Evaluation of methane-utilising bacteria products as feed ingredients for monogastric animals

Highly efficient ammonium removal through nitrogen assimilation by a hydrogen-oxidizing bacterium, Ideonella sp. TH17

Ideonella sp. TH17, an autotrophic hydrogen-oxidizing bacterium (HOB), was successfully enriched and isolated from activated sludge in a domestic wastewater treatment plant (WWTP). Batch experiments were conducted to identify the cell growth and ammonium (NH₄⁺-N) removal, and to verify the pathways of nitrogen utilization under different conditions. At a representative NH₄⁺-N concentration of 100 mg/L in domestic wastewater, it was the first time that a HOB strain achieved a nearly 100% ammonium removal. More than 90% of NH₄⁺-N was assimilated to biomass nitrogen by strain TH17. Only a little of N₂ (<10% of initial NH₄⁺-N) was detected without N₂O emission in aerobic denitrification process. Autotrophic NH₄⁺-N assimilation contributed predominantly to biomass nitrogen production, supplemented by assimilatory nitrate (NO₃^--N) reduction under aerobic conditions. A total of 17 amino acids, accounting for 54.25 ± 1.98% of the dry biomass, were detected in the bacterial biomass harvested at 72 h. These results demonstrated that the newly isolated strain TH17 was capable of removing NH₄⁺-N and recovering nutrients from wastewater efficiently. A new solution was thus provided by this HOB strain for ammonium treatment in sustainable WWTPs of future.

The indispensable role of assimilation in methane driven nitrate removal

Methane is a greenhouse gas that can be released from sludge anaerobic fermentation in wastewater treatment plants. Methane is also an alternative additional carbon source for deep nitrate removal of secondary effluent. A sequencing experiment was conducted to study the efficacy of nitrate removal with methane as the sole carbon source. The maximum nitrate removal rate was 17.2 mg-N·L^-1·d^-1. Nitrate removal was confirmed to arise via two pathways: aerobic methane oxidation coupled to denitrification (AME-D) contributed to 55% of the nitrate removal with the rest stemming from assimilation by methanotrophs. Additional study revealed that nitrate assimilated by methanotrophs was used for the synthesis of proteins, resulting in a protein content of 52.2% dry weight. Metagenomic sequencing revealed a high abundance of nitrate assimilation and glutamine synthetase genes, which were primarily provided by methanotrophs (mainly Methylomonas). Assimilatory nitrate removal by methanotrophs has a high potential for advanced nitrogen removal and for alleviating methane emissions. The nitrogen-rich biomass produced by nitrate absorption could also be used as a biofertilizer for nitrogen recycling.

Sulfide restrains the growth of Methylocapsa acidiphila converting renewable biogas to single cell protein

Methane-oxidizing bacteria (MOB) that can use biogas and recycled nitrogen from wastewater as a sustainable feedstock for single cell protein (SCP) synthesis are receiving increasing attention. Though promising, limited knowledge is available on the alternative strains especially the ones that can tolerant to strict environments such as acidic conditions. Furthermore, how would the hydrogen sulfide affect the MOB (especially the alternative strains) for SCP synthesis when crude biogas is used as feedstock is still unknown. In this study, the capability of an acidic-tolerant methanotrophic bacterium Methylocapsa acidiphila for SCP production using raw biogas and the associated inhibitory effect of sulfide on the bioconversion was for the first time investigated. Results showed that the inhibitory effect of sulfide on the growth of M. acidiphila was observed starting from 8.13 mg L^-1 Na₂S (equivalent to approximately 1000 ppm of H₂S in crude biogas). The total amino acid content in the dry biomass decreased more than two times due to sulfide inhibition compared with the control samples without the presence of sulfide (585.96 mg/g dry biomass), while the proportion of essential amino acids in the total amino acid was not affected when the concentration of Na₂S was lower than 5.73 mg L^-1. The performance of M. acidiphila in a sulfide-rich environment was further studied at different operational conditions. The feeding gas with a CH₄/O₂ ratio of 6:4 could help to alleviate the sulfide inhibition, compared with other ratios (4:6 and 8:2). Moreover, the sequential supply of the feed gas could also alleviate sulfide inhibition. In addition, the MOB's growth rate was higher when applying a higher mixing rate of 120 rpm, compared with 70 rpm and 0, due to a better gas-liquid mass transfer. The inoculum size of 20% and 10% resulted in a faster growth rate compared with the 5%. Furthermore, M. acidiphila could assimilate either NH₄⁺ or NO₃^- as nitrogen source with a similar growth rate, giving it the potential to recycle nitrogen from a wide range of wastewaters. The results will not only create new knowledge for better understanding the role of hydrogen sulfide in the assimilation of raw biogas by acid-tolerant M. acidiphila but also provide technical insights into the development of an efficient and robust process for the waste-to-protein conversion.

Evaluation of a Bacterial Single-Cell Protein in Compound Diets for Rainbow Trout (Oncorhynchus mykiss) Fry as an Alternative Protein Source

Simple Summary

Fish meal (FM), as the main protein source, is used in aquafeeds due to its good nutritional profile and palatability. In recent years, because of the high cost and uncertainty in FM supply, studies have been focused to identify and evaluate alternative protein ingredients to minimize FM and reducethe cost of formulated feeds. Currently, plant protein ingredients and animal by-products are used as alternative protein sources to FM, but these components have some nutritional limitations, such as beingrich in anti-nutritional elements and deficient in certain essential amino acids. Among alternative protein sources, single-cell protein (SCP) such as bacteria, yeasts and microalgae, is considered a promising substitute for animal- or plant-derived ingredients. In this work, we aimed to evaluate the replacement of FM with a bacterial SCP, a by-product of the monosodium L-glutamic acid produced by microbial fermentation of vegetal raw materials, in diets for rainbow trout (Oncorhynchus mykiss) fry. Results indicated that the maximum replacement of FM by SCP in terms of growth and feed efficiency performance was up to 50%, while the broken-line regression analyses using DHA muscle content and weight gain showed that this value ranged between 46.9 to 52% SCP depending on the parameter considered.

Abstract

A 60-day trial was conducted in rainbow trout (Oncorhynchus mykiss) fry (initial weight = 2.5 ± 0.6 g) to evaluate the potential use of a bacterial single-cell protein (SCP) as an alternative protein source. Five experimental diets with different levels of fishmeal replacement (0, 25, 50, 75 and 100%) and no amino acid supplementation were tested. At the end of the trial, we found that fry fed diets, replacing 25 and 50% of fishmeal with bacterial SCP, were 9.1 and 21.8% heavier, respectively, than those fed the control diet (p < 0.05), while Feed Conversion Ratio (FCR) values were also lower in comparison to the reference group. These results were also supported by Protein Efficiency Ratio (PER) and Lipid Efficiency Ratio (LER) values that improved in fish fed diets replacing 50% fishmeal by bacterial SCP. The inclusion of SCP enhanced Feed intake (FI) (p < 0.05), although FI was reduced at higher inclusion levels (>50%), which was associated to feed palatability. High levels of bacterial SCP (>50%) affected the muscular amino acid and fatty acid profiles, imbalances that were associated to their dietary content. The broken-line regression analysis using muscle DHA content and weight gain data showed that the maximum levels of fishmeal replacement by bacterial SCP were 46.9 and 52%, respectively.

Cultivation of methanotrophic bacteria in a novel bubble-free membrane bioreactor for microbial protein production

Microbial protein is proposed as an alternative protein source with low environmental impact. Methane oxidizing bacteria are already produced at commercial scale from natural gas. However, their productivity is limited because of the creation of explosive atmospheres in the fermenters during production. This work demonstrates the applicability of bioreactors with a membrane-based gas supply via diffusion. Methanotrophic bacteria were successfully cultivated, with growth yields from 0.26 to 0.43 g-VSS g-CH₄^-1, slightly below those observed in analogous fermenters relying on bubbling. However, ammonia yields ranged from 5.2 to 6.9 g-VSS g-NH₃^-1, indicating higher nitrogen assimilation than in conventional fermenters. Indeed, protein content increased during the operational period reaching up to 51% of dry weight. The amino acid profile included the majority of the essential amino acids, demonstrating suitability as feed ingredient. Never during the operational period was an explosive atmosphere established in the reactor. Thus, bubble-free membrane bioreactors are a promising technology for microbial protein production relying on explosive gas mixtures.

ASAS-NANP SYMPOSIUM: RUMINANT/NONRUMINANT FEED COMPOSITION: Challenges and opportunities associated with creating large feed composition tables

Traditional feed composition tables have been a useful tool in the field of animal nutrition throughout the last 70 yr. The objective of this paper is to discuss the challenges and opportunities associated with creating large feed ingredient composition tables. This manuscript will focus on three topics discussed during the National Animal Nutrition Program (NANP) Symposium in ruminant and nonruminant nutrition carried out at the American Society of Animal Science Annual Meeting in Austin, TX, on July 11, 2019, namely: 1) Using large datasets in feed composition tables and the importance of standard deviation in nutrient composition as well as different methods to obtain accurate standard deviation values, 2) Discussing the importance of fiber in animal nutrition and the evaluation of different methods to estimate fiber content of feeds, and 3) Description of novel feed sources, such as insects, algae, and single-cell protein, and challenges associated with the inclusion of such feeds in feed composition tables. Development of feed composition tables presents important challenges. For instance, large datasets provided by different sources tend to have errors and misclassifications. In addition, data are in different file formats, data structures, and feed classifications. Managing such large databases requires computers with high processing power and software that are also able to run automated procedures to consolidate files, to screen out outlying observations, and to detect misclassified records. Complex algorithms are necessary to identify misclassified samples and outliers aimed to obtain accurate nutrient composition values. Fiber is an important nutrient for both monogastrics and ruminants. Currently, there are several methods available to estimate the fiber content of feeds. However, many of them do not estimate fiber accurately. Total dietary fiber should be used as the standard method to estimate fiber concentrations in feeds. Finally, novel feed sources are a viable option to replace traditional feed sources from a nutritional perspective, but the large variation in nutrient composition among batches makes it difficult to provide reliable nutrient information to be tabulated. Further communication and cooperation among different stakeholders in the animal industry are required to produce reliable data on the nutrient composition to be published in feed composition tables.

The Application of Single-Cell Ingredients in Aquaculture Feeds—A Review

Single-cell ingredients (SCI) are a relatively broad class of materials that encompasses bacterial, fungal (yeast), microalgal-derived products or the combination of all three microbial groups into microbial bioflocs and aggregates. In this review we focus on those dried and processed single-cell organisms used as potential ingredients for aqua-feeds where the microorganisms are considered non-viable and are used primarily to provide protein, lipids or specific nutritional components. Among the SCI, there is a generalised dichotomy in terms of their use as either single-cell protein (SCP) resources or single-cell oil (SCO) resources, with SCO products being those oleaginous products containing 200 g/kg or more of lipids, whereas those products considered as SCP resources tend to contain more than 300 g/kg of protein (on a dry basis). Both SCP and SCO are now widely being used as protein/amino acid sources, omega-3 sources and sources of bioactive molecules in the diets of several species, with the current range of both these ingredient groups being considerable and growing. However, the different array of products becoming available in the market, how they are produced and processed has also resulted in different nutritional qualities in those products. In assessing this variation among the products and the application of the various types of SCI, we have taken the approach of evaluating their use against a set of standardised evaluation criteria based around key nutritional response parameters and how these criteria have been applied against salmonids, shrimp, tilapia and marine fish species.

Coproducts of algae and yeast-derived single cell oils: A critical review of their role in improving biorefinery sustainability

Oleaginous microalgae and yeast are of increasing interest as a renewable resource for single cell oils (SCOs). These have applications in fuels, feed and food products. In order to become cost competitive with existing terrestrial oils, a biorefinery approach is often taken where several product streams are valorised alongside the SCO. Whilst many life cycle assessment (LCA) and Techno-economic (TEA) studies have employed this biorefinery approach to SCO production, a systematic analysis of their implications is missing. This review evaluates the economic and environmental impacts associated with the use of coproducts. Overall, protein production plays the greatest role in determining viability, with coproduct strategy crucial to considering in the early stages of research and development.

Cyberlindnera jadinii yeast as a protein source for broiler chickens: effects on growth performance and digestive function from hatching to 30 days of age

Europe is heavily dependent on imported feed protein sources such as soybean meal (SBM); thus, investigating local sustainable alternatives is crucial to increase self-sufficiency. This study evaluated the effects of the inactivated yeast Cyberlindnera jadinii grown on local lignocellulosic sugars on the growth performance and digestive function of Ross 308 broiler chickens. A total of 1,000 male chicks were allocated to 20 pens. There were 5 replicate pens with 50 birds each, from 1 to 30 D after hatch. The birds were offered one conventional wheat–oat–SBM–based control diet and 3 diets with increasing levels of C. jadinii replacing 10, 20, and 30% of dietary crude protein (CP), whereas SBM levels were gradually decreased. The feed intake and weight gain of the birds decreased linearly, and feed conversion ratio increased linearly (P < 0.01) with increasing dietary levels of C. jadinii. Nevertheless, growth performance and feed intake were similar between the birds fed with control diets and diets containing 10% CP from C. jadinii in the starter and grower periods. The apparent ileal digestibility (AID) of dry matter, crude fat, organic matter, and carbohydrates was higher in control diets than in diets with 30% C. jadinii CP (P < 0.05) and decreased (P < 0.01) with incremental levels of dietary C. jadinii. Regardless, the AID of CP, starch, ash, and phosphorus was unaffected. Ileal villus height on day 10 was maintained in birds fed with diets containing 30% C. jadinii CP compared with the birds fed with control diets but was lower for birds fed with diets containing 10 and 20% C. jadinii protein (P < 0.05). To conclude, up to 10% C. jadinii CP can replace SBM CP in broiler chicken diets, maintaining growth performance and digestive function, whereas higher levels of C. jadinii may decrease bird performance. Altogether, this suggests the potential of C. jadinii as a local-based protein source in broiler chicken diets, contributing to a more sustainable feed.

Recent advances in single cell protein use as a feed ingredient in aquaculture

The global demand for high-quality, protein-rich foods will continue to increase as the global population grows, along with income levels. Aquaculture is poised to help fulfill some of this demand, and is thus the fastest growing animal protein industry. A key challenge for it, though, is sourcing a sustainable, renewable protein ingredient. Single cell protein (SCP) products, protein meals based on microbial or algal biomass, have the potential to fulfill this need. Here, we review potential sources of SCP strains and their respective production processes, highlight recent advances on identification of new SCP strains and feedstocks, and, finally, review new feeding trial data on important aquaculture species, specifically Atlantic salmon, rainbow trout, and whiteleg shrimp.

Thermophilic methanotrophs: in hot pursuit

Methane is a potent greenhouse gas responsible for 20–30% of global climate change effects. The global methane budget is ∼500–600 Tg y−1, with the majority of methane produced via microbial processes, including anthropogenic-mediated sources such as ruminant animals, rice fields, sewage treatment facilities and landfills. It is estimated that microbially mediated methane oxidation (methanotrophy) consumes >50% of global methane flux each year. Methanotrophy research has primarily focused on mesophilic methanotrophic representatives and cooler environments such as freshwater, wetlands or marine habitats from which they are sourced. Nevertheless, geothermal emissions of geological methane, produced from magma and lithosphere degassing micro-seepages, mud volcanoes and other geological sources, contribute an estimated 33–75 Tg y−1 to the global methane budget. The aim of this review is to summarise current literature pertaining to the activity of thermophilic and thermotolerant methanotrophs, both proteobacterial (Methylocaldum, Methylococcus, Methylothermus) and verrucomicrobial (Methylacidiphilum). We assert, on the basis of recently reported molecular and geochemical data, that geothermal ecosystems host hitherto unidentified species capable of methane oxidation at higher temperatures.

Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals

Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg⁻¹, respectively. Consequently, the biomass can be viewed as an appropriate feed and/or feed additive for supplementation with macroelements and certain microelements. Moreover, all consortia demonstrated higher content of unsaturated acids than saturated ones. Thus, methanotrophic bacteria seem to be a good solution, in natural supplementation of animal diets.

Engineering the Dark Food Chain

Meeting global food needs in the face of climate change and resource limitation requires innovative approaches to food production. Here, we explore incorporation of new dark food chains into human food systems, drawing inspiration from natural ecosystems, the history of single cell protein, and opportunities for new food production through wastewater treatment, microbial protein production, and aquaculture. The envisioned dark food chains rely upon chemoautotrophy in lieu of photosynthesis, with primary production based upon assimilation of CH₄ and CO₂ by methane- and hydrogen-oxidizing bacteria. The stoichiometry, kinetics, and thermodynamics of these bacteria are evaluated, and opportunities for recycling of carbon, nitrogen, and water are explored. Because these processes do not require light delivery, high volumetric productivities are possible; because they are exothermic, heat is available for downstream protein processing; because the feedstock gases are cheap, existing pipeline infrastructure could facilitate low-cost energy-efficient delivery in urban environments. Potential life-cycle benefits include: a protein alternative to fishmeal; partial decoupling of animal feed from human food; climate change mitigation due to decreased land use for agriculture; efficient local cycling of carbon and nutrients that offsets the need for energy-intensive fertilizers; and production of high value products, such as the prebiotic polyhydroxybutyrate.

Environmental Benefits of Novel Nonhuman Food Inputs to Salmon Feeds

Global population growth and changing diets increase the importance, and challenges, of reducing the environmental impacts of food production. Farmed seafood is a relatively efficient way to produce protein and has already overtaken wild fisheries. The use of protein-rich food crops, such as soy, instead of fishmeal in aquaculture feed diverts these important protein sources away from direct human consumption and creates new environmental challenges. Single cell proteins (SCPs), including bacteria and yeast, have recently emerged as replacements for plant-based proteins in salmon feeds. Attributional life cycle assessment is used to compare salmon feeds based on protein from soy, methanotrophic bacteria, and yeast ingredients. All ingredients are modeled at the industrial production scale and compared based on seven resource use and emissions indicators. Yeast protein concentrate showed drastically lower impacts in all categories compared to soy protein concentrate. Bacteria meal also had lower impacts than soy protein concentrate for five of the seven indicators. When these target meals were incorporated into complete feeds the relative trends remain fairly constant, but benefits of the novel ingredients are dampened by high impacts from the nontarget ingredients. Particularly, primary production requirements (PPR) are about equal and constant across all feeds for both analyses since PPR was driven by fishmeal and oil. The bacteria-based feed has the highest climate change impacts due to the use of methane to feed the bacteria who then release carbon dioxide. Overall, the results of this study suggest that incorporating SCP ingredients into salmon feeds can help reduce the environmental impacts of salmon production. Continued improvements in SCP production would further increase the sustainability of salmon farming.

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Background: Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like Escherichia coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers.

Results: Here, we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature.

Conclusion: The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies toward improved SCP production processes in M. capsulatus.

Meeting Global Feed Protein Demand: Challenge, Opportunity, and Strategy

Feed protein supplements are one of the most expensive and limiting feed ingredients. This review offers a comprehensive analysis of how the expected expansion of animal production, driven by the rising world population and living standards for more animal-sourced foods, is creating a global shortage of feed protein supply. Because ruminants, chickens, and pigs contribute to 96% of the global supply of animal protein and aquaculture is growing fast, means of meeting the feed protein requirements of these species are elaborated. Geographic variation and interdependence among China, Europe, and North America in the demand and supply of feed protein are compared. The potential and current state of exploration into alternative feed proteins, including microalgae, insects, single-cell proteins, and coproducts, are highlighted. Strategic innovations are proposed to upgrade feed protein processing and assessment, improve protein digestion by exogenous enzymes, and genetically select feed-efficient livestock breeds. An overall successful and sustainable solution in meeting global feed protein demands will lead to a substantial net gain of human-edible animal protein with a minimal environmental footprint.

Decoupling Livestock from Land Use through Industrial Feed Production Pathways

One of the main challenges for the 21st century is to balance the increasing demand for high-quality proteins while mitigating environmental impacts. In particular, cropland-based production of protein-rich animal feed for livestock rearing results in large-scale agricultural land-expansion, nitrogen pollution, and greenhouse gas emissions. Here we propose and analyze the long-term potential of alternative animal feed supply routes based on industrial production of microbial proteins (MP). Our analysis reveals that by 2050, MP can replace, depending on socio-economic development and MP production pathways, between 10-19% of conventional crop-based animal feed protein demand. As a result, global cropland area, global nitrogen losses from croplands and agricultural greenhouse gas emissions can be decreased by 6% (0-13%), 8% (-3-8%), and 7% (-6-9%), respectively. Interestingly, the technology to industrially produce MP at competitive costs is directly accessible for implementation and has the potential to cause a major structural change in the agro-food system.

Production of single cell protein from agro-waste using Rhodococcus opacus

Livestock and fish farming are rapidly growing industries facing the simultaneous pressure of increasing production demands and limited protein required to produce feed. Bacteria that can convert low-value non-food waste streams into singe cell protein (SCP) present an intriguing route for rapid protein production. The oleaginous bacterium Rhodococcus opacus serves as a model organism for understanding microbial lipid production. SCP production has not been explored using an organism from this genus. In the present research, R. opacus strains DSM 1069 and PD630 were fed three agro-waste streams: (1) orange pulp, juice, and peel; (2) lemon pulp, juice, and peel; and (3) corn stover effluent, to determine if these low-cost substrates would be suitable for producing a value-added product, SCP for aquafarming or livestock feed. Both strains used agro-waste carbon sources as a growth substrate to produce protein-rich cell biomass suggesting that that R. opacus can be used to produce SCP using agro-wastes as low-cost substrates.

Methane to bioproducts: the future of the bioeconomy?

Methanotrophs have been studied since the 1970s, but interest has increased tremendously in recent years due to their potential to transform methane into valuable bioproducts. The vast quantity of available methane and the low price of methane as natural gas have helped to spur this interest. The most well-studied, biologically-derived products from methane include methanol, polyhydroxyalkanoates, and single cell protein. However, many other high-interest chemicals such as biofuels or high-value products such as ectoine could be made industrially relevant through metabolic engineering. Although challenges must be overcome to achieve commercialization of biologically manufactured methane-to-products, taking a holistic view of the production process or radically re-imagining pathways could lead to a future bioeconomy with methane as the primary feedstock.

Single Cell Protein-State-of-the-Art, Industrial Landscape and Patents 2001-2016

By 2050, the world would need to produce 1,250 million tonnes of meat and dairy per year to meet global demand for animal-derived protein at current consumption levels. However, growing demand for protein will not be met sustainably by increasing meat and dairy production because of the low efficiency of converting feed to meat and dairy products. New solutions are needed. Single cell protein (SCP), i.e., protein produced in microbial and algal cells, is an option with potential. Much of the recent interest in SCP has focused on the valorisation of side streams by using microorganisms to improve their protein content, which can then be used in animal feed. There is also increased use of mixed populations, rather than pure strains in the production of SCP. In addition, the use of methane as a carbon source for SCP is reaching commercial scales and more protein-rich products are being derived from algae for both food and feed. The following review addresses the latest developments in SCP production from various organisms, giving an overview of commercial exploitation, a review of recent advances in the patent landscape (2001–2016) and a list of industrial players in the SCP field.

Autotrophic nitrogen assimilation and carbon capture for microbial protein production by a novel enrichment of hydrogen-oxidizing bacteria

Domestic used water treatment systems are currently predominantly based on conventional resource inefficient treatment processes. While resource recovery is gaining momentum it lacks high value end-products which can be efficiently marketed. Microbial protein production offers a valid and promising alternative by upgrading low value recovered resources into high quality feed and also food. In the present study, we evaluated the potential of hydrogen-oxidizing bacteria to upgrade ammonium and carbon dioxide under autotrophic growth conditions. The enrichment of a generic microbial community and the implementation of different culture conditions (sequenced batch resp. continuous reactor) revealed surprising features. At low selection pressure (i.e. under sequenced batch culture at high solid retention time), a very diverse microbiome with an important presence of predatory Bdellovibrio spp. was observed. The microbial culture which evolved under high rate selection pressure (i.e. dilution rate D = 0.1 h(-1)) under continuous reactor conditions was dominated by Sulfuricurvum spp. and a highly stable and efficient process in terms of N and C uptake, biomass yield and volumetric productivity was attained. Under continuous culture conditions the maximum yield obtained was 0.29 g cell dry weight per gram chemical oxygen demand equivalent of hydrogen, whereas the maximum volumetric loading rate peaked 0.41 g cell dry weight per litre per hour at a protein content of 71%. Finally, the microbial protein produced was of high nutritive quality in terms of essential amino acids content and can be a suitable substitute for conventional feed sources such as fishmeal or soybean meal.

A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation

Methane, a carbon source for methanotrophic bacteria, is the principal component of natural gas and is produced during anaerobic digestion of organic matter (biogas). Methanotrophs are a viable source of single cell protein (feed supplement) and can produce various products, since they accumulate osmolytes (e.g. ectoine, sucrose), phospholipids (potential biofuels) and biopolymers (polyhydroxybutyrate, glycogen), among others. Other cell components, such as surface layers, metal chelating proteins (methanobactin), enzymes (methane monooxygenase) or heterologous proteins hold promise as future products. Here, scenarios are presented where ectoine, polyhydroxybutyrate or protein G are synthesised as the primary product, in conjunction with a variety of ancillary products that could enhance process viability. Single or dual-stage processes and volumetric requirements for bioreactors are discussed, in terms of an annual biomass output of 1000 tonnesyear(-1). Product yields are discussed in relation to methane and oxygen consumption and organic waste generation.

Microbial protein: future sustainable food supply route with low environmental footprint

Microbial biotechnology has a long history of producing feeds and foods. The key feature of today's market economy is that protein production by conventional agriculture based food supply chains is becoming a major issue in terms of global environmental pollution such as diffuse nutrient and greenhouse gas emissions, land use and water footprint. Time has come to re‐assess the current potentials of producing protein‐rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass, producible with a lower environmental footprint compared with other plant or animal‐based alternatives. A major driver is the need to no longer disintegrate but rather upgrade a variety of low‐value organic and inorganic side streams in our current non‐cyclic economy. In this context, microbial bioconversions of such valuable matters to nutritive microbial cells and cell components are a powerful asset. The worldwide market of animal protein is of the order of several hundred million tons per year, that of plant protein several billion tons of protein per year; hence, the expansion of the production of microbial protein does not pose disruptive challenges towards the process of the latter. Besides protein as nutritive compounds, also other cellular components such as lipids (single cell oil), polyhydroxybuthyrate, exopolymeric saccharides, carotenoids, ectorines, (pro)vitamins and essential amino acids can be of value for the growing domain of novel nutrition. In order for microbial protein as feed or food to become a major and sustainable alternative, addressing the challenges of creating awareness and achieving public and broader regulatory acceptance are real and need to be addressed with care and expedience.

Bacillus amyloliquefaciens SQR9 induces dendritic cell maturation and enhances the immune response against inactivated avian influenza virus

The objective of this study was to evaluate the stimulatory effects of Bacillus amyloliquefaciens SQR9 on dendritic cells (DCs) and to verify its ability to enhance the immune response by modulating DC maturation. The results demonstrated that B. amyloliquefaciens SQR9 can adhere to the nasal epithelium and be taken up by DCs in the nasal mucosa, thereby inducing DC maturation and resulting in increased CD80, CD86, CD40 and MHCII expression and cytokine secretion. The frequencies of CD4(+) and CD8(+) T cells and CD69(+) memory T cells were increased in spleens after nasal immunization with virus plus B. amyloliquefaciens SQR9 compared to immunization with inactivated H9N2 AIV alone. Moreover, the levels of sIgA in the nasal cavity, the trachea, and the lung and the levels of IgG, IgG1, and IgG2a in serum were significantly increased in mice administered WIV plus SQR9 compared to mice administered H9N2 WIV alone. The results of this study demonstrated that B. amyloliquefaciens SQR9 can stimulate DC maturation to effectively induce an immune response. In conclusion, an effective immune response may result from the uptake of H9N2 by DCs in the nasal mucosa, thereby stimulating DC maturation and migration to cervical lymph nodes to initiate immune response.

Methane as a resource: can the methanotrophs add value?

Methane is an abundant gas used in energy recovery systems, heating, and transport. Methanotrophs are bacteria capable of using methane as their sole carbon source. Although intensively researched, the myriad of potential biotechnological applications of methanotrophic bacteria has not been comprehensively discussed in a single review. Methanotrophs can generate single-cell protein, biopolymers, components for nanotechnology applications (surface layers), soluble metabolites (methanol, formaldehyde, organic acids, and ectoine), lipids (biodiesel and health supplements), growth media, and vitamin B12 using methane as their carbon source. They may be genetically engineered to produce new compounds such as carotenoids or farnesene. Some enzymes (dehydrogenases, oxidase, and catalase) are valuable products with high conversion efficiencies and can generate methanol or sequester CO2 as formic acid ex vivo. Live cultures can be used for bioremediation, chemical transformation (propene to propylene oxide), wastewater denitrification, as components of biosensors, or possibly for directly generating electricity. This review demonstrates the potential for methanotrophs and their consortia to generate value while using methane as a carbon source. While there are notable challenges using a low solubility gas as a carbon source, the massive methane resource, and the potential cost savings while sequestering a greenhouse gas, keeps interest piqued in these unique bacteria.

Candida utilis and Chlorella vulgaris counteract intestinal inflammation in Atlantic salmon (Salmo salar L.)

Intestinal inflammation, caused by impaired intestinal homeostasis, is a serious condition in both animals and humans. The use of conventional extracted soybean meal (SBM) in diets for Atlantic salmon and several other fish species is known to induce enteropathy in the distal intestine, a condition often referred to as SBM induced enteropathy (SBMIE). In the present study, we investigated the potential of different microbial ingredients to alleviate SBMIE in Atlantic salmon, as a model of feed-induced inflammation. The dietary treatments consisted of a negative control based on fish meal (FM), a positive control based on 20% SBM, and four experimental diets combining 20% SBM with either one of the three yeasts Candida utilis (CU), Kluyveromyces marxianus (KM), Saccharomyces cerevisiae (SC) or the microalgae Chlorella vulgaris (CV). Histopathological examination of the distal intestine showed that all fish fed the SC or SBM diets developed characteristic signs of SBMIE, while those fed the FM, CV or CU diets showed a healthy intestine. Fish fed the KM diet showed intermediate signs of SBMIE. Corroborating results were obtained when measuring the relative length of PCNA positive cells in the crypts of the distal intestine. Gene set enrichment analysis revealed decreased expression of amino acid, fat and drug metabolism pathways as well as increased expression of the pathways for NOD-like receptor signalling and chemokine signalling in both the SC and SBM groups while CV and CU were similar to FM and KM was intermediate. Gene expression of antimicrobial peptides was reduced in the groups showing SBMIE. The characterisation of microbial communities using PCR-DGGE showed a relative increased abundance of Firmicutes bacteria in fish fed the SC or SBM diets. Overall, our results show that both CU and CV were highly effective to counteract SBMIE, while KM had less effect and SC had no functional effects.

Prevention of soya-induced enteritis in Atlantic salmon (Salmo salar) by bacteria grown on natural gas is dose dependent and related to epithelial MHC II reactivity and CD8α+ intraepithelial lymphocytes

An experiment was carried out to study the preventive effect of bacterial meal (BM) produced from natural gas against plant-induced enteropathy in Atlantic salmon (Salmo salar). Salmon were fed a diet based on fish meal (FM) or seven diets with 200 g/kg solvent-extracted soyabean meal (SBM) to induce enteritis in combination with increasing levels of BM from 0 to 300 g/kg. Salmon fed a SBM-containing diet without BM developed typical SBM-induced enteritis. The enteritis gradually disappeared with increasing inclusion of BM. By morphometry, no significant (P>0.05) differences in the size of stretches stained for proliferating cell nuclear antigen were found with 150 g/kg BM compared with the FM diet. Increasing BM inclusion caused a gradual decline in the number of cluster of differentiation 8 α positive (CD8α+) intraepithelial lymphocytes, and fish fed BM at 200 g/kg or higher revealed no significant difference from the FM diet. Histological sections stained with antibody for MHC class II (MHC II) showed that fish with intestinal inflammation had more MHC II-reactive cells in the lamina propria and submucosa, but less in the epithelium and brush border, compared with fish without inflammation. There were no significant (P>0.05) differences in growth among the diets, but the highest levels of BM slightly reduced protein digestibility and increased the weight of the distal intestine. In conclusion, the prevention of SBM-induced enteritis by BM is dose dependent and related to intestinal levels of MHC II- and CD8α-reactive cells.

The noncommensal bacterium Methylococcus capsulatus (Bath) ameliorates dextran sulfate (Sodium Salt)-Induced Ulcerative Colitis by influencing mechanisms essential for maintenance of the colonic barrier function

Dietary inclusion of a bacterial meal has recently been shown to efficiently abolish soybean meal-induced enteritis in Atlantic salmon. The objective of this study was to investigate whether inclusion of this bacterial meal in the diet could abrogate disease development in a murine model of epithelial injury and colitis and thus possibly have therapeutic potential in human inflammatory bowel disease. C57BL/6N mice were fed ad libitum a control diet or an experimental diet containing 254 g/kg of body weight BioProtein, a bacterial meal consisting of Methylococcus capsulatus (Bath), together with the heterogenic bacteria Ralstonia sp., Brevibacillus agri, and Aneurinibacillus sp. At day 8, colitis was induced by 3.5% dextran sulfate sodium (DSS) ad libitum in the drinking water for 6 days. Symptoms of DSS treatment were less profound after prophylactic treatment with the diet containing the BioProtein. Colitis-associated parameters such as reduced body weight, colon shortening, and epithelial damage also showed significant improvement. Levels of acute-phase reactants, proteins whose plasma concentrations increase in response to inflammation, and neutrophil infiltration were reduced. On the other, increased epithelial cell proliferation and enhanced mucin 2 (Muc2) transcription indicated improved integrity of the colonic epithelial layer. BioProtein mainly consists of Methylococcus capsulatus (Bath) (88%). The results that we obtained when using a bacterial meal consisting of M. capsulatus (Bath) were similar to those obtained when using BioProtein in the DSS model. Our results show that a bacterial meal of the noncommensal bacterium M. capsulatus (Bath) has the potential to attenuate DSS-induced colitis in mice by enhancing colonic barrier function, as judged by increased epithelial proliferation and increased Muc2 transcription.

Bacteria grown on natural gas prevent soybean meal-induced enteritis in Atlantic salmon

Dietary inclusion of solvent extracted soybean meal (SBM) is associated with inflammation in the distal intestine of salmonid fish, commonly referred to as SBM-induced enteritis. The enteritis is linked to alcohol soluble components in SBM, but the mechanisms have not been established. Previous studies show that bacterial meal (BM) containing mainly Methylococcus capsulatus grown on natural gas is a suitable protein source for salmonids. The BM is rich in nucleotides, phospholipids, and small peptides that might be beneficial for intestinal homeostasis. In this study, a fish meal (FM)-based control diet (FM diet) and diets with 200 g/kg SBM (SBM diet), 300 g/kg BM (BM diet), and 300 g/kg BM and 200 g/kg SBM (BM-SBM diet) were fed to juvenile Atlantic salmon (Salmo salar) for 80 d. Dietary inclusion of SBM reduced growth (P = 0.007). Inclusion of BM reduced digestibility of protein (P = 0.002) and lipids (P = 0.011) and increased (P < 0.01) the relative weights (g/kg whole body) of total gut, liver, and stomach, and mid and distal intestine. Fish fed the SBM diet developed enteritis, lacked carbonic anhydrase 12 in the brush border of epithelial cells in distal intestine, and had more epithelial cells reacting for proliferating cell nuclear antigen compared with fish fed the other diets. Fish fed the same amount of SBM combined with BM showed no signs of inflammation in the distal intestine. Our results demonstrate that BM grown on natural gas can be used to prevent SBM-induced enteritis in Atlantic salmon.

Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b

Methylosinus trichosporium OB3b (for "oddball" strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from M. trichosporium OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the M. trichosporium OB3b genome is the first reported from a member of the Methylocystaceae family in the order Rhizobiales.