Faster-growing salt-loving microbes could make protein from biogas instead of natural gas

A team of researchers at Ghent University has identified two methane-eating bacteria that may outperform the industrial workhorse of microbial protein production, opening a path toward protein grown on biogas and seawater rather than fossil natural gas and freshwater. The study, published in Frontiers in Chemical Engineering, systematically compared Methylosinus sp. and Methylomonas methanica against Methylococcus capsulatus, the species that underpins commercial products such as FeedKind. The results suggest that the conventional choice of microbe may not be the optimal one for a future in which protein is fermented from waste-derived methane under salty, less-than-ideal conditions.

Microbial protein, also called single-cell protein, is the protein-rich biomass of bacteria, yeasts, fungi or microalgae grown on substrates ranging from sugars to gases. Its appeal is rooted in stark resource arithmetic: producing protein this way requires roughly 40,000 times less land and 20 times less water than beef, while bacterial biomass can contain 50 to 82 percent protein by dry weight, approaching raw chicken and exceeding whole egg or soybean. Because bacteria can feed on gaseous carbon sources, methane from biogas offers a route that sidesteps the pesticides, heavy metals and pathogens that can contaminate liquid waste streams, since those contaminants do not survive the anaerobic digestion step that generates the gas.

The bottleneck has always been the microbe. Methane fermentation suffers from poor gas-to-liquid mass transfer, so methane growers tend to be slower and less productive than organisms fed soluble sugars. Methylococcus capsulatus, the incumbent, is also sensitive to impurities such as hydrogen sulfide, which effectively locks industrial processes into using natural gas or carefully upgraded biomethane rather than raw biogas. The Ghent team reasoned that alternative methane-oxidizing bacteria, or methanotrophs, might sidestep some of these constraints. Gamma-proteobacteria such as Methylomonas methanica use the ribulose monophosphate pathway for carbon assimilation, a biochemically more efficient route than the serine pathway, promising higher biomass yields and less wasted carbon and energy.

In head-to-head comparisons under identical gas fermentation conditions, the challengers delivered. Methylosinus sp. reached a maximum specific growth rate of 0.75 per hour, nearly 1.9 times that of M. capsulatus, while M. methanica achieved 0.65 per hour. Methylomonas methanica also produced a biomass concentration of 0.53 grams per liter, 2.5 times higher than the 0.21 grams per liter of the conventional species. There was a catch: M. capsulatus still made the most protein-dense biomass, at 58 percent of cell dry weight, compared with 45 percent for M. methanica and just 18 percent for Methylosinus sp. Fast growth, it turns out, tends to come at the expense of protein content, a trade-off that echoes broader principles of microbial physiology linking growth rate to macromolecular composition and cell size.

The researchers then asked whether co-cultivation could shift that balance. Methanotrophs release metabolic intermediates such as methanol, formate and acetate during methane oxidation, compounds that can accumulate and stress the methane growers themselves. Non-methanotrophic methylotrophs, which consume these one-carbon compounds, were proposed as cleanup crew. The team paired each methanotroph with two established biotechnology organisms: the methylotrophic bacterium Methylorubrum extorquens and the methylotrophic yeast Komagataella phaffii, formerly known as Pichia pastoris. The outcome was strikingly species-dependent. Co-cultures with M. capsulatus or Methylosinus sp. showed little change, but when M. methanica was grown with K. phaffii, the protein content of the mixed biomass rose significantly to 64 percent of cell dry weight, a 1.42-fold increase, without any loss of growth performance.

Protein quality improved as well. The essential amino acid content of the M. methanica and K. phaffii co-culture reached 126 grams per kilogram of cell dry weight, 1.27 times the pure culture value of 99 grams per kilogram, and well above the 87 grams per kilogram of the co-culture with M. extorquens. Benchmarking the biomass against common foods, the researchers calculated that 111 grams of the co-culture product, with lysine as the limiting amino acid, would cover an adult’s daily essential amino acid requirements, compared with 148 grams of pure M. methanica and 258 grams of the M. extorquens co-culture. The co-culture biomass also contained a higher fraction of sulfur-containing amino acids such as methionine, at 6 percent of essential amino acids versus 4 percent in soybean meal, which is often deficient in this respect. Notably, because protein content is expressed relative to total dry biomass, the increase cannot be explained simply by adding yeast cells, hinting at genuinely altered carbon allocation whose mechanism remains to be unraveled.

The most eye-catching result came from stressing the winning bacterium with salt. When the medium was supplemented with 20 grams of sodium chloride per liter, the protein content of M. methanica jumped to 81 percent of cell dry weight, 1.8 times the salt-free control, while growth rates and biomass concentrations were barely affected across salt levels from 10 to 35 grams per liter. The 35 gram per liter condition approximates seawater, meaning the organism, originally isolated from a seawater enrichment culture, can grow protein in ocean-strength brine. That matters because saline cultivation could let future factories use brackish water, desalination brines or seawater instead of scarce freshwater, and high salt also suppresses contaminating microbes, easing sterility demands. The mechanism likely involves osmotic adaptation reshaping cellular composition, but the researchers caution that targeted compositional analyses are needed to pin down what is actually changing inside the cells.

The study also tackled the question of feedstock purity, with consequences for process sustainability. When M. methanica was grown on synthetic biogas, a methane and carbon dioxide mixture of 65 and 35 percent by volume, the protein content of the biomass rose 1.5-fold compared with purified methane, and protein yields per unit of methane consumed climbed from 0.37 to 0.56 grams of protein per gram of methane. Real biogas from a local maize farm, containing 78 percent methane, boosted protein content 1.3-fold and yields to 0.40 grams per gram. Crucially, pH remained stable in the biogas cultures and methane was never limiting, so the effect appears tied to the altered gas composition itself rather than to acidification or starvation. Because raw biogas contains carbon dioxide that purified methane does not, the result suggests that skipping the energy-intensive biogas upgrading step could actually improve product quality, a counterintuitive bonus for circular-economy schemes that convert organic waste to methane and then to food.

The trade-offs were equally illuminating on the pH front. When the researchers allowed the medium to acidify from around pH 6.8 down to 4.6 during growth, biomass concentration collapsed to about a quarter of the pH-controlled value, but the protein content of what biomass remained rose to 45 percent of cell dry weight, 1.55 times the pH-controlled level of 29 percent. Because total protein productivity depends on both biomass and protein fraction, pH-controlled cultivation still won on overall protein output, achieving 2.7 milligrams of protein per liter per hour versus 1.1 without control. The broader lesson is that upstream cultivation choices, from species selection to pH strategy to salinity to gas composition, act as adjustable dials that shift the balance between how much biomass a bioreactor produces and how protein-rich that biomass is.

Caveats remain before any of this reaches a dinner plate. The experiments were run in sealed serum bottles at small scale, where gas-liquid mass transfer, mixing and oxygen availability differ substantially from industrial bioreactors, so the performance gains cannot be directly extrapolated to production. Methylomonas methanica and its co-culture partner would also face a complete safety evaluation and regulatory approval pathway, something M. capsulatus has already cleared in both the European Union and the United States. The researchers note that biogas impurities such as hydrogen sulfide and ammonia were not fully assessed, although sulfur impurities could conceivably enrich the biomass in sulfur amino acids. Still, the study delivers the first quantitative comparison of these fast-growing methanotrophs against the industrial standard, and it sketches a concrete recipe for a future protein factory: Methyomonas methanica fermented with Komagataella phaffii, on unupgraded biogas, in saltwater, tuning the dials of stress and partnership to match the market’s demand for either volume or quality.

Subject of Research: Microbial protein production from biogas using alternative methanotrophic bacteria and methylotrophic co-cultures under saline conditions

Article Title: Methylomonas methanica and Methylosinus sp. co-cultivated with methylotrophs under saline conditions for microbial protein production from biogas as alternatives to natural-gas- based production using Methylococcus capsulatus

Article References: Kerckhof, F.-M., Benmeridja, N., Rabaey, K., Boon, N., De Vrieze, J., & Sakarika, M. (2026). Methylomonas methanica and Methylosinus sp. co-cultivated with methylotrophs under saline conditions for microbial protein production from biogas as alternatives to natural-gas- based production using Methylococcus capsulatus. Frontiers in Chemical Engineering, 8, Article 1912929. https://doi.org/10.3389/fceng.2026.1912929

Image Credits: AI Generated

DOI: 10.3389/fceng.2026.1912929

Keywords: microbial protein, methanotrophs, Methylomonas methanica, Methylococcus capsulatus, biogas, co-culture, Komagataella phaffii, salinity, single-cell protein, food sustainability, methane fermentation, essential amino acids