Continuous n-valerate formation from propionate and methanol in an anaerobic chain elongation open-culture bioreactor

Modelling anaerobic sulfide removal by sulfide shuttling bacteria

Sulfide oxidizing bacteria are used in industrial biodesulfurization processes to convert sulfide to sulfur. These bacteria can spatially separate sulfide removal from terminal electron transfer, thereby acting as sulfide shuttles. The mechanisms underlying sulfide shuttling are not yet clear. In this work, newly obtained sulfide removal data were used to develop a new model for anaerobic sulfide removal and this model was shown to be an improvement over two previously published models. The new model describes a fast chemical step and a consecutive slow enzymatic step. The improved model includes the effect of pH, with higher total sulfide removal at increasing pH, as well as partial sulfide removal at higher sulfide concentrations. The two-stage model is supported by recent developments in anaerobic sulfide removal research and contributes to a better understanding of the underlying mechanisms. The model is a step toward accurately modelling anaerobic sulfide removal in industrial systems.

Two-stage conversion of syngas and pyrolysis aqueous condensate into L-malate

Hybrid thermochemical-biological processes have the potential to enhance the carbon and energy recovery from organic waste. This work aimed to assess the carbon and energy recovery potential of multifunctional processes to simultaneously sequestrate syngas and detoxify pyrolysis aqueous condensate (PAC) for short-chain carboxylates production. To evaluate relevant process parameters for mixed culture co-fermentation of syngas and PAC, two identical reactors were run under mesophilic (37 °C) and thermophilic (55 °C) conditions at increasing PAC loading rates. Both the mesophilic and the thermophilic process recovered at least 50% of the energy in syngas and PAC into short-chain carboxylates. During the mesophilic syngas and PAC co-fermentation, methanogenesis was completely inhibited while acetate, ethanol and butyrate were the primary metabolites. Over 90% of the amplicon sequencing variants based on 16S rRNA were assigned to Clostridium sensu stricto 12. During the thermophilic process, on the other hand, Symbiobacteriales, Syntrophaceticus, Thermoanaerobacterium, Methanothermobacter and Methanosarcina likely played crucial roles in aromatics degradation and methanogenesis, respectively, while Moorella thermoacetica and Methanothermobacter marburgensis were the predominant carboxydotrophs in the thermophilic process. High biomass concentrations were necessary to maintain stable process operations at high PAC loads. In a second-stage reactor, Aspergillus oryzae converted acetate, propionate and butyrate from the first stage into L-malate, confirming the successful detoxification of PAC below inhibitory levels. The highest L-malate yield was 0.26 ± 2.2 molL-malate/molcarboxylates recorded for effluent from the mesophilic process at a PAC load of 4% v/v. The results highlight the potential of multifunctional reactors where anaerobic mixed cultures perform simultaneously diverse process roles, such as carbon fixation, wastewater detoxification and carboxylates intermediate production. The recovered energy in the form of intermediate carboxylates allows for their use as substrates in subsequent fermentative stages.

Methanol as a co-substrate with CO2 enhances butyrate production in microbial electrosynthesis

Methanol is a promising feedstock for the bio-based economy as it can be derived from organic waste streams or produced electrochemically from CO2. Acetate production from CO2 in microbial electrosynthesis (MES) has been widely studied, while more valuable compounds such as butyrate are currently attracting attention. In this study, methanol was used as a co-substrate with CO2 to enhance butyrate production in MES. Feeding with CO2 and methanol resulted in the highest butyrate production rates and titres of 0.36 ± 0.01 g L-1 d-1 and 8.6 ± 0.2 g L-1, respectively, outperforming reactors with only CO2 feeding (0.20 ± 0.03 g L-1 d-1 and 5.2 ± 0.1 g L-1, respectively). Methanol acted as electron donor and as carbon source, both of which contributed ca. 50% of the carbon in the products. Eubacterium was the dominant genus with 52.6 ± 2.5% relative abundance. Thus, we demonstrate attractive route for the use of the C1 substrates, CO2 and methanol, to produce mainly butyrate. KEY POINTS: • Butyrate was the main product from methanol and CO2 in MES • Methanol acted as both carbon and electron source in MES • Eubacterium dominating microbial culture was enriched in MES.

CO2 supply is a powerful tool to control homoacetogenesis, chain elongation and solventogenesis in ethanol and carboxylate fed reactor microbiomes

Anaerobic fermentation technology enables the production of medium chain carboxylates and alcohols through microbial chain elongation. This involves steering reactor microbiomes to yield desired products, with CO2 supply playing a crucial role in controlling ethanol-based chain elongation and facilitating various bioprocesses simultaneously. In the absence of CO2 supply (Phase I), chain elongation predominantly led to n-caproate with a high selectivity of 96 Cmol%, albeit leaving approximately 80% of ethanol unconverted. During this phase, C. kluyveri and Proteiniphilum-related species dominated the reactors. In Phase II, with low CO2 input (2.0 NmL L-1 min-1), formation of n-butyrate, butanol, and hexanol was stimulated. Increasing CO2 doses in Phase III (6 NmL L-1 min-1) led to CO2 utilization via homoacetogenesis, coinciding with the enrichment of Clostridium luticellarii, a bacterium that can use CO2 as an electron acceptor. Lowering CO2 dose to 0.5 NmL L-1 min-1 led to a shift in microbiome composition, diminishing the dominance of C. luticellarii while increasing C. kluyveri abundance. Additionally, other Clostridia, Proteiniphilum, and Lactobacillus sakei-related species became prevalent. This decrease in CO2 load from 6 to 0.5 NmL L-1 min-1 minimized excessive ethanol oxidation from 30%-50% to 0%-3%, restoring a microbiome favoring net n-butyrate consumption and n-caproate production. The decreased ethanol oxidation coincided with the resurgence of hydrogen formation at partial pressures above 1%. High concentrations of butyrate, caproate, and ethanol in the reactor, along with low acetate concentration, promoted the formation of butanol and hexanol. It is evident that CO2 supply is indispensable for controlling chain elongation in an open culture and it can be harnessed to stimulate higher alcohol formation or induce CO2 utilization as an electron acceptor.

Medium chain Fatty acids production from Food Waste via homolactic fermentation and lactate/ethanol elongation: Electron balance and thermodynamic assessment

This study explored the potential of Food Waste (FW) extract as a suitable substrate for Medium Chain Fatty Acids (MCFAs) production, in a single-phase reactor, where both fermentation and Chain Elongation (CE) processes occurred simultaneously. A continuous experiment was conducted with an Organic Loading Rate (OLR) = 20 gCOD L-1 d-1 and was fed in batch mode twice a week with pH = 6. In addition, four batch tests were performed, to assess the effects on the MCFAs production of caproate inhibition, hydrogen partial pressure (PH2) and different lactate/acetate ratios. Thermodynamics and electron flux were calculated to gain insights into the process pathways. Due to the presence of aminoacids, fermentation was mostly homolactic and both lactate and ethanol were produced as Electron Donors (EDs); the average MCFAs production efficiency was ∼ 12 %, although after 4 weeks the elongation process was halted, resulting in EDs accumulation. This occurred regardless of inoculum selection and the presence of caproate as a possible inhibitor, suggesting that EDs accumulation was due to the elongation process kinetics being slower than those of the fermentation step, thus calling for a longer Hydraulic Retention Time (HRT). It's worth noting that lactate was prevalently self-elongated to butyrate, whereas ethanol elongation only took place after lactate depletion, but was more efficient since it required other Electron Acceptors (EAs) such as butyrate, propionate or valerate. Moreover, the selected pH limited the acrylate pathway to a reasonable extent, whereas the high PH2 prevented both ethanol and lactate oxydation to acetate.

Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii

Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.

Functional Redundancy Secures Resilience of Chain Elongation Communities upon pH Shifts in Closed Bioreactor Ecosystems

For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions, and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Gradual pH increase from 5.5 to 6.5 induced dramatic shifts in community composition, whereas product range and yields returned to previous states after transient fluctuations. To understand community responses to pH perturbations over long-term reactor operation, we applied Aitchison PCA clustering, linear mixed-effects models, and random forest classification on 16S rRNA gene amplicon sequencing and process data. Different pH preferences of two key chain elongation species─one Clostridium IV species related to Ruminococcaceae bacterium CPB6 and one Clostridium sensu stricto species related to Clostridium luticellarii─were determined. Network analysis revealed positive correlations of Clostridium IV with lactic acid bacteria, which switched from Olsenella to Lactobacillus along the pH increase, illustrating the plasticity of the food web in chain elongation communities. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.

Formate-induced CO tolerance and methanogenesis inhibition in fermentation of syngas and plant biomass for carboxylate production

BACKGROUND

Production of monocarboxylates using microbial communities is highly dependent on local and degradable biomass feedstocks. Syngas or different mixtures of H2, CO, and CO2 can be sourced from biomass gasification, excess renewable electricity, industrial off-gases, and carbon capture plants and co-fed to a fermenter to alleviate dependence on local biomass. To understand the effects of adding these gases during anaerobic fermentation of plant biomass, a series of batch experiments was carried out with different syngas compositions and corn silage (pH 6.0, 32 °C).

RESULTS

Co-fermentation of syngas with corn silage increased the overall carboxylate yield per gram of volatile solids (VS) by up to 29% (0.47 ± 0.07 g gVS-1; in comparison to 0.37 ± 0.02 g gVS-1 with a N2/CO2 headspace), despite slowing down biomass degradation. Ethylene and CO exerted a synergistic effect in preventing methanogenesis, leading to net carbon fixation. Less than 12% of the electrons were misrouted to CH4 when either 15 kPa CO or 5 kPa CO + 1.5 kPa ethylene was used. CO increased the selectivity to acetate and propionate, which accounted for 85% (electron equivalents) of all products at 49 kPa CO, by favoring lactic acid bacteria and actinobacteria over n-butyrate and n-caproate producers. Inhibition of n-butyrate and n-caproate production by CO happened even when an inoculum preacclimatized to syngas and lactate was used. Intriguingly, the effect of CO on n-butyrate and n-caproate production was reversed when formate was present in the broth.

CONCLUSIONS

The concept of co-fermenting syngas and plant biomass shows promise in three aspects: by making anaerobic fermentation a carbon-fixing process, by increasing the yields of short-chain carboxylates (propionate and acetate), and by minimizing electron losses to CH4. Moreover, a model was proposed for how formate can alleviate CO inhibition in certain acidogenic bacteria. Testing the fermentation of syngas and plant biomass in a continuous process could potentially improve selectivity to n-butyrate and n-caproate by enriching chain-elongating bacteria adapted to CO and complex biomass.

Anaerobic sulphide removal by haloalkaline sulphide oxidising bacteria

Sulphide is a toxic and corrosive compound and requires removal from waste streams. Recent discoveries show that sulphide oxidising bacteria (SOB) from modern desulphurisation plants are able to spatially separate sulphide removal and oxygen reduction when exposed to intermittent anaerobic and aerobic environments. Here, SOB act as electron shuttles between electron donor and acceptor. The underlying mechanisms for electron shuttling are of yet unknown. To investigate the anaerobic sulphide removal of SOB, batch experiments and mathematical models were applied. The sulphide removal capacity decreased at increasing biomass concentrations. At 0.6 mgN/L SOB could remove up to 8 mgS/mgN in 30 min. It was found that biological activity determines sulphide removal, alongside chemical processes. Anaerobic oxidation of electron carriers was determined to only explain 0.1% of charge storage, where irreversible cleavage of long chain polysulphides could explain full sulphide storage. Different sulphide removal and intracellular storage processes are postulated.

Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability

It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.

The effect of anode potential on electrogenesis, methanogenesis and sulfidogenesis in a simulated sewer condition

Methane emissions from the sewer system are considered to be a non-negligible source of aggravating the greenhouse effect. Meanwhile, the sewer system has long been plagued by sulfide-induced corrosion problems. This study explored the possibility of using a bioelectrochemical system to intensify the competition between electroactive bacteria, methanogens and sulfate-reducing bacteria, thereby reducing the production of methane and sulfide. Dual-chamber bioelectrochemical reactors were constructed and operated in fed-batch mode with the coexistence of Electroactive bacteria, Methanogenic archaea and Sulfate-reducing bacteria. Acetate was supplied as the sole carbon source. The results indicated that electrogenesis induced by the anode potentials of -0.42 V and -0.2 V (vs. Ag/AgCl) had advantages over methanogenesis and sulfidogenesis in consuming acetate. The stimulated electrogenesis by anode potentials resulted in a decrease in pH. Methane production was suppressed in the reactors with anode potentials of -0.42 and -0.2 V compared to open circuit controls. In contrast to methane, the capacity for sulfide production was facilitated in the reactors with the anode potentials of -0.42 V and -0.2 V compared to open circuit controls. 16s rRNA gene analysis showed that Geobacter was the most abundant genus on the anode biofilm in the anode potential-controlled reactor, while acetoclastic methanogens dominated in open circuit controls. Methanosaeta and Methanosarcina were the most abundant methanogens in open circuit controls. Collectively, our study demonstrates that the use of electrodes with anode potential control can help to control methane emissions, but could not yet prevent sulfide production, which requires further research.

Host and microbial-derived metabolites for Clostridioides difficile infection: Contributions, mechanisms and potential applications

Clostridioides difficile infection (CDI), which mostly occurs in hospitalized patients, is the most common and costly health care-associated disease. However, the biology of C. difficile remains incompletely understood. Current therapeutics are still challenged by the frequent recurrence of CDI. Advances in metabolomics facilitate our understanding of the etiology of CDI, which is not merely an alteration in the structure of the gut microbial community but also a dysbiosis metabolic setting promoting the germination, expansion and virulence of C. difficile. Therefore, we summarized the gut microbial and metabolic profiles for CDI under different conditions, such as those of postantibiotic treatment and postfecal microbiota transplantation. The current understanding of the role of host and gut microbial-derived metabolites as well as other nutrients in preventing or alleviating the disease symptoms of CDI will also be provided in this review. We hope that a specific nutrient-centric dietary strategy or the administration of certain nutrients to the colon could serve as an alternate line of investigation for the prophylaxis and mitigation of CDI in the future. Nevertheless, rigorously designed basic studies and randomized controlled trials need to be conducted to assess the functional mechanisms and effects of such therapeutics.

Efficient production of medium chain fatty acids in microbial electrosynthesis with simultaneous bio-utilization of carbon dioxide and ethanol

Microbial electrosynthesis (MES) is a promising technology for chemicals production driven by renewable energy. However, how the medium chain fatty acids (MCFAs) production in MES is affected by the method of chain elongation is not clear, and no direct evidence is provided yet for a simultaneous bio-utilization of CO₂ and ethanol. In this study, different methods of chain elongation in MES reactors were investigated. During in-situ chain elongation, a maximum caproate concentration of 11.9 ± 0.6 g L^-1 was achieved, while the C6 specificity (56.4% ± 0.5%) was much lower than that of ex-situ chain elongation (78.7% ± 1.5%). Carbon distribution and reduction degree balance indicated a simultaneous bio-utilization of CO₂ and ethanol, and it was validated by the isotope tracer technique. MCFAs-forming microbes, acetogens, and electrochemically active microorganisms were enriched. This study provides fundamental insights relevant to the carbon and electron fluxes driven by electricity.

Increase Dietary Fiber Intake Ameliorates Cecal Morphology and Drives Cecal Species-Specific of Short-Chain Fatty Acids in White Pekin Ducks

The current study was to investigate the modulatory effects of total dietary fiber (TDF) levels on cecal morphology and the response of microbiota to maintain gut health for duck growth. A total of 192 14-day-old male white Pekin ducks were randomly allocated to three dietary groups and fed diets, containing 12.4, 14.7, and 16.2% TDF, respectively, until 35 days under the quantitative feed intake. Each dietary group consisted of eight replicate cages of eight birds. The results revealed that 14.7 and 16.2% TDF groups significantly promoted growth performance and improved villus height, the ratio of villus to crypt, muscle layer thickness, and goblet cells per villus of cecum in ducks. qPCR results showed that the transcriptional expression of Claudin-1, Muc2, IGF-1, and SLC16A1 was significantly upregulated in cecum in 14.7 and 16.2% TDF groups. Meanwhile, the concentration of IGF-1 in circulating was significantly increased in 14.7 and 16.2% TDF groups while that of DAO was significantly decreased in 16.2% TDF group. Furthermore, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum were conspicuously improved in 14.7 and 16.2% TDF groups while that of propionate was significantly decreased. In addition, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum presented negative correlations with the concentration of DAO in circulating. 16S rRNA gene sequencing results showed that the 14.7% TDF group importantly elevated the microbial richness. Simultaneously, butyrate-producing bacteria like the family Lachnospiraceae, Oscillospiraceae, and Erysipelatoclostridiaceae were enriched as biomarkers in the 16.2% TDF group. Correlation network analysis revealed that the associations between specific bacteria and short-chain fatty acids (SCFAs) induced by different TDF levels, and the correlations among bacteria were also witnessed. For example, the genus Monoglobus and CHKCI002 showed a positive correlation with butyrate, and there was a positively coexistent association between Monoglobus and CHKCI002. In summary, these data revealed that increasing the TDF level could enhance the cecal morphology and drive cecal species-specific of SCFAs in ducks.

Syntrophic propionate-oxidizing bacteria in methanogenic systems

The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.

Reverse β-oxidation pathways for efficient chemical production

Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.

Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways

Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.

Concentration-dependent effects of nickel doping on activated carbon biocathodes

In microbial electrosynthesis (MES), microorganisms grow on a cathode electrode as biofilm, or in the catholyte as planktonic biomass, and utilize CO2 for their growth and metabolism. Modification of the...

Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H₂/CO₂. Two stirred tank reactors and two bubble column reactors were operated with H₂/CO₂ gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O₂ L⁻¹ d⁻¹, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH₄ was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O₂ concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O₂ below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L⁻¹ d⁻¹ depending on the reactor (control reactors 0.1–0.8 mmol L⁻¹ d⁻¹). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H₂ availability was high. After air contamination stopped completely, production of n-caproate and CH₄ recovered, with n-caproate production rates of 1.4–1.8 mmol L⁻¹ d⁻¹ (control 0.7–2.1 mmol L⁻¹ d⁻¹). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.

Diverse Profile of Fermentation Byproducts From Thin Stillage

The economy of biorefineries is influenced not only by biofuel production from carbohydrates but also by the production of valuable compounds from largely underutilized industrial residues. Currently, the demand for many chemicals that could be made in a biorefinery, such as succinic acid (SA), medium-chain fatty acids (MCFAs), and lactic acid (LA), is fulfilled using petroleum, palm oil, or pure carbohydrates as raw materials, respectively. Thin stillage (TS), the residual liquid material following distillation of ethanol, is an underutilized coproduct from the starch biofuel industry. This carbon-rich material has the potential for chemical upgrading by microorganisms. Here, we explored the formation of different fermentation products by microbial communities grown on TS using different bioreactor conditions. At the baseline operational condition (6-day retention time, pH 5.5, 35°C), we observed a mixture of MCFAs as the principal fermentation products. Operation of a bioreactor with a 1-day retention time induced an increase in SA production, and a temperature increase to 55°C resulted in the accumulation of lactic and propionic acids. In addition, a reactor operated with a 1-day retention time at 55°C conditions resulted in LA accumulation as the main fermentation product. The prominent members of the microbial community in each reactor were assessed by 16S rRNA gene amplicon sequencing and phylogenetic analysis. Under all operating conditions, members of the Lactobacillaceae family within Firmicutes and the Acetobacteraceae family within Proteobacteria were ubiquitous. Members of the Prevotellaceae family within Bacteroidetes and Lachnospiraceae family within the Clostridiales order of Firmicutes were mostly abundant at 35°C and not abundant in the microbial communities of the TS reactors incubated at 55°C. The ability to adjust bioreactor operating conditions to select for microbial communities with different fermentation product profiles offers new strategies to explore and compare potentially valuable fermentation products from TS and allows industries the flexibility to adapt and switch chemical production based on market prices and demands.

Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities

Electron donor scarcity is seen as one of the major issues limiting economic production of medium-chain carboxylates from waste streams. Previous studies suggest that co-fermentation of hydrogen in microbial communities that realize chain elongation relieves this limitation. To better understand how hydrogen co-feeding can support chain elongation, we enriched three different microbial communities from anaerobic reactors (A, B, and C with ascending levels of diversity) for their ability to produce medium-chain carboxylates from conventional electron donors (lactate or ethanol) or from hydrogen. In the presence of abundant acetate and CO₂, the effects of different abiotic parameters (pH values in acidic to neutral range, initial acetate concentration, and presence of chemical methanogenesis inhibitors) were tested along with the enrichment. The presence of hydrogen facilitated production of butyrate by all communities and improved production of i-butyrate and caproate by the two most diverse communities (B and C), accompanied by consumption of acetate, hydrogen, and lactate/ethanol (when available). Under optimal conditions, hydrogen increased the selectivity of conventional electron donors to caproate from 0.23 ± 0.01 mol e^-/mol e^- to 0.67 ± 0.15 mol e^-/mol e^- with a peak caproate concentration of 4.0 g L^-1. As a trade-off, the best-performing communities also showed hydrogenotrophic methanogenesis activity by Methanobacterium even at high concentrations of undissociated acetic acid of 2.9 g L^-1 and at low pH of 4.8. According to 16S rRNA amplicon sequencing, the suspected caproate producers were assigned to the family Anaerovoracaceae (Peptostreptococcales) and the genera Megasphaera (99.8% similarity to M. elsdenii), Caproiciproducens, and Clostridium sensu stricto 12 (97-100% similarity to C. luticellarii). Non-methanogenic hydrogen consumption correlated to the abundance of Clostridium sensu stricto 12 taxa (p < 0.01). If a robust methanogenesis inhibition strategy can be found, hydrogen co-feeding along with conventional electron donors can greatly improve selectivity to caproate in complex communities. The lessons learned can help design continuous hydrogen-aided chain elongation bioprocesses.

Microbial Regulation of Host Physiology by Short-chain Fatty Acids

Our ancestral diet consisted of much more nondigestible fiber than that of many societies today. Thus, from an evolutionary perspective the human genome and its physiological and nutritional requirements are not well aligned to modern dietary habits. Fiber reaching the colon is anaerobically fermented by the gut bacteria, which produce short-chain fatty acids (SCFAs) as metabolic by-products. SCFAs play a role in intestinal homeostasis, helping to explain why changes in the microbiota can contribute to the pathophysiology of human diseases. Recent research has shown that SCFAs can also have effects on tissues and organs beyond the gut, through their circulation in the blood. SCFAs not only signal through binding to cognate G-protein-coupled receptors on endocrine and immune cells in the body but also induce epigenetic changes in the genome through effects on the activity of histone acetylase and histone deacetylase enzymes. Furthermore, epigenetic imprinting likely occurs in utero, highlighting the importance of the maternal diet in early life. Here we review current understanding of how SCFAs impact on human and animal physiology and discuss the potential applications of SCFAs in the prevention and treatment of human diseases.

Enhanced bio-production from CO2 by microbial electrosynthesis (MES) with continuous operational mode

Technologies able to convert CO2 to various feedstocks for fuels and chemicals are emerging due to the urge of reducing greenhouse gas emissions and de-fossilizing chemical production. Microbial electrosynthesis (MES) has been shown a promising technique to synthesize organic products particularly acetate using microorganisms and electrons. However, the efficiency of the system is low. In this study, we demonstrated the simple yet efficient strategy in enhancing the efficiency of MES by applying continuous feeding regime. Compared to the fed-batch system, continuous operational mode provided better control of pH and constant medium refreshment, resulting in higher acetate production rate and more diverse bio-products, when the cathodic potential of -1.0 V Ag/AgCl and dissolved CO2 were provided. It was observed that hydraulic retention time (HRT) had a direct effect on the pattern of production, acetate production rate and coulombic efficiency. At HRT of 3 days, pH was around 5.2 and acetate was the dominant product with the highest production rate of 651.8 ± 214.2 ppm per day and a significant coulombic efficiency of 90%. However at the HRT of 7 days, pH was lower at around 4.5, and lower but stable acetate production rate of 280 ppm per day and a maximum coulombic efficiency of 80% was obtained. In addition, more diverse and longer chain products, such as butyrate, isovalerate and caproate, were detected with low concentrations only at the HRT of 7 days. Although microbial community analysis showed the change in the planktonic cells communities after switching the fed-batch mode to continuous feeding regime, Acetobacterium still remained as the responsible bacteria for CO2 reduction to acetate, dominating the cathodic biofilm.

Taming the Sentinels: Microbiome-Derived Metabolites and Polarization of T Cells

A global increase in the prevalence of metabolic syndromes and digestive tract disorders, like food allergy or inflammatory bowel disease (IBD), has become a severe problem in the modern world. Recent decades have brought a growing body of evidence that links the gut microbiome’s complexity with host physiology. Hence, understanding the mechanistic aspects underlying the synergy between the host and its associated gut microbiome are among the most crucial questions. The functionally diversified adaptive immune system plays a central role in maintaining gut and systemic immune homeostasis. The character of the reciprocal interactions between immune components and host-dwelling microbes or microbial consortia determines the outcome of the organisms’ coexistence within the holobiont structure. It has become apparent that metabolic by-products of the microbiome constitute crucial multimodal transmitters within the host–microbiome interactome and, as such, contribute to immune homeostasis by fine-tuning of the adaptive arm of immune system. In this review, we will present recent insights and discoveries regarding the broad landscape of microbiome-derived metabolites, highlighting the role of these small compounds in the context of the balance between pro- and anti-inflammatory mechanisms orchestrated by the host T cell compartment.

Parameters influencing the development of highly conductive and efficient biofilm during microbial electrosynthesis: the importance of applied potential and inorganic carbon source

Cathode-driven applications of bio-electrochemical systems (BESs) have the potential to transform CO2 into value-added chemicals using microorganisms. However, their commercialisation is limited as biocathodes in BESs are characterised by slow start-up and low efficiency. Understanding biosynthesis pathways, electron transfer mechanisms and the effect of operational variables on microbial electrosynthesis (MES) is of fundamental importance to advance these applications of a system that has the capacity to convert CO2 to organics and is potentially sustainable. In this work, we demonstrate that cathodic potential and inorganic carbon source are keys for the development of a dense and conductive biofilm that ensures high efficiency in the overall system. Applying the cathodic potential of -1.0 V vs. Ag/AgCl and providing only gaseous CO2 in our system, a dense biofilm dominated by Acetobacterium (ca. 50% of biofilm) was formed. The superior biofilm density was significantly correlated with a higher production yield of organic chemicals, particularly acetate. Together, a significant decrease in the H2 evolution overpotential (by 200 mV) and abundant nifH genes within the biofilm were observed. This can only be mechanistically explained if intracellular hydrogen production with direct electron uptake from the cathode via nitrogenase within bacterial cells is occurring in addition to the commonly observed extracellular H2 production. Indeed, the enzymatic activity within the biofilm accelerated the electron transfer. This was evidenced by an increase in the coulombic efficiency (ca. 69%) and a 10-fold decrease in the charge transfer resistance. This is the first report of such a significant decrease in the charge resistance via the development of a highly conductive biofilm during MES. The results highlight the fundamental importance of maintaining a highly active autotrophic Acetobacterium population through feeding CO2 in gaseous form, which its dominance in the biocathode leads to a higher efficiency of the system.

Cryopreservation and fast recovery of enriched syngas-converting microbial communities

Over the last decades, the use of mixed microbial communities has attracted increasing scientific attention due to their potential biotechnological applications in several emerging technological platforms such as the carboxylate, bioplastic, syngas and bio-electrochemical synthesis platforms. However, this increasing interest has not been accompanied by a parallel development of suitable cryopreservation techniques for microbial communities. While cryopreservation methods for the long-term storage of axenic cultures are well established, their effectiveness in preserving the microbial diversity and functionality of microbial communities has rarely been studied. In this study, the effect of the addition of different cryopreservation agents on the long-term storage of microbial communities at -80 °C was studied using a stable enrichment culture converting syngas into acetate and ethanol. The cryopreservation agents considered in the study were glycerol, dimethylsulfoxide, polyvinylpyrrolidone, Tween 80 and yeast extract, as well as with no addition of cryopreservation agent. Their effectiveness was evaluated based on the microbial activity recovery and the maintenance of the microbial diversity and community structure upon revival of the microbial community. The results showed that the commonly used glycerol and no addition of cryopreservation agent were the least recommendable methods for the long-term frozen storage of microbial communities, while Tween 80 and polyvinylpyrrolidone were overall the most effective. Among the cryoprotectants studied, polyvinylpyrrolidone and especially Tween 80 were the only ones assuring reproducible results in terms of microbial activity recovery and microbial community structure preservation.

Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate

Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day^-1, with a concurrent production of n-butyrate of 7.9 mM day^-1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

Concurrent use of methanol and ethanol for chain-elongating short chain fatty acids into caproate and isobutyrate

Microbial chain elongation (MCE) is a bioprocess that could utilise a mixed-culture fermentation to valorise organic waste. MCE converting ethanol and short chain fatty acids (SCFA; derived from organic waste) to caproate has been studied extensively and implemented. Recent studies demonstrated the conversion of SCFAs and methanol or ethanol into isomerised fatty acids as novel products, which may expand the MCE application and market. Integrating caproate and isomerised fatty acid production in one reactor system is theoretically feasible given the employment of a mixed culture and may increase the economic competence of MCE; however, the feasibility of such has never been demonstrated. This study investigated the feasibility of using two electron donors, i.e. methanol and ethanol, for upgrading SCFAs into isobutyrate and caproate concurrently in MCE Results show that supplying methanol and ethanol in MCE simultaneously converted acetate and/or butyrate into caproate and isobutyrate, by a mixed-culture microbiome. The butyrate supplement stimulated the caproate production rate from 1.5 to 2.6 g/L.day and induced isobutyrate production (1.5 g/L.day). Further increasing ethanol feeding rate from 140 to 280 mmol carbon per litre per day enhanced the direct use of butyrate for caproate production, which improved the caproate production rate to 5.9 g/L.day. Overall, the integration of two electron donors, i.e. ethanol and methanol, in one chain-elongation reactor system for upgrading SCFAs was demonstrated. As such, MCE could be applied to valorise organic waste (water) streams into a wider variety of value-added biochemical.

Competition Between Butyrate Fermenters and Chain-Elongating Bacteria Limits the Efficiency of Medium-Chain Carboxylate Production

Medium-chain carboxylates such as n-caproate and n-caprylate are valuable chemicals, which can be produced from renewable feedstock by anaerobic fermentation and lactate-based microbial chain elongation. Acidogenic microbiota involved in lactate-based chain elongation and their interplay with lactic acid bacteria have not been characterized in detail yet. Here, the metabolic and community dynamics were studied in a continuous bioreactor with xylan and lactate as sole carbon sources. Four succession stages were observed during 148 days of operation. After an adaptation period of 36 days, a relatively stable period of 28 days (stage I) was reached with n-butyrate, n-caproate and n-caprylate productivities of 7.2, 8.2 and 1.8 gCOD L-1 d-1, respectively. After a transition period, the process changed to another period (stage II), during which 46% more n-butyrate, 51% less n-caproate and 67% less n-caprylate were produced. Co-occurrence networks of species based on 16S rRNA amplicon sequences and correlations with process parameters were analyzed to infer ecological interactions and potential metabolic functions. Diverse functions including hydrolysis of xylan, primary fermentation of xylose to acids (e.g., to acetate by Syntrophococcus, to n-butyrate by Lachnospiraceae, and to lactate by Lactobacillus) and chain-elongation with lactate (by Ruminiclostridium 5 and Pseudoramibacter) were inferred from the metabolic network. In stage I, the sub-network characterized by strongest positive correlations was mainly related to the production of n-caproate and n-caprylate. Lactic acid bacteria of the genus Olsenella co-occurred with potentially chain-elongating bacteria of the genus Pseudoramibacter, and their abundance was positively correlated with n-caproate and n-caprylate concentrations. A new sub-network appeared in stage II, which was mainly related to n-butyrate production and revealed a network of different lactic acid bacteria (Bifidobacterium) and potential n-butyrate producers (Clostridium sensu stricto 12). The synergy effects between lactate-producing and lactate-consuming bacteria constitute a division of labor cooperation of mutual benefit. Besides cooperation, competition between different taxa determined the bacterial community assembly over the four succession stages in this resource-limited system. During long-term reactor operation under constant conditions, chain-elongating bacteria were outcompeted by butyrate-producing bacteria, leading to the increase of n-butyrate yield at the cost of medium-chain carboxylate yields in this closed model system.

A Thin Layer of Activated Carbon Deposited on Polyurethane Cube Leads to New Conductive Bioanode for (Plant) Microbial Fuel Cell

Large-scale implementation of (plant) microbial fuel cells is greatly limited by high electrode costs. In this work, the potential of exploiting electrochemically active self-assembled biofilms in fabricating three-dimensional bioelectrodes for (plant) microbial fuel cells with minimum use of electrode materials was studied. Three-dimensional robust bioanodes were successfully developed with inexpensive polyurethane foams (PU) and activated carbon (AC). The PU/AC electrode bases were fabricated via a water-based sorption of AC particles on the surface of the PU cubes. The electrical current was enhanced by growth of bacteria on the PU/AC bioanode while sole current collectors produced minor current. Growth and electrochemical activity of the biofilm were shown with SEM imaging and DNA sequencing of the microbial community. The electric conductivity of the PU/AC electrode enhanced over time during bioanode development. The maximum current and power density of an acetate fed MFC reached 3 mA·m−2 projected surface area of anode compartment and 22 mW·m−3 anode compartment. The field test of the Plant-MFC reached a maximum performance of 0.9 mW·m−2 plant growth area (PGA) at a current density of 5.6 mA·m−2 PGA. A paddy field test showed that the PU/AC electrode was suitable as an anode material in combination with a graphite felt cathode. Finally, this study offers insights on the role of electrochemically active biofilms as natural enhancers of the conductivity of electrodes and as transformers of inert low-cost electrode materials into living electron acceptors.

Microbial electrochemical stimulation of caproate production from ethanol and carbon dioxide

The production of value added chemicals from CO₂ is of critical importance for the practical application of microbial electrosynthesis (MES). Here, a binary electron donor (ED) design (using electrode and ethanol) was introduced to provide an efficient caproate production with the bioconversion of both CO₂ and ethanol. A maximum caproate production rate of 2.41 ± 0.69 g L^-1 d^-1, and a final concentration of 7.66 ± 1.38 g L^-1 was achieved. Caproate production selectivity based on the substrate increased to 91.47 ± 0.58% (Binary EDs) from 32.22 ± 32.58% (open circuit Electrode ED). An observed amount of 23.43 ± 0.69% of carbon within the final binary ED products originated from the CO₂. This work proves for the first time the potential of caproate production from CO₂ utilization and ethanol upgrading using solid electrodes to regulate the chain elongation process.

Microbial reduction of organosulfur compounds at cathodes in bioelectrochemical systems

Organosulfur compounds, present in e.g. the pulp and paper industry, biogas and natural gas, need to be removed as they potentially affect human health and harm the environment. The treatment of organosulfur compounds is a challenge, as an economically feasible technology is lacking. In this study, we demonstrate that organosulfur compounds can be degraded to sulfide in bioelectrochemical systems (BESs). Methanethiol, ethanethiol, propanethiol and dimethyl disulfide were supplied separately to the biocathodes of BESs, which were controlled at a constant current density of 2 A/m² and 4 A/m². The decrease of methanethiol in the gas phase was correlated to the increase of dissolved sulfide in the liquid phase. A sulfur recovery, as sulfide, of 64% was found over 5 days with an addition of 0.1 ​mM methanethiol. Sulfur recoveries over 22 days with a total organosulfur compound addition of 1.85 ​mM were 18% for methanethiol and ethanethiol, 17% for propanethiol and 22% for dimethyl disulfide. No sulfide was formed in electrochemical nor biological control experiments, demonstrating that both current and microorganisms are required for the conversion of organosulfur compounds. This new application of BES for degradation of organosulfur components may unlock alternative strategies for the abatement of anthropogenic organosulfur emissions.

Syngas-aided anaerobic fermentation for medium-chain carboxylate and alcohol production: the case for microbial communities

Syngas fermentation has been successfully implemented in commercial-scale plants and can enable the biochemical conversion of the driest fractions of biomass through synthesis gas (H₂, CO₂, and CO). The process relies on optimized acetogenic strains able to reach and maintain high productivity of ethanol and acetate. In parallel, microbial communities have shown to be the best choice for the production of valuable medium-chain carboxylates through anaerobic fermentation of biomass, demanding low technical complexity and being able to realize simultaneous hydrolysis of the substrate. Each of the two technologies benefits from different strong points and has different challenges to overcome. This review discusses the rationales for merging these two seemingly disparate technologies by analyzing previous studies and drawing opinions based on the lessons learned from such studies. For keeping the technical demands of the resulting process low, a case is built for using microbial communities instead of pure strains. For that to occur, a shift from conventional syngas-based to "syngas-aided" anaerobic fermentation is suggested. Strategies for tackling the intricacies of working simultaneously with communities and syngas, such as competing pathways, and thermodynamic aspects are discussed as well as the stoichiometry and economic feasibility of the concept. Overall, syngas-aided anaerobic fermentation seems to be a promising concept for the biorefinery of the future. However, the effects of process parameters on microbial interactions have to be understood in greater detail, in order to achieve and sustain feasible medium-chain carboxylate and alcohol productivity.

Activated Carbon Mixed with Marine Sediment is Suitable as Bioanode Material for Spartina anglica Sediment/Plant Microbial Fuel Cell: Plant Growth, Electricity Generation, and Spatial Microbial Community Diversity

Wetlands cover a significant part of the world’s land surface area. Wetlands are permanently or temporarily inundated with water and rich in nutrients. Therefore, wetlands equipped with Plant-Microbial Fuel Cells (Plant-MFC) can provide a new source of electricity by converting organic matter with the help of electrochemically active bacteria. In addition, sediments provide a source of electron donors to generate electricity from available (organic) matters. Eight lab-wetlands systems in the shape of flat-plate Plant-MFC were constructed. Here, four wetland compositions with activated carbon and/or marine sediment functioning as anodes were investigated for their suitability as a bioanode in a Plant-MFC system. Results show that Spartina anglica grew in all of the plant-MFCs, although the growth was less fertile in the 100% activated carbon (AC100) Plant-MFC. Based on long-term performance (2 weeks) under 1000 ohm external load, the 33% activated carbon (AC33) Plant-MFC outperformed the other plant-MFCs in terms of current density (16.1 mA/m2 plant growth area) and power density (1.04 mW/m2 plant growth area). Results also show a high diversity of microbial communities dominated by Proteobacteria with 42.5%–69.7% relative abundance. Principal Coordinates Analysis shows clear different bacterial communities between 100% marine sediment (MS100) Plant-MFC and AC33 Plant-MFC. This result indicates that the bacterial communities were affected by the anode composition. In addition, small worms (Annelida phylum) were found to live around the plant roots within the anode of the wetland with MS100. These findings show that the mixture of activated carbon and marine sediment are suitable material for bioanodes and could be useful for the application of Plant-MFC in a real wetland. Moreover, the usage of activated carbon could provide an additional function like wetland remediation or restoration, and even coastal protection.