Tartrate fermentation with H2 production by a new member of Sporomusaceae enriched from rice paddy soil.

In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.

Inhalation of diesel exhaust particulate matter accelerates weight gain via regulation of hypothalamic appetite-related genes and gut microbiota metabolism.

Mice exposed to diesel exhaust particulate matter (DEPM) exhibited accelerated weight gain. Several hypothalamic genes, hormones (serum Hypothalamic-Pituitary-Adrenal (HPA) axis hormones and gastrointestinal peptide tyrosine tyrosine (PYY)), metabolites (intrahepatic triglyceride (IHTG) and fecal short-chain fatty acids (SCFAs)), and gut microbiota structure, which may influence obesity and appetite regulation, were examined. The result suggested that DEPM-induced accelerated weight gain may be associated with increased expression of hypothalamic Gamma-aminobutyric acid (GABA) type B receptor, tight junction protein, and orexin receptors, in addition with decreased IHTG and repressed HPA axis. Moreover, changes in the structure of intestinal microbiota are also related to weight changes, especially for phylum Firmicutes, genus Lactobacillus, and the ratio of relative abundance of Firmicutes and Bacteroidetes (F/B). DEPM exposure also caused widespread increase in the levels of intestinal SCFAs, the concentrations of propionic acid and isobutyric acid were associated with weight gain rate and the abundance of some bacteria. Although DEPM exposure caused changes in expression of hypothalamic serotonin, NPY, and melanocortin receptors, they were not associated with weight changes. Furthermore, no significant difference in gastrointestinal PYY and expression of hypothalamic receptors for leptin, insulin, and glucagon-like peptide 1 receptors was observed between DEPM-exposed and control mice.

The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia.

Cells are unceasingly confronted by oxidative stresses that oxidize proteins on their cysteines. The thioredoxin (Trx) system, which is a ubiquitous system for thiol and protein repair, is composed of a thioredoxin (TrxA) and a thioredoxin reductase (TrxB). TrxAs reduce disulfide bonds of oxidized proteins and are then usually recycled by a single pleiotropic NAD(P)H-dependent TrxB (NTR). In this work, we first analyzed the composition of Trx systems across Bacteria. Most bacteria have only one NTR, but organisms in some Phyla have several TrxBs. In Firmicutes, multiple TrxBs are observed only in Clostridia, with another peculiarity being the existence of ferredoxin-dependent TrxBs. We used Clostridioides difficile, a pathogenic sporulating anaerobic Firmicutes, as a model to investigate the biological relevance of TrxB multiplicity. Three TrxAs and three TrxBs are present in the 630Δerm strain. We showed that two systems are involved in the response to infection-related stresses, allowing the survival of vegetative cells exposed to oxygen, inflammation-related molecules and bile salts. A fourth TrxB copy present in some strains also contributes to the stress-response arsenal. One of the conserved stress-response Trx system was found to be present both in vegetative cells and in the spores and is under a dual transcriptional control by vegetative cell and sporulation sigma factors. This Trx system contributes to spore survival to hypochlorite and ensure proper germination in the presence of oxygen. Finally, we found that the third Trx system contributes to sporulation through the recycling of the glycine-reductase, a Stickland pathway enzyme that allows the consumption of glycine and contributes to sporulation. Altogether, we showed that Trx systems are produced under the control of various regulatory signals and respond to different regulatory networks. The multiplicity of Trx systems and the diversity of TrxBs most likely meet specific needs of Clostridia in adaptation to strong stress exposure, sporulation and Stickland pathways.

Metabolism of novel potential syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats.

Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH4. In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics. In addition to the reported SAOB classified in the genera Tepidanaerobacter, Desulfotomaculum, and Thermodesulfovibrio, we identified a number of potential SAOB that are affiliated with Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. The potential SAOB possessing the glycine-mediated acetate oxidation pathway dominates SAOB communities. Moreover, formate appeared to be the main product of the acetate degradation by the most active potential SAOB. We identified the methanogen partner of these potential SAOB in the acetate-fed chemostat as Methanosarcina thermophila. The dominated potential SAOB in each chemostat had similar metabolic characteristics, even though they were in different fatty-acid-fed chemostats. These novel syntrophic lineages are prevalent and may play critical roles in thermophilic methanogenic reactors. This study expands our understanding of the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders and presents novel insights into how they interact with methanogens.IMPORTANCECombining reactor operation with omics provides insights into novel uncultured syntrophic acetate degraders and how they perform in thermophilic anaerobic digesters. This improves our understanding of syntrophic acetate degradation and contributes to the background knowledge necessary to better control and optimize anaerobic digestion processes.

Genetic tools for the electrotroph Sporomusa ovata and autotrophic biosynthesis.

Sporomusa ovata is a Gram-negative acetogen of the Sporomusaceae family with a unique physiology. This anerobic bacterium is a core microbial catalyst for advanced CO2-based biotechnologies including gas fermentation, microbial electrosynthesis, and hybrid photosystem. Until now, no genetic tools exist for S. ovata, which is a critical obstacle to its optimization as an autotrophic chassis and the acquisition of knowledge about its metabolic capacities. Here, we developed an electroporation protocol for S. ovata. With this procedure, it became possible to introduce replicative plasmids such as pJIR751 and its derivatives into the acetogen. This system was then employed to demonstrate the feasibility of heterologous expression by introducing a functional ß-glucuronidase enzyme under the promoters of different strengths in S. ovata. Next, a recombinant S. ovata strain producing the non-native product acetone both from an organic carbon substrate and from CO2 was constructed. Finally, a replicative plasmid capable of integrating itself on the chromosome of the acetogen was developed as a tool for genome editing, and gene deletion was demonstrated. These results indicate that S. ovata can be engineered and provides a first-generation genetic toolbox for the optimization of this biotechnological workhorse.IMPORTANCES. ovata harbors unique features that make it outperform most microbes for autotrophic biotechnologies such as a capacity to acquire electrons from different solid donors, a low H2 threshold, and efficient energy conservation mechanisms. The development of the first-generation genetic instruments described in this study is a key step toward understanding the molecular mechanisms involved in these outstanding metabolic and physiological characteristics. In addition, these tools enable the construction of recombinant S. ovata strains that can synthesize a wider range of products in an efficient manner.

Advancing the fitness of gut commensal bacteria.

Nutrient starvation of beneficial bacteria helps them colonize the human gut.

Monitoring of a microbial community during bioaugmentation with hydrogenotrophic methanogens to improve methane yield of an anaerobic digestion process.

Methane production by microbial fermentation of municipal waste is a challenge for better yield processes. This work describes the characterization of a hydrogenotrophic methanogen microbial community used in a bioaugmentation procedure to improve the methane yield in a thermophilic anaerobic process, digesting the organic fraction of municipal solid waste. The performance of the bioaugmentation was assessed in terms of methane production and changes in the microbial community structure. The results showed that bioaugmentation slightly improved the cumulative methane yield (+ 4%) in comparison to the control, and its use led to an acceleration of the methanogenesis stage. We observed associated significant changes in the relative abundance of taxa and their interactions, using high throughput DNA sequencing of V3-16S rRNA gene libraries, where the abundance of the archaeal hydrogenotrophic genus Methanoculleus (class Methanomicrobia, phylum Euryarchaeota) and the bacterial order MBA08 (class Clostridia, phylum Firmicutes) were dominant. The relevant predicted metabolic pathways agreed with substrate degradation and the anaerobic methanogenic process. The purpose of the study was to evaluate the effect of the addition of hydrogenotrophic methanogens in the generation of methane, while treating organic waste through anaerobic digestion.

Fermentation of resistant starch from the starch-ferulic acid inclusion complex compared with high-amylose corn starch.

Fermentation of resistant starch from the starch-ferulic acid inclusion complex, one representative of the starch-polyphenol inclusion complex, was investigated in this study. It was found that this complex-based resistant starch, high-amylose corn starch and the mixture of ferulic acid and high-amylose corn starch were mainly utilized at the initial 6 h as indicated by the gas production and pH. Besides, the supplement of high-amylose corn starch, the mixture and the complex promoted production of short-chain fatty acids (SCFAs), reduced the ratio of Firmicutes/Bacteroidetes (F/B) and selectively stimulated the proliferation of some beneficial bacteria. Specifically, the production of SCFAs in the control and high-amylose starch, mixture and complex groups was 29.33 mM, 140.82 mM, 144.12 mM, and 167.4 mM after fermentation for 48 h, respectively. Moreover, the F/B ratio of those groups was 1.78, 0.78, 0.8 and 0.69, respectively. These results suggested that the supplement of the complex-based resistant starch led to the most SCFAs and the lowest F/B ratio (P < 0.05). Moreover, the complex group had the largest abundance of beneficial bacteria, including Bacteroides, Bifidobacterium and Lachnospiraceae_UCG-001 (P < 0.05). In summary, the resistant starch from the starch-ferulic acid inclusion complex exhibited stronger prebiotic activity than high-amylose corn starch and the mixture.

Serotonin Transporter (SERT) Expression Modulates the Composition of the Western-Diet-Induced Microbiota in Aged Female Mice.

Background. The serotonin transporter (SERT), highly expressed in the gut and brain, is implicated in metabolic processes. A genetic variant of the upstream regulatory region of the SLC6A4 gene encoding SERT, the so-called short (s) allele, in comparison with the long (l) allele, results in the decreased function of this transporter, altered serotonergic regulation, an increased risk of psychiatric pathology and type-2 diabetes and obesity, especially in older women. Aged female mice with the complete (Sert-/-: KO) or partial (Sert+/-: HET) loss of SERT exhibit more pronounced negative effects following their exposure to a Western diet in comparison to wild-type (Sert+/+: WT) animals. Aims. We hypothesized that these effects might be mediated by an altered gut microbiota, which has been shown to influence serotonin metabolism. We performed V4 16S rRNA sequencing of the gut microbiota in 12-month-old WT, KO and HET female mice that were housed on a control or Western diet for three weeks. Results. The relative abundance of 11 genera was increased, and the abundance of 6 genera was decreased in the Western-diet-housed mice compared to the controls. There were correlations between the abundance of Streptococcus and Ruminococcaceae_UCG-014 and the expression of the pro-inflammatory marker Toll-like-Receptor 4 (Tlr4) in the dorsal raphe, as well as the expression of the mitochondrial activity marker perixome-proliferator-activated-receptor-cofactor-1b (Ppargc1b) in the prefrontal cortex. Although there was no significant impact of genotype on the microbiota in animals fed with the Control diet, there were significant interactions between diet and genotype. Following FDR correction, the Western diet increased the relative abundance of Intestinimonas and Atopostipes in the KO animals, which was not observed in the other groups. Erysipelatoclostridium abundance was increased by the Western diet in the WT group but not in HET or KO animals. Conclusions. The enhanced effects of a challenge with a Western diet in SERT-deficient mice include the altered representation of several gut genera, such as Intestinimonas, Atopostipes and Erysipelatoclostridium, which are also implicated in serotonergic and lipid metabolism. The manipulation of these genera may prove useful in individuals with the short SERT allele.

Leucine-Restricted Diet Ameliorates Obesity-Linked Cognitive Deficits: Involvement of the Microbiota-Gut-Brain Axis.

Leucine restriction (LR) improves insulin resistance and promotes white adipose tissue browning. However, the effect of LR on obesity-associated cognitive impairment remains unclear. The present study found that an 8-week LR dramatically improved high-fat diet (HFD)-induced cognitive decline by preventing synaptic dysfunction, increasing the expressions of neurotrophic factors, and inhibiting neuroinflammation in memory-related brain regions. Moreover, LR notably reshaped the structure of gut microbiota, which was manifested by downregulating the Firmicutes/Bacteroidetes ratio, reducing the relative abundance of inflammation-related bacteria including Acetatifactor, Helicobacter, Mucispirillum, and Oscillibacter but increasing short-chain fatty acid (SCFA)-producing bacterial genera including Alistipes, Allobaculum, Odoribacter, and Olsenella. Notably, HFD-caused SCFA reduction, gut barrier damage, and LPS leakage were recovered by LR. Our findings suggested that LR could serve as an effective approach to attenuate obesity-induced cognitive deficits, which may be achieved by balancing gut microbiota homeostasis and enhancing SCFA production.

Integrated genome-centric metagenomic and metaproteomic analyses unravel the responses of the microbial community to ammonia stress.

Ammonia is a major inhibitor in anaerobic digestion of nitrogen-rich organic wastes. In this study, integrated genome-centric metagenomic and metaproteomic analyses were used to identify the key microorganisms and metabolic links causing instability by characterizing the process performance, microbial community, and metabolic responses of key microorganisms during endogenous ammonia accumulation. The identification of 89 metagenome-assembled genomes and analysis of their abundance profile in different operational phases permitted the identification of key taxa (Firmicutes and Proteobacteria) causing poor performance. Metabolic reconstruction indicated that the key taxa had the genetic potential to participate in the metabolism of C2C5 volatile fatty acids (VFAs). Further investigation suggested that during Phase I, the total ammonia nitrogen (TAN) level was maintained below 2000 mg N/L, and the reactor showed a high methane yield (478.30 ± 33.35 mL/g VS) and low VFAs concentration. When the TAN accumulated to > 2000 mg N/L, acid accumulation, mainly of acetate, began to occur, and the methane yield gradually decreased to 330.44 mL/g VS (Phase II). During this phase, the VFA degradation functions of the community were mainly mediated by Firmicutes. Approximately 61.54% of significant differentially expressed proteins (DEPs) related to acetate metabolism in Firmicutes were down-regulated, which led to an increase in acetate concentration to 4897.91 ± 1558.96 mg/L. However, the reactor performance showed spontaneous recovery without any interference (Phase III), during which Firmicutes gradually adapted to the high ammonia conditions. Approximately 75% of the significant DEPs related to acetate metabolism of Proteobacteria were also up-regulated in Phase III compared with Phase II; thus, VFA-related metabolic functions of the community were enhanced, which resulted in a decrease in the total VFA concentration to 195.39 mg/L. When the TAN increased above 4000 mg N/L, the system gradually showed acid accumulation dominated by propionate, accompanied by a second decrease in methane yield (Phase IV). During this phase, the number of up-regulated and down-regulated proteins related to acetate metabolism of Firmicutes and butyrate/valerate metabolism of Proteobacteria was comparable with that of Phase III, indicating that the metabolic functions related to acetate, butyrate, and valerate of the microbial community were not significantly affected. However, for propionate metabolism, the expression activity of fumarate hydratase from Firmicutes and Proteobacteria was severely inhibited by ammonia, as shown by down-regulation ratios of 63.64% and 85.71%, respectively. No protein with the same function that was not inhibited by ammonia could be detected, and the fumarate degradation function of the microbial community was severely damaged, leading to blocked propionate metabolism and irreversible deterioration of reactor performance. This study has provided a new perspective on the microecological mechanisms of ammonia inhibition.

Impact of High-Fiber or High-Protein Diet on the Capacity of Human Gut Microbiota To Produce Tryptophan Catabolites.

This study investigated the effect of high-fiber-low-protein (HF) and high-protein-low-fiber (HP) diets on microbial catabolism of tryptophan in the proximal colon (PC) and distal colon(DC) compartments of the Simulator of the Human Intestinal Microbial Ecosystem. The microbiota in PC and DC was dominated by Bacteroidetes and Firmicutes, in which Bacteroidetes were more abundant in DC (∼60% versus 50%) and Firmicutes were more abundant in PC (∼40% versus 25%). Most of the tryptophan catabolites were determined at a higher concentration in PC samples than in DC samples, but the overall concentration of tryptophan catabolites was over 10-fold higher in DC samples than that in PC samples. Interestingly, indole-3-propionic acid and oxindole were only identified in DC samples. A two-week dietary intervention by the HF diet enriched the abundance of Firmicutes in PC, whereas the HP diet enriched the abundance of Proteobacteria. Compared to the HP diet, the HF diet favored the microbial production of indole-3-acetic acid, indole-3-lactic acid, indole-3-aldehyde, and indole-3-propionic acid in both PC and DC compartments. To conclude, these findings increase the understanding of the effect of diets on the microbial production of tryptophan catabolites in the colon.

Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale.

Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.

Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil.

The effect of dietary lead on the intestinal microbiome has not been fully elucidated. To determine if there was an association between microflora modulation, predicted functional genes, and Pb exposure, mice were provided diets amended with increasing concentrations of a single lead compound, lead acetate, or a well characterized complex reference soil containing lead, i.e. 6.25-25 mg/kg Pb acetate (PbOAc) or 7.5-30 mg/kg Pb in reference soil SRM 2710a having 0.552 % Pb among other heavy metals such as Cd. Feces and ceca were collected following 9 days of treatment and the microbiome analyzed by 16 S rRNA gene sequencing. Treatment effects on the microbiome were observed in both feces and ceca of mice. Changes in the cecal microbiomes of mice fed Pb as Pb acetate or as a constituent in SRM 2710a were statistically different except for a few exceptions regardless of dietary source. This was accompanied by increased average abundance of functional genes associated with metal resistance, including those related to siderophore synthesis and arsenic and/or mercury detoxification. Akkermansia, a common gut bacterium, was the highest ranked species in control microbiomes whereas Lactobacillus ranked highest in treated mice. Firmicutes/Bacteroidetes ratios in the ceca of SRM 2710a treated mice increased more than with PbOAc, suggestive of changes in gut microbiome metabolism that promotes obesity. Predicted functional gene average abundance related to carbohydrate, lipid, and/or fatty acid biosynthesis and degradation were greater in the cecal microbiome of SRM 2710a treated mice. Bacilli/Clostridia increased in the ceca of PbOAc treated mice and may be indicative of increased risk of host sepsis. Family Deferribacteraceae also was modulated by PbOAc or SRM 2710a possibly impacting inflammatory response. Understanding the relationship between microbiome composition, predicted functional genes, and Pb concentration, especially in soil, may provide new insights into the utility of various remediation methodologies that minimize dysbiosis and modulate health effects, thus assisting in the selection of an optimal treatment for contaminated sites.

Refactoring and Heterologous Expression of Class III Lanthipeptide Biosynthetic Gene Clusters Lead to the Discovery of N,N-Dimethylated Lantibiotics from Firmicutes.

Class III lanthipeptides are an emerging subclass of lanthipeptides, representing an underexplored trove of new natural products with potentially broad chemical diversity and important biological activity. Bioinformatic analysis of class III lanthipeptide biosynthetic gene cluster (BGC) distribution has revealed their high abundance in the phylum Firmicutes. Many of these clusters also feature methyltransferase (MT) genes, which likely encode uncommon class III lanthipeptides. However, two hurdles, silent BGCs and low-yielding pathways, have hindered the discovery of class III lanthipeptides from Firmicutes. Here, we report the design and construction of a biosynthetic pathway refactoring and heterologous overexpression strategy which seeks to overcome these hurdles, simultaneously activating and increasing the production of these Firmicutes class III lanthipeptides. Applying our strategy to MT-containing BGCs, we report the discovery of new class III lanthipeptides from Firmicutes bearing rare N,N-dimethylations. We reveal the importance of the first two amino acids in the N-terminus of the core peptide in controlling the MT dimethylation activity. Leveraging this feature, we engineer class III lanthipeptides to enable N,N-dimethylation, resulting in significantly increased antibacterial activity. Furthermore, the refactoring and heterologous overexpression strategy showcased in this study is potentially applicable to other ribosomally synthesized and post-translationally modified peptide BGCs from Firmicutes, unlocking the genetic potential of Firmicutes for producing peptide natural products.

Changes in the bacterial community colonizing extracted and non-extracted tannin-rich plants in the rumen of dromedary camels.

Leguminous trees and saltbushes provide potential alternatives to conventional feeds to overcome feed deficiency in arid and semi-arid countries. However, these plants are rich in antinutritional factors that have adverse effects on rumen microbiota and the host- animal. Some rumen microbiota detoxifies plants' secondary metabolites; thus, understanding plant-microbe interaction in the rumen could improve the plants' utilization. This study investigated the bacterial colonization and degradation of non-extracted and extracted tanniniferous plants: Atriplex halimus, Acacia saligna, and Leucaena leucocephala, in the rumen of three fistulated camels at 6 and 12 hours. The results showed that these plants have high nutritional value and tannins contents. The rumen degradation and microbial diversity of plant-attached bacteria varied according to plant type and phenols' extraction. Atriplex and leucaena showed higher microbial diversity at 6 and 12h, respectively. Bacteroidetes and Firmicutes were the main bacterial phyla, and the main genera were Prevotella, RC9_gut_group, Butyrivibrio that overrepresented in non-extracted plants (P<0.05). Fibrobacteres and Anaerovibrio showed sensitivity to plant toxins and Ruminococcus attached to plants with lower tannins. Several bacterial genera in the camel rumen have the potential to resist antinutritional factors in fodder plants, which could be used to improve the performance of grazing animals.

Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes.

A variety of electron transfer mechanisms link bacterial cytosolic electron pools with functionally diverse redox activities in the cell envelope and extracellular space. In Listeria monocytogenes, the ApbE-like enzyme FmnB catalyzes extracytosolic protein flavinylation, covalently linking a flavin cofactor to proteins that transfer electrons to extracellular acceptors. L. monocytogenes uses an energy-coupling factor (ECF) transporter complex that contains distinct substrate-binding, transmembrane, ATPase A, and ATPase A' subunits (RibU, EcfT, EcfA, and EcfA') to import environmental flavins, but the basis of extracytosolic flavin trafficking for FmnB flavinylation remains poorly defined. In this study, we show that the EetB and FmnA proteins are related to ECF transporter substrate-binding and transmembrane subunits, respectively, and are essential for exporting flavins from the cytosol for flavinylation. Comparisons of the flavin import versus export capabilities of L. monocytogenes strains lacking different ECF transporter subunits demonstrate a strict directionality of substrate-binding subunit transport but partial functional redundancy of transmembrane and ATPase subunits. Based on these results, we propose that ECF transporter complexes with different subunit compositions execute directional flavin import/export through a broadly conserved mechanism. Finally, we present genomic context analyses that show that related ECF exporter genes are distributed across members of the phylum Firmicutes and frequently colocalize with genes encoding flavinylated extracytosolic proteins. These findings clarify the basis of ECF transporter export and extracytosolic flavin cofactor trafficking in Firmicutes. IMPORTANCE Bacteria import vitamins and other essential compounds from their surroundings but also traffic related compounds from the cytosol to the cell envelope where they serve various functions. Studying the foodborne pathogen Listeria monocytogenes, we find that the modular use of subunits from a prominent class of bacterial transporters enables the import of environmental vitamin B2 cofactors and the extracytosolic trafficking of a vitamin B2-derived cofactor that facilitates redox reactions in the cell envelope. These studies clarify the basis of bidirectional small-molecule transport across the cytoplasmic membrane and the assembly of redox-active proteins within the cell envelope and extracellular space.

Ameliorating Effects of Vitamin K2 on Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice.

Ulcerative colitis (UC) is a chronic recurrent inflammatory illness of the gastrointestinal system. The purpose of this study was to explore the alleviating effect of vitamin K2 (VK2) on UC, as well as its mechanism. C57BL/6J mice were given 3% DSS for seven days to establish UC, and they then received VK2 (15, 30, or 60 mg/kg·bw) and 5-aminosalicylic acid (100 mg/kg·bw) for two weeks. We recorded the clinical signs, body weights, colon lengths, and histological changes during the experiment. We detected the inflammatory factor expressions using enzyme-linked immunosorbent assay (ELISA) kits, and we detected the tight junction proteins using Western blotting. We analyzed the intestinal microbiota alterations and short-chain fatty acids (SCFAs) using 16S rRNA sequencing and targeted metabolomics. According to the results, VK2 restored the colon lengths, improved the colonic histopathology, reduced the levels of proinflammatory cytokines (such as IL-1ß, TNF-α, and IL-6), and boosted the level of the immunosuppressive cytokine IL-10 in the colon tissues of the colitis mice. Moreover, VK2 promoted the expression of mucin and tight junction proteins (such as occludin and zonula occludens-1) in order to preserve the intestinal mucosal barrier function and prevent UC in mice. Additionally, after the VK2 intervention, the SCFAs and SCFA-producing genera, such as Eubacterium_ruminantium_group and Faecalibaculum, were elevated in the colon. In conclusion, VK2 alleviated the DSS-induced colitis in the mice, perhaps by boosting the dominant intestinal microflora, such as Faecalibaculum, by reducing intestinal microflora dysbiosis, and by modulating the expression of SCFAs, inflammatory factors, and intestinal barrier proteins.

Carbon Reduction and Pollutant Abatement by a Bio-Ecological Combined Process for Rural Sewage.

In order to explore the treatment effect of a bio-ecological combined process on pollution reduction and carbon abatement of rural domestic wastewater under seasonal changes, the rural area of Lingui District, Guilin City, Guangxi Province, China was selected to construct a combined process of regulating a pond, biological filter, subsurface flow constructed wetland, and ecological purification pond. The influent water, effluent water, and the characteristics of pollutant treatment in each unit were investigated. The results showed that the average removal rates of COD, TN, and NH3-N in summer were 87.57, 72.18, and 80.98%, respectively, while they were 77.46, 57.52, and 64.48% in winter. There were significant seasonal differences in wastewater treatment results in Guilin. Meanwhile, in view of the low carbon:nitrogen ratio in the influent and the poor decontamination effect, the method of adding additional carbon sources such as sludge fermentation and rice straw is proposed to strengthen resource utilization and achieve carbon reduction and emission reduction. The treatment effect of ecological units, especially constructed wetland units, had a high contribution rate of TN treatment, but it was greatly impacted by seasons. The analysis of the relative abundance of the microbial community at the phylum level in constructed wetlands revealed that Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetota, and Actinobacteria were the dominant phyla. The relative abundance of microbial communities of Proteobacteria, Chloroflexi, and Acidobacteria decreased to a large extent from summer to winter, while Firmicutes, Bacteroidetes, and Planctomycetota increased to varying degrees. These dominant bacteria played an important role in the degradation of pollutants such as COD, NH3-N, and TN in wetland systems.

Microbial communities that drive the degradation of flax pectin and hemicellulose during dew retting with Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 addition.

In this study, the combined addition of Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 to flax degradation increased the degradation rates of pectin (74.7 %) and pectinic acid (59.3 %) and increased the maximum activities of pectinase (610.66 ± 7.03 U/mL) and mannanase (656.97 ± 13.16 U/mL). 16S rRNA sequencing showed that the added bacterial agent (Bacillus) was the dominant bacterium, and its addition increased the relative abundance (RA) of Firmicutes and decreased the RA of Bacteroidetes. The core bacterial community linked to degradation (Firmicutes) was determined by RDA. Network analysis showed that the number of bacteria related to pectin and hemicellulose degradation increased with the addition of the bacteria combination. SEM analysis showed that Bacillus was positively correlated with the degradation of pectic substances. These results provide new ideas for improving the utilization of agricultural waste resources and promoting sustainable development in modern agriculture.