Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate

Research on the conversion of biowaste to MCCAs: A review of recent advances in the electrochemical synergistic anaerobic pathway

Medium-chain carboxylic acids (MCCAs) show great promise as commercial chemicals due to their high energy density, significant product value, and wide range of applications. The production of MCCAs from waste biomass through coupling chain extension with anaerobic fermentation represents a new and innovative approach to biomass utilization. This review provides an overview of the principles of MCCAs production through coupled chain extension and anaerobic fermentation, as well as the extracellular electron transfer pathways and microbiological effects involved. Emphasis is placed on the mechanisms, limitations, and microbial interactions in MCCAs production, elucidating metabolic pathways, potential influencing factors, and the cooperative and competitive relationships among various microorganisms. Additionally, this paper delves into a novel technology for the bio-electrocatalytic generation of MCCAs, which promotes electron transfer through the use of different three-dimensional electrodes, various electrical stimulation methods, and hydrogen-assisted approaches. The insights and conclusions from previous studies, as well as the identification of existing challenges, will be valuable for the further development of high-product-selectivity strategies and environmentally friendly treatments.

Advancements in medium chain fatty acids production through chain elongation: Key mechanisms and innovative solutions for overcoming rate-limiting steps

The depletion of fossil fuels has prompted an urgent search for alternative chemicals from renewable sources. Current technology in medium chain fatty acids (MCFAs) production though chain elongation (CE) is becoming increasingly sustainable, hence the motivation for this review, which provides the detailed description, insights and analysis of the metabolic pathways, substrates type, inoculum and fermentation process. The main rate-limiting steps of microbial MCFAs production were comprehensively revealed and the corresponding innovative solutions were also critically evaluated. Innovative strategies such as substrate pretreatment, electrochemical regulation, product separation, fermentation parameter optimization, and electroactive additives have shown significant advantages in overcoming the rate-limiting steps. Furthermore, novel regulatory strategies such as quorum sensing and electronic bifurcation are expected to further increase the MCFAs yield. Finally, the techno-economic analysis was carried out, and the future research focuses were also put forward.

Gut microbiota derived short-chain fatty acids in physiology and pathology: An update

Short-chain fatty acids (SCFAs) are essential molecules produced by gut bacteria that fuel intestinal cells and may also influence overall health. An imbalance of SCFAs can result in various acute and chronic diseases, including diabetes, obesity and colorectal cancer (CRC). This review delves into the multifaceted roles of SCFAs, including a brief discussion on their source and various gut-residing bacteria. Primary techniques used for detection of SCFAs, including gas chromatography, high-performance gas chromatography, nuclear magnetic resonance and capillary electrophoresis are also discussed through this article. This review study also compiles various synthesis pathways of SCFAs from diverse substrates such as sugar, acetone, ethanol and amino acids. The different pathways through which SCFAs enter cells for immune response regulation are also highlighted. A major emphasis is the discussion on diseases associated with SCFA dysregulation, such as anaemia, brain development, CRC, depression, obesity and diabetes. This includes exploring the relationship between SCFA levels across ethnicities and their connection with blood pressure and CRC. In conclusion, this review highlights the critical role of SCFAs in maintaining gut health and their implications in various diseases, emphasizing the need for further research on SCFA detection, synthesis and their potential as diagnostic biomarkers. Future studies of SCFAs will pave the way for the development of novel diagnostic tools and therapeutic strategies for optimizing gut health and preventing diseases associated with SCFA dysregulation.

Conversion of wine lees and waste activated sludge into caproate and heptanoate: Thermodynamic and microbiological insights

In this study, wine lees and waste activated sludge (WAS) were co-fermented for the first time in a 4:1 ratio (COD basis) at 20, 40, 70 and 100 gCOD/L, in batch at 37 °C and pH 7.0. The substrates were successfully converted to caproate (C6) and heptanoate (C7) with a high selectivity (40.2 % at 40 gCOD/L). The rapidly-growing chain-elongating microbiome was enriched inClostridiaceaeandOscillospiraceae, representing together 3.4-8.8 % of the community. Substrate concentrations higher than 40 gCOD/L negatively affected C6 and C7 selectivities and yields, probably due to microbial inhibition by high ethanol concentrations (15.82-22.93 g/L). At 70 and 100 gCOD/L, chain elongation shifted from ethanol-based to lactate-based, with a microbiome enriched in the lactic acid bacteriaRoseburia intestinalis(27.3 %) andEnterococcus hirae(13.8 %). The partial pressure of H2(pH2) was identified by thermodynamic analysis as a fundamental parameter for controlling ethanol oxidation and improving C6 and C7 selectivities.

Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction

Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as n-caproate (C6) and n-caprylate (C8), from organic substrates such as wastes. Even though the production of n-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for n-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed. n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2 and O2 between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the Clostridia class. Several Oscillibacter spp., including Oscillibacter valericigenes, were positively correlated with n-caprylate production rates, while Clostridium kluyveri was positively correlated with n-caproate production. Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of n-caprylate production rates. This study provides insight into microbiota that are associated with n-caprylate production in open-culture reactors and provides ideas for further work.IMPORTANCEMicrobial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including n-caproate (C6) and n-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for n-caproate or n-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from n-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.

Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human

An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.

The phenotype and genotype of fermentative prokaryotes

Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.

Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage

Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein. KEY POINTS: • Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %. • The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway. • The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.

Rumen microbial community and milk quality in Holstein lactating cows fed olive oil pomace as part in a sustainable feeding strategy

The use of alternative feed ingredients from the Agro-industry could be an efficient tool to improve the sustainability of dairy cow production. Since the richness in polyphenols, olive oil pomace (OOP), produced during olive oil milling, seems a promising by-product to ameliorate milk's nutritional value. The aim of this study was to test the use of OOP produced by means of a new technology (biphasic with stone deprivation) in dairy cow feeding strategy to evaluate the effect on animal performances, rumen microbiota, biohydrogenation processes and milk quality by a multidisciplinary approach. Forty multiparous Italian-Friesian dairy cows, at middle lactation, were randomly allotted into two homogenous groups and fed respectively a commercial diet (CON) and the experimental diet (OOPD) obtained by adding OOP to CON as partial replacement of maize silage. The two diets were formulated to be isoproteic and isoenergetic. The same diets were tested also in an in vitro trial aimed to evaluate their rumen degradability (% DEG). The dietary supplementation with OOP did not affect DM intake, rumen % DEG and milk production. The milk's nutritional quality was improved by increasing several important functional fatty acids (FAs; i.e., linoleic acid, conjugated linoleic acid, oleic acid, vaccenic acid). This finding was related to a decrease in rumen liquor biohydrogenation rate of unsaturated FAs. The stochiometric relation between volatile FA production in the rumen and methanogenesis suggested that OOP lowers the methane potential production (CON = 0.050 mol/L vs OOPD = 0.024 mol/L, SEM = 0.005, P = 0.0011). Rumen microbiota and fungi community did not be strongly altered by OOP dietary inclusion because few bacteria were affected at the genus level only. Particularly, Acetobacter, Prevotellaceae_UCG-004, Prevotellaceae_UCG-001, Eubacterium coprostanoligenes, Lachnospira, Acetitomaulatum, Lachnospiraceae_NK3A20 group were more abundant with OOPD condition (P < 0.05). Data reported in this study confirm that the use of OOP in dairy cow feeding can be an interesting strategy to improve milk nutritional quality increasing functional FA content without compromising the rumen degradability of the diet or causing strong perturbation of rumen ecosystem and maintaining animal performances.

Effects of Circadian Rhythm and Feeding Modes on Rumen Fermentation and Microorganisms in Hu Sheep

All organisms have a biological clock system which is strongly tied to how well an organism digests food and develops. This study aimed to understand the effects of circadian rhythm and feeding modes on rumen fermentation and microorganisms in Hu sheep. Forty-five healthy Hu sheep were randomly divided into three treatment groups of 15 sheep in each group, wherein they were fed the same concentrate and roughage. Under the condition that the nutrient-feeding amount was consistent throughout the day, the concentrate-to-forage ratio was dynamically adjusted during the day and night. Rumen fluid collected after the feeding experiment was used to determine the study parameters; the results showed a connection between rumen fermentation and the circadian clock. Volatile fatty acids (VFAs), pH, and NH3-N were significantly influenced by the fermentation duration (p < 0.05). The activities of digestive enzymes also showed a relationship with nutrition and circadian rhythm, and there were differences in the digestive enzyme activities of amylase, lipase, and cellulase (p < 0.05). Dominant microorganisms, such as Saccharomycetes and Mucor, were more abundant in the daytime of the high-concentrate fed group. The correlation among the study objectives was evident from the differences in enzyme activity and microbial diversity among the treatment groups. On the basis of the circadian rhythm characteristics of Hu sheep, changes in the feeding mode of Hu sheep and only adjusting the proportion of concentrate and forage in the morning and evening showed that feeding diets with the high-concentrate ratio in the day significantly reduced rumen PH and increased NH3-N concentration (p < 0.05). Under this feeding pattern, the activities of major digestive enzymes in the rumen, such as amylase and lipase, were significantly increased (p < 0.05), and the microbial diversity was also improved.

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.

Biological production of medium-chain carboxylates through chain elongation: An overview

Medium chain carboxylates (MCCs) have wide applications in various industries, but the traditional MCCs production methods are costly and unsustainable. Anaerobic fermentation offers a more scalable, economical and eco-friendly platform for producing MCCs through chain elongation which converts short chain carboxylates and electron donor into more valuable MCCs. However, the underlying microbial pathways are not well understood. In this review, biological production of MCCs through chain elongation is introduced elaborately, including the metabolic pathways, electron donor and substrates, microorganisms and influencing factors. Then, the strategies for enhancing MCCs production are extensively analyzed and summarized, along with the technologies for MCCs separation from the fermentation broth. Finally, challenges and perspectives concerning the large-scale MCCs production are proposed, providing suggestions for the future research. Extensive review demonstrated that anaerobic fermentation has great potential in achieving economical and sustainable MCCs production from complex organic substrates, including organic waste streams, which would significantly broaden the application of MCCs, especially in the renewable energy field. An interdisciplinary approach with knowledge from microbiology and biochemistry to chemical separations and environmental engineering is required to use this promising technology as a valorization method for converting organic biomass or organic wastes into valuable MCCs.

A Citrus Fruit Extract High in Polyphenols Beneficially Modulates the Gut Microbiota of Healthy Human Volunteers in a Validated In Vitro Model of the Colon

The effect of a Citrus Fruit Extract high in the polyphenols hesperidin and naringin (CFE) on modulation of the composition and activity of the gut microbiota was tested in a validated, dynamic in vitro model of the colon (TIM-2). CFE was provided at two doses (250 and 350 mg/day) for 3 days. CFE led to a dose-dependent increase in Roseburia, Eubacterium ramulus, and Bacteroides eggerthii. There was a shift in production of short-chain fatty acids, where acetate production increased on CFE, while butyrate decreased. In overweight and obesity, acetate has been shown to increase fat oxidation when produced in the distal gut, and stimulate secretion of appetite-suppressive neuropeptides. Thus, the data in the in vitro model point towards mechanisms underlying the effects of the polyphenols in CFE with respect to modulation of the gut microbiota, both in composition and activity. These results should be confirmed in a clinical trial.

Adaptability of a caproate-producing bacterium contributes to its dominance in an anaerobic fermentation system

The transformation of diverse feedstocks into medium-chain fatty acids (MCFAs) by mixed cultures is a promising biorefinery route because of the high value of MCFAs. A particular concern is how to maintain the microbial consortia in mixed cultures to achieve stable MCFA production. Chinese strong aroma-type liquor (Baijiu) fermentation system continually produces caproic acid for decades through a spontaneous inoculation of anaerobes from pit mud into fermented grains. Therefore, illuminating the dominant caproate-producing bacterium (CPB) in pit mud and how the CPB sustains in the spontaneous fermentation system will benefit to reveal the microbiological mechanisms of the stable caproate production. Here, we examined pit mud samples across four Chinese strong aroma-type Baijiu producing areas and found that a caproate-producing Caproicibacterium sp. was widely distributed in these distilleries with relative abundance ranging from 1.4% to 35.5% and an average abundance of 11.4%. Through controlling carbon source availability, we achieved different simplified caproate-producing consortia and found that the growth advantage of Caproicibacterium sp. was highly dependent on glucose. Then two strains, named Caproicibacterium sp. LBM19010 and Caproicibacterium sp. JNU-WLY1368, were isolated from pit mud of two regions. The metabolic versatility of this bacterium utilizing starch, maltose, glucose and lactate reflected its adaptability to the fermentation environment where these carbon sources coexist. The simultaneous utilization of glucose and lactate contributed to the balance between cell growth and pH homeostasis. This study reveals that multiple adaptation strategies employed by the predominant CPB promotes its stability and dominance in a saccharide- and lactate-rich anaerobic habitat. IMPORTANCE Chinese strong aroma-type liquor (Baijiu) fermentation environment is a typical medium-chain fatty acid producing system with complex nutrients. Although several studies have revealed the correlation between microbial community composition and abiotic factors, the adaptation mechanisms of dominant species to abiotic environment are still unknown in this special anaerobic habitat. This study identified the predominant CPB in Chinese strong aroma-type Baijiu fermentation system. Metabolic versatility and flexibility of the dominant CPB with a small-size genome indicated that this bacterium can effectively exploit available carbon and nitrogen sources, which could be a key factor to promote its ecological success in a multi-species environment. The understanding of growth and metabolic features of CPB responsible for its dominance in microbial community will not only contribute to the improvement of Chinese strong aroma-type Baijiu production but also expand its potential industrial applications in caproate production.

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge

Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d^-1), or BCA (6 g d^-1). The basal diet consisted of corn silage and dried distiller’s grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1–4: 40% corn; d 5–8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.

Caffeic acid modulates methane production and rumen fermentation in an opposite way with high-forage or high-concentrate substrate in vitro

BACKGROUND

Plant secondary metabolites, including tannins, saponins and phenolic acids, possess potential methane (CH₄ ) inhibition bioactivity. Caffeic acid (CA), as one of the typical phenolic acids, serves as a promising rumen CH₄ inhibitor, but the underlying mechanisms and investigations with typical formulated rations are still not well documented. Therefore, a batch culture study was conducted to investigate the effects of CA on methanogenesis, rumen fermentation and growth of ruminal microorganisms when high-forage or high-concentrate substrates are fermented.

RESULTS

After 48 h incubations, adding CA up to 40 g kg^-1 dry matter linearly reduced (P < 0.05) the disappearance of dry matter, neutral detergent fiber (NDFD), total gas, methanogenesis, total volatile fatty acid and 16S rDNA copy numbers of Ruminococcus albus and Butyrivibrio fibrisolvens, and increased 16S rDNA copy numbers of methanogens for the high-forage treatment. For the high-concentrate treatment, CA exerted opposite effects (P < 0.05) on the above variables, except that CA did not affect (P > 0.05)16S rDNA copy numbers of methanogens or R. albus.

CONCLUSION

Caffeic acid inhibited in vitro methanogenesis and rumen fermentation with high-forage substrate incubation. Contrarily, CA benefited in vitro fermentation and enhanced methanogenesis with high-concentrate substrate incubation. It suggests that CA modulates methanogenesis and rumen fermentation mainly by affecting the growth of cellulolytic bacteria in vitro. © 2020 Society of Chemical Industry.

Chain elongators, friends, and foes

Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut

BACKGROUND

Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects ("leaky gut"). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder-non-responder phenotypes observed in vivo.

RESULTS

Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype.

CONCLUSIONS

Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. Video abstract.

Effect of ultrasonic pretreatment on chain elongation of saccharified residue from food waste by anaerobic fermentation

Converting biowaste into value-added products has raised the researchers' interests. In this study, bioconversion was applied to produce chain acids from food waste by anaerobic fermentation. To improve the caproic acid production, different pretreatments (i.e., ultrasonic, hydrothermal, and alkaline-thermal) were used for investigating their effects on the acidogenic production and microbial communities. The results showed that ultrasonic and hydrothermal pretreatments (207.8 and 210.1 mg COD/g VS, respectively) were very efficient for enhancing the caproic acid production, compared to the alkaline-thermal pretreated samples and control samples (72.6 and 97.5 mg COD/g VS, respectively). The ultrasonic pretreatment was beneficial for reducing volatile fatty acids (VFAs) during the caproic acid production, resulting in converting more lactic acid to caproic acid by adding the hydrothermal pretreatment. The microbial community analysis showed that the acidogenic bacteria Caproiciproducens dominated the fermentation in this bioconversion process of food waste into chain acids. The Caproiciproducens mainly degraded the proteins and carbohydrates from the saccharified residues of food waste to produce caproic acids through chain elongation procedure. The investigation and optimized method may help develop the bioconversion technology for producing VFAs products from food wastes.

Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria

The platform chemicals n-caproate and iso-butyrate can be produced by anaerobic fermentation from agro-industrial residues in a process known as microbial chain elongation. Few lactate-consuming chain-elongating species have been isolated and knowledge on their shared genetic features is still limited. Recently we isolated three novel clostridial strains (BL-3, BL-4, and BL-6) that convert lactate to n-caproate and iso-butyrate. Here, we analyzed the genetic background of lactate-based chain elongation in these isolates and other chain-elongating species by comparative genomics. The three strains produced n-caproate, n-butyrate, iso-butyrate, and acetate from lactate, with the highest proportions of n-caproate (18%) for BL-6 and of iso-butyrate (23%) for BL-4 in batch cultivation at pH 5.5. They show high genomic heterogeneity and a relatively small core-genome size. The genomes contain highly conserved genes involved in lactate oxidation, reverse β-oxidation, hydrogen formation and either of two types of energy conservation systems (Rnf and Ech). Including genomes of another eleven experimentally validated chain-elongating strains, we found that the chain elongation-specific core-genome encodes the pathways for reverse β-oxidation, hydrogen formation and energy conservation, while displaying substantial genome heterogeneity. Metabolic features of these isolates are important for biotechnological applications in n-caproate and iso-butyrate production.

Fermentation of Organic Residues to Beneficial Chemicals: A Review of Medium-Chain Fatty Acid Production

Medium-chain fatty acids (MCFAs) have a variety of uses in the production of industrial chemicals, food, and personal care products. These compounds are often produced through palm refining, but recent work has demonstrated that MCFAs can also be produced through the fermentation of complex organic substrates, including organic waste streams. While “chain elongation” offers a renewable platform for producing MCFAs, there are several limitations that need to be addressed before full-scale implementation becomes widespread. Here, we review the history of work on MCFA production by both pure and mixed cultures of fermenting organisms, and the unique metabolic features that lead to MCFA production. We also offer approaches to address the remaining challenges and increase MCFA production from renewable feedstocks.

Performance and community structure dynamics of microbial electrolysis cells operated on multiple complex feedstocks

BACKGROUND

Microbial electrolysis is a promising technology for converting aqueous wastes into hydrogen. However, substrate adaptability is an important feature, seldom documented in microbial electrolysis cells (MECs). In addition, the correlation between substrate composition and community structure has not been well established. This study used an MEC capable of producing over 10 L/L-day of hydrogen from a switchgrass-derived bio-oil aqueous phase and investigated four additional substrates, tested in sequence on a mature biofilm. The additional substrates included a red oak-derived bio-oil aqueous phase, a corn stover fermentation product, a mixture of phenol and acetate, and acetate alone.

RESULTS

The MECs fed with the corn stover fermentation product resulted in the highest performance among the complex feedstocks, producing an average current density of 7.3 ± 0.51 A/m2, although the acetate fed MECs outperformed complex substrates, producing 12.3 ± 0.01 A/m2. 16S rRNA gene sequencing showed that community structure and community diversity were not predictive of performance, and replicate community structures diverged despite identical inoculum and enrichment procedure. The trends in each replicate, however, were indicative of the influence of the substrates. Geobacter was the most dominant genus across most of the samples tested, but its abundance did not correlate strongly to current density. High-performance liquid chromatography (HPLC) showed that acetic acid accumulated during open circuit conditions when MECs were fed with complex feedstocks and was quickly degraded once closed circuit conditions were applied. The largest net acetic acid removal rate occurred when MECs were fed with red oak bio-oil aqueous phase, consuming 2.93 ± 0.00 g/L-day. Principal component analysis found that MEC performance metrics such as current density, hydrogen productivity, and chemical oxygen demand removal were closely correlated. Net acetic acid removal was also found to correlate with performance. However, no bacterial genus appeared to correlated to these performance metrics strongly, and the analysis suggested that less than 70% of the variance was accounted for by the two components.

CONCLUSIONS

This study demonstrates the robustness of microbial communities to adapt to a range of feedstocks and conditions without relying on specific species, delivering high hydrogen productivities despite differences in community structure. The results indicate that functional adaptation may play a larger role in performance than community composition. Further investigation of the roles each microbe plays in these communities will help MECs to become integral in the 21st-century bioeconomy to produce zero-emission fuels.

Profiling the effects of physicochemical indexes on the microbial diversity and its aroma substances in pit mud

Microbial diversity of pit mud (PM) plays a significant role in Baijiu's flavour. Here we explored the microbial community structures and aroma substances of Wenwang Winery with high-throughput sequencing coupling with headspace solid-phase microextraction-gas chromatography-mass spectrometry. We discovered that the odorant was mainly derived from 14 aroma compounds because of their OAVs ≥ 1 (OAV, the ratio of substance concentration to aroma threshold; s, on behalf of the plural), such as ethyl hexanoate (2438), ethyl octanoate (975), caproic acid (52) and etc. Moreover we also revealed that Lactobacillaceae (97·08%) was the mainly bacterial microbial community in 2-year-old PM, companied by the primarily fungi including Aspergillaceae (55·45%), Unclassified Ascomycota (11·13%) and Dipodascaceae (5·72%). Compared with the 2-year-old PM, bacterial floras in 20-year-old PM and 30-year-old PM were more abundant (i.e. Dysgonomonadaceae, Clostridium and Synerggstaceas), while no fungi were detected. Besides, the physicochemical analysis showed that the content of Lactobacillaceae was inversely associated with moisture, pH and ammonia nitrogen. By further Spearman's correlation coefficient analysis, we verified that the content of Lactobacillaceae was positively correlated with ethyl hexanoate, while negatively correlated with ethyl octanoate and caproic acid. Meanwhile, ethyl octanoate and caproic acid were positively correlated with most flora including Ruminococcaceae, Dysgonomonadaceae and Clostridiacea, which were related to physicochemical indexes. This work demonstrates promise for adjusting the physicochemical indexes of PM to affect the micro-organisms and aroma, which may provide a reference for the production of high-quality Baijiu.

Review on the production of medium and small chain fatty acids through waste valorization and CO2 fixation

The developing approaches in the recovery of resources from biowastes for the production of renewable value-added products and fuels, using microbial cultures as bio-catalyst have now became promising aspect. In the path of anaerobic digestion, the microorganisms are assisting transformation of a complex organic feedstock/waste to biomass and biogas. This potentiality consequently leads to the production of intermediate precursors of renewable value-added products. Particularly, a set of anaerobic pathways in the fermentation process, yields small-chain fatty acids (SCFA), and medium-chain fatty acids (MCFA) via chain elongation pathways from waste valorization and CO₂ fixation. This review focuses on the production of SCFA and MCFA from CO₂, synthetic substrates and waste materials. Moreover, the review introduces the metabolic engineering of Escherichia coli and Saccharomyces cerevisiae for SCFAs/MCFAs production. Furtherly, it concludes that future critical research might target progress of this promising approach as a valorization of complex organic wastes.

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function

Dietary high protein and low carbohydrate levels compromise colonic microbiota and bile acid metabolism, which underlies a detrimental gut environment. However, it remains unclear if the diet-induced changes in colonic health are due to a change in hindgut nutrient availability and what key intermediates link the microbe-epithelium dialogue. To specifically alter the hindgut nutrient substrate availability, here we used a cecally cannulated pig model to infuse corn starch and casein hydrolysate directly into the cecum to generate a stepwise change of carbohydrate/nitrogenous compound (C/N) ratio. Pigs were cecally infused daily with either saline (Control), corn starch (Starch), or casein hydrolysate (Casein) (n = 8 per group), respectively, for 19 days. After infusion, C/N ratios in colonic digesta were 16.33, 12.56, and 8.54 for the starch, control, and casein groups, respectively (P < 0.05). Relative to the control group, casein infusion showed greater abundance of the bacteria (Eubacterium) capable of bile acid 7α-dehydroxylation (baiJ), higher levels of expression of bacterial genes encoding the baiJ enzyme, and higher levels of secondary bile acid (deoxycholic acid [DCA] and lithocholic acid [LCA]), while the starch infusion showed the opposite effect. Correspondingly, casein infusion downregulated expression of genes encoding tight junction proteins (ZO-1 and OCLD) and upregulated expression of genes encoding epidermal growth factor receptor (EGFR). The ratio of C/N was linearly related with the concentrations of DCA and LCA and gene expression levels of ZO-1, occludin, and EGFR. Caco-2 cell experiments further showed that DCA and LCA downregulated expression of genes involved in barrier function (ZO-1 and OCLD) and upregulated the gene expression of EGFR and Src. Inhibition of EGFR and Src could abolish DCA- and LCA-induced downregulation of ZO-1, indicating that DCA and LCA impair gut barrier function via enhancing the EGFR-Src pathway. These results suggest that the ratio of C/N in the large intestine is an important determinant of microbial metabolism and gut barrier function in the colon. The findings provide evidence that microbe-related secondary bile acid metabolism may mediate the interplay between microbes and gut barrier function.

IMPORTANCE High-fiber or high-protein diets could alter gut microbiota and health in the large intestine, but factors involved in the effects remain unclear. The present study for the first time demonstrates that the starch- and casein-induced C/N ratio in the hindgut is an important factor. Using the cannulated pig model, we found that the distinct C/N ratio induced by cecal infusion of corn starch or casein hydrolysate was linearly correlated with microbial metabolites (secondary bile acids) and tight junction proteins (ZO-1 and OCLD). Cell culture study further demonstrates that the gut microbial metabolites (DCA and LCA) could impair the intestinal barrier function via the EGFR-Src pathway. These suggest that DCA and LCA were key metabolites mediating microbe-epithelium dialogue when the hindgut C/N ratios were altered by cecal infusion of corn starch or casein hydrolysate. These findings provide new insight into the impact of C/N ratio in the large intestine on colonic health and provide a new framework for therapeutic strategy in gut health through targeted manipulation of hindgut microbiota by increasing the carbohydrate level in the large intestine.

Inclusion of Soluble Fiber in the Gestation Diet Changes the Gut Microbiota, Affects Plasma Propionate and Odd-Chain Fatty Acids Levels, and Improves Insulin Sensitivity in Sows

The transition from pregnancy to lactation is characterized by a progressive decrease in insulin sensitivity. Propionate increases with dietary fiber consumption and has been shown to improve insulin sensitivity. Recent studies suggest that plasma odd-chain fatty acids [OCFAs; pentadecanoic acid (C15:0) and heptadecanoic acid (C17:0)] that inversely correlated with insulin resistance are synthesized endogenously from gut-derived propionate. The present study investigated the effects of soluble fiber during gestation on gut microbiota, plasma non-esterified fatty acids and insulin sensitivity in sows. Sows were allocated to either control or 2.0% guar gum plus pregelatinized waxy maize starch (SF) dietary treatment during gestation. The SF addition changes the structure and composition of gut microbiota in sows. Genus Eubacterium increased by SF addition may promote intestinal propionate production. Moreover, the dietary SF increased circulating levels of plasma OCFAs, especially C17:0. The SF-fed sows had a higher insulin sensitivity and a lower systemic inflammation level during perinatal period. Furthermore, the plasma C15:0 and C17:0 was negatively correlated with the area under curve of plasma glucose after meal and plasma interleukin-6. In conclusion, dietary SF improves insulin sensitivity and alleviates systemic inflammation in perinatal sows, potentially related to its stimulating effect on propionate and OCFAs production.

Road to full bioconversion of biowaste to biochemicals centering on chain elongation: A mini review

Production of biochemicals from waste streams has been attracting increasing worldwide interest to achieve climate protection goals. Chain elongation (CE) for production of medium-chain carboxylic acids (MCCAs, especially caproate, enanthate and caprylate) from diverse biowaste has emerged as a potential economic and environmental technology for a sustainable society. The present mini review summarizes the research utilizing various synthetic or real waste-derived substrates available for MCCA production. Additionally, the microbial characteristics of the CE process are surveyed and discussed. Considering that a large proportion of recalcitrantly biodegradable biowaste and residues cannot be further utilized by CE systems and remain to be treated and disposed, we propose here a loop concept of bioconversion of biowaste to MCCAs making full use of the biowaste with zero emission. This could make possible an alternative technology for synthesis of value-added products from a wide range of biowaste, or even non-biodegradable waste (such as, plastics and rubbers). Meanwhile, the remaining scientific questions, unsolved problems, application potential and possible developments for this technology are discussed.

Genome Sequence of the Caproic Acid-Producing Bacterium Caproiciproducens galactitolivorans BS-1T (JCM 30532)

Caproiciproducens galactitolivorans BS-1^T is an anaerobic bacterium that produces acetate, butyrate, and caproate. The genome has a size of 2.57 Mbp and harbors 2,439 predicted protein-coding genes.

Caproiciproducens galactitolivorans BS-1^T is an anaerobic bacterium that produces acetate, butyrate, and caproate. The genome has a size of 2.57 Mbp and harbors 2,439 predicted protein-coding genes.

Characterization of microbial community profiles associated with quality of Chinese strong-aromatic liquor through metagenomics

AIMS

Microorganisms in fermentation pits (FPs) play key roles for Chinese-strong-aromatic-liquor (CSAL) production. However, the microbial community in the FPs is still poorly understood. Here, the aim of this study was to reveal the diversity and potential functions of microbiota in FPs.

METHODS AND RESULTS

Sequencing-by-synthesis-based metagenomic sequencing and annotation results revealed that the microbiota of FPs was primarily composed of Firmicutes (54·6%), Euryarchaeota (15·3%), Bacteroidetes (10·1%), Gammaproteobacteria (5·8%), Opisthokonta (5·7%) and Unclassified_Bacteria (2·3%). And 133 genera were identified as the dominant genera of this fermentative food. Lactobacillus, Sedimentibacter, Syntrophomonas, Methanoculleus, Methanobacterium, Bacillus, Clostridium, Galactomyces, Candida, Pichia, Penicillium and Aspergillus were defined as active populations for biosynthesizing the characteristic volatile compounds of CSAL. The study also revealed that the microbial community structures changed significantly with different cellar ages and over different geographical regions. (i) The presence of Bacteroidetes was the most distinctive feature that characterized the different FPs ages. (ii) Distinct contents of Gammaproteobacteria and Euryarchaeota were observed at different positions in the FPs. (iii) Euryarchaeota markedly contributed to the generation of the character of the liquors with distinct geographical associations.

CONCLUSIONS

This study demonstrated that the changes of microbial communities determined the different quality characteristics of CSAL.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research contributes to a deeper understanding of the FPs microbial composition and shows a new microbial resource for biotechnological applications.

Medium chain carboxylic acids production from waste biomass: Current advances and perspectives

Alternative chemicals to diverse fossil-fuel-based products is urgently needed to mitigate the adverse impacts of fossil fuel depletion on human development. To this end, researchers have focused on the production of biochemical from readily available and affordable waste biomass. This is consistent with current guidelines for sustainable development and provides great advantages related to economy and environment. The search for suitable biochemical products is in progress worldwide. Therefore, this review recommends a biochemical (i.e., medium chain carboxylic acids (MCCAs)) utilizing an emerging biotechnological production platform called the chain elongation (CE) process. This work covers comprehensive introduction of the CE mechanism, functional microbes, available feedstock types and corresponding utilization strategies, major methods to enhance the performance of MCCAs production, and the challenges that need to be addressed for practical application. This work is expected to provide a thorough understanding of the CE technology, to guide and inspire researchers to solve existing problems in depth, and motivate large-scale MCCAs production.

Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production

BACKGROUND

Heifers emit more enteric methane (CH₄ ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for these pre-production animals. Given its direct role in CH₄ production, altering the rumen microbiota is another potential avenue for reducing CH₄ production by ruminants. However, to identify effective microbial targets, a better understanding of the rumen microbiota and its relationship to CH₄ production across heifer development is needed.

RESULTS

Here, we investigate the relationship between rumen bacterial, archaeal, and fungal communities as well as CH₄ emissions and a number of production traits in prepubertal (PP), pubertal (PB), and pregnant heifers (PG). Overall, PG heifers emitted the most CH₄ , followed by PB and PP heifers. The bacterial genus Acetobacter and the archaeal genus Methanobrevibacter were positively associated, while Eubacterium and Methanosphaera were negatively associated with raw CH₄ production by heifers. When corrected for dietary intake, both Eubacterium and Methanosphaera remained negatively associated with CH₄ production.

CONCLUSION

We suggest that Eubacterium and Methanosphaera represent likely targets for CH₄ mitigation efforts in heifers as they were negatively associated with CH₄ production and not significantly associated with production traits. © 2018 Society of Chemical Industry.

Metabolic Interactions of a Chain Elongation Microbiome

Carbon chain elongation (CCE), a reaction within the carboxylate platform that elongates short-chain to medium-chain carboxylates by mixed culture, has attracted worldwide interest. The present study provides insights into the microbial diversity and predictive microbial metabolic pathways of a mixed-culture CCE microbiome on the basis of a comparative analysis of the metagenome and metatranscriptome. We found that the microbial structure of an acclimated chain elongation microbiome was a highly similar to that of the original inoculating biogas reactor culture; however, the metabolic activities were completely different, demonstrating the high stability of the microbial structure and flexibility of its functions. Additionally, the fatty acid biosynthesis (FAB) pathway, rather than the well-known reverse β-oxidation (RBO) pathway for CCE, was more active and pivotal, though the FAB pathway had more steps and consumed more ATP, a phenomenon that has rarely been observed in previous CCE studies. A total of 91 draft genomes were reconstructed from the metagenomic reads, of which three were near completion (completeness, >97%) and were assigned to unknown strains of Methanolinea tarda, Bordetella avium, and Planctomycetaceae The last two strains are likely new-found active participators of CCE in the mixed culture. Finally, a conceptual framework of CCE, including both pathways and the potential participators, was proposed.IMPORTANCE Carbon chain elongation means the conversion of short-chain volatile fatty acids to medium-chain carboxylates, such as n-caproate and n-caprylate with electron donors under anaerobic condition. This bio-reaction can both expand the resource of valuable biochemicals and broaden the utilization of low-grade organic residues in a sustainable biorefinery context. Clostridium kluyveri is conventionally considered model microbe for carbon chain elongation which uses the reverse β-oxidation pathway. However, little is known about the detailed microbial structure and function of other abundant microorganism in a mixed culture (or open culture) of chain elongation. We conducted the comparative metagenomic and metatranscriptomic analysis of a chain elongation microbiome to throw light on the underlying functional microbes and alternative pathways.

Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system

BACKGROUND

Nowadays, the vast majority of chemicals are either synthesised from fossil fuels or are extracted from agricultural commodities. However, these production approaches are not environmentally and economically sustainable, as they result in the emission of greenhouse gases and they may also compete with food production. Because of the global agreement to reduce greenhouse gas emissions, there is an urgent interest in developing alternative sustainable sources of chemicals. In recent years, organic waste streams have been investigated as attractive and sustainable feedstock alternatives. In particular, attention has recently focused on the production of caproate from mixed culture fermentation of low-grade organic residues. The current approaches for caproate synthesis from organic waste are not economically attractive, as they involve the use of two-stage anaerobic digestion systems and the supplementation of external electron donors, both of which increase its production costs. This study investigates the feasibility of producing caproate from food waste (FW) without the supplementation of external electron donors using a single-phase reactor system.

RESULTS

Replicate leach-bed reactors were operated on a semi-continuous mode at organic loading of 80 g VS FW l-1 and at solid retention times of 14 and 7 days. Fermentation, rather than hydrolysis, was the limiting step for caproate production. A higher caproate production yield 21.86 ± 0.57 g COD l-1 was achieved by diluting the inoculating leachate at the beginning of each run and by applying a leachate recirculation regime. The mixed culture batch fermentation of the FW leachate was able to generate 23 g caproate COD l-1 (10 g caproate l-1), at a maximum rate of 3 g caproate l-1 day-1 under high H2 pressure. Lactate served as the electron donor and carbon source for the synthesis of caproate. Microbial community analysis suggested that neither Clostridium kluyveri nor Megasphaera elsdenii, which are well-characterised caproate producers in bioreactors systems, were strongly implicated in the synthesis of caproate, but that rather Clostridium sp. with 99% similarity to Ruminococcaceae bacterium CPB6 and Clostridium sp. MT1 likely played key roles in the synthesis of caproate. This finding indicates that the microbial community capable of caproate synthesis could be diverse and may therefore help in maintaining a stable and robust process.

CONCLUSIONS

These results indicate that future, full-scale, high-rate caproate production from carbohydrate-rich wastes, associated with biogas recovery, could be envisaged.

Computational and experimental analysis of organic degradation positively regulated by bioelectrochemistry in an anaerobic bioreactor system

Methane production was tested in membrane-less microbial electrolysis cells (MECs) under closed-circuit (R_CC) and open-circuit (R_OC) conditions, using glucose as a substrate, to understand the regulatory effects of bioelectrochemistry in anaerobic digestion systems. A dynamic model was built to simulate methane productions and microbial dynamics of functional populations, which were colonized in groups R_CC and R_OC during the start-up stage. The experiment results showed significantly greater methane production in R_CC than R_OC, the average methane production of R_CC was 0.131 m³/m³/d, which was 1.4 times higher than that of R_OC (0.055 m³/m³/d). The simulation results revealed that bioelectrochemistry had a significant influence on the abundance of microorganisms involved in acidogenesis and methanogenesis. The abundance of glucose-uptaking microorganisms was 87% of the total biomass in R_OC without applied voltage, which was 20% higher than that in R_CC (67%) when external voltages were applied between the anode and cathode. The abundance of hydrogenotrophic methanogens in R_CC was 6% higher than that in R_OC. The simulation results were verified through 16S rDNA high-throughput sequencing analysis. An electron balance analysis revealed that alteration of the acidogenesis type led to more acetate and hydrogen production from glucose fermentation, compared with the situation without bioelectrochemistry. An additional pathway from acetate to hydrogen was introduced by bioelectrolysis. These two factors resulted in significant enhancement of methane production in R_CC. Bioelectrolysis process directly contributed to 26% of the total methane production after the start-up stage. When the applied voltages were cut down or decreased, R_CC could maintain considerable methane productions, because the microbial communities and electron transfer pathways were already formed. Starting-up with high voltage, but operating under low voltage, could be an energy-favorable strategy for accelerating biogas production in bioelectro-anaerobic bioreactors.

Hops (Humulus lupulus L.) Bitter Acids: Modulation of Rumen Fermentation and Potential As an Alternative Growth Promoter

Antibiotics can improve ruminant growth and efficiency by altering rumen fermentation via selective inhibition of microorganisms. However, antibiotic use is increasingly restricted due to concerns about the spread of antibiotic-resistance. Plant-based antimicrobials are alternatives to antibiotics in animal production. The hops plant (Humulus lupulus L.) produces a range of bioactive secondary metabolites, including antimicrobial prenylated phloroglucinols, which are commonly called alpha- and beta-acids. These latter compounds can be considered phyto-ionophores, phytochemicals with a similar antimicrobial mechanism of action to ionophore antibiotics (e.g., monensin, lasalocid). Like ionophores, the hop beta-acids inhibit rumen bacteria possessing a classical Gram-positive cell envelope. This selective inhibition causes several effects on rumen fermentation that are beneficial to finishing cattle, such as decreased proteolysis, ammonia production, acetate: propionate ratio, and methane production. This article reviews the effects of hops and hop secondary metabolites on rumen fermentation, including the physiological mechanisms on specific rumen microorganisms, and consequences for the ruminant host and ruminant production. Further, we propose that hop beta-acids are useful model natural products for ruminants because of (1) the ionophore-like mechanism of action and spectrum of activity and (2) the literature available on the plant due to its use in brewing.

Ruminal tryptophan-utilizing bacteria degrade ergovaline from tall fescue seed extract

The objectives of this study were to evaluate degradation of ergovaline in a tall fescue [ (Schreb.) Darbysh.] seed extract by rumen microbiota ex vivo and to identify specific bacteria capable of ergovaline degradation in vitro. Rumen cell suspensions were prepared by harvesting rumen fluid from fistulated wether goats ( = 3), straining, and differential centrifugation. Suspensions were dispensed into anaerobic tubes with added Trypticase with or without extract (∼10 μg kg ergovaline). Suspensions were incubated for 48 h at 39°C. Samples were collected at 0, 24, and 48 h for ergovaline analysis and enumeration of hyper-ammonia producing (HAB) and tryptophan-utilizing bacteria. Ergovaline values were analyzed by repeated measures using the mixed procedure of SAS. Enumeration data were log transformed for statistical analysis. When suspensions were incubated with extract, 11 to 15% of ergovaline disappearance was observed over 48 h ( = 0.02). After 24 h, suspensions with added extract had 10-fold less HAB than controls ( = 0.04), but treatments were similar by 48 h ( = 1.00). However, after 24 h and 48 h, suspensions with extract had 10-fold more tryptophan-utilizing bacteria ( < 0.01) that were later isolated and identified by their 16S RNA gene sequence as . The isolates and other known rumen pure cultures ( JB1, B159, HD4, B, F, MD1, SR) were evaluated for the ability to degrade ergovaline in vitro. Pure culture cell suspensions were incubated as described above and samples were taken at 0 and 48 h for ergovaline analysis. Data were analyzed using the ANOVA procedure of SAS. All HAB, including the isolates, tested degraded ergovaline (54 to 75%; < 0.05). B14 was also able to degrade ergovaline but to a lesser capacity (12%; < 0.05), but all other bacteria tested did not degrade ergovaline. The results of this study indicate which rumen bacteria may play an important role in ergovaline degradation and that microbiological strategies for controlling their activity could have ramifications for fescue toxicosis and other forms of ergotism in ruminants.

Effect of high-oleic-acid soybeans on production performance, milk fatty acid composition, and enteric methane emission in dairy cows

The objective of this study was to investigate the effect of 3 soybean sources differing in fatty acid profile and processing method on productivity, milk composition, digestibility, rumen fermentation, and enteric methane emission in lactating dairy cows. The soybean sources were conventional, high-linoleic-acid variety extruded soybean meal (ESBM; 8.7% ether extract with 15% oleic and 54% linoleic acids); extruded Plenish (DuPont Pioneer, Johnston, IA), high-oleic-acid variety soybean meal (EPSBM; 8.4% ether extract with 73% oleic and 8% linoleic acids); and whole, heated Plenish soybeans (WPSB; 20.2% ether extract). The study involved 15 Holstein cows in a replicated 3 × 3 Latin square design experiment with three 28-d periods. The inclusion rate of the soybean sources in the diet was (dry matter basis) 17.1, 17.1, and 7.4% for ESBM, EPSBM, and WPSB, respectively, which resulted in ether extract concentration of the diets of 3.99, 3.94, and 4.18%, respectively. Compared with ESBM, the Plenish diets tended to increase dry matter intake and decreased feed efficiency (but had no effect on energy-corrected milk feed efficiency). The Plenish diets increased milk fat concentration on average by 5.6% and tended to increase milk fat yield, compared with ESBM. The WPSB diet tended to increased milk true protein compared with the extruded soybean meal diets. Treatments had no effect on rumen fermentation and enteric methane or carbon dioxide emissions, except pH was higher for WPSB versus EPSBM. The Plenish diets decreased the prevalence of Ruminococcus and increased that of Eubacterium and Treponema in whole ruminal contents. Total-tract apparent digestibility of organic matter and crude protein were decreased by WPSB compared with ESBM and EPSBM. Compared with the other treatments, urinary N excretion was increased by EPSBM and fecal N excretion was greater for WPSB. Treatments had marked effects on milk fatty acid profile. Generally, the Plenish diets increased mono-unsaturated (mostly cis-9 18:1) and decreased polyunsaturated, total trans-, and conjugated linoleic fatty acids concentrations in milk fat. In this study, compared with conventional, high-linoleic-acid variety extruded soybean meal, the Plenish soybean diets increased milk fat concentration and tended to increase fat yield, decreased feed efficiency, and modified milk fatty acid profile in a manner expected from the greater concentration of oleic acid in Plenish soybean oil.

Chain Elongation with Reactor Microbiomes: Open-Culture Biotechnology To Produce Biochemicals

Chain elongation into medium-chain carboxylates, such as n-caproate and n-caprylate, with ethanol as an electron donor and with open cultures of microbial consortia (i.e., reactor microbiomes) under anaerobic conditions is being developed as a biotechnological production platform. The goal is to use the high thermodynamic efficiency of anaerobic fermentation to convert organic biomass or organic wastes into valuable biochemicals that can be extracted. Several liter-scale studies have been completed and a first pilot-plant study is underway. However, the underlying microbial pathways are not always well understood. In addition, an interdisciplinary approach with knowledge from fields ranging from microbiology and chemical separations to biochemistry and environmental engineering is required. To bring together research from different fields, we reviewed the literature starting with the microbiology and ending with the bioprocess engineering studies that already have been performed. Because understanding the microbial pathways is so important to predict and steer performance, we delved into a stoichiometric and thermodynamic model that sheds light on the effect of substrate ratios and environmental conditions on product formation. Finally, we ended with an outlook.

Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle

The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a 1-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5 and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P < 0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P < 0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.

Biochemical and genetic diversity of carbohydrate-fermenting and obligate amino acid-fermenting hyper-ammonia-producing bacteria from Nellore steers fed tropical forages and supplemented with casein

Background

Dietary protein plays a major role in ruminant nutrition, and protein supplementation is a widespread practice among farmers in the tropics. Ruminal bacteria are the main agents of dietary protein and amino acid degradation, yet few studies have focused on the isolation and characterization of hyper-ammonia-producing bacteria in animals fed tropical diets or supplemented with rumen-degradable proteins. This work investigated the bacterial community diversity of the rumen of Nellore steers fed tropical forages, with or without casein supplementation. We also isolated and characterized ruminal bacteria showing high levels of ammonia production.

Results

Polymerase chain reaction–denaturing gradient gel electrophoresis analysis indicated no differences in the ruminal bacterial community composition between the control and supplemented animals. Amino acid-fermenting bacteria (n = 250) were isolated from crossbred Nellore steers fed Tifton 85 (Cynodon sp.) using trypticase as the sole carbon and organic nitrogen source in the enrichment and isolation media. The deamination rates in isolates obtained from steers supplemented with casein showed a higher incidence of deamination rates >350 nmol NH₃ mg protein⁻¹ min⁻¹ (P < 0.05), whereas isolates obtained from steers without supplementation showed deamination rates <200 nmol NH₃ mg protein⁻¹ min⁻¹. Although most isolates (84%) could ferment carbohydrates, none could hydrolyze proteins or use urea to sustain growth. All isolates were sensitive to lasalocid and monensin (1 μmol l⁻¹), and similarity analysis of the 16S rRNA sequences indicated a predominance of bacteria from the order Clostridiales, with variable homology (73–99%) to known bacterial species.

Conclusions

These results expand what is known about the biochemical and genetic diversity of hyper-ammonia-producing bacteria, and emphasize the role of carbohydrate-fermenting bacteria in ammonia production in the rumen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0369-9) contains supplementary material, which is available to authorized users.

Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.

The effect of essential oils of Zataria multiflora and Mentha spicata on the in vitro rumen fermentation, and growth and deaminative activity of amino acid-fermenting bacteria isolated from Mehraban sheep

Gas (CO2 and CH4) and ammonia production in the rumen represent major sources of lost carbon and nitrogen, respectively. The essential oils of some plants have been shown to decrease gas and ammonia production by selectively inhibiting rumen microbes. Particularly, those of Zataria multiflora (ZEO; thymol 21%, carvacrol 32%) and Mentha spicata (SEO; carvone 55%) were evaluated in vitro as ruminant-feed additives. The experiments employed mixed rumen microbes and a hyper-ammonia-producing bacterium (HAP) isolated from the rumen of a Mehraban sheep. Both ZEO and SEO decreased in vitro fibre digestibility and also gas production by mixed rumen microbes that were fermenting a typical growing-lamb diet. ZEO decreased ammonia concentration in mixed culture of rumen microbes, but SEO exerted the opposite effect. A bacterial isolate (MT8) was obtained from the rumen of a Mehraban sheep, and the 16S rRNA gene sequence indicated that it was most closely related to Clostridium bifermentans. Isolate MT8 exhibited rapid ammonia production when peptides were the growth substrate, which indicated that MT8 was a HAP. Both oils inhibited the growth and ammonia production of isolate MT8. However, ZEO decreased ammonia production at lower doses, and to a greater degree, than did SEO. These results indicated that both essential oils could potentially be used to modulate rumen fermentation. The detrimental effects on fibre digestion could be problematic in high-forage diets, and this requires further investigation. Isolate MT8 is the first described HAP from the Mehraban sheep rumen. Results on ammonia production by isolate MT8 and mixed rumen microbes indicate differential mode of action of each oil on this parameter.

Board-invited review: Rumen microbiology: leading the way in microbial ecology

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.

Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid

The objective of this experiment, part of a larger study, was to investigate changes in rumen bacterial, archaeal, and fungal diversity in cows fed medium-chain saturated fatty acids. In the main study, 6 lactating dairy cows were dosed intraruminally with 240 g/(cow · d) of stearic (SA, control), lauric (LA), or myristic (MA) acid in a replicated 3 × 3 Latin square design trial. Experimental periods were 28 d, and cows were transfaunated between periods. Lauric acid decreased protozoal counts in the rumen by 96% compared with SA and MA (compared with SA, MA had no effect on ruminal protozoa). Whole ruminal contents samples were collected 2, 4, 6, 8, 10, 14, 18, and 24 h after the morning feeding on d 23 of each experimental period, stored frozen, and later composited by cow and period for microbial profile analyses, which involved tag-encoded flexible (FLX) amplicon pyrosequencing to provide diversity analyses of gastrointestinal bacterial, archaeal, and fungal populations of the cattle. The LA treatment, either directly or through its effect on protozoa, had a profound effect on the microbial ecology of the rumen. Ruminal populations of Prevotella, Bacteroides, and Enterorhabdus were decreased (P = 0.04 to P < 0.001) by more than 2-fold in LA treatments compared with SA, and Clostridium populations were decreased (P = 0.01) in LA- compared with MA-treated cows. The proportion of Ruminococcus was not affected by treatment, although the LA treatment had the least proportion of Ruminococcus. Proportions of Eubacterium, Butyrivibrio, Olsenella, and Lactobacillus genera were increased (P = 0.03 to 0.01) by LA compared with MA or SA. The LA treatment, possibly through its effect on protozoa physically associated with archaea, resulted in an increase (P = 0.01) in the archaeal methanogenic genus Methanosphaera and a decrease (P = 0.01) in Methanobrevibacter. Few changes in fungal populations caused by treatment were detected. Collectively, results indicate that LA, either through antiprotozoal or direct antimicrobial effects, altered bacterial and archaeal populations in the rumen of dairy cows, but effects on fungal populations were not clear.