Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009

Enhancing biohydrogen production from xylose through natural FeS2 ore: Mechanistic insights

In this study, we investigated the advantages of utilizing natural FeS2 ore in the context of dark fermentative hydrogen production within a fermentation system employing heat-treated anaerobic granular sludge with xylose as the carbon source. The results demonstrated a significant improvement in both hydrogen production and the maximum rate, with increases of 2.58 and 4.2 times, respectively. Moreover, the presence of FeS2 ore led to a reduction in lag time by more than 2-3 h. The enhanced biohydrogen production performance was attributed to factors such as the intracellular NADH/NAD+ ratio, redox-active components of extracellular polymeric substances, secreted flavins, as well as the presence of hydrogenase and nitrogenase. Furthermore, the FeS2 ore served as a direct electron donor and acceptor during biohydrogen production. This study shed light on the underlying mechanisms contributing to the improved performance of biohydrogen production from xylose during dark fermentation through the supplementation of natural FeS2 ore.

Enhancing and monitoring spore production in Clostridium butyricum using pH-based regulation strategy and a robust soft sensor based on back-propagation neural networks

Clostridium butyricum is a probiotic that forms anaerobic spores and plays a crucial role in regulating gut microbiota. However, the total viable cell count and spore yield of C. butyricum in industrial production are comparatively low. To this end, we investigated the metabolic characteristics of the strain and proposed three distinct pH regulation strategies for enhancing spore production. In addition, precise measurement of fermentation parameters such as substrate concentration, total viable cell count, and spore concentration is crucial for successful industrial probiotics production. Nevertheless, online measurement of these intricate parameters in the fermentation of C. butyricum poses a considerable challenge owing to the complex, nonlinear, multivariate, and strongly coupled characteristics of the production process. Therefore, we analyzed the capacitance and conductivity acquired from a viable cell sensor as the core parameters for the fermentation process. Subsequently, a robust soft sensor was developed using a seven-input back-propagation neural network model with input variables of fermentation time, capacitance, conductivity, pH, initial total sugar concentration, ammonium ion concentration, and calcium ion concentration. The model enables the online monitoring of total viable biomass count, substrate concentrations, and spore yield, and can be extended to similar fermentation processes with pH changes as a characteristic feature.

Microalgae-bacterial granular consortium: Striding towards sustainable production of biohydrogen coupled with wastewater treatment

Anthropogenic activities have drastically affected the environment, leading to increased waste accumulation in atmospheric bodies, including water. Wastewater treatment is an energy-consuming process and typically requires thousands of kilowatt hours of energy. This enormous energy demand can be fulfilled by utilizing the microbial electrolysis route to breakdown organic pollutants in wastewater which produces clean water and biohydrogen as a by-product of the reaction. Microalgae are the promising microorganism for the biohydrogen production, and it has been investigated that the interaction between microalgae and bacteria can be used to boost the yield of biohydrogen. Consortium of algae and bacteria resulting around 50-60% more biohydrogen production compared to the biohydrogen production of algae and bacteria separately. This review summarises the recent development in different microalgae-bacteria granular consortium systems successfully employed for biohydrogen generation. We also discuss the limitations in biohydrogen production and factors affecting its production from wastewater.

Fantastic [FeFe]-Hydrogenases and Where to Find Them

[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.

Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia

BACKGROUND

Bio-hydrogen production via dark fermentation of low-value waste is a potent and simple mean of recovering energy, maximising the harvesting of reducing equivalents to produce the cleanest fuel amongst renewables. Following several position papers from companies and public bodies, the hydrogen economy is regaining interest, especially in combination with circular economy and the environmental benefits of short local supply chains, aiming at zero net emission of greenhouse gases (GHG). The biomasses attracting the largest interest are agricultural and urban green wastes (pruning of trees, collected leaves, grass clippings from public parks and boulevards), which are usually employed in compost production, with some concerns over the GHG emission during the process. Here, an alternative application of green wastes, low-value compost and intermediate products (partially composted but unsuitable for completing the process) is studied, pointing at the autochthonous microbial consortium as an already selected source of implementation for biomass degradation and hydrogen production. The biocatalysts investigated as mainly relevant for hydrogen production were the [FeFe]-hydrogenases expressed in Clostridia, given their very high turnover rates.

RESULTS

Bio-hydrogen accumulation was related to the modulation of gene expression of multiple [FeFe]-hydrogenases from two strains (Clostridium beijerinckii AM2 and Clostridium tyrobutyricum AM6) isolated from the same waste. Reverse Transcriptase quantitative PCR (RT-qPCR) was applied over a period of 288 h and the RT-qPCR results showed that C. beijerinckii AM2 prevailed over C. tyrobutyricum AM6 and a high expression modulation of the 6 different [FeFe]-hydrogenase genes of C. beijerinckii in the first 23 h was observed, sustaining cumulative hydrogen production of 0.6 to 1.2 ml H₂/g VS (volatile solids). These results are promising in terms of hydrogen yields, given that no pre-treatment was applied, and suggested a complex cellular regulation, linking the performance of dark fermentation with key functional genes involved in bio-H₂ production in presence of the autochthonous consortium, with different roles, time, and mode of expression of the involved hydrogenases.

CONCLUSIONS

An applicative outcome of the hydrogenases genes quantitative expression analysis can be foreseen in optimising (on the basis of the acquired functional data) hydrogen production from a nutrient-poor green waste and/or low added value compost, in a perspective of circular bioeconomy.

A Win-Loss Interaction on Fe0 Between Methanogens and Acetogens From a Climate Lake

Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe⁰-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe⁰, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win-loss) interaction on Fe⁰ between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe⁰. Since abiotic H₂ failed to explain the high metabolic rates on Fe⁰, we examined whether cell exudates (spent media filtrate) promoted the H₂-evolving reaction on Fe⁰ above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H₂ than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H₂ evolution from Fe⁰ and found candidate H₂-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H₂-evolving reaction on Fe⁰, explaining the significant H₂ evolved by spent media exposed to Fe⁰. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H₂-consuming neighbors-Methanobacterium-fare five times better in their presence. The particular enzymes and constituents promoting H₂ evolution from Fe⁰ remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.

Molecular mechanism of ethanol-H2 co-production fermentation in anaerobic acidogenesis: Challenges and perspectives

Ethanol-type fermentation (ETF) is one of three fermentation types during the acidogenesis of the anaerobic biological treatment. Ethanoligenens, a representative genus of ETF, displays acidophilic, autoaggregative, and ethanol-H₂ co-producing characteristics and facilitates subsequent methanogenesis. Here, the latest advances in the molecular mechanisms of the metabolic regulation of ethanol-H₂ co-producing bacteria based on multi-omics studies were comprehensively reviewed. Comparative genomics demonstrated a low genetic similarity between Ethanoligenens and other hydrogen-producing genera. FeFe‑hydrogenases (FeFe-H₂ases) and pyruvate ferredoxin oxidoreductase (PFOR) played critical roles in the ethanol-H₂ co-metabolic pathway of Ethanoligenens. Global transcriptome analysis revealed that highly expressed [FeFe]-H₂ases and ferredoxins drove hydrogen production by Ethanoligenens at low pH conditions (4.0-4.5). Quantitative proteomic analysis also proved that this genus resists acetic acid-induced intracellular acidification through the up-regulated expression of pyrimidine metabolism related proteins. The autoaggregation of Ethanoligenen facilitated its granulation with acetate-oxidizing bacteria in co-culture systems and mitigated a fast pH drop, providing a new approach for solving a pH imbalance and improving hydrogen production. In-depth studies of the regulatory mechanism underlying ethanol-H₂ co-production metabolism and the syntrophic interactions of ethanol-H₂ co-producing Ethanoligenens with other microorganisms will provide insights into the improvement of bioenergy recovery in anaerobic biotechnology. The coupling of ETF with other biotechnologies, which based on the regulation of electron flow direction, syntrophic interaction, and metabolic flux, can be potential strategies to enhance the cascade recovery of energy and resources.

Rapid recruitment of hydrogen-producing biofilms for hydrogen production in a moving bed biofilm reactor by a sequential immobilization and deoxygenization approach

To reduce start-up time and enhance hydrogen production efficiency, a sequential immobilization and deoxygenization (SIDO) strategy for hydrogen production was investigated in continuous-flow moving bed biofilm reactors (MBBRs). The pre-immobilization process accelerated the initial enrichment of hydrogen-producing bacteria (HPB) and promoted the biofilm formation, which contribute to higher hydrogen production efficiency in SIDO-MBBRs compared to a non-immobilized reactor. A similar deoxygenization effect was achieved by inoculation with Pseudomonas aeruginosa compared with N₂ sparging, and the P. aeruginosa pre-immobilized MBBR (Pse-MBBR) showed a higher H₂ yield in the initial stage of operation. Microbial community analysis found a higher abundance of putative HPB in the range of 82.82-96.56%, with the predominant populations in the SIDO-MBBR assigned to genera Clostridium and Enterobacter. The results suggest that the SIDO-MBBR is an effective approach for rapid recruitment of HPB and start-up of fermentative hydrogen production.

Metabolism, morphology and transcriptome analysis of oscillatory behavior of Clostridium butyricum during long-term continuous fermentation for 1,3-propanediol production

BACKGROUND

Oscillation is a special cell behavior in microorganisms during continuous fermentation, which poses threats to the output stability for industrial productions of biofuels and biochemicals. In previous study, a spontaneous oscillatory behavior was observed in Clostridium butyricum-intensive microbial consortium in continuous fermentation for 1,3-propanediol (1,3-PDO) production from glycerol, which led to the discovery of oscillation in species C. butyricum.

RESULTS

Spontaneous oscillations by C. butyricum tended to occur under glycerol-limited conditions at low dilution rates. At a glycerol feed concentration of 88 g/L and a dilution rate of 0.048 h^-1, the oscillatory behavior of C. butyricum was observed after continuous operation for 146 h and was sustained for over 450 h with an average oscillation period of 51 h. During oscillations, microbial glycerol metabolism exhibited dramatic periodic changes, in which productions of lactate, formate and hydrogen significantly lagged behind that of other products including biomass, 1,3-PDO and butyrate. Analysis of extracellular oxidation-reduction potential and intracellular ratio of NAD⁺/NADH indicated that microbial cells experienced distinct redox changes during oscillations, from oxidized to reduced state with decreasing of growth rate. Meanwhile, C. butyricum S3 exhibited periodic morphological changes during oscillations, with aggregates, elongated shape, spores or cell debris at the trough of biomass production. Transcriptome analysis indicated that expression levels of multiple genes were up-regulated when microbial cells were undergoing stress, including that for pyruvate metabolism, conversion of acetyl-CoA to acetaldehyde as well as stress response.

CONCLUSION

This study for the first time systematically investigated the oscillatory behavior of C. butyricum in aspect of occurrence condition, metabolism, morphology and transcriptome. Based on the experimental results, two hypotheses were put forward to explain the oscillatory behavior: disorder of pyruvate metabolism, and excessive accumulation of acetaldehyde.

Analysis of the core genome and pangenome of Clostridium butyricum

Clostridium butyricum is an anaerobic bacterium that inhabits broad niches. Clostridium butyricum is known for its production of butyrate, 1,3-propanediol, and hydrogen. This study aimed to present a comparative pangenome analysis of 24 strains isolated from different niches. We sequenced and annotated the genome of C. butyricum 3-3 isolated from the Chinese baijiu ecosystem. The pangenome of C. butyricum was open. The core genome, accessory genome, and strain-specific genes comprised 1011, 4543, and 1473 genes, respectively. In the core genome, Carbohydrate metabolism was the largest category, and genes in the biosynthetic pathway of butyrate and glycerol metabolism were conserved (in the core or soft-core genome). Furthermore, the 1,3-propanediol operon existed in 20 strains. In the accessory genome, numerous mobile genetic elements belonging to the Replication, recombination, and repair (L) category were identified. In addition, genome islands were identified in all 24 strains, ranging from 2 (strain KNU-L09) to 53 (strain SU1), and phage sequences were found in 17 of the 24 strains. This study provides an important genomic framework that could pave the way for the exploration of C. butyricum and future studies on the genetic diversification of C. butyricum.

The complete genome sequence of Ethanoligenens harbinense reveals the metabolic pathway of acetate-ethanol fermentation: A novel understanding of the principles of anaerobic biotechnology

Ethanol-type fermentation is one of three main fermentation types in the acidogenesis of anaerobic treatment systems. Non-spore-forming Ethanoligenens is as a typical genus capable of ethanol-type fermentation in mixed culture (i.e. acetate-ethanol fermentation). This genus can produce ethanol, acetate, CO₂, and H₂ using carbohydrates, and has application potential in anaerobic bioprocesses. Here, the complete genome sequences and methylome of Ethanoligenens harbinense strains with different autoaggregative and coaggregative abilities were obtained using the PacBio single-molecule real-time sequencing platform. The genome size of E. harbinense strains was about 2.97-3.10 Mb with 55.5% G+C content. 3020-3153 genes were annotated, most of which were methylated at specific sites or motifs. The methylation types included 6mA, 4mC, and unknown types. Comparative genomic analysis demonstrated low levels of genetic similarity between E. harbinense and other well-known hydrogen-producing bacteria (i.e., Clostridium and Thermoanaerobacter) in phylogenesis. Hydrogen production of E. harbinense was catalyzed by genes that encode [FeFe]‑hydrogenases and that were synthesized by three maturases of [FeFe]-H₂ase. The metabolic mechanism of H₂-ethanol co-production fermentation, catalyzed by pyruvate ferredoxin oxidoreductase was proposed. This study provides genetic and evolutionary information of a model genus for the further investigation of the metabolic pathway and regulatory network of ethanol-type fermentation and anaerobic bioprocesses for waste or wastewater treatment.

Granular activated carbon supplementation alters the metabolic flux of Clostridium butyricum for enhanced biohydrogen production

In this work, the effects of granular activated carbon (GAC) supplementation on hydrogen fermentation were investigated in Clostridium butyricum. Maximum hydrogen production rate and ultimate hydrogen volume increased up to 1.7 and 1.9 fold, respectively, with 1 g/L GAC supplementation. Indicators of stable hydrogen production, such as acetate and butyrate formation increased with increasing GAC concentration. To identify the factors for hydrogen production enhancement, transcriptome analysis was conducted. Functional genes related to hydrogen production increased by GAC supplementation (1.75 fold for pfor and 1.48 fold for oxct). On the other hand, functional genes related to hydrogen consumption decreased (1.78 fold for ldh, 0.67 fold for adh, 1.64 fold for hbd, 2.4 fold for crt, and 0.71 fold for buk). Considered together, these results suggested that GAC supplementation increased biohydrogen production by changing the metabolic flux associated with hydrogen production and consumption pathways.

Enhanced biohydrogen production from nutrient-free anaerobic fermentation medium with edible fungal pretreated rice straw

An edible fungal pretreatment of rice straw was proposed for enhanced hydrogen production while reducing the chemical cost for traditional biological hydrogen production from lignocellulose. In this research, rice straw was pretreated by edible fungus Gymnopus contrarius J2 at room temperature under static conditions for 15 d at first. The highest hydrogen yield of 5.71 mmol g-1-pretreated rice straw was obtained, 74% higher than the counterpart without pretreatment. Chemical composition analysis demonstrated that lignin removal was up to 22.4% with a little cellulose and hemicellulose loss of 13.3% and 17.1%, respectively, which is in favor of hydrogen production. Additionally, microscopic structure observation combined with FT-IR and XRD analysis illustrated the structural disruption of pretreated rice straw, and the crystalline index of rice straw can be decreased by 46.2% after pretreatment, which might account for the hydrogen production enhancement. The results also indicated that the hydrogen yield from pretreated rice straw was not affected without the addition of yeast extract and vitamins to the culture medium, which is substantial evidence that edible fungal pretreated rice straw could provide prerequisite nutrients for hydrogen-producing bacteria. Overall, edible fungal pretreatment has great potential under the mild conditions for high hydrogen yields and thus leads to a new direction to realize a highly efficient and economically competitive biological hydrogen production process from lignocellulosic biomass.

Transcription of [FeFe]-Hydrogenase Genes during H2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil

Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H₂ production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H₂ production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H₂ production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H₂ production was differently regulated among the paralogs in H₂ producers isolated from paddy field soil.

Catalytic hydrolysis of starch for biohydrogen production by using a newly identified amylase from a marine bacterium Catenovulum sp. X3

An identified cold-adaptive, organic solvents-tolerant alkaline α-amylase (HP664) from Catenovulum sp. strain X3 was heterologously expressed and characterized in E. coli, and it was further applied to starch saccharification for biohydrogen production. The recombinant HP664 belongs to a member of glycoside hydrolase family 13 (GH13), with a molecular weight of 69.6kDa without signal peptides, and also shares a relatively low similarity (49%) to other reported amylases. Biochemical characterization demonstrated that the maximal enzymatic activity of HP664 was observed at 35°C and pH 9.0. Most metal ions inhibited its activity; however, low polar organic solvents (e.g., benzene and n-hexane) could enhance the activity by 35-50%. Additionally, HP664 also exhibited the catalytic capability on various polysaccharides, including potato starch, amylopectin, dextrin and agar. In order to increase the bioavailability of starch for H₂ production, HP664 was utilized to elevate fermentable oligosaccharide level, and the results revealed that the maximal hydrolytic percentage of starch was up to 44% with 12h of hydrolysis using 5.63U of HP664. Biohydrogen fermentation of the starch hydrolysate by Clostridium sp. strain G1 yielded 297.7mL of H₂ after 84h of fermentation, which is 3.73-fold higher than the control without enzymatic treatment of HP664.

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

BACKGROUND

The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled.

RESULTS

We reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example, Clostridium maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions, Clostridium grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than iCbu641 perturbations for improving PDO yields.

CONCLUSIONS

The agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing Clostridium strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.

Microbial cell immobilization in biohydrogen production: a short overview

The high dependence on fossil fuels has escalated the challenges of greenhouse gas emissions and energy security. Biohydrogen is projected as a future alternative energy as a result of its non-polluting characteristics, high energy content (122 kJ/g), and economic feasibility. However, its industrial production has been hampered by several constraints such as low process yields and the formation of biohydrogen-competing reactions. This necessitates the search for other novel strategies to overcome this problem. Cell immobilization technology has been in existence for many decades and is widely used in various processes such as wastewater treatment, food technology, and pharmaceutical industry. In recent years, this technology has caught the attention of many researchers within the biohydrogen production field owing to its merits such as enhanced process yields, reduced microbial contamination, and improved homogeneity. In addition, the use of immobilization in biohydrogen production prevents washout of microbes, stabilizes the pH of the medium, and extends microbial activity during continuous processes. In this short review, an insight into the potential of cell immobilization is presented. A few immobilization techniques such as entrapment, adsorption, encapsulation, and synthetic polymers are discussed. In addition, the effects of process conditions on the performance of immobilized microbial cells during biohydrogen production are discussed. Finally, the review concludes with suggestions on improvement of cell immobilization technologies in biohydrogen production.

Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria

The syntrophic degradation of branched-chain fatty acids (BCFAs) such as 2-methylbutyrate and isobutyrate is an essential step in the production of methane from proteins/amino acids in anaerobic ecosystems. While a few syntrophic BCFA-degrading bacteria have been isolated, their metabolic pathways in BCFA and short-chain fatty acid (SCFA) degradation as well as energy conservation systems remain unclear. In an attempt to identify these pathways, we herein performed comparative genomics of three syntrophic bacteria: 2-methylbutyrate-degrading “Syntrophomonas wolfei subsp. methylbutyratica” strain JCM 14075^T (=4J5^T), isobutyrate-degrading Syntrophothermus lipocalidus strain TGB-C1^T, and non-BCFA-metabolizing S. wolfei subsp. wolfei strain Göttingen^T. We demonstrated that 4J5 and TGB-C1 both encode multiple genes/gene clusters involved in β-oxidation, as observed in the Göttingen genome, which has multiple copies of genes associated with butyrate degradation. The 4J5 genome possesses phylogenetically distinct β-oxidation genes, which may be involved in 2-methylbutyrate degradation. In addition, these Syntrophomonadaceae strains harbor various hydrogen/formate generation systems (i.e., electron-bifurcating hydrogenase, formate dehydrogenase, and membrane-bound hydrogenase) and energy-conserving electron transport systems, including electron transfer flavoprotein (ETF)-linked acyl-CoA dehydrogenase, ETF-linked iron-sulfur binding reductase, ETF dehydrogenase (FixABCX), and flavin oxidoreductase-heterodisulfide reductase (Flox-Hdr). Unexpectedly, the TGB-C1 genome encodes a nitrogenase complex, which may function as an alternative H₂ generation mechanism. These results suggest that the BCFA-degrading syntrophic strains 4J5 and TGB-C1 possess specific β-oxidation-related enzymes for BCFA oxidation as well as appropriate energy conservation systems to perform thermodynamically unfavorable syntrophic metabolism.