, blood lipid
reducing, antitumor
Haematococcus pluvialis Astaxanthin Antioxidant, antihypertensive, anti-inflammatory,
anticancer, photoprotective
Dunaliella salina β-carotene Antioxidant, anticancer, eye protective
Porphyridiophyceae (red algae) Porphyridium sp. Phycoerythrin-polyunsaturated Antiviral (herpes), antibacterial, antioxidant,
fatty acids immunomodulatory
Bacillariophyceae Phaeodactylum tricornutum Fucuxanthin Insulin resistance improving, anticancer, anti-
inflammatory, eye- and cardiovascular-protective

applications, as the cultivation processes can be optimized in a have a relatively low content of nucleic acids, which makes
controlled culture. A better understanding of microalgae biology, them more suitable for edible applications [50]. They can be
genetics, and cultivation processes will lead to a bioproduction grown using traditional fermentation approaches or
platform that is environmentally friendly and economically bioreactors; although growing microalgae in open ponds is
viable [37]. also common, it risks biological and chemical contaminations
Over the last 2 decades, microalgae research has attracted [51].
great interest for the potential to produce high-value com- In recent years, employing microalgae as an innovative plat-
pounds, biofuels, and waste effluent remediation [40]. Previ- form for food, feed, and health products is generating immense
ously, in addition to the cost of harvesting, extraction, and interest. The primary focus of these attempts was to use micro-
refinement, most of the research was geared toward biofuel algae to produce compounds that are used as food supplements,
application where the photosynthesis requirement was a signif- additives, or ingredients [48]. Currently, microalgae products
icant cost barrier [41]. It currently is estimated that the cost of are available in several pharmaceutical forms such as tablets,
producing 1 L of microalgae-based biodiesel in photobioreactors liquid or capsules, and baking ingredients for pasta and snacks
with 60% oil content is $3.96–$10.56. This is 10-fold greater [24,48]. These products include β-glucan content, food in-
than the cost of producing 1 L of soybean-based biodiesel [42]. gredients, and whole-cell products produced using food-grade
From 70%–80% of the total cost is attributed to the downstream microalgae species such as Arthrospira, Arthrospira, Chlorella,
processing of microalgal biomass where energy consumption Dunaliella, Aphanizomenon, Euglena [52–54]. Microalgae are also
represents the most expensive factor in the process [43]. used to produce feed for aquaculture, where they mainly provide
Microalgae-based waste removal of chemicals or nutrients might livestock with fatty acids (e.g., omega-3 fatty acids), pigments,
be achieved by either conversion to different forms or accumu- and carotenoids, while their high protein content contributed to
lation in biomass. However, harvesting at low cost and dealing fish nutrition [55]. Because of their high nutrient contents,
with contaminants are still potential challenges for its wider several microalgae species have been used in aquaculture as a
applications [44–46]. live feed for bivalve molluscs (i.e., mussels, clams oysters, and
clams) of all growth stages [56].
Microalgae Utilization in Food and Health In addition to utilization for producing health products, food
Industries ingredients, and feed, microalgae are a promising source of
Microalgae can be used as a key platform for alternative alternative proteins mainly due to their generally high protein
protein production due to several positive reasons: 1) Some content ranging from 6% to 71 % of dry matter [49]; for example,
microalgae contain relatively high concentrations of essential A. platensis was reported with 630 g protein/kg dry mass [20].
amino acids including lysine, tryptophan, methionine, threo- Furthermore, the composition of IAA in A. platensis is nearly the
nine, histidine, valine, and isoleucine that are comparable with same as that of animal protein and exceeds that of most
those reported in oyster larvae and eggs [35,36]; 2) they also plant-derived protein [57]. Similarly, Chlorella and Arthrospira
contain polyunsaturated fatty acids including omega-3 fatty species are promising due to their best protein quality [49]. Ac-
acids, such as docosahexaenoic acid and eicosapentaenoic acid, cording to the recommended requirements of essential amino
carotenoids, chlorophyll, and pigments; 3) they can be used as a acids by the World Health Organization and the Food and Agri-
source of vitamins such as vitamin A, ascorbic acid (vitamin C), culture Organization, these 2 species have proteins with balanced
nicotinic acid, tocopherol (vitamin E), thiamin (vitamin B1), amino acid profiles suitable for human requirements [58,59]. The
riboflavin (vitamin B2), pyridoxin (vitamin B-6), cobalamin amino acid profiles of these 2 species are also similar to that of
(vitamin B-12), folic acid, pantothenic acid, and biotin (vitamin animal-based protein foods such as eggs [60]. By making use of
H), in addition to fiber and other valuable nutrients [47]; 4) the ability of these species to grow heterotrophically, i.e., in the
some microalgae are heterotrophic where they can grow on absence of light, and of utilizing an external carbon source, So-
both light and carbon source at comparable rates to other mi- phie’s Bionutrients, a food-based startup, plans to generate
crobes; and 6) they require simple and defined media to grow microalgae-based food protein as fast as yeast; their first proto-
[24,48,49]. Furthermore, many microalgae strains are type contains 50% protein by dry biomass weight. Microalgae are
high-protein producers with up to 70% dry weight (DW) pro- also unique in its seafood umami flavor, and hence, they are a
tein contents. Additionally, compared to bacteria, microalgae potential alternative to conventional seafood [61]. Nevertheless,

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M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

the microalgae contribution to global food security is still limited Kluyveromyces marxianus on whey, Fusarium graminearum on
due to several challenges faced by the new field. molasses, Candida utilis on starch, and Cellulomonas sp. on
bagasse [50]. Moreover, more than fifty types of media are used
Challenges to Microalgae Utilization for Protein for microalgae cultivation [79], and some of them such as f/2
Production medium (enriched seawater medium, National Centre for Marine
Conventional protein sources including plant proteins are Algae and Microbiota, Maine) cost ~$55/L. Similarly,
widely consumed worldwide due to their relatively high protein cost-effective storage techniques are well established and re-
digestibility [62,63]. In contrast, microalgae represent an age-old ported to maintain the microorganism viable and free of
high-protein product for human consumption [49], and its com- contamination and genetic alterations by bacteria and fungi,
mercial application has not virtually materialized and is restricted including cryopreservation and lyophilization that are highly
to only a few species such as Chlorella vulgaris, Scenedesmus obli- utilized [80,81]. Common ways to conserve microalgae are
quus, Dunaliella sp., and Arthrospira platensis [59,64,65]. This either by routine serial subculturing or cryopreservation [79].
limitation, for instance, might correlate with their safety as some The former method is a labor- and consumable-intensive process.
microalgae species belonging to diatoms, dinoflagellates, and In addition, the long continuous subculturing may result in cul-
cyanobacteria were reported to produce toxins [66]. In addition, ture degeneration and loss of essential morphological and
allergenicity was also recorded with consumption of microalga physiological features with the high possibility of cross
species such as Arthrospira platensis [67,68]. Overall, the safety contaminations [79,82]. On the other hand, cryopreservation
data for existing microalgae are still very limited, and the future provides an alternative approach that overcomes such draw-
selected candidates will have to undergo several toxicological and backs, and nevertheless, it has also been reported to cause cul-
allergen tests to confirm their safety, which introduces re- ture death of some algae strains [83].
strictions to their commercial applications. For large-scale cultivation, a few studies have been conducted
Currently, only Chlorella vulgaris and Arthrospira sp. are sold on on cost-effective cultivation of algae using several systems, such
the market shelves, usually as health supplements in tablets or as photobioreactors, polyethylene sleeve, and open ponds [84].
powdered form. These are of dried cell biomass without further Norsker et al. [65] reported costs of €4.15, €4.95, and €5.96/kg of
cellular extraction [69]. Bioactive compounds of much higher price algae for horizontal tubular photobioreactors, open ponds, and
also are being extracted and purified from other algae species (e.g., flat panel photobioreactors, respectively. The authors believed
Dunaliella salina and Haematococcus pluvialis), but food protein in- that through optimizing the cost factors, such as mixing, irradia-
gredients from microalgae are still at the premarket stage [70]. The tion, photosynthesis, and medium components, the cost declined
low level of exploitation of these highly nutritious microbes is to €0.68/kg. Another economic study reported the overall costs
linked to the missing data on the algal biology, toxicity, food safety, ranging €1.4–€2.5 [85]. Furthermore, the cultivation process is a
and optimal growth conditions and feed [71]. species-specific and non-generic process due to the variations of
Compared to animal source proteins, microalgae have char- species nutrients, light, temperature, pH, and other requirements
acteristic strong cellulosic indigestible cell walls that are asso- of culture conditions [86]. Similarly, downstream processing is
ciated with lower digestibility and further limit their also species-specific. This process includes harvesting, drying,
acceptability [63,72]. Thus, post-harvesting treatments are and by-product purification [87]. Furthermore, the variation
required to disrupt the cell wall and make the extracted protein among alga species in geometric, cell weight, and mucilage
more accessible for digestive proteases. This requires a down- secretion also makes such processes species-specific and requires
stream process such as enzymatic hydrolysis using pancreatin considerable research to be optimized [88,89].
enzymes, which was reported to improve the in vitro hydrolysate Microalgae are generally slow-growing compared to bacterial
digestibility of Chlorella vulgaris and Arthrospira platensis by 70% or yeast culture in nutrient media, and growth is limited by the
and 97%, respectively [73]. daylight cycle, CO2 availability, and photoinhibition during the
In addition to digestibility, the microalgae sensory quality peak of day. For photosynthetic modes of cell production, open
presents another challenge. Although the desirable sensory pond systems of cultivation remain the cheaper option, but
qualities of the conventional protein sources represent a major productivity and contamination risks by bacteria, protozoa, and
cause of wider consumer satisfaction, in contrast, the green other algae are typical limitations [90]. Furthermore, less than a
color, odor, and fishy smell associated with microalgae are meter of culture depth poses light penetration limitation to the
considered undesirable features for consumer choice [28,74]. cells [91]. Several photobioreactors are designed to reduce the
Volatile sulfur and diketone compounds were reported to have light penetration depth problem but, often, performance
fishy odors in microalgae [75]. Unpleasant odors might be increases with the increase of both equipment capital and
mitigated by various routes such as changing medium compo- operational cost [92]. Fouling, aeration, and light-source direc-
nents, altering harvest time, and cooking [76,77]. Overall, the tion are some of the operational challenges involved. Hence,
organoleptic assessment of microalgae is important for its use as several commercial approaches have focused on heterotrophic
a source of alternative protein and further research is required to species capable of higher productivity when supplied with
improve their digestibility and sensory quality. nutrient media [93].
Microalga cultivation is expensive and the possibilities to
decrease its production cost remain a major challenge [78]. Systems Biology and Machine Learning Approaches
Culture conditions of microalgae such as temperature, pH, light, Help Tackle the Challenges
aeration, and nutrients potentially influence their overall pro- Most of the challenges faced in the utilization of microalgae
duction cost and biomass yield. Cheap carbon sources were are centralized around the understanding of their biology and
successfully used to produce single cell protein, including genetics. For instance, the process of growing and optimizing

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M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

microalgae in the laboratory as a source of alternative proteins produce large volumes of data, such as multiomics data, that
requires an adequate understanding of microalga biology that require advanced data mining and analytics to generate a holistic
involves many variables and multiple steps. This, therefore, view of the microalga biology at the systems level. Thus, data
makes it a highly complex process that requires long time in- analytics and machine learning approaches are required for the
vestment and high-cost and labor-intensive experiments. The success of the research and process. Alternatively, systems
processes face multiple levels of challenges starting with the biology approaches, which include biosimulation using mathe-
identification of food-safe strains, evaluating their protein pro- matical models (e.g., nonparametric steady-state or dynamic in
duction capacities, and assessing their abilities to grow under silico models) [96], can provide mechanistic understanding and
laboratory/bioreactor conditions [94,95]. These steps also predictive opportunity of microalgae research (Figure 1).

FIGURE 1. Systems biology and machine learning pipeline. (A) Microalgae data can be stored or retrieved from private/public databases. They
can contain gene/protein sequences and structures and omics data (transcriptomics, proteomics, and metabolomics). (B) The data from (A) can be
used to perform biostatistics, data analytics, and machine learning to identify expression correlations; co-regulated clusters; and differentially
activated genes, proteins, or metabolites between samples. Metabolites and enzyme data can be used to develop and test a genome-scale model to
identify growth constraints, as well as kinetic models, which could highlight bottlenecks in metabolic fluxes. (C) The model-optimized microalga
strains can then be experimentally tested for better yield, especially at a commercial scale. DE, deferential expression; SOM, self-organization map.

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M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

Due to the overwhelming interest in using microalgae to pro- which replaced the traditional way of measuring the occurrences
duce biofuel and high-value products (i.e., pharmaceuticals, food of single isolates within a mixed culture. Theoretical models can
supplements, and pigments), there is a large amount of previously also be used to predict, control, and optimize the culture and
published genome and transcriptome data of different microalga growth conditions of microalgae and to direct their metabolism.
species under different growth conditions [97–99]. Genomic For example, it was postulated that lipid yield can be increased
(DNA-sequencing) and transcriptomic (RNA-sequencing) studies by 5 times to reach a realistic maximum of 0.5 g triacylglycerol
play a crucial role in the qualitative and quantitative improvement (TAG)/mol photons [121].
of microalgal biomass [98,100]. Currently, the Gene Expression Another aspect of theoretical or computational models is
Omnibus database has over 6350 gene expression datasets for based on metabolic network stoichiometry. Here, thousands of
algae, and the Genome Online Database has 230 alga genome metabolites and their reactions can be simulated with reasonable
sequencing projects [101,102]. The genomic and transcriptomic computational cost and prediction outcome, especially when
information can be used to assess metabolic pathways and their biological restrictions, such as growth constraints, are added
respective genes of the enzymes that are involved. Furthermore, a [77]. In one study, Betenbaugh et al. [99] developed such a
good annotation of the whole genome, alongside a comparative constraint-based genome-scale model and optimized metabolic
transcriptomic approach, not only allows gaining insight into the fluxes for sustainable growth with increased nutrient supply and
metabolic pathways and their key-enzymes but also enables iden- lipid productivity in Chlorella vulgaris.
tification of regulatory factors, transcriptional factors, and pro- Another area of mathematical models that have been widely
moters of gene expression [103–105]. used for microbial metabolic optimization research is kinetic
Computational models developed for biological applications models. These models are based on ordinary differential equa-
require actual experimental data to be used in the building, tions applied to each biochemical reaction in a metabolic
training, and testing processes of these models [106]. Data are network [96]. Although sparingly applied in microalga research
usually obtained through well-defined experiments. Quantitative so far, they have been used to simulate dynamic lipid metabo-
high-throughput transcriptomic data measuring the dynamic lisms, TAG synthesis, and growth under multiple cultivation
gene expression profiles of the microalgae, under multiple growth conditions and have led to novel insights. Lenka et al. [122] have
conditions, can be analyzed to identify differentially expressed provided a succinct review of several modeling applications in
(DE) genes between the conditions. These can be subsequently the microalga lipid and TAG yield increase.
clustered into distinct expression patterns. Such specific clusters The culture, harvesting, and extraction costs are a major
with the aid of bioinformatic databases, such as UniProt data- limitation to the commercialization of microalgae. The organic
bases, Gene Ontology Resource [107], Kyoto Encyclopaedia of carbon sources are indispensable for microalga growth, and they
Genes and Genomes (KEGG) [108], PathwaysCommons [109], account for >80% of the overall cost of the used culture medium
and Reactome [110], can rapidly highlight genes and their [123]. Cheap carbon sources such as CO2, lignocellulosic
pathways that are involved in alternative protein production biomass, organic acids, and other wastes might be explored to
[111]. For example, KEGG databases highlight genes that are reduce the overall production cost [124]. Screening of genes and
differentially present between different strains and species, and enzymes that can degrade such substrates among microalga
these can be used to focus on alternative protein pathways [112]. species using available databases, such as the KEGG database,
To illustrate the utility of mathematical approaches, there are might potentially save time, cost, and resources in experimental
several extrinsic environmental factors reported to potentially conformation compared to the traditional laboratory screening
affect the tubular photobioreactors and open pond large-scale process, which is expensive and labor- and time-consuming [96].
culturing processes of microalgae, including fluctuation of Furthermore, metabolic engineering might also be used to
daily temperatures, dissolved oxygen, and light intensity [113, encode the desired hydrolytic enzymes into selected microalgae.
114]. Applying predictive microbiology mathematical models to Similar approaches have been successfully applied to improve
correlate such changes and predict the microalgae growth per- the capability of industrial microbes to break down substrates
formance, one could optimize the culturing process and decrease that cannot be degraded naturally [125,126].
the overall costs. For example, the Geeraerd and Van Impe Natural mutations were reported among alga isolates that
Inactivation Model Fitting Tool has been successfully applied to produced the generally desired lighter-colored green biomass.
bacteria, yeast, and filamentous fungi growth performance To investigate such positive attributes systematically, computa-
covering both classical log-linear and nonlinear performance tional genomics approaches might be used to identify novel
curves of microbial survivors [115,116]. These tools and equa- secondary metabolite-related genes, such as that of carotenoids,
tions were reported to evaluate the growth performance of mi- that can be biochemically determined using the available data-
croorganisms under several variables including pH, inoculum bases with the well-known Escherichia coli expression systems.
size, temperature, mixed culture, and incubation time to deter- Such approaches could be aimed to modulate and improve the
mine the actual growth behavior in a particular or desirable sensory quality of green microalgae [127,128]. For example,
environment [117–120]. Overall, the authors of these studies computational techniques unleashed the phylogenetics of the
used their observations to develop a model describing the impact carotenoid pathways and helped study their gene expression and
of several variables and their combined effects on the growth of mutations, thereby providing better opportunities for increasing
the target microorganism. For example, Ram et al. [120] illus- production rates [129].
trated a possible way to overcome the laborious and expensive High-throughput data analytics also play a major role in
traditional way of evaluating the microbial fitness of different recent microalga research. A transcriptome-wide analysis by
stains in a mixed culture. In this study, a computational approach Azaman et al. [130] on Chlorella sorokiniana showed 2000
was created from growth curves of mono- and mixed cultures, upregulated and downregulated genes related to lutein

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biosynthesis, fatty acid biosynthesis, TAG accumulation, starch TABLE 2

biosynthesis, sucrose biosynthesis, etc. under the mixotrophic Overview of some key contributions of systems biology and AI in
condition. In another work, by studying differentially activated microalga research
genes from transcriptome-wide data, Kobayashi et al. [131] Methodology Key contributions Reference
illustrated a safe way to produce green Chlamydomonas rein-
Computational analysis of Identify suppressor [140]
hardtii with a chlorophyll-deficient mutant by the deletion of MFA data: using proteins of methionine
phytoene synthase. Here, an understanding of the gene regula- mathematical and and cysteine biosynthesis
tion mechanism might increase consumer acceptance of micro- statistical approaches to Increase carbon fixation [141]
algae as an alternative protein source, since the dark process and analyze and biomass through the
MFA data identification of an
green–colored biomass generally decreases customer desire, as
alternative pathway for
discussed above. isoleucine synthesis
Machine learning (ML) algorithms can also be used to analyze Investigate and increase [142]
the transcriptome data and protein structure data of many the astaxanthin synthesis
available microalgae datasets to predict the connection between Control the hydrogen [143]
production through the
genes and pathways/networks to reveal novel gene regulation
regulation of hydrogenase
mechanisms [132,133]. Some of the data analytic and AI and poly-
methods, such as PCA, random forest, k-means clustering, and β-hydroxybutyrate
support vector machine, can be utilized to predict key pathways synthase
and rank them based on their expression levels and statistical Genome-scale metabolic Predict alternative [144]
model: a mathematical metabolic routes for fixed
scores [96]. This will subsequently allow for testing and vali-
approach for simulating carbon through an
dating the best ranking pathways biosynthetically on stable metabolism in genome- analysis of all possible
microalgae for enhanced production of alternative protein [134, scale reconstructions. It double reaction
135]. Thus, advanced data mining and analytics methods (e.g., uses steady-state knockouts
AI) can provide breakthroughs through analyses and predictions assumptions and
stoichiometry of all
that cannot be achieved otherwise [96].
known reactions of the
Another area of ML models under current development is metabolic pathway
related to those attempting to integrate complex dynamic omics Dynamic or kinetic Control the growth of the [145]
data [136]. Here, the models are first developed to learn between modeling: microalgae in the
high-throughput omics “training” data linking an input to an computational bioreactors with artificial
modeling of metabolic lights
output (e.g., proteomics with metabolomics in wildtype). Next,
pathways using Predict the [146]
the trained model is to be tested on a different “test” data (e.g., enzymes kinetics and photosynthetic apparatus
under mutant or different growth condition) to finalize a rate laws status (open, closed, and
machine-learned connectivity model that, without knowing the damaged reaction
detailed mechanistic understanding of the cell system, will be centers) under different
lighting conditions
able to guide synthetic biology applications [137–139]. How-
Optimize the growth of [147]
ever, such models are yet to be developed or tested in microalga microalgae for increased
research, partly due to the lack of expertise or domain knowl- biomass through the
edge in the cross-disciplinary area. Table 2 lists current examples simulation of the
of systems biology and machine learning contributions to production in a virtual
microalga research. system
Machine learning: data Analyze microscopic [148]
In conclusion, overpopulation, the COVID-19 pandemic, and analytics, imaging for the
ongoing geopolitical conflicts are some of the major challenges bioinformatics, and classification,
faced in today’s world that are negatively impacting global food deep learning using identification, and growth
security. Increasing food production through most of the artificial neural stage estimation of
currently available approaches (agriculture, livestock, and fish- networks microalgae
Analyze microscopic [149]
ing) to match the increasing demand is not possible due to imaging for the
limited resources, environmental impact, and increased aware- identification of
ness of healthier diets. This raises the need for unconventional individual microalgae in a
solutions and fundamental changes in the current food system. free or symbiosis state
Alternative food and proteins sources are 2 potential solutions to Improve the design of a [150]
semicontinuous algal
close the gap between food supply and demand. Microalgae can cultivation to overcome
be a potential platform for alternative proteins production. They the mutual shading that
are known for their high protein content and producing proteins limited the growth
rich in essential amino acids, and can grow in different envi- Define and diagnose algal [151]
ronments using cheap and recyclable feed, such as wastes. They cultures under stress
conditions to save them
are also being successfully used as a live feed in aquaculture. from imminent crashing
Utilizing microalgae to produce alternative proteins require by utilizing 4 biomarkers
overcoming of several limitations, such as finding the most Predict phosphorylation [152]
suitable strains, reducing the cost of cultivation, harvesting and site from mass
extraction, increasing the yield from the proteins, eliminating (continued on next page)

7
M. Helmy et al. Advances in Nutrition 14 (2023) 1–11

TABLE 2 (continued ) writing, and supervised the entire study; and all authors: read
Methodology Key contributions Reference and approved the final manuscript.
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