ATP formation associated with fumarate and nitrate reduction in growing cultures of Veillonella alcalescens

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate

Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.

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.

Fumarate and nitrite reduction by Prevotella nigrescens and Prevotella buccae isolated from Chronic Periodontitis patients

OBJECTIVE

This study is an investigation of anaerobic nitrite and fumarate reduction/respiration abilities of two characterised Prevotella species namely Prevotella nigrescens (SS6B) and Prevotella buccae (GS6B) isolated from the periodontal pockets of chronic periodontitis (ChP) patients.

METHODS

Isolation and identification of the periodontal bacteria from 20 patients showing clinical symptoms of ChP. Characterisation of anaerobic nitrite and fumarate reduction was done in P. nigrescens (SS6B) and P. buccae (GS6B) using reduction assays, inhibition assays with use of specific inhibitors, growth assays and enzyme activity assays. Degenerate PCR was used to detect and amplify nitrite reductase (nrfA) and fumarate reductase (frdA) gene sequences in these Prevotella isolates. In addition, molecular and in silico analysis of the amplified anaerobic reductase gene sequences was performed using NCBI conserved domain analysis, Interpro database and MegaX.

RESULTS

We provided experimental evidence for presence of active nitrite and fumarate reductase activities through enzyme activity, reduction, inhibitor and growth assays. Moreover, we were able to detect presence of 505 bps nrfA gene fragment and 400 bps frdA gene fragment in these Prevotella spp. These fragments show similarity to multiheme ammonia forming cytochrome c nitrite reductases and fumarate reductases flavoprotein subunit, respectively.

CONCLUSION

Anaerobic nitrite and fumarate respiration abilities in P. nigrescens and P. buccae isolates appear to be important for detoxification process and growth, respectively.

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine

Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.

Palm oil protects α-linolenic acid from rumen biohydrogenation and muscle oxidation in cashmere goat kids

Background

In ruminants, dietary C18:3n-3 can be lost through biohydrogenation in the rumen; and C18:3n-3 that by-passes the rumen still can be lost through oxidation in muscle, theoretically reducing the deposition of C18:3n-3, the substrate for synthesis of poly-unsaturated fatty acids (n-3 LCPUFA) in muscle. In vitro studies have shown that rumen hydrogenation of C18:3n-3 is reduced by supplementation with palm oil (rich in cis-9 C18:1). In addition, in hepatocytes, studies with neonatal rats have shown that cis-9 C18:1 inhibits the oxidation of C18:3n-3. It therefore seems likely that palm oil could reduce both rumen biohydrogenation of C18:3n-3 and muscle oxidation of C18:3n-3. The present experiment tested whether the addition of palm oil to a linseed oil supplement for goat kids would prevent the losses of C18:3n-3 and thus improve the FA composition in two muscles, Longissimus dorsi and Biceps femoris. To investigate the processes involved, we studied the rumen bacterial communities and measured the mRNA expression of genes related to lipid metabolism in Longissimus dorsi. Sixty 4-month-old castrated male Albas white cashmere kids were randomly allocated among three dietary treatments. All three diets contained the same ingredients in the same proportions, but differed in their fat additives: palm oil (PMO), linseed oil (LSO) or mixed oil (MIX; 2 parts linseed oil plus 1 part palm oil on a weight basis).

Results

Compared with the LSO diet, the MIX diet decreased the relative abuandance of Pseudobutyrivibrio, a bacterial species that is positively related to the proportional loss rate of dietary C18:3n-3 and that has been reported to generate the ATP required for biohydrogenation (reflecting a decrease in the abundance of rumen bacteria that hydrogenate C18:3n-3 in MIX kids). In muscle, the MIX diet increased concentrations of C18:3n-3, C20:5n-3, C22:6n-3, and n-3 LCPUFA, and thus decreased the n-6/n-3 ratio; decreased the mRNA expression of CPT1β (a gene associated with fatty acid oxidation) and increased the mRNA expression of FADS1 and FADS2 (genes associated with n-3 LCPUFA synthesis), compared with the LSO diet. Interestingly, compared to Longissimus dorsi, Biceps femoris had greater concentrations of PUFA, greater ratios of unsaturated fatty acids/saturated fatty acids (U/S), and poly-unsaturated fatty acids/saturated fatty acids (P/S), but a lesser concentration of saturated fatty acids (SFA).

Conclusions

In cashmere goat kids, a combination of linseed and palm oils in the diet increases the muscle concentration of n-3 LCPUFA, apparently by decreasing the relative abundance of rumen bacteria that are positively related to the proportional loss rate of dietary C18:3n-3, by inhibiting mRNA expression of genes related to C18:3n-3 oxidation in muscle, and by up-regulating mRNA expression of genes related to n-3 LCPUFA synthesis in muscle, especially in Longissimus dorsi.

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids1

This study investigated the effects of dietary supplementation with alternative sources of α-linolenic acid on growth, the composition of rumen microbiota, and the interactions between rumen microbiota and long-chain fatty acid (FA) concentrations, in goat kids. Sixty 4-month-old castrated male Albas white cashmere kids (average BW 18.6 ± 0.1 kg) were randomly allocated among three dietary treatments: (i) basal diet without supplementation (Control), (ii) basal diet supplemented with linseed oil (LSO), (iii) basal diet supplemented with heated linseed grain (HLS). The concentrate:forage ratio was 5:5 and the LSO and HLS treatments provided the kids with similar dietary FA profiles. The diets were fed for 104 d, consisting of 14 d for adaptation followed by 90 d of experimental observation. Treatment did not significantly influence BW, DMI, or bacterial richness or diversity. On the other hand, the relative abundance of bacteria participating in hydrogenation differed significantly among the three groups: the Veillonellaceae and Christensenellaceae were more abundant in LSO kids, Prevotellaceae were more abundant in HLS kids, and the Fibrobacteriaceae were more abundant in Control kids (P < 0.05). Spearman correlation analysis indicated that Ruminobacter, Selenomonas_1, Fretibacterium, Prevotellaceae_UCG-001, Succinimonas, and Ruminococcaceae_NK4A214_group were the genera that participated in hydrogenation of long-chain FAs. HLS-fed kids had a lower relative abundance of Ruminobacter, but a higher abundance of Prevotellaceae_UCG-001 and Fretibacterium than LSO-fed kids. These changes were associated with greater rumen concentrations of C18:3n3 and n-3 PUFA, but lower concentrations of n-6 PUFA and lower n-6/n-3 ratios, in HLS than in LSO-fed kids. In conclusion, feeding kids with HLS increased rumen concentrations of C18:3n3 and n-3 PUFA, but decreased the n-6/n-3 ratio by decreasing the abundance of bacteria that hydrogenate C18:3n3 and increasing the abundance of bacteria that hydrogenate C18:2n6.

Citric acid wastewater as electron donor for biological sulfate reduction

Citrate-containing wastewater is used as electron donor for sulfate reduction in a biological treatment plant for the removal of sulfate. The pathway of citrate conversion coupled to sulfate reduction and the microorganisms involved were investigated. Citrate was not a direct electron donor for the sulfate-reducing bacteria. Instead, citrate was fermented to mainly acetate and formate. These fermentation products served as electron donors for the sulfate-reducing bacteria. Sulfate reduction activities of the reactor biomass with acetate and formate were sufficiently high to explain the sulfate reduction rates that are required for the process. Two citrate-fermenting bacteria were isolated. Strain R210 was closest related to Trichococcus pasteurii (99.5% ribosomal RNA (rRNA) gene sequence similarity). The closest relative of strain S101 was Veillonella montepellierensis with an rRNA gene sequence similarity of 96.7%. Both strains had a complementary substrate range.

Comparison of Batch Culture Growth and Fermentation of a PoultryVeillonellaIsolate and SelectedVeillonellaSpecies Grown in a Defined Medium

The objective of this study was to develop a defined medium for quantitating nutritional requirements and fermentation products of a poultry cecal isolate of Veillonella and to compare these parameters with representative Veillonella species. The poultry isolate is one of 29 organisms from a continuous-flow culture that has been shown to be effective against Salmonella colonization in broilers. When the Veillonella species were grown in anaerobic batch culture, propionate and acetate were the only volatile fatty acids detected. Lactate was needed to provide energy for the growth of the Veillonella in the defined medium. The poultry isolate had significantly (p< 0.05) higher Y(lactate)(g of dry cell weight per mole of lactate utilized) and dry cell weight than the other Veillonella species when grown on amino acid supplemented defined media. Cultures of the Veillonella species in the defined medium grown with supplemented amino acids aspartate, threonine, arginine, and serine indicated that these amino acids were metabolized to acetate and propionate. Amino acid analysis on media inoculated with either V. atypica or the poultry isolate also indicated that these organisms may have different amino acid preferences. For nearly all of the amino acid supplemented media combinations the poultry isolate utilized significantly (p< 0.05) more threonine and serine whereas V. atypica utilized significantly (p< 0.05) more aspartate. The defined medium supported growth of all of the Veillonella species tested and should enable further in-depth physiological studies to be conducted on the poultry Veillonella studies.

Anaerobic growth of Salmonella typhimurium on L(+)- and D(-)-tartrate involves an oxaloacetate decarboxylase Na+ pump

We show here that the Enterobacterium Salmonella typhimurium LT2 has the capacity to grow anaerobically on L(+)- or D(-)-tartrate as sole carbon and energy source. Growth on these substrates was Na(+)-dependent and involved the L(+)- or D(-)-tartrate-inducible expression of oxaloacetate decarboxylase. The induced decarboxylase was closely related to the oxaloacetate decarboxylase Na+ pump of Klebsiella pneumoniae as shown by the sensitivity towards avidin, the location in the cytoplasmic membrane, activation by Na+ ions, and Western blot analysis with antiserum raised against the K. pneumoniae oxaloacetate decarboxylase. Participation of an oxaloacetate decarboxylase Na+ pump in L(+)-tartrate degradation by S. typhimurium is in accord with results from DNA analyses. The deduced protein sequence of the open reading frame identified upstream of the recently sequenced oxaloacetate decarboxylase genes is clearly homologous with the beta-subunit of L-tartrate dehydratase from Escherichia coli. Southern blot analysis with S. typhimurium chromosomal DNA indicated the presence of probably more than one gene for oxaloacetate decarboxylase.

Growth yield increase and ATP formation linked to succinate decarboxylation in Veillonella parvula

Veillonella parvula strain 259 (= DSM 2007) was able to grow on a mineral salts medium supplemented with (per litre) 1 g yeast extract, 1 g Tween-80, and 3 mg putrescine.2 HCl, with 6 mM thioglycolate as reductant and lactate as growth substrate. Succinate did not serve as a growth substrate, but when added in conjunction with lactate, it was decarboxylated to propionate and resulted in a measurable increase in growth yield, corresponding to the formation of 2.4 g cell dry mass per mol succinate. A growth yield increase linked to succinate metabolism occurred only while lactate was also being metabolised. Experiments with cell suspensions showed that succinate decarboxylating activity was constitutive. Addition of succinate produced clear increases in cellular ATP levels in ATP-depleted washed cells.

Fermentation of L-tartrate by a newly isolated gram-negative glycolytic bacterium

Enrichments on L-tartrate from a freshwater lake sediment yielded a pure culture of anaerobic bacterium designated strain 16Lt1. The rod-shaped organism was motile, did not form spores, and had a gram-negative wall structure. No cytochromes were detected. The mol % G + C of the DNA was 58. The new strain was microaerotolerant, and grew optimally at 30 degrees C and neutral pH in freshwater medium. A wide range of carbohydrates was fermented, with formate, acetate, ethanol, lactate and succinate being the end-products detected. L-tartrate and citrate were fermented to formate, acetate and CO2. L-tartrate was fermented by the dehydratase pathway, and glucose by the Embden-Meyerhof-Parnas pathway. Fumarate was reduced, but nitrate, sulfate, sulfur and thiosulfate were not used as terminal electron acceptors. Glucose metabolism was constitutive, whereas L-tartrate-degrading activity was inducible. When glucose and L-tartrate were both present as substrates, growth was diauxic with glucose being metabolized first. The growth rate and growth yield were higher on glucose than on L-tartrate. Strain 16Lt1 has been deposited with the Deutsche Sammlung von Mikroorganismen as 'Bacteroides' sp. DSM6268.

Sodium ion transport decarboxylases and other aspects of sodium ion cycling in bacteria

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L-serine enhances the anaerobic lactate metabolism of Veillonella dispar ATCC 17745

Under anaerobic conditions, the rate of metabolism of lactate by starved resting cells of Veillonella dispar ATCC 17745 was very low. Because pyruvate was metabolized well by the starved cells, oxidation of lactate to pyruvate, which is the first step of the lactate metabolism, must have been limited in the cells. In the starved cells, the levels of the metabolic intermediates, oxalacetate or fumarate, of which reductions to malate or to succinate could be coupled with lactate oxidation to pyruvate and initiate lactate metabolism, were quite low, suggesting that these had been reduced during the starvation steps under strictly anaerobic conditions. Thus, the starved cells were unable to start the anaerobic lactate metabolism because of shortage of such reducible substrates. L-serine greatly enhanced anaerobic lactate metabolism of the starved cells. This enhancement may have been due to metabolism of L-serine itself and conversion to oxalacetate and fumarate, which made it possible to begin lactate oxidation.

Production and degradation of formate by Veillonella dispar ATCC 17745

Under strictly anaerobic conditions, the resting cells of V. dispar ATCC 17745 produced formate as well as acetate and propionate from pyruvate or from lactate. Pyruvate formate-lyase activity was found when the activity was assayed under strictly anaerobic conditions. Under aerobic conditions, however, the resting cells did not produce formate from pyruvate or from lactate, though the cells actively metabolized pyruvate or lactate (mainly to acetate). This was ascribed to pyruvate formate-lyase activity being easily lost when the cell-free extract was exposed to the air. A part of the produced formate was further degraded to CO2 by the resting cells.

Competition for L-lactate betweenDesulfovibrio, Veillonella, andAcetobacterium species isolated from anaerobic intertidal sediments

Almost equal numbers ofDesulfovibrio, Veillonella, andAcetobacterium species were found in agar shake dilutions of anaerobic intertidal brackish sediments applying L-lactate as the only energy source and sulfate as electron acceptor. Pure cultures of these bacteria were studied in more detail in batch cultures as well as in L-lactate-limited chemostats. The maximal specific growth rates on L-lactate were determined in washout experiments and amounted to 0.16, 0.30, and 0.06 h(-1) forDesulfovibrio baculatus H.L21,Veillonella alcalescens NS.L49, andAcetobacterium NS.L40, respectively. Competition for L-lactate was studied in energy-limited chemostats at a dilution rate of 0.02 h(-1).D. baculatus H.L21 turned out to be the best competitor at low L-lactate concentrations provided that sufficient sulfate and iron were present.V. alcalescens NS.L49 was favored by the absence of sulfate and iron. Coexistence ofD. baculatus H.L21 andV. alcalescens NS.L49 was observed in a L-lactate-limited chemostat with additional sulfate and citrate. Syntrophic growth ofV. alcalescens NS.L49 andAcetobacterium NS.L40 occurred in a L-lactate-limited chemostat in the absence of sulfate. No coexistence betweenD. baculatus H.L21 andAcetobacterium NS.L40 was observed in a L-lactate-limited chemostat without sulfate. Addition of calcium-saturated illite to an energy-limited mixed culture ofV. alcalescens NS.L49 andAcetobacterium NS.L40 induced iron limitation and subsequent washout of theAcetobacterium species. Finally, the ecological niches of the 3 species in relation to the consumption of lactate were discussed.

Purification and characterization of a new sodium-transport decarboxylase. Methylmalonyl-CoA decarboxylase from Veillonella alcalescens

Upon resolution of the particulate cell fraction of Veillonella alcalescens by gel chromatography, membranes and ribosomes were clearly resolved. Methylmalonyl-CoA decarboxylase was bound to the membranes and not to ribosomes as reported earlier. Membrane vesicles containing methylmalonyl-CoA decarboxylase were prepared by disrupting V. alcalescens cells with a French pressure chamber. About 64% of the decarboxylase was oriented in these vesicles with the substrate binding site facing to the outside. The vesicles performed a rapid accumulation of Na+ ions in response to the decarboxylation of methylmalonyl-CoA. Decarboxylation and transport were highly uncoupled. The efficiency of the transport was considerably increased if methylmalonyl-CoA decarboxylation was retarded by using a low temperature or by slowly generating the substrate enzymically from propionyl-CoA. Under optimized conditions Na+ was concentrated inside the inverted vesicles eight-times higher than in the incubation medium. Methylmalonyl-CoA decarboxylase was solubilized from the membranes with Triton X-100 and purified about 20-fold by affinity chromatography on monomeric avidin-Sepharose columns. The decarboxylase was specifically activated by Na+ ions (apparent Km approximately equal to 0.6 mM). Whereas (S)-methylmalonyl-CoA was the superior substrate (apparent Km approximately equal to 7 microM), malonyl-CoA was also decarboxylated (apparent Km approximately equal to 35 microM). The decarboxylation of methylmalonyl-CoA yielded CO2 and not HCO-3 as the primary reaction product. Analysis of the purified enzyme by dodecylsulfate gel electrophoresis indicated the presence of four different polypeptides alpha, beta, gamma, delta with Mr 60 000, 33 000, 18 5000 and 14 000. The latter of these polypeptides was clearly visible only after silver staining but not after staining with Coomassie brilliant blue. A low molecular weight polypeptide with similar staining properties was also found in oxaloacetate decarboxylase. Methylmalonyl-CoA decarboxylase contained about 1 mol covalently bound biotin per 125 500 g protein which was localized exclusively in the gamma-subunit. This subunit therefore represents the biotin carboxyl carrier protein of methylmalonyl-CoA decarboxylase. A new very sensitive method for the detection of biotin-containing proteins is described.

Fumarate reduction and product formation by the Reiter strain of Treponema phagedenis

The catabolic pathways for butyrate, acetate, succinate, and ethanol formation by the Reiter strain of Treponema phagedenis were investigated. Enzyme activities were demonstrated for glucose catabolism to pyruvate by the Embden-Meyerhof-Parnas pathway. Butyrate formation from acetyl-coenzyme A (acetyl-CoA) does not generate ATP by substrate level phosphorylation and involves NAD+-dependent 3-hydroxybutyryl-CoA dehydrogenase and NAD(P)+-independent butyryl-CoA dehydrogenase activities. Butyrate is formed from butyryl-CoA in a CoA transphorase reaction. Phosphate acetyltransferase and acetate kinase activities convert acetyl-CoA to acetate. An NADP+-dependent alcohol dehydrogenase participates in ethanol formation; however, the manner in which acetyl-CoA is reduced to acetaldehyde is unclear. A membrane-associated fumarate reductase was found which utilized reduced ferredoxin or flavin nucleotides as physiological electron donors. Additional electron carriers may also be involved in electron transfer for fumarate reduction. Strains of Treponema denticola, T. vincentii, and T. minutum utilized fumarate without succinate formation, whereas strains of T. phagedenis and T. refringens formed succinate from exogenously supplied fumarate.