Functional conservation of microbial communities determines composition predictability in anaerobic digestion.

A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.

The microbiology of Power-to-X applications.

Power-to-X (P2X) technologies will play a more important role in the conversion of electric power to storable energy carriers, commodity chemicals and even food and feed. Among the different P2X technologies, microbial components form cornerstones of individual process steps. This review comprehensively presents the state-of-the-art of different P2X technologies from a microbiological standpoint. We are focusing on microbial conversions of hydrogen from water electrolysis to methane, other chemicals and proteins. We present the microbial toolbox needed to gain access to these products of interest, assess its current status and research needs, and discuss potential future developments that are needed to turn todays P2X concepts into tomorrow's technologies.

Granular activated carbon stimulates biogas production in pilot-scale anaerobic digester treating agro-industrial wastewater.

This work examines the continuous addition (5 g/L) of conductive granular activated carbon (GAC) in an integrated pilot-scale unit containing an anaerobic digester (180 L) and an aerobic submerged membrane bioreactor (1600 L) connected in series for the treatment of agro-industrial wastewater. Biogas production increased by 32 % after the addition of GAC. Methanosaeta was the dominant methanogen in the digester, and its relative abundance increased after the addition of GAC. The final effluent after post-treatment with the aerobic membrane bioreactor had a total solids content <0.01 g/L and a chemical oxygen demand between 120 and 150 mg/L. A simple cost analysis showed that GAC addition is potentially profitable, but alternatives ways of retaining the GAC in the system need to be found. Overall, this study provides useful scientific data for the possible application of GAC in full-scale biogas projects.

Steering the product spectrum in high-pressure anaerobic processes: CO2 partial pressure as a novel tool in biorefinery concepts.

BACKGROUND: Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor. RESULTS: Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided. CONCLUSIONS: Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.

Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning.

Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH4 production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH4 production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH4 production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.

Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion.

Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH4 daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH4 daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.

Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure.

Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.

Labile carbon feedstocks trigger a priming effect in anaerobic digestion: An insight into microbial mechanisms.

The mechanisms underlying the advanced performance in anaerobic co-digestion (AcoD) are crucial but remain elusive. This study conducted AcoD of swine manure, rice straw and apple waste (AW, mainly consisting of labile carbon) or fructose (a pure labile carbon), and monitored microbial community abundances, activities and transcriptional profiles in the digestate and on straw. The transformation efficiencies of manure (not straw) to CH4 were promoted in AcoD co-fed manure and AW (by 39 ± 13%) or fructose (by 65 ± 14%), compared to the control mono-fed manure, implying labile carbon could trigger a priming effect underlying AcoD advantage. Although digestate-associated and straw-associated communities existed in a same bioreactor, the priming effect mainly linked to the former and was attributed to enhancements in deterministic turnover of active communities, in activities of Firmicutes taxa involved in substrate hydrolysis, and in acetoclastic methanogenesis. These findings provide novel insights to elaborate AcoD processes.

Molybdate effectively controls sulphide production in a shrimp pond model.

The production of shrimp is often performed in earthen outdoor ponds in which the high input of feed and faeces on the bottom can result in deterioration of the water quality, which negatively impacts the animals and the environment. Here, we investigate the potential of sodium molybdate (Na2MoO4·2H2O), sodium nitrate (NaNO3) and sodium percarbonate (Na2CO3·1.5H2O2) to control sulphide production in a simulated shrimp pond bottom system that included the sediment, overlaying artificial seawater and organic matter input in the form of shrimp feed and shrimp faeces. Sediment depth gradient measurements of oxygen, H2S and pH were obtained during 7 days of incubation using microelectrodes. The most significant impact in terms of H2S, was observed for 50 mg/L sodium molybdate. At the water-sediment interface, there was up to 73% less H2S detected for this treatment in comparison to a control treatment, while in the deeper layers of the sediment it was up to 47% less H2S. The residual sulphate concentrations in the molybdate treated samples were 16 ± 4% higher than the control, indicating an inhibition in sulphate reduction. Nitrate and sodium percarbonate treatments also showed a limited capacity to decrease H2S entering in the water column, yet no clear difference in H2S concentrations in the sediment compared to the control were observed. Molybdate treatment appears to work through the inhibition of sulphate reducing bacteria in situ for the control of H2S production better than the chemical oxygen boosters or nitrate treatment.

Engineering microbial technologies for environmental sustainability: choices to make.

Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.

From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria.

Increasing efforts are directed towards the development of sustainable alternative protein sources among which microbial protein (MP) is one of the most promising. Especially when waste streams are used as substrates, the case for MP could become environmentally favorable. The risks of using organic waste streams for MP production-the presence of pathogens or toxicants-can be mitigated by their anaerobic digestion and subsequent aerobic assimilation of the (filter-sterilized) biogas. Even though methane and hydrogen oxidizing bacteria (MOB and HOB) have been intensively studied for MP production, the potential benefits of their co-cultivation remain elusive. Here, we isolated a diverse group of novel HOB (that were capable of autotrophic metabolism), and co-cultured them with a defined set of MOB, which could be grown on a mixture of biogas and H2/O2. The combination of MOB and HOB, apart from the CH4 and CO2 contained in biogas, can also enable the valorization of the CO2 that results from the oxidation of methane by the MOB. Different MOB and HOB combinations were grown in serum vials to identify the best-performing ones. We observed synergistic effects on growth for several combinations, and in all combinations a co-culture consisting out of both HOB and MOB could be maintained during five days of cultivation. Relative to the axenic growth, five out of the ten co-cultures exhibited 1.1-3.8 times higher protein concentration and two combinations presented 2.4-6.1 times higher essential amino acid content. The MP produced in this study generally contained lower amounts of the essential amino acids histidine, lysine and threonine, compared to tofu and fishmeal. The most promising combination in terms of protein concentration and essential amino acid profile was Methyloparacoccus murrelli LMG 27482 with Cupriavidus necator LMG 1201. Microbial protein from M. murrelli and C. necator requires 27-67% less quantity than chicken, whole egg and tofu, while it only requires 15% more quantity than the amino acid-dense soybean to cover the needs of an average adult. In conclusion, while limitations still exist, the co-cultivation of MOB and HOB creates an alternative route for MP production leveraging safe and sustainably-produced gaseous substrates.

Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles.

The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, ß-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.

In vitro and in vivo digestion of red cured cooked meat: oxidation, intestinal microbiota and fecal metabolites.

Mechanisms explaining epidemiological associations between red (processed) meat consumption and chronic disease risk are not yet elucidated, but may involve oxidative reactions, microbial composition alterations, inflammation and/or the formation of toxic bacterial metabolites. First, in vitro gastrointestinal digestion of 23 cooked beef-lard minces, to which varying doses of nitrite salt (range 0-40 g/kg) and sodium ascorbate (range 0-2 g/kg) were added, showed that nitrite salt decreased protein carbonylation up to 3-fold, and inhibited lipid oxidation, demonstrated by up to 4-fold lower levels of 'thiobarbituric acid reactive substances', 32-fold lower 4-hydroxynonenal, and 21-fold lower hexanal values. The use of ascorbate increased the antioxidant effect of low nitrite salt levels, whereas it slightly increased protein carbonylation at higher doses of nitrite salt. The addition of a low dose of ascorbate without nitrite salt slightly promoted oxidation during digestion, whereas higher doses had varying antioxidant effects. Second, 40 rats were fed a diet of cooked chicken- or beef-lard minces, either or not cured, for three weeks. Beef, compared to chicken, consumption increased lipid oxidation (2- to 4-fold) during digestion, and gut protein fermentation (cecal iso-butyrate, (iso-)valerate, and fecal indole, cresol), but oxidative stress and inflammation were generally not affected. Cured, compared to fresh, meat consumption significantly increased stomach protein carbonylation (+16%), colonic Ruminococcaceae (2.1-fold) and cecal propionate (+18%), whereas it decreased cecal butyrate (-25%), fecal phenol (-69%) and dimethyl disulfide (-61%) levels. Fecal acetaldehyde and diacetyl levels were increased in beef-fed rats by 2.8-fold and 5.9-fold respectively, and fecal carbon disulfide was 4-fold higher in rats consuming cured beef vs. fresh chicken. Given their known toxicity, the role of acetaldehyde and carbon disulfide in the relation between meat consumption and health should be investigated in future studies.

Cow manure stabilizes anaerobic digestion of cocoa waste.

Anaerobic digestion of a mono-feedstock often causes low methane yields and process instability. An effective strategy to overcome these barriers is co-digestion with animal manure. The obtained process improvement is often attributed to buffer capacity, nutrients, vitamins and trace metals, and microorganisms present in manure, but it remains unknown which factor plays the key role in digester performance. Here, we investigated anaerobic digestion of cocoa waste in four different treatments: mono-digestion, addition of synthetic nutrients, co-digestion with sterile cow manure, and co-digestion with raw cow manure. Co-digestion with raw manure resulted in the highest methane yield of 181 ± 39 L kg-1 VS (volatile solids), similar to the co-digestion with sterile manure, i.e., 162 ± 52 L kg-1 VS. The supplementation of synthetic nutrients to the anaerobic digestion of cocoa waste only temporarily increased methane yield, indicating that this will tackle a lack of nutrients in the short term, but has a limited long-term contribution to the stabilization of the process. Hence, because of the inability of synthetic nutrients to stabilize the digestion process and the similarity between the digesters fed sterile and raw manure, both at the physico-chemical and microbial level, the key contribution of manure co-digestion with cocoa seems to be the provision of buffering capacity.

Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production.

Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.

Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets.

BACKGROUND: Early-life antibiotic administration is known to affect gut microbiota and host adiposity, but the effects of antibiotic exposure on skeletal muscle properties remain unknown. The present study evaluated the changes in skeletal muscle properties including myofiber characteristics and composition, as well as intramuscular fat (IMF) content in skeletal muscle of piglets when exposed to a tylosin-containing diet. RESULTS: A total of 18 piglets (28 days of age) were randomly allocated into two groups: control basal diet (Control) and Control + 100 mg tylosin phosphate/kg of feed (Antibiotic). The trial lasted for 39 days. High-throughput amplicon sequencing revealed that no significant difference in initial gut microbiota composition was existed between Control and Antibiotic groups. Antibiotic administration increased body weight and growth rate and decreased feed to gain ratio of pigs (P < 0.05). The carcass lean and fat volumes of pigs were increased by the tylosin administration (P < 0.05). Antibiotic treatment increased myofiber density and the expression of genes related to type I and type IIb myofibers in longissimus muscle (P < 0.05). The IMF content in longissimus muscle was increased by antibiotic exposure (P < 0.05). Antibiotic administration increased expression of genes related to fatty acid uptake and de novo synthesis, and decreased expression of genes related to triglyceride hydrolysis (P < 0.05). Tylosin administration affected taxonomic distribution and beta diversity of the caecal and colonic microbiota of piglets. CONCLUSION: These results confirm that the growth performance, myofiber composition and muscle lipid metabolism are affected by antibiotic administration, which may be associated with an altered gut microbiota, suggesting that the gut microbiota could be served as a potential target for modulating skeletal muscle properties of host.

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals.

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.

Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.

Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L-1. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.

Red and processed meat consumption within two different dietary patterns: Effect on the colon microbial community and volatile metabolites in pigs.

Pigs were fed either red and processed meat or chicken meat within either a prudent or a Western dietary pattern for four weeks (2 × 2 full factorial design). The colon microbial community and volatile organic compounds were assessed (either quantified or based on their presence). Results show that Lactobacilli were characteristic for the chicken × prudent dietary pattern treatment and Paraprevotella for the red and processed meat × prudent dietary pattern treatment. Enterobacteriaceae and Desulfovibrio were characteristic for the chicken × Western dietary pattern treatment and Butyrivibrio for the red and processed meat × Western dietary pattern treatment. Campylobacter was characteristic for chicken consumption and Clostridium XIVa for red and processed meat, irrespective of the dietary pattern. Ethyl valerate and 1-methylthio-propane were observed more frequently in pigs fed red and processed meat compared to chicken meat. The prevalence of 3-methylbutanal was >80% for pigs receiving a Western dietary pattern, whereas for pigs fed a prudent dietary pattern the prevalence was <35%. The concentration of butanoic acid was significantly higher when the prudent dietary pattern was given, compared to the Western dietary pattern, but no differences for other short chain fatty acids or protein fermentation products were observed.

The next frontier of the anaerobic digestion microbiome: From ecology to process control.

The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.