Deep Dive: Beyond the bottlenecks

Transforming alternative proteins from promising innovations to mainstream products requires overcoming critical hurdles in production, cost efficiency, and supply chain logistics. As Lloyd Fuller reveals here, the companies that refine their processes, optimize resources, and secure strategic partnerships will be best positioned to accelerate large-scale adoption

Just a few years ago, the alternative protein sector was the darling of investors. Now, though, it faces a starkly different reality. No longer are investors simply betting on future potential; they’re demanding tangible evidence of a clear path to profitability. This fundamental shift necessitates that companies demonstrate not only cutting-edge technology but also a robust business plan capable of delivering solid returns. In such a tighter funding environment, success hinges on optimizing production processes, meticulously managing costs, and forging strategic partnerships that can accelerate scaleup. These imperatives, in turn, require careful consideration of critical trade-offs, the identification and elimination of key bottlenecks, and a deep understanding of the complex interplay between upstream and downstream operations. To navigate this challenging landscape, companies are seeking effective strategies.

The January 2025 Protein Production Technology International webinar, From Molecule to Market: Exploring the Journey from Discovery to Commercialization, sponsored by Beckman Coulter Life Sciences, provided valuable insights into some of these very strategies, offering a glimpse into what will ultimately distinguish the winners from the also-rans in this evolving space.

One size does not fit all

What all the assembled panelists agreed upon was that the need for effective scaling strategies is paramount. Scaling strategies in the alternative protein sector are anything but monolithic. Companies adopt diverse approaches, often tailored to their specific technologies and target markets. Some initially pursue large commodity markets before strategically pivoting to more specialized, higher-value niches. Consider Perfect Day, for example, which initially targeted the vast dairy market with its precision-fermented whey protein, positioning itself as a direct competitor to traditional dairy proteins. The company has since strategically expanded into higher-value applications. Similarly, Impossible Foods launched its products with a high-profile entry into premium food service, securing partnerships with high-end restaurants and Burger King for its Impossible Whopper, before subsequently expanding into retail channels. Other companies, in contrast, opt for a more phased approach, incrementally introducing commodity proteins into specific products. These diverse strategic decisions, each with their own implications, have cascading effects, influencing everything from R&D priorities to manufacturing footprints, and therefore demand careful deliberation regarding the long-term strategic vision.

Overcoming bottlenecks in scaling

As webinar attendees learned, scaling up in alternative proteins presents a complex web of bottlenecks, which vary depending on the specific production platform. However, certain common threads run throughout the sector. Karthik Anekella-Anderson, Global Marketing Manager, Food & Alternative Proteins at Pall Corporation, believes cultivating a “food science mindset” is important – and not just when a company is ready to scale up. “This means thinking early about the ingredients you’ll use, the necessary certifications, and whether you’re developing a consumer-facing product or an ingredient,” he explains.

This forward-thinking approach also extends to supply chain management. Anekella-Anderson also highlights the critical role of managing Minimum Order Quantities (MOQs) and mitigating supply chain vulnerabilities. “Many small companies struggle because they can’t order a truckload of a particular flavor or ingredient for a small trial, yet that’s the supplier’s MOQ.” This underscores the importance of understanding supply chain dynamics and developing robust sourcing strategies from the outset.

Beyond ingredient sourcing, cultivating a ‘scale-up mindset’ is crucial. Processes should be designed with scalability and sustainability in mind from day one. Anekella-Anderson illustrates this point with the example of filtration technology. “Fermentation, for example, has traditionally used diatomaceous earth for filtration, but many companies are now moving away from it due to sustainability and worker safety concerns. Cross-flow filtration using membranes is emerging as a viable alternative,” he says.

Pilot-scale testing and resource optimization

This proactive approach to process design must be supported by adequate resources. Access to pilot-scale facilities is non-negotiable for rigorously testing processes and generating critical data on parameters such as flow rates, oxygen demand, and cleaning protocols. Furthermore, resource optimization plays a vital part. Resource optimization, particularly water usage and side stream management, is often an overlooked but vital factor. “More often than not, the limiting factor isn’t the process itself but the availability of utilities, water resources, and waste management,” stresses Anekella-Anderson. This necessitates considering the total cost of ownership, encompassing both resource consumption and waste disposal.

The importance of considering the entire production process cannot be overstated. Downstream processing (DSP) frequently lags behind upstream development, creating a significant bottleneck in the scaling process. Brian Jacobson, Associate Director of Strategic Operations at the University of Illinois at Urbana-Champaign, cautions, “Especially in today’s environment, we need to move away from the idea that titer is the only metric that matters when scaling fermentation. But unless you have a clear plan for what comes next and understand your downstream operations, that 50 grams per liter can quickly turn into 1 gram per liter.”

Believing that many companies often fixate on achieving high titers, and neglect the crucial downstream steps, Jacobson stresses the importance of maintaining balance between upstream and downstream processes. “DSP is just as critical to the success of the overall process, both technically and on the business side,” he says. “Many of those lessons can be learned much more cost-effectively earlier in the process.”

Balanced approach

A balanced approach is also crucial within upstream processing itself. Strain engineering is fundamental to upstream development and, in that respect, Chris Saenz, Segment Development Manager – Biomanufacturing, North America from Beckman Coulter Life Sciences, highlights the importance of chassis selection. “Once you have your core plasmid, selecting and optimizing the right chassis organism becomes critical. Each chassis has its own strengths and weaknesses. Screening for production efficiency and optimizing media parameters early – before reaching larger reaction vessels – is essential.” Companies can accelerate the optimization process by adopting either a sequential or parallel processing approach. “One of our key product offerings is a 48×2mL fermenter, which allows companies to screen a large number of conditions simultaneously,” reveals Saenz, describing the advantages of parallel processing. “We’ve seen this approach help teams identify strong candidates faster.”

The field of strain engineering is also benefiting from technological advancements, with AI-guided protein design transforming the process. While Saenz notes the increasing use of predictive models, he points out a key challenge. “One major hurdle is the lack of seamless integration across different tool vendors – each has its own software stack, which makes interoperability cumbersome.”

Data integration, meanwhile, is also crucial for accurate financial projections. High-quality data is the bedrock of robust techno-economic analysis (TEA) modeling. But inaccurate TEA data, often resulting from underdeveloped DSP processes, can lead to flawed financial projections. “That’s why it’s critical to establish partnerships early, both with a reliable TEA provider and with a CDMO or manufacturing partner,” continues Jacobson. “Having those relationships in place ensures that the data you’re using aligns with the actual scaling conditions.”

Of course, CDMOs can play a role in scaling up, but selecting the right one is critical. “Having someone on your team who can manage the tech transfer from pilot to demo and then from demo to production is vital,” suggests Adam Leman, Lead Scientist, Fermentation, at The Good Food Institute.

Profitability and investor expectations

Yet even with the right manufacturing partner, scaling alone is not enough – companies must also navigate a shifting financial landscape. The current funding environment demands a laser focus on profitability, forcing startups to prove not only that they can scale but that they can do so sustainably. Describing the current state of play, Mihir Pershad of Umami Bioworks says, “I think we’re now in year three of this new funding reality, particularly for alternative proteins. It’s becoming clear that this is the new normal.”

To survive and thrive, Pershad emphasizes the importance of co-development partnerships. “At Umami Bioworks, we’ve always been B2B-focused, but we’ve increasingly targeted large enterprise customers – not just as buyers but as co-development partners.” This collaborative approach allows companies to share risks and resources, accelerating the path to commercialization. Beyond partnerships, demonstrating clear milestones and exploring adjacent markets are also critical strategies for attracting investment.

Pershad adds, “Ultimately, staying alive is step one, and investors today want to see that companies have a path to ‘default alive’ as quickly as possible.” He also points out the importance of minimum viable scale, stating, “For startups, the key is recognizing that investors and customers have different risk appetites.” Therefore, finding the right balance between demonstrating progress and managing investor expectations is crucial for long-term success.

This focus on profitability must be balanced with other critical factors, particularly sustainability, but balancing sustainability and profitability presents a key challenge. Anekella-Anderson explains the importance of considering alternative processes. “Take wet extraction of plant protein isolates, for example. The most common approach today uses acids and bases. However, there are membrane separation techniques that eliminate the need for harsh chemicals, which helps preserve functionality and improves sustainability.”

Sustainability and batch-to-batch consistency

Adopting sustainable practices not only benefits the environment but can also enhance a company’s image and appeal to environmentally conscious consumers. Furthermore, ensuring batch-to-batch consistency is equally critical for maintaining product quality and customer trust. Anekella-Anderson emphasizes the importance of early planning. “Ultimately, anticipating these challenges at the lab scale – rather than waiting until full-scale production – allows companies to proactively implement the right tools and processes for batch-to-batch consistency, regulatory compliance, and efficient product release.” Consequently, robust quality control systems and validated analytical methods become increasingly important.

Beyond process optimization and sustainability, market transitions also require careful consideration. Transitioning from one market to another, such as from pet food to human food, requires careful planning. Simo Ellilä, CEO of Enifer, discusses the Finnish company’s approach. “We’re building a plant that is viable for pet food, but from the very beginning, we’ve designed it with the future transition to human food in mind,” he says. “This forward-thinking approach allows companies to capitalize on initial market opportunities while laying the groundwork for future expansion.”

Ultimately, balancing innovation with investor expectations demands a clear focus on commercial viability. “One way we tackle this is through a dashboard mentality – boiling everything down to just two or three key metrics that consolidate all the necessary technical progress,” continues Pershad. By focusing on key metrics, companies can communicate their progress to investors and demonstrate their commitment to achieving commercial success.

Regulatory challenges of using industrial side streams

Navigating regulatory approval can also be challenging for companies working with undefined raw materials like industrial side streams. For Enifer, which specializes in biomass fermentation, proving the safety of its products while demonstrating the sustainability benefits of upcycling presents both opportunities and hurdles.

“Our process is relatively straightforward compared to some other approaches,” says Ellilä. “We focus on solid-liquid separation and product recovery, while ensuring that we meet both cost and environmental targets – what we call the double bottom line. A fundamental part of this is using side stream raw materials, which helps us reduce both production costs and environmental impact. However, this also introduces regulatory complexities.”

Regulatory agencies are accustomed to evaluating fermentation processes using well-defined substrates, such as glucose. However, introducing a more variable feedstock can create additional scrutiny. “Most agencies expect a unique, standardized input, so when you come to them with ‘raw material X’, it raises questions,” Ellilä suggests. “To address this, we simplify the safety validation process by proving the safety of our strains and production methods on defined media. Then, we run comparison batches to show our product meets the same specifications, regardless of the feedstock used.”

Communicating sustainability and market viability

This variability also extends to Life Cycle Assessments (LCA), which can be challenging to communicate to both regulators and customers. “If you conduct LCAs properly, the feedstock plays a significant role in the results,” suggests Ellilä. “That means our sustainability metrics vary depending on the raw material used, so we need to work within acceptable ranges and clearly explain those parameters to customers.”

Convincing the market to embrace this variability remains an ongoing conversation. “The food industry is used to standardized feedstocks and products, which makes upcycling more difficult to position,” Ellilä acknowledges. “However, it’s about reframing the conversation – yes, there’s some variability, but that’s also what enables us to hit competitive price points and strong LCA metrics. We work closely with customers to define mutually agreed specifications, ensuring that both product quality and sustainability indicators remain within an acceptable range.”

For Enifer, shifting this mindset requires continuous dialogue and education, balancing the need for consistency with the benefits that upcycled ingredients bring to both cost and sustainability targets.

A similar balancing act exists in cultivated meat, where companies must navigate both technological advancements and shifting political landscapes. While upcycled ingredients face regulatory hurdles tied to variability, cultivated meat companies contend with broader geopolitical and policy challenges. Concerns about regulatory approval processes, particularly in the USA, raise questions about the industry’s trajectory. As Pershad, an American building a cultivated meat company abroad (in Singapore), observes, “Political realities change, and you have to have an understanding of regulatory risk and be able to prioritize.” He suggests that companies should not be “too married to the home country” and advocates for a diversified approach, noting that “there’s a handful of countries where food security is national security, and those are the best countries to be working with right now”. He cites Singapore, the UAE, and China as examples of markets where cultivated meat is being prioritized for these very reasons.

GFI’s Leman echoes that sentiment, suggesting that while regulatory actions are unpredictable, companies can emphasize the advantages of cultivated meat that align with government interests. “One of the really cool opportunities we have here in the USA,” Leman suggests, “is building up a completely new bio manufacturing industry that uses locally sourced feedstocks [and] local talent.” He also pinpoints the potential for increased protein security, arguing that biomanufacturing offers “a closed system” that can provide “stable, predictable production”, as well as consistent pricing, unlike animal-derived protein supply chains.

He also emphasizes the scale of the opportunity, noting that with a global population approaching 10 billion by 2050, “there’s room for a lot of different operators, and room for a lot of different manufacturing here”. Ultimately, he thinks most governments will recognize the value of investing in such stable and scalable food production systems. The question remains, however, which commercial applications will lead the charge, and whether fermentation or cellular agriculture will take the lead.

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