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The expanding field of alternative proteins represents a transformative approach to addressing global food security and sustainability challenges. Among these, fermentation-derived alternative proteins cultivated from microorganisms such as fungi, bacteria, and algae offer a promising avenue for sustainable protein production. This review explores the selection and utilization of raw materials to produce microbial proteins through fermentation processes. Critical raw materials include agricultural byproducts, industrial waste streams, and specifically designed feedstocks, which not only mitigate environmental footprint but also enhance the economic viability of production systems. The utilization of lignocellulosic biomass and molasses has demonstrated considerable promise, attributed to their abundant and renewable nature. The review underscored the necessity of exploring specific areas to enhance the viability of producing microbial protein from diverse raw materials. These areas include improving pre-treatment strategies to enhance substrate suitability for fermentation, optimizing fermentation processes for increased yield and reduced costs, and developing more resilient microorganisms capable of thriving on varied substrates. These strategies are crucial for advancing the production of alternative proteins through fermentation, in addition to raw material selection, which is vital in the scalability and sustainability of alternative protein production through fermentation, emphasizing the need for continued research and innovation in this field.
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REVIEW
Systems Microbiology and Biomanufacturing
https://doi.org/10.1007/s43393-024-00294-4
diets mainly centred on meat, which demands substantial
resources for production, including water, energy, feedstock,
fertilizers, pesticides, and veterinary medicines. This evolv-
ing dietary landscape, driven by population growth and ris-
ing wealth, emphasizes adopting sustainable consumption
and production practices to ensure food security and envi-
ronmental sustainability [1, 2]. Animal-based protein value
is also linked to signicant health risks, including cardio-
vascular diseases and cancer [3, 4]. These pressing issues
highlight the urgent need for alternative protein sources that
promise lower environmental impacts and enhanced sus-
tainability with a promise to achieve the Sustainable Devel-
opment Goal of Zero Hunger.
The alternative protein market is expected to reach
$290 billion by 2035, underscoring the signicance of these
innovative food sources [5, 6]. Alternative proteins encom-
pass a diverse range of sources, including plant-based pro-
teins (e.g., peas, soy, and rice), proteins from cultivated
animal cells, insect-based proteins with robust nutritional
Introduction
The global population is expected to reach 10 billion by
2050, leading to a substantial increase in food demand. This
surge is accompanied by rising wealth, especially in rapidly
industrializing nations where improving incomes are lead-
ing to changes in dietary preferences. As wealth expands,
there is a notable shift towards higher-quality, protein-rich
Lachi Wankhede and Gaurav Bhardwaj contributed equally.
Satinder Kaur Brar
satinder.brar@lassonde.yorku.ca
1 Department of Civil Engineering, Lassonde School of
Engineering, York University,
North York, Toronto, Ontario M3J 1P3, Canada
2 Department of Bioprocess Engineering and Biotechnology,
Federal University of Paraná (UFPR), Curitiba,
PR 81530-900, Brazil
Abstract
The expanding eld of alternative proteins represents a transformative approach to addressing global food security and
sustainability challenges. Among these, fermentation-derived alternative proteins cultivated from microorganisms such
as fungi, bacteria, and algae oer a promising avenue for sustainable protein production. This review explores the selec-
tion and utilization of raw materials to produce microbial proteins through fermentation processes. Critical raw materials
include agricultural byproducts, industrial waste streams, and specically designed feedstocks, which not only mitigate
environmental footprint but also enhance the economic viability of production systems. The utilization of lignocellulosic
biomass and molasses has demonstrated considerable promise, attributed to their abundant and renewable nature. The
review underscored the necessity of exploring specic areas to enhance the viability of producing microbial protein from
diverse raw materials. These areas include improving pre-treatment strategies to enhance substrate suitability for fermen-
tation, optimizing fermentation processes for increased yield and reduced costs, and developing more resilient microor-
ganisms capable of thriving on varied substrates. These strategies are crucial for advancing the production of alternative
proteins through fermentation, in addition to raw material selection, which is vital in the scalability and sustainability of
alternative protein production through fermentation, emphasizing the need for continued research and innovation in this
eld.
Keywords Alternative proteins · Lignocellulosic biomass · Agricultural waste · Wastewater and · Gas stream
Received: 22 May 2024 / Revised: 10 July 2024 / Accepted: 15 July 2024
© Jiangnan University 2024
Raw material selection for sustainable fermentation-derived
alternative protein production: a review
LachiWankhede1· GauravBhardwaj1· Gilberto Vinícius de MeloPereira2· Carlos RicardoSoccol2·
Satinder KaurBrar1
1 3
Systems Microbiology and Biomanufacturing
proles, and microbial proteins produced by bacteria,
yeasts, fungi, and algae [7, 8]. Each category oers distinct
advantages and integrates various aspects of human con-
sumption and animal feed.
Among these alternatives, microbial proteins, produced
through fermentation, are particularly noteworthy for their
eciency and versatility. These proteins can be generated
rapidly with minimal resource input, presenting signicant
advantages over traditional agricultural methods. The scal-
able and adaptable fermentation process allows for using a
wide array of substrates, including low-value byproducts
and agricultural residues, strengthening the sustainability of
microbial proteins and aiding in signicant waste reduction
[9, 10].
A variety of microorganisms are utilized for protein pro-
duction through fermentation. These encompass bacteria
such as Corynebacterium glutamicum [11], yeast like Sac-
charomyces cerevisiae [12], fungi including Aspergillus
[13], and algae such as Spirulina [14]. Each microorganism
has specic substrate preferences and production capabili-
ties, enabling the tailored production of proteins depending
on the desired functional characteristics and applications.
The substrates used in microbial fermentation encompass
a broad spectrum, ranging from simple sugars like glucose to
more complex substrates such as lignocellulosic waste and
even unconventional waste streams, including gas streams
and municipal and industrial euents [1517]. Simple sug-
ars, derived from agricultural products and byproducts such
as sugarcane and corn, are favoured in fermentation due to
their ease of assimilation by a wide range of microorgan-
isms, facilitating ecient microbial growth and protein syn-
thesis. Lignocellulosic waste, which includes materials such
as wood chips and agricultural residues, contains complex
polymers of cellulose, hemicellulose, and lignin [15]. These
components require pretreatment to convert them into fer-
mentable sugars, which can then be utilized by specially
adapted or engineered microbial strains to produce proteins.
Additionally, gas streams, primarily composed of methane
and carbon dioxide, are used in innovative ways; methane
can be transformed into proteins by methanotrophic bacte-
ria, while carbon dioxide, in the presence of hydrogen or
through photosynthetic processes in organisms like cya-
nobacteria, also serves as a substrate for protein produc-
tion [16]. These diverse substrates reect the versatility
of microbial fermentation technologies and highlight the
potential for converting various waste streams into valuable
protein products, thus contributing to the sustainability of
the production systems (Figure 1).
This review aims to comprehensively examine the raw
materials employed in microbial protein production through
fermentation and explore how these substrates interact with
dierent microorganisms to optimize protein yield and
functionality. By systematically analyzing current research
and identifying emerging trends, this review will highlight
innovative approaches and pinpoint gaps in the existing
knowledge, guiding future research and development eorts
Fig. 1 Integrated overview of the global context, substrate utilization, and the sustainable benets of microbial alternative proteins
1 3
Systems Microbiology and Biomanufacturing
toward more ecient and sustainable protein production
systems.
Microorganisms used for alternative protein
production
Fungi
Fungi are remarkably diverse, encompassing macroscopic
mushrooms, microscopic yeasts vital for fermentation, and
lamentous moulds with expansive networks of hyphae
essential for decomposition. They hold great potential for
producing alternative proteins and sustainable substitutes
for animal-based products. Dierent fungal species from
the genera Saccharomyces, Penicillium, Mucor, Candida,
Aspergillus, Monascus, Neurospora, Actinomucor, Tricho-
sporon, Amylomyces, Zygosaccharomyces, Torulopsis,
Rhizopus, Hansenula, and Endomyces are involved in bio-
technological food applications, showcasing their versatility
and broad applicability in the food industry [18, 19]. These
organisms are primarily cultivated through fermentation
processes, including solid-state and submerged fermenta-
tion, which are ecient, scalable, and require signicantly
less space and resources than traditional livestock produc-
tion [20]. Additionally, lamentous fungi can colonize and
decompose a wide range of substrates, including agricul-
tural byproducts, through their distinctive hyphal growth.
This ability not only supports a circular economy by trans-
forming waste into valuable fungal biomass but also aids
signicantly in waste reduction. The extensive network of
fungal hyphae penetrates these substrates, eectively break-
ing down complex organic materials, which enhances the
ecient production of fungal proteins and other valuable
metabolites [21].
For instance, the mycelium of Fusarium venenatum is
used to produce Quorn™. This widely recognized meat
substitute contains about 45% protein with a high Protein
Digestibility-Corrected Amino Acid Score (PDCAAS) of
0.91 [22]. Fungal proteins boast a wealth of essential amino
acids and other vital nutrients, including vitamins and min-
erals, rendering them highly nutritious [23]. The unique tex-
tural properties of fungal laments enable them to mimic
the brous structure of meat, which is particularly useful in
creating meat analogues like burgers and sausages.
Yeasts, primarily represented by Saccharomyces cerevi-
siae, play a pivotal role due to their exceptional fermenta-
tion abilities and ecient protein production. Recognized
for their sustainability and nutritional richness, yeast pro-
teins are viable alternatives to animal-based proteins. Yeast
proteins can be easily extracted using mechanical, enzy-
matic, or chemical methods that disrupt the yeast cell walls,
rendering the proteins readily available [2426]. Yeast pro-
teins, which constitute about 35–60% of their dry weight,
oer a complete amino acid prole and are enhanced with
minerals, lipids, and essential nutrients such as a high con-
tent of B vitamins [27, 28].
Furthermore, the high digestibility of yeast proteins, with
an in vitro rate of approximately 81.06%, surpasses many
plant proteins and compares favourably with soybean and
sh proteins [29]. This superior digestibility enhances their
nutritional value and broadens their application in food
products, where they can improve texture and avour. Addi-
tionally, yeast proteins can be processed into hydrolysates
and peptides with antioxidant and anti-inammatory prop-
erties, enhancing their health benets [30]. This blend of
nutritional richness and functional versatility underscores
the potential of yeast proteins in dietary applications and
sustainable food production.
However, protein production from fungi, including yeasts
and moulds, faces signicant challenges. A prominent issue
is the high content of nucleic acids, primarily RNA, across
these organisms, which can lead to health problems such as
gout if consumed in large amounts [31]. Eective strategies
such as heat treatment reduce high nucleic acid levels in
fungal-based foods, including yeasts, ensuring their safety
and benets for consumption. Enhancing the sensory quali-
ties of these proteins and rening the distinct avours of
yeast proteins for broader food industry appeal remains a
challenge. Ongoing research aims to reduce the production
costs of fungal proteins to improve their competitiveness
with traditional protein sources, addressing both economic
and consumer acceptance issues.
Fungi present a promising and sustainable alternative to
animal-based proteins, with signicant potential for future
developments in food technology. Their unique character-
istics and adaptability to mass production make them a key
focus for innovations to meet the global protein demand.
Additionally, fungal protein production oers substantial
environmental and economic benets, such as lower green-
house gas emissions, reduced water usage, and minimal
land requirements compared to traditional animal protein
sources. These advantages are crucial for developing more
sustainable and resource-ecient food production methods,
underlining the critical role of fungi in enhancing environ-
mental sustainability and addressing the urgent need for
more ecient food systems.
Algae
Algae, comprising microalgae and macroalgae, are a
diverse group of photosynthetic organisms found in marine
and freshwater environments. They are gaining recognition
as an ecient alternative protein source. Due to their rapid
1 3
Systems Microbiology and Biomanufacturing
traditional animal proteins, increasing the utility of algae
primarily in roles that complement rather than replace meat
proteins. While algae oer signicant benets as food addi-
tives and supplements due to their nutrient-rich proles,
their direct use as stand-alone alternatives for meat in con-
sumer diets faces challenges, including textural dierences
and consumer acceptance. This aligns with the growing
consumer interest in sustainable and ethically produced
food options, driving the research and development in this
eld forward.
Bacteria
Bacteria also represent a signicant group of microorgan-
isms with potential for alternative protein production, oer-
ing advantages in terms of rapid growth rates and high
protein yield eciencies. They are increasingly being uti-
lized to produce alternative proteins, achieving 50–80% dry
cell weight (DCW), thereby oering sustainable substitutes
for animal-based products [43]. For example, methane-
utilizing bacteria such as Methylococcus capsulatus can
ferment natural gas into high-quality bacterial protein. The
biomass produced is an excellent source of protein, known
for its good digestibility and favourable amino acid com-
position [44]. However, the use of genetically modied
bacteria raises concerns about antibiotic resistance. This
issue arises because these bacteria often contain antibiotic
resistance genes used as selectable markers during genetic
modication. There is a risk that these genes could transfer
to pathogenic bacteria, enhancing their resistance. Careful
management is needed to prevent the transfer of resistance
genes and ensure public health safety [45].
The eld of precision fermentation is revolutionizing
the production of specic milk and egg proteins through
bacterial fermentation. This innovative technology utilizes
microbial fermentation to recombinantly create proteins,
presenting a sustainable alternative to traditional animal-
based agriculture by signicantly reducing its environmen-
tal footprint [46]. Additionally, single-cell proteins (SCPs)
produced by bacteria provide a practical and sustainable
alternative to conventional animal-based protein sources.
Bacteria can rapidly convert simple substances like natu-
ral gases or agricultural waste into proteins rich in essen-
tial nutrients [47, 48], making bacterial alternative proteins
exceptionally reliable, especially in areas where traditional
farming is challenging due to environmental conditions
[49].
Furthermore, bacterial proteins have diverse applications
beyond nutrition. For instance, lactic acid bacteria (LAB)
can produce bioactive peptides with multifunctional prop-
erties, which are increasingly used in the food industries
as natural preservatives and nutraceuticals. This highlights
growth rates [32] and high photosynthetic eciency, algae
represent a sustainable alternative to animal-based products.
They do not compete with terrestrial agricultural resources,
enhancing their environmental benets. Furthermore, some
algae can have protein content that exceeds 70% of their
dry weight, as noted by Espinosa-Ramírez et al. [33]. Algae
are rich in essential co-nutrients such as carbohydrates and
lipids, which, in some species, can constitute 20 to 50% of
their composition [34]. This combination of high nutritional
value and sustainable cultivation practices supports the
shift toward more sustainable protein sources, underscoring
algae’s potential in future food systems.
Algae, including microalgae and macroalgae forms, hold
signicant promise as they are not typically used to replace
conventional protein sources but are utilized as food addi-
tives and supplements. This is due to their rich composition
of nutrients well suited for such applications, particularly in
nutraceuticals, which include proteins, essential fatty acids
like omega-3 and omega-6, vitamins such as B12 and D,
etc [35]. Microalgae species like Arthrospira, Chlorella,
Dunaliella, and Haematococcus are ocially recognized
for human consumption by the European Food Safety
Authority. These microorganisms are particularly noted for
their high protein concentrations, often surpassing 70%, and
their robust proles of essential amino acids, making them
competitive with other plant proteins such as soybeans or
chickpeas [36, 37].
Macroalgae, such as Ochrophyta, Chlorophyta, and
Rhodophyta, visible without magnication and possess-
ing complex multicellular structures, have been utilized in
Asian culinary traditions for a long time. These species also
play a crucial role in producing hydrocolloids like alginate,
agar, and carrageenan, staples in the food industry. Though
macroalgae generally have lower protein contents, ranging
from 9 to 22% dry matter, they are valued for their essential
amino acid content [33].
Despite these promising attributes, protein extraction
from algae involves several challenges, including ecient
large-scale extraction techniques and overcoming the sen-
sory and textural limitations that might aect consumer
acceptance when used in food products, such as meat ana-
logs. Advanced methods, such as mechanical crushing, ultra-
sonic sonication, and enzymatic treatment, are employed to
enhance the yield and functionality of the extracted proteins
[3841]. These proteins can then be incorporated into meat
analogs through extrusion, a process that texturizes them to
replicate the brous structure of meat [42]. However, the
development of algae-based meat alternatives is still in the
early stages of research. Further exploration is required to
optimize processing conditions and improve the end prod-
uct’s sensory properties, such as taste and texture. The
goal is to develop sustainable and nutritious alternatives to
1 3
Systems Microbiology and Biomanufacturing
Classication of raw materials
In microbial protein fermentation, selecting appropriate
raw materials is crucial for maximizing eciency and sus-
tainability. These substrates, varied in origin and proper-
ties, must be abundant, non-toxic, and conducive to rapid
microbial growth. The potential of these materials to be
transformed into valuable biological products underpins
the “wealth from waste” concept, emphasizing the eco-
nomic and environmental benets of using inexpensive
waste materials [51]. However, the global acceptance of
the “waste-to-protein” approach requires careful consid-
eration of regional perceptions and standards [52]. Figure
2 presents an overview of various raw materials and their
LAB’s capability to generate proteinaceous compounds that
benet the food industry and the animal and pharmaceutical
sectors [50]. These advantages collectively showcase bacte-
rial proteins’ broad potential and versatility in contributing
to more sustainable and ecient food production systems.
These bacterial-based technologies pave the way for more
sustainable, ecient, and environmentally friendly protein
production systems, signifying a signicant shift in how we
approach food and feed production.
Fig. 2 Compatibility of raw materials with dierent microbial groups according to [5360]
1 3
Systems Microbiology and Biomanufacturing
production despite challenges in handling and fermenta-
tion. The variability in protein content, especially noted in
lignocellulosic biomass, suggests that results may depend
signicantly on the type and treatment of the biomass. The
subsequent sections categorize raw materials according to
their characteristics, emphasizing their inuence on the
scalability and eectiveness of the process.
Lignocellulosic biomass and agricultural waste
Lignocellulosic and agricultural wastes represent a substan-
tial category of substrates to produce alternative proteins,
oering a sustainable approach to managing agricultural
byproducts while producing valuable proteins. These wastes
typically consist of residues from crops such as straw, husks,
and stalks, rich in cellulose, hemicellulose, and lignin. Con-
verting these complex carbohydrates into microbial biomass
aids in waste reduction but also helps generate alternative,
nutrient-rich protein sources. Converting lignocellulosic
waste into alternative proteins involves preliminary steps
like pre-treatment, which helps break down the complex
structure of plant materials, making them more accessible
for microbial consumption. This is often followed by fer-
mentation, where microorganisms such as bacteria, yeast, or
fungi utilize the sugars derived from the pre-treated waste to
grow and produce protein [65, 66]. Various lignocellulosic
biomass and agricultural wastes can be used as substrates
with dierent microbial strains, as shown in Table 1. The
highest protein production is achieved by Rhodopseudomo-
nas gelatinosa using wheat bran as a substrate, with a protein
content of 65.0% [54]. This indicates that this combination
is particularly eective for producing protein, potentially
due to the biochemical properties of the microbial strain or
the nutrient composition of wheat bran. Candida tropicalis
shows high eciency with multiple substrates, producing
nearly 61% protein with soy molasses [55] and about 60%
with sugarcane bagasse [56]. This suggests that Candida
tropicalis is a versatile strain capable of high protein pro-
duction across dierent substrate types.
Further studies on fungal strains revealed that Aspergil-
lus niger and Aspergillus terreus could eectively use wheat
bran, corn cob, and rice husk, yielding protein contents of
36.84%, 22.41%, and 14.52% respectively [67]. These nd-
ings highlight the potential of fungi to decompose complex
plant materials into simpler, utilizable forms. Bakratas et al.
cultivated Pleurotus ostreatus on agro-industrial hydrolysate
in a 3.5 L stirred tank bioreactor, resulting in a total protein
content of 44.8% [68], pointing to the eciency of certain
fungi in addition to the pretreatment of lignocellulosic sub-
strates into valuable proteins. These studies collectively
emphasize the potential of using microbial fermentation
to transform lignocellulosic and agricultural wastes into
suitability for fermentation by dierent microbial groups
alongside potential protein content ranges.
Lignocellulosic biomass and agriculture waste, which
include materials such as agro-industry waste, soy molas-
ses, and millet bran, are compatible with bacteria and mush-
rooms for protein production, with protein content ranging
from 12.5 to 65.0% [53, 54]. Food and fruit waste, consist-
ing of materials like apple pomace and mango waste, are
suitable for algae, bacteria, and mushroom fermentation,
with protein content between 26.6% and 58.6% [61]. Waste-
water and industrial euent, which include sources such as
dairy wastewater, are primarily processed by algae and bac-
teria, yielding protein contents from 31.1 to 65.0% [62, 63].
Lastly, gas streams incorporating biogas and methane are
suitable for algae fermentation and oer the highest protein
potential, ranging from 33.0 to 88.0% [60, 64]. This cat-
egory presents intriguing possibilities for high-yield protein
Table 1 Protein production from lignocellulosic biomass and agricul-
ture waste as a substrate
Lignocellulosic & Agriculture Waste
Substrate Microbial Strain Protein (%) Reference
Wheat bran Rhodopseudomo-
nas gelatinosa
65.0 [53]
Hempstalk
waste
Cellulomonas 12.5 [54]
Soy molasses Candida tropicalis 60.99 [69]
Wheat bran Candida utilis
and Rhizopus
oligosporus
41.02 [70]
Millet bran Candida tropicalis 9.19 [71]
Sugarcane
bagasse
Candida tropicalis 60.05 [72]
Wheat bran/
Corn cob/
Rice husk
Aspergillus niger 36.84/22.41/14.52 [65]
Wheat bran/
Corn cob/
Rice husk
Aspergillus terreus 26.18/24.43/15.61 [67]
Corn cob Arachniouts sp. 18.87 [73]
De-oiled rice
bran
Trichoderma viride/
Aspergillus oryzae/
Aspergillus niger
44/43/39.2 [74]
Hydrolysate Pleurotus ostreatus
LGAM 1123
44.8 [68]
Soybean hull Bacillus subtilis 12.27 [75]
Maize stover/
Rice straw
Yarrowia lipolytica 16.23/14.75 [76]
Corncob
hydrolysate/
Miscanthus
straw
Candida intermedia 40/17 [77]
Corn cobs Aspergillus niger 30.4 [78]
Rice straw Trichoderma reesei 9.71 [79]
Coee husk Aspergillus niger 33.6 [80]
Ammoniated
corn straw
Penicillium sp. and
Torula allii
35.41 [81]
1 3
Systems Microbiology and Biomanufacturing
In exploring alternative protein production from food and
fruit waste, various studies have highlighted the potential
of dierent substrates and microbial strains, as shown in
Table 2, to achieve high protein yields. Notably, mango peel
extract fermented with Pichia pinus resulted in the highest
recorded protein content at 62.2% [82], showcasing the e-
cacy of high-sugar substrates in supporting vigorous yeast
activity and substantial protein synthesis. Similar success
was observed with Chlorella sp. using tofu and tempeh
waste, producing 52.24% and 52% protein content, respec-
tively [83], likely due to the high nitrogen content inherent
to soy processing byproducts. Additionally, Saccharomyces
cerevisiae grown on cucumber peels achieved a protein
yield of 53.4% [84], indicating the suitability of cucumber
peels as a balanced nutrient source for yeast.
However, some studies have shown variability and lower
yields, such as Saccharomyces cerevisiae used with multi-
fruit waste, which displayed protein contents ranging from
9.64 to 48.32% [85]. This variability suggests mixed fruit
wastes may not consistently provide the necessary nutrients
for optimal yeast growth. Additionally, Trichoderma viride
fermented with banana peel extract yielded a moderate pro-
tein content of 29.76% [86], likely hindered by the di-
culty in decomposing the brous material of banana peels.
Unusual ndings underscored the importance of substrate
selection, as evidenced by signicant variations in protein
yield from Saccharomyces cerevisiae across dierent fruit
wastes, ranging from 26.26 to 58.62% [87]. This variability
highlights that while some fruits are well-suited for yeast
fermentation, others lack essential nutrients, emphasizing
the critical role of substrate suitability in optimizing protein
production.
Furthermore, a co-cultivation strategy involving Bacillus
amyloliquefaciens and Candida utilis in citrus pomace was
notably eective, achieving a protein content of 40.04%
[88], suggesting that such synergistic microbial relation-
ships can enhance the breakdown of complex substrates
and improve yield. This phenomenon is likely attributed to
the eective breakdown of the pomace’s intricate constitu-
ents by enzymes derived from Bacillus amyloliquefaciens,
notably including amylases, proteases, and lipases. Subse-
quently, Candida utilis eciently metabolizes these simpler
compounds, yielding protein-rich biomass. Thus, the micro-
bial co-cultivation approach, where bacteria and yeast work
together, maximizes the transformation of waste into high-
value products, illustrating the potential of integrated bio-
technological solutions in sustainable waste management
and production systems.
Utilizing food and fruit wastes as substrates for alter-
native protein production is crucial for addressing global
waste management and food security challenges. These
nutrient-rich waste materials oer a sustainable solution by
signicant amounts of alternative proteins. Beyond achiev-
ing high protein content, the practical application of these
substrates critically depends on their economic feasibility
and scalability. Challenges, such as the cost of preprocess-
ing these materials and the complexities of scaling up pro-
duction, are pivotal. Addressing these challenges is crucial
for ensuring that such substrates can serve as sustainable
and economically viable alternatives to conventional pro-
tein sources.
Food and fruit waste
Food and fruit waste as substrates for alternative protein
production through microbial processes oers a sustainable
approach to reducing waste and enhancing food security.
These waste materials, rich in sugars, bres, and essential
nutrients, provide an excellent carbon and energy source for
microbial fermentation. Specic microbial strains are cul-
tivated to eciently metabolize the organic compounds in
the waste, facilitating rapid microbial growth and protein
synthesis. This makes the process cost-eective and eco-
friendly and allows for customization to improve the nutri-
tional or functional properties of the biomass, such as its
amino acid composition, vitamin content, and digestibility
[52].
Table 2 Protein production from Food and fruit waste as a substrate
Food & Fruit Waste
Substrate Microbial Strain Protein
(%)
Refer-
ence
Apple pomace Mucor indicus 29.0 [55]
Tofu waste Chlorella sp. 52.24 [83]
Tempeh waste Chlorella sp. 52 [83]
Orange & Lemon
waste
Rhodococcus opacus PD630 52.1–56.9 [61]
Orange & Lemon
waste
Rhodococcus opacus DSM
1069
42.2–45.8 [61]
Fruit waste Lactobacillus 24.67 [89]
Mango peel
extract
Pichia pinus 62.2 [82]
Fruit waste Saccharomyces cerevisiae 26.26–
58.62
[87]
Papaya extract Saccharomyces cerevisiae 34.0 [90]
Cucumber peel Saccharomyces cerevisiae 53.4 [84]
Mango waste Candida utilis 56.40 [91]
Food waste Saccharomyces cerevisiae 39 [92]
Multi-Fruit waste Saccharomyces cerevisiae 9.64–
48.32
[85]
Fruit peels Palmyrah Toddy Yeast 29.5–52.4 [93]
Multifood waste Saccharomyces cerevisiae 40.19 [94]
Orange waste Aspergillus niger 46.50-
52.48
[95]
Banana peel
extract
Trichoderma viride 29.76 [86]
Citrus pomace Bacillus amyloliquefaciens
and Candida utilis
40.04 [88]
1 3
Systems Microbiology and Biomanufacturing
resource. Consequently, various types of wastewater have
been utilized as substrates to produce microbial protein
(Table 3).
Exploring wastewater and industrial euents as sub-
strates for alternative protein production reveals diverse
outcomes across various microbial strains, demonstrating
the critical inuence of substrate characteristics on protein
yield. Notable high protein yields achieved in studies such
as Rhodopseudomonas palustris with latex rubber sheet
wastewater (65.0%) [63] show the potential of specic
microorganisms to convert complex euents eciently.
This particular study also highlighted the importance of
optimizing the fermentation process, where the use of Rho-
dopseudomonas palustris P1, along with fermented pine-
apple extract, not only eectively removed pollutants but
also facilitated the production of high-quality SCP as a
byproduct. This optimization shows how tailored fermenta-
tion strategies can signicantly enhance protein yield and
process eciency.
Similarly, Haematococcus pluvialis with synthetic
brewery wastewater achieved a high yield of 64.9% [97],
indicating that certain strains are exceptionally adept at uti-
lizing specic wastewater types for protein synthesis. These
results suggest that the careful selection of microbial strains
combined with precise adjustments in the fermentation pro-
cess can maximize the utilization of waste substrates, turn-
ing them into valuable protein sources.
Conversely, lower protein yields, such as those seen in
the treatment of dairy wastewater with Chlorella vulgaris
and Yarrowia lipolytica (31.1% [62]), highlight the chal-
lenges posed by substrates that may lack a balanced nutrient
prole essential for optimal microbial growth. This suggests
further optimization of microbial strains and fermentation
conditions to boost protein production. Similarly, the vari-
ability in protein content observed with Chlorella vulgaris
in municipal euent (42–55%) [57] underscores the inu-
ence of even minor dierences in wastewater composition
on production eciency. These ndings emphasize the
importance of a comprehensive understanding of microbial
ecology and substrate chemistry to achieve consistent and
ecient protein yields.
Overall, these studies collectively illustrate the impor-
tance of selecting appropriate microorganisms and carefully
characterizing waste substrates to maximize the eciency
of protein production. Optimizing these factors is crucial for
advancing the use of wastewater and industrial euents in
sustainable protein production, which helps manage waste
and contributes to environmental sustainability by pro-
viding an eco-friendly alternative to conventional protein
sources. The feasibility of scaling up these processes and
their economic viability are essential. Factors such as the
consistency of waste composition, processing costs, and the
transforming waste into valuable protein sources through
microbial fermentation. However, selecting appropriate
substrates is essential to optimize the eciency of these
bioconversion processes. Variations in protein yields under-
score the need for careful evaluation of waste materials to
ensure adequate nutrient utilization by microbial cultures,
thereby enhancing the viability and eectiveness of protein
production while advancing sustainable food technologies.
Beyond the biochemical potential, assessing the scalability
and economic feasibility of using food and fruit wastes as
substrates is crucial. These materials must be available in
sucient quantities and at a cost that makes the processes
nancially viable commercially. The economic aspects,
including the cost of collecting, storing, and preprocessing
these wastes, play a signicant role in their practical appli-
cation. Addressing these factors is critical to realizing the
full potential of food and fruit wastes in sustainable protein
production.
Wastewater and industrial euents
Wastewater is rich in organic and inorganic nutrients essen-
tial for microbial growth, making it an ideal medium for
producing alternative proteins [96]. It aligns with sustain-
ability goals by transforming a waste stream into a valuable
Table 3 Protein production from wastewater & industrial euent as
a substrate
Wastewater & Industrial Euents
Substrate Microbial Strain Protein (%) Refer-
ence
Industrial process
wastewater
Chlorella sp. 46–65 [58]
Wet market wastewater Scenesdesmus
obliquus
50.72 [98]
Industrial wastewater Chlorella
sorokiniana
52.5 [17]
Dairy wastewater Chlorella vulgaris
and Yarrowia
lipolytica
31.1 [62]
Municipal wastewater Rhodopseudomonas
sp.
60.1 [99]
Municipal euent Chlorella vulgaris 42–55 [57]
Sugar industry
wastewater
Rhodopseudomonas
faecalis
50-51.5 [100]
Starch-processing
wastewater
Aspergillus oryzae 45.7 [101]
Synthetic brewery
wastewater
Haematococcus
pluvialis
64.9 [97]
Latex rubber sheet
wastewater
Rhodopseudomonas
palustris
65.0 [63]
Fiber sludge Pleurotus ostreatus
LGAM 1123
44.8 [68]
parboiled rice euent Aphanothece
microscopica
42 [102]
Corn stover euent Rhodococcus opacus 52.7 [61]
1 3
Systems Microbiology and Biomanufacturing
potent and consistent substrate, further optimizing micro-
bial protein synthesis [104].
However, despite these promising results, producing pro-
teins from gas streams involves signicant challenges that
must be carefully managed. Issues like gas solubility and
transfer eciency are critical; not all microorganisms can
utilize methane or carbon dioxide eectively. Engineering
microbial strains for the optimal metabolism of these gases
is crucial. Additionally, maintaining precise process control
and optimization, including appropriate pressure, tempera-
ture, and pH levels, is essential but challenging, aecting
the stability and activity of microbial cultures [102].
Scaling these processes from laboratory to industrial
levels also presents substantial economic and technical
challenges. Ensuring nancial viability while adhering to
regulatory and safety standards is essential for integrating
this technology into existing industrial landscapes. The
scale-up of gas fermentation processes must address these
issues to ensure that production is technically feasible and
commercially viable.
While gas streams oer a promising substrate for produc-
ing alternative proteins, realizing their full potential requires
overcoming substantial technical hurdles. Addressing these
challenges through innovative engineering solutions, rigor-
ous process optimization, and strategic microbial selection
will be vital in advancing this technology and making it a
reliable component of sustainable protein production strate-
gies. Scaling production to economically viable quantities is
essential, focusing on cost-eectiveness and market dynam-
ics. Using Generally Recognized As Safe (GRAS) microor-
ganisms is vital for ensuring safety and enhancing consumer
acceptance, which mitigates health risks and increases these
proteins’ marketability. Future developments should inte-
grate these elements to create a sustainable, safe, and eco-
nomically viable protein production platform.
Challenges and future aspects
Producing alternative proteins through fermentation using
substrates such as lignocellulosic biomass, agricultural
waste, wastewater, and gas streams oers promising oppor-
tunities, albeit with challenges. These complex substrates
require pretreatment to make them more accessible for
microbial fermentation, enhancing cost eciency and envi-
ronmental sustainability. Scaling these processes from labo-
ratory to industrial levels incurs costs. For instance, cultured
meat production costs remain high, with perfusion biore-
actors costing about $51 per kg and fed-batch bioreactors
costing $37 per kg, signicantly above consumer expecta-
tions of around $25 per kg. Even after accounting for pack-
aging and distribution, costs can reach at least $50 per kg,
infrastructure for large-scale operations must be evaluated.
Innovations in technology and integrated systems will be
crucial to improve economic and environmental outcomes,
making this approach viable for broader industrial adoption.
Gas streams
In the innovative realm of using gas streams for alternative
protein production, the potential of various substrates and
microbial strains to achieve high protein yields is notably
demonstrated in several fundamental studies, as described
in Table 4. The utilization of upgraded biogas with a com-
bination of Methylophilus sp., Methylomonas sp., and
Comamonadaceae sp. achieved the highest protein con-
tent reported at 88% [64]. Similarly, Methylophilales and
Methylococcales grown on biogas reached impressive pro-
tein yields of 87% [103], while Methylophilus sp., using
pure methane, produced a yield of 79% [59]. These excep-
tional outcomes highlight the eciency of methanotrophs
and related bacteria in converting methane into substantial
amounts of protein through their unique metabolic pathways
that allow direct conversion of methane to cellular biomass.
The superior protein yields from methane and other gas
streams can be attributed to the ‘methanotrophs’ ability to
utilize methane as their sole carbon and energy source. This
direct conversion process is highly ecient, minimizing
energy loss and maximizing protein synthesis. Moreover,
the gaseous nature of methane ensures rapid substrate trans-
fer to microbial cells, enhancing growth and protein pro-
duction rates. Upgraded biogas, rened to increase methane
concentration and remove contaminants, provides a more
Table 4 Protein production from gas streams as a substrate
Gas Streams
Substrate Microbial Strain Pro-
tein
(%)
Refer-
ence
Biogas Methylophilus sp. and
Methylomonas
76 [106]
Biogas Methylococcus capsulatus 52 [107]
Biogas Methylophilales and
Methylococcales
87 [103]
Pure methane Methylophilus sp. 79 [59]
Upgraded
biogas
Methylophilus sp., Methylomonas
sp., and Comamonadaceae sp.
88 [64]
Light + CO2Arthrospira maxima (Spirulina
maxima)
60–71 [108]
Light + CO2Arthospira platensis Spirulina
platensis
46–63 [109]
Light + CO2Euglena gracilis 50–70 [110]
Light + CO2Scenesdesmus obliquus 33 [60]
Light + CO2Chlorella pyrenoidosa 45 [111]
Municipal
euent + CO2
Chlorella vulgaris 42–55 [57]
NH4 and CO2Hydrogen-oxidizing bacteria 71.0 [112]
1 3
Systems Microbiology and Biomanufacturing
they also present specic challenges that must be addressed
to optimize their practical application.
Lignocellulosic biomass and agricultural waste are abun-
dant and renewable, rich in complex carbohydrates that can
be transformed into fermentable sugars for microbial use.
However, the eciency of this transformation is limited by
the complex nature of these materials, requiring advanced
pretreatment to release usable sugars. Developing more
eective enzymatic treatments and genetically engineered
microbes could enhance the conversion process, making
it more ecient and sustainable. As a substrate, wastewa-
ter provides a nutrient-rich medium supporting microbial
growth, reducing the need for synthetic growth substrates
and lowering production costs. However, the variable com-
position of wastewater can aect microbial performance
and protein yield, necessitating the development of versa-
tile microbial strains and robust fermentation strategies to
manage these variations eectively. Gas streams, especially
those containing methane and carbon dioxide, oer an
innovative approach by converting greenhouse gases into
protein. While this method shows high potential yields, it
faces challenges like gas solubility, transfer eciency, and
precise process control. Advances in bioreactor technology
and microbial adaptation are crucial for optimizing the use
of these gases.
Despite the promising aspects of these substrates, scaling
these processes to industrial levels remains economically
challenging. The production costs must be competitive,
and regulatory and safety standards must be met to ensure
consumer acceptance and market success. Overcoming
these hurdles is crucial for viability, requiring innovations
in microbial strain selection, process optimization, and sub-
strate pretreatment. GRAS microorganisms are essential
to ensure safety and enhance market integration. Future
advancements may rely on biotechnological innovations,
such as improved genetic engineering of microbes, incor-
porating articial intelligence for process optimization, and
developing integrated bioreneries that support a circular
economy.
In summary, leveraging various waste substrates for
microbial protein production oers a pathway to more sus-
tainable and ecient food systems. However, realizing the
full potential of these substrates requires overcoming signif-
icant technical, economic, and regulatory challenges. Thus,
advancing sustainable microbial fermentation technologies
will help enhance global food security.
Acknowledgements This research was funded by the Natural Sci-
ences and Engineering Research Council of Canada (NSERC) CRE-
ATE Program 554777-2021, Training in Advanced Biotechnology for
Environmental Sustainability (TABES), and James and Joanne Love
Chair in Environmental Engineering.
Author contributions Lachi Wankhede: Conceptualization, Literature
highlighting the urgent need for reduction [113]. Optimiza-
tions could focus on feedstock materials, energy use in bio-
reactor operations, high production costs in cultured meat,
and downstream processing. Developing low-cost hydroly-
sate media might reduce fed-batch process costs below $25/
kg, but the capital-intensive perfusion process remains cost-
lier. Streamlining these aspects could signicantly lower
costs, align with consumer expectations, and enhance the
economic viability of cultured meat.
Advancements in genetic engineering and bioprocess-
ing technologies, including automation and enhanced pro-
cess controls integrated with articial intelligence, have
the potential to streamline production processes, increase
yields, and reduce labour and error rates. Specically, these
technologies can optimize fermentation conditions continu-
ously and predictively, leading to more ecient resource use
and shorter production cycles. Such improvements enhance
the scalability and stability of fermentation processes and
contribute to signicant cost reductions by minimizing
waste, optimizing energy use, and improving overall pro-
cess eciency [114]. Emerging technologies like Clustered
Regularly Interspaced Short Palindromic Repeat (CRISPR)
for targeted microbial enhancements and real-time data
acquisition sensors are also pivotal in advancing fermenta-
tion eciency [115]. Furthermore, integrated bioreneries
could enhance economic viability by allowing producers to
diversify products from a single raw material source, thus
supporting a circular economy that minimizes waste, opti-
mizes resource use, and reduces environmental footprints.
Promoting policy support with incentives and favour-
able regulations is crucial for the widespread adoption of
sustainable fermentation technologies. Demonstrating their
benets, collaborating with stakeholders, and advocating
for subsidies and regulatory reforms can position these tech-
nologies as viable alternatives to traditional protein sources,
enhancing their market adoption. Tackling these challenges
and applying technological advances will be essential for
advancing and sustaining alternative protein production
through fermentation, ensuring a resilient and ecient food
system for the future.
Conclusion
The study concludes that selecting raw materials is para-
mount for the sustainable production of alternative pro-
teins through microbial fermentation. This process shows
excellent potential in addressing global food security and
environmental sustainability challenges. Our systematic
evaluation of diverse substrates such as lignocellulosic
biomass, agricultural waste, wastewater, and gas streams
reveals that while each substrate oers unique advantages,
1 3
Systems Microbiology and Biomanufacturing
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Declarations
Conict of interest Carlos Ricardo Soccol, a co-author of this paper,
is the Editor of Systems Microbiology and Biomanufacturing. He was
blinded to this paper during the review/handling process, and Ashok
Pandey, the Co-Editor-in-Chief, independently handled the paper.
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