Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production

Identification and Characterization of Two Novel Members of the Family Eubacteriaceae, Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov., Isolated from Human Feces

Members of Eubacteriaceae are involved in host health and diseases. Two Gram-stain-positive, strictly anaerobic, non-motile, non-spore-forming, and rod-shaped bacterial strains, HA2171T and HA2172T, were isolated from the feces of Chinese healthy donors. Based on 16S rRNA gene sequences, HA2171T and HA2172T belonged to the family Eubacteriaceae. Physiological and biochemical characterizations indicated that HA2171T and HA2172T were neutrophilic, mesophilic, and tolerant to low-concentration NaCl. The major cellular fatty acids (>10.0%) of HA2171T were C16:0, C14:0, C18:1ω7c, and C17:0 2-OH, and those of HA2172T were C14:0 and C16:0. MK-6 was the respiratory quinone in both strains. Phylogenetic and phylogenomic analyses showed that HA2171T was closest to Anaerofustis stercorihominis ATCC BAA-858T and that HA2172T as closest to Pseudoramibacter alactolyticus ATCC 23263T. Genome annotation revealed that the HA2171T and HA2172T were able to metabolize carbohydrates and produce acetate and butyrate. HA2172T contains genes associated with hydrogen sulfide production, which is a potential risk for diseases. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, we propose that HA2171T and HA2172T represent two novel species, and the names Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov. are proposed.

Up-flow anaerobic sludge blanket bioreactor for the production of carboxylates: effect of inocula on process performance and microbial communities

This research investigated the acidogenic fermentation (AF) of sugar cane molasses in an up-flow anaerobic sludge blanket (UASB) reactor for the production of carboxylates. The first step was to assess the optimum process temperature (25, 35 or 55 ºC) using two different granular inocula, one from a brewery company (BGS) and other from a paper plant company (PGS). These experiments determined that the most suitable temperature for carboxylates production was 25 ºC, obtaining higher bioconversions (27.3 ± 0.3% using PGS and 39.2 ± 0.2% using BGS), despite the low pH value recorded (4.0-4.2). Then, both inocula were tested in UASB reactors. As a consequence of the operational conditions (25 ºC, pH = 5.5-6, organic loading rate (OLR) = 3 gCOD·L-1·d-1 and hydraulic retention time (HRT) = 10 d), the microbial communities changed from those typical for biogas production to those specialised in the production of volatile fatty acids (VFAs). Indeed, the highest bioconversion efficiency (70.1%) was obtained with BGS, where uncultured Eubacteriaceae family microorganisms (56.0%) prevailed, enhancing the production of butyric acid (59.5 ± 2.4%w/w). Consequently, this inoculum was used to further identify the OLR threshold that should not be exceeded to attain optimal carboxylates production. OLR of 6 gCOD·L-1·d-1 resulted in a decrease in bioconversion efficiency (59.5%). The VFAs pool was dominated by butyric acid (63.0 ± 1.4%w/w at an OLR of 4.5 gCOD·L-1·d-1 and 52.8 ± 2.2%w/w at 6 gCOD·L-1·d-1). The microbial community became even more specialised, increasing the presence of Firmicutes and Actinobacteriota phyla, proving that the imposed conditions favoured the production of VFAs when operating semicontinuously fed UASB reactors.

pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes

The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step. This approach will improve our comprehension of metabolic functions of uncultured species.

A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review

The increasing reliance on fossil fuels and the growing accumulation of organic waste necessitates the exploration of sustainable energy alternatives. Anaerobic digestion (AD) presents one such solution by utilizing secondary biomass to produce biogas while reducing greenhouse gas emissions. Given the crucial role of microbial activity in anaerobic digestion, a deeper understanding of the microbial community is essential for optimizing biogas production. While metagenomics has emerged as a valuable tool for unravelling microbial composition and providing insights into the functional potential in biodigestion, it falls short of interpreting the functional and metabolic interactions, limiting a comprehensive understanding of individual roles in the community. This emphasizes the significance of expanding the scope of metagenomics through innovative tools that highlight the often-overlooked, yet crucial, role of microbiota in biomass digestion. These tools can more accurately elucidate microbial ecological fitness, shared metabolic pathways, and interspecies interactions. By addressing current limitations and integrating metagenomics with other omics approaches, more accurate predictive techniques can be developed, facilitating informed decision-making to optimize AD processes and enhance biogas yields, thereby contributing to a more sustainable future.

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.

Long hydraulic retention time mediates stable volatile fatty acids production against slight pH oscillations

The effect of operational conditions on the stability of acidogenic fermentation (AF) devoted to volatile fatty acids (VFAs) production still presents numerous gaps to achieve high yields and fully understand the responses of open microbiomes associated to this technology. To cope with that, this investigation was designed to assess the stability of VFAs production via AF of agro-food wastes at high hydraulic retention times (HRTs) (20 and 30 d) and pH oscillations (5.8-6.2). Similar bioconversion efficiencies (∼50 %) were reached regardless of the HRT, revealing that HRT of 20 d can be considered as a threshold from which, no further improvement was achieved. The combination of long HRTs, 25 °C and acid pHs promoted a robust microbiome that resulted in a stable outcome against pH variations, being Clostridiales order identified as key player of AF stability. These conditions mediated a high selectivity in the VFAs production profile, with acetic and butyric acids, prevailing in the VFAs pool (∼80 % of total VFAs) at HRT 20 d. The selection of appropriated conditions was shown to be critical to maximize the hydrolysis and acidogenesis of the substrate and attain a stable effluent against pH oscillations.

Two-stage biohydrogen and methane production from sugarcane-based sugar and ethanol industrial wastes: A comprehensive review

The transition to renewable energy sources is crucial to ensure a sustainable future. Although the sugar and ethanol industries benefit from this transition, there are untapped opportunities to utilize the waste generated from the sugar and ethanol process chains through two-stage anaerobic digestion (TSAD). This review comprehensively discusses the utilization of various sugarcane-based industrial wastes by TSAD for sequential biohydrogen and methane production. Factors influencing TSAD process performance, including pH, temperature, hydraulic retention time, volatile fatty acids and alkalinity, nutrient imbalance, microbial population, and inhibitors, were discussed in detail. The potential of TSAD to reduce emissions of greenhouse gases is demonstrated. Recent findings, implications, and promising future research related to TSAD, including the integration of meta-omics approaches, gene manipulation and bioaugmentation, and application of artificial intelligence, are highlighted. The review can serve as important literature for the implementation, improvement, and advancements in TSAD research.

Microbial co-cultures for biochemicals production from lignocellulosic biomass: A review

Global reliance on fossil oil should shift to cleaner alternatives to get a decarbonized society. One option to achieve this ambitious goal is the use of biochemicals produced from lignocellulosic biomass (LCB). The inherent low biodegradability of LCB and the inhibitory compounds that might be released during pretreatment are two main challenges for LCB valorization. At microbiological level, constraints are mostly linked to the need for axenic cultures and the preference for certain carbon sources (i.e., glucose). To cope with these issues, this review focuses on efficient LCB conversion via the sugar platform as well as an innovative carboxylate platform taking advantage of the co-cultivation of microorganisms. This review discusses novel trends in the use of microbial communities and co-cultures aiming at different bioproducts co-generation in single reactors as well as in sequential bioprocess combination. The outlook and further perspectives of these alternatives have been outlined for future successful development.

Hydraulic Retention Time as an Operational Tool for the Production of Short-Chain Carboxylates via Anaerobic Fermentation of Carbohydrate-Rich Waste

The carboxylate platform is a sustainable and cost-effective way to valorize wastes into biochemicals that replace those of fossil origin. Short-chain fatty acids (SCFAs) are intermediates generated during anaerobic fermentation (AF) and are considered high-value-added biochemicals among carboxylates. This investigation aimed to produce SCFAs through the AF of sugar beet molasses at 25 °C and semi-continuous feeding mode in completely stirred tank reactors. A particular focus was devoted to the role of hydraulic retention time (HRT) variation in SCFAs production and distribution profile. The highest SCFAs concentration (44.1 ± 2.3 gCOD/L) was reached at the HRT of 30 days. Caproic acid accounted for 32.5-35.5% (COD-concentration basis) at the long HRTs of 20 and 30 days due to the carbon chain elongation of shorter carboxylic acids. The findings of this study proved that HRT could be used to steer the anaerobic process toward the targeted SCFAs for specific uses. Furthermore, the successful operation at low-temperature conditions (i.e., 25 °C) makes the process economically promising.