Production of short-chain fatty acids (SCFAs) as chemicals or substrates for microbes to obtain biochemicals

Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste

Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5T, was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L-1, 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5T was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5T grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112T (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5T belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5T is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5T (= DSM 112743T = ATCC TSD-267T) being the type of strain. This study highlights the biotechnological potential of strain m5T, specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.

13C-Labelled Glucose Reveals Shifts in Fermentation Pathway During Cathodic Electro-Fermentation with Mixed Microbial Culture

Cathodic Electro-Fermentation (CEF) is an innovative approach to manage the spectrum of products deriving from anaerobic fermentation. Herein, mixed microbial culture fermentation using a ternary mixture containing labelled 13C glucose and non-labelled acetate and ethanol was studied to identify the role of polarization on the metabolic pathways of glucose fermentation. CEF at an applied potential of -700 mV (vs. SHE, Standard Hydrogen Electrode) enhanced the production yield of acetate, propionate, and butyrate (0.90±0.10, 0.22±0.03, and 0.34±0.05 mol/mol; respectively) compared to control tests performed at open circuit potential (OCP) (0.54±0.09, 0.15±0.04, and 0.20±0.001 mol/mol, respectively). Results indicate that CEF affected the 13C labelled fermented product levels and their fractional 13C enrichments, allowing to establish metabolic pathway models. This work demonstrates that, under cathodic polarization, the abundance of both fully 13C labelled propionate and butyrate isotopomers increased compared to control tests. The effect of CEF is mainly due to intermediates initially produced from the glucose metabolic transformation in the presence of non-labelled acetate and ethanol as external substrates. These findings represent a significant advancement in current knowledge of CEF, which offers a promising tool to control mixed cultures bioprocesses.

Epigenetic Regulatory Processes Involved in the Establishment and Maintenance of Skin Homeostasis-The Role of Microbiota

Epigenetic mechanisms are central to the regulation of all biological processes. This manuscript reviews the current understanding of diverse epigenetic modifications and their role in the establishment and maintenance of normal skin functions. In healthy skin, these mechanisms allow for the precise control of gene expression, facilitating the dynamic balance between cell proliferation and differentiation necessary for effective barrier function. Furthermore, as the skin ages, alterations in epigenetic marks can lead to impaired regenerative capacity and increased susceptibility to environmental stressors. The interaction between skin microbiota and epigenetic regulation will also be explored, highlighting how microbial communities can influence skin health by modulating the host gene expression. Future research should focus on the development of targeted interventions to promote skin development, resilience, and longevity, even in an ever-changing environment. This underscores the need for integrative approaches to study these complex regulatory networks.

Clostridium carboxidivorans and Rhodosporidium toruloides as a platform for the valorization of carbon dioxide to microbial oils

There is growing scientific interest in oleaginous yeasts producing microbial oils as precursors of biofuels and potential substitutes for fossil fuels. Due to the high cost of substrates commonly metabolized by yeasts, volatile fatty acids (VFAs) are gaining interest as alternative cheap and sustainable carbon sources, which can be obtained from solid, liquid and gas pollutants. In this research, Rhodosporidium toruloides was proven to be able to accumulate microbial oils from VFAs obtained from the fermentation of syngas by Clostridium carboxidivorans. Using CO2 and CO as carbon sources from the syngas mixture and H2 as energy source, this acetogen produced, via the Wood-Ljungdahl pathway, a mixture of acetic, butyric and caproic acids. It was first revealed that R. toruloides exhibited minimal inhibition at concentrations below 12 g/L when exposed to a mixture of VFAs, which included acetic, butyric and even hexanoic acids. The yeast was then grown on the culture medium derived from the acetogenic fermentation of syngas. Between the two yeast strains tested of the same species, R. toruloides DSM 4444 reached a total VFAs consumption of 69.1 g/L, supplied by successive additions of acids to the reactor, yielding a maximum lipid content of 29.7% w/w cell. The lipid profile obtained in this case, in terms of abundance followed the order C18:1 > C16:0 ≥ C18:0 > C18:2>others; in which the dominant compound (C18:1), represented approximately 50% of the total. This research opens new possibilities in the cultivation of oleaginous yeasts for the production of biofuels and bioproducts from C1 gases.

Mechanistic Insights on Microbiota-Mediated Development and Progression of Esophageal Cancer

Esophageal cancer (EC) is one of the most common malignant tumors worldwide, and its two major types, esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), present a severe global public health problem with an increasing incidence and mortality. Established risk factors include smoking, alcohol consumption, and dietary habits, but recent research has highlighted the substantial role of oral microbiota in EC pathogenesis. This review explores the intricate relationship between the microbiome and esophageal carcinogenesis, focusing on the following eight significant mechanisms: chronic inflammation, microbial dysbiosis, production of carcinogenic metabolites, direct interaction with epithelial cells, epigenetic modifications, interaction with gastroesophageal reflux disease (GERD), metabolic changes, and angiogenesis. Certain harmful bacteria, such as Porphyromonas gingivalis and Fusobacterium nucleatum, are specifically implicated in sustaining irritation and tumor progression through pathways including NF-κB and NLRP3 inflammasome. Additionally, the review explores how microbial byproducts, including short-chain fatty acids (SCFAs) and reactive oxygen species (ROS), contribute to DNA harm and disease advancement. Furthermore, the impact of reflux on microbiota composition and its role in esophageal carcinogenesis is evaluated. By combining epidemiological data with mechanistic understanding, this review underscores the potential to target the microbiota-immune system interplay for novel therapeutic and diagnostic strategies to prevent and treat esophageal cancer.

Strategies for producing probiotic biomass and postbiotics from Akkermansia muciniphila in submerged cultivations incorporating prebiotic sources

This research propounds an innovative technology focused on sustainability to increase the biomass yield of Akkermansia muciniphila, the next-generation probiotic, using prebiotic sources to replace or reduce animal mucin levels. A series of experimental design approaches were developed aiming to optimize the growth of Akkermansiamuciniphila by incorporating extracts of green leafy vegetables and edible mushroom into the cultivation media. Experiments using kale extract (KE), Brassica oleracea L., associated with lyophilized mushroom extract (LME) of Pleurotus ostreatus were the most promising, highlighting the assays with 0.376% KE and 0.423% LME or 1.05% KE and 0.5% LME, in which 3.5 × 1010 CFU (Colony Forming Units) mL- 1 was achieved - higher than in experiments in optimized synthetic media. Such results enhance the potential of using KE and LME not only as mucin substitutes, but also as a source to increase Akkermansia muciniphila biomass yields and release short-chain fatty acids. The work is relevant to the food and pharmaceutical industries in the preparation of the probiotic ingredient.

High-throughput screening of non-conventional yeasts for conversion of organic waste to microbial oils via carboxylate platform

Converting waste into high-value products promotes sustainability by reducing waste and creating new revenue streams. This study investigates the potential of diverse yeasts for microbial oil production by utilizing short-chain fatty acids (SCFAs) that can be produced from organic waste and focuses on identifying strains with the best SCFA utilisation, tolerance and lipid production. A collection of 1434 yeast strains was cultivated with SCFAs as the sole carbon source. Eleven strains emerged as candidates with promising growth rates and high lipid accumulation. Subsequent fermentation experiments in liquid SCFA-rich media, which focused on optimizing lipid accumulation by adjusting the carbon to nitrogen (C/N) ratio, showed an increase in lipid content at a C/N ratio of 200:1, but with a concurrent reduction in biomass. Two strains were characterized by their superior ability to produce lipids compared to the reference strain Yarrowia lipolytica CECT124: Y. lipolytica EXF-17398 and Pichia manshurica EXF-7849. Characterization of these two strains indicated that they exhibit a biotechnologically relevant balance between maximizing lipid yield and maintaining growth at high SCFA concentrations. These results emphasize the potential of using SCFAs as a sustainable feedstock for oleochemical production, offering a dual benefit of waste valorisation and microbial oil production.

Effect of electron acceptors on product selectivity and carbon flux in carbon chain elongation with Megasphaera hexanoica

Megasphaera hexanoica is a bacterial strain following the reverse β-oxidation pathway to synthesize caproate (CA) using lactate (LA) as an electron donor (ED) and acetate (AA) or butyrate (BA) as electron acceptors (EA). Differences in the type and concentration of EA lead to distinctions in product distribution and energy bifurcation of carbon fluxes in ED pathways, thereby affecting CA production. In this study, the effect of various ratios of AA, BA, and AA+BA as EA on carbon flux and CA specific titer during the carbon chain elongation in M. hexanoica was explored. The results indicated that the maximum levels of CA were 18.81 mM and 31.48 mM when the molar ratios of LA/AA and LA/BA were 10:1 and 3:1, respectively. Meanwhile, when AA and BA were used as combined EA (LA, AA, and BA molar amounts of 100, 23, and 77 mM), a maximum CA production of 39.45 mM was obtained. Further analysis revealed that the combined EA exhibited a CA production carbon flux of 49 % (4.3 % and 19.5 % higher compared to AA or BA, respectively) and a CA production specific titer of 45.24 mol (80.89 % and 58.51 % higher compared to AA or BA, respectively), indicating that the effective carbon utilization rate and CA production efficiency were greatly improved. Finally, a scaled-up experiment was conducted in a 1.2 L (working volume) automated bioreactor, implying high biomass (optical density at 600 nm or OD600 = 1.809) and a slight decrease in CA production (28.45 mM). A decrease in H2 production (4.11 g/m3) and an increase in CO2 production (0.632 g/m3) demonstrated the appropriate metabolic adaptation of M. hexanoica to environmental changes such as stirring shear.

Effect of Pediococcus acidilactici and mango seed polyphenols on the fermentative profile of the indigestible fraction of yam bean

Yam bean is an important source of dietary fiber and other components that comprise the total indigestible fraction (TIF), which can be fermented by the colonic microbiota and produce metabolites with beneficial health effects. Therefore, the objective of this study was to evaluate the in vitro colonic fermentation of yam bean TIF and the changes caused by the addition of a polyphenolic extract of mango seed and the lactic acid bacteria Pediococcus acidilactici. The mango seed extract was obtained by ultrasound-assisted extraction, and the microbial growth rate and viability of P. acidilactici were determined using a Neubauer chamber. Yam bean TIF was isolated by triple enzymatic hydrolysis and subjected to in vitro colonic fermentation in combination with treatments with mango seed extract and P. acidilactici suspensions. Changes in pH, total soluble phenols (TSP), and antioxidant capacity (AOX) were evaluated. Furthermore, the production of metabolites was quantified by HPLC-DAD-MS and GC-MS. The Growth rate of P. acidilactici was 0.1097 h-1 with 97.5 % viability at 7 h of incubation. All TIF treatments showed a high capacity of fermentation, and the addition of mango seed extract increased the TSP content and AOX in DPPH and FRAP assays. A total of Forty-six volatile metabolites were detected, with highlighting the presence of esters, benzenes, aldehydes, and short-chain fatty acids. Five phenolic compounds associated with mango by-products were quantified during all fermentation process, despite the concentration of the extract. P. acidilactici did not substantially modify the fermentative profile of TIF. However, further studies such as the evaluation of the abundance of microbial communities may be necessary to observe whether it can generate changes during colonic fermentation.

Energy and nutrient recovery from municipal and industrial waste and wastewater-a perspective

This publication highlights the latest advancements in the field of energy and nutrient recovery from organics rich municipal and industrial waste and wastewater. Energy and carbon rich waste streams are multifaceted, including municipal solid waste, industrial waste, agricultural by-products and residues, beached or residual seaweed biomass from post-harvest processing, and food waste, and are valuable resources to overcome current limitations with sustainable feedstock supply chains for biorefining approaches. The emphasis will be on the most recent scientific progress in the area, including the development of new and innovative technologies, such as microbial processes and the role of biofilms for the degradation of organic pollutants in wastewater, as well as the production of biofuels and value-added products from organic waste and wastewater streams. The carboxylate platform, which employs microbiomes to produce mixed carboxylic acids through methane-arrested anaerobic digestion, is the focus as a new conversion technology. Nutrient recycling from conventional waste streams such as wastewater and digestate, and the energetic valorization of such streams will also be discussed. The selected technologies significantly contribute to advanced waste and wastewater treatment and support the recovery and utilization of carboxylic acids as the basis to produce many useful and valuable products, including food and feed preservatives, human and animal health supplements, solvents, plasticizers, lubricants, and even biofuels such as sustainable aviation fuel.

ONE-SENTENCE SUMMARY

Multifaceted waste streams as the basis for resource recovery are essential to achieve environmental sustainability in a circular economy, and require the development of next-generation waste treatment technologies leveraging a highly adaptive mixed microbial community approach to produce new biochemicals, biomaterials, and biofuels from carbon-rich organic waste streams.

Cutaneotrichosporon curvatum and Yarrowia lipolytica as key players for green chemistry: efficient oil producers from food waste via the carboxylate platform

Cutaneotrichosporon curvatum and Yarrowia lipolytica can accumulate microbial oils using short-chain fatty acids (SCFA) as carbon sources. SCFAs-rich media often contain significant amounts of nitrogen that prevent high carbon:nitrogen (C:N) ratios necessary to boost lipid production. This work assessed the intrinsic ability of C. curvatum and Y. lipolytica to produce high amounts of microbial oils from these unusual carbon sources. Results demonstrated that minor differences in SCFA concentration (only 2 g/L) had a significant effect on yeast growth and lipid production. A C:N of 80 promoted yeast growth at all SCFA concentrations and favored SCFA consumption at 19 g/L SCFAs. The different SCFA uptake preferences in C. curvatum and Y. lipolytica highlighted the importance of considering the SCFA profile to select a suitable yeast strain for microbial oils production. At the most challenging SCFA concentration (19 g/L), 57.2% ±1.6% (w/w) and 78.4 ± 0.6% (w/w) lipid content were obtained in C. curvatum and Y. lipolytica, respectively. These values are among the highest reported for wild-type strains. To circumvent the challenges associated with media with high nitrogen content, this report also proved struvite precipitation as an effective method for increasing lipid production (from 17.9 ± 3.9% (w/w) to 41.9 ± 2.6% (w/w)) after nitrogen removal in food waste-derived media.

Impact of Ivermectin on the Gut Microbial Ecosystem

Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME® (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor's starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.

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.