Hydrogen as an energy source for the human pathogen Bilophila wadsworthia

Research progress on the correlation between gut microbiota and preeclampsia: microbiome changes, mechanisms and treatments

Preeclampsia is a specific disease during pregnancy and is a significant factor in the increased mortality in perinatal women. Gut microbiota, an intricate and abundant microbial community in the digestive tract, is crucial for host metabolism, immunity, and nutrient absorption. The onset and progression of preeclampsia are closely correlated with the changes in maternal gut microbiota. Research purpose was to compile the existing bits of present scientific data and to close the gap in the knowledge of changes in gut microbiota in preeclampsia and their association with preeclampsia. We searched studies from two electronic databases (PubMed and Web of Science) included from 2014 to 2023. This review is divided into three parts. In the first part, the author elaborates longitudinal differences of maternal gut microbiota during different gestation periods. In the second part, we discuss that gut microbiota can lead to the occurrence of preeclampsia by systemic immune response, influencing the release of active peptides, short-chain fatty acids, trimethylamine-N-oxide (TMAO) and other metabolites, vascular factors and Microorganism-immune axis. In the third part, we proposed that a high-fiber diet combined with drugs and microecological regulators may be therapeutic in enhancing or preventing the emergence and evolution of preeclampsia, which needs further exploration. Although the pathogenesis of preeclampsia is still nebulous and there is no clear and valid clinical treatment, our study provides new ideas for the pathogenesis, prevention and treatment of preeclampsia.

The causal role of intestinal microbiome in development of pre-eclampsia

The correlation of pre-eclampsia (PE) and intestinal microbiome has been widely demonstrated in existing research, whereas their causal relationship has been rarely explored. The causal relationship between intestinal microbiome and PE risk was examined using large-scale genome-wide association studies (GWAS) summary statistics. To be specific, the causal microbial taxa for PE were identified using the two-sample Mendelian randomization (MR) method. The results were verified to be robust through comprehensive sensitive analyses, and the independence of causal relationship was ensured through novel multivariable MR analyses. The possibility of reverse relationships was ruled out through reverse-direction MR analyses. Lastly, the biofunction was explored through enrichment analysis, and a series of validations of PE results in a second GWAS were performed to confirm the results. After correction, four microbial taxa, including Streptococcus genus for PE (FDR q = 0.085), Olsenella genus for PE (FDR q = 0.085), Enterobacteriales order for PE (FDR q = 0.0134), and Akkermansia genus for PE (FDR q = 0.015), had a causal relationship to diverse joint PE (FDR q < 0.15). Moreover, when three different methods were employed on basis of the nominal significance (P < 0.05), five suggestive microbial taxa took on significance. The effect of heterogeneity and horizontal pleiotropy was excluded through sensitive analysis, and the possibility of horizontal pleiotropy of BMI was ruled out through multivariable MR analysis. The protective mechanism of the identified taxa against PE was illustrated through GO enrichment analysis and KEGG pathways. A number of microbial taxa had a causal relationship to PE. The result of this study provides more insights into intestinal microbiome in the pathology of PE.

Concentration-dependent effects of nickel doping on activated carbon biocathodes

In microbial electrosynthesis (MES), microorganisms grow on a cathode electrode as biofilm, or in the catholyte as planktonic biomass, and utilize CO2 for their growth and metabolism. Modification of the...

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

Background

Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H₂S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves the glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethanesulfonate) into acetaldehyde and sulfite.

Results

We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis.

Conclusions

We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H₂S production in the human gut.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02386-w.

Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.

NMN Maintains Intestinal Homeostasis by Regulating the Gut Microbiota

The aim of this study was to determine the effects of long-term Nicotinamide mononucleotide (NMN) treatment on modulating gut microbiota diversity and composition, as well as its association with intestinal barrier function. In this study, C57BL/6J mice were fed different concentrations of NMN, and their feces were collected for detection of 16S rDNA and non-targeted metabolites to explore the effects of NMN on intestinal microbiota and metabolites. The results revealed that NMN increased the abundance of butyric acid-producing bacteria (Ruminococcae_UCG-014 and Prevotellaceae_NK3B31_group) and other probiotics (Akkermansia muciniphila), while the abundance of several harmful bacteria (Bilophila and Oscillibacter) were decreased after NMN treatment. Meanwhile, the level of bile acid-related metabolites in feces from the G1 group (0.1 mg/ml) was significantly increased compared to the control group, including cholic acid, taurodeoxycholic acid, taurocholic acid, glycocholic acid, and tauro-β-muricholic acid. In addition, long-term NMN treatment affected the permeability of the intestinal mucosa. The number of goblet cells and mucus thickness increased, as well as expression of tight junction protein. These results demonstrate that NMN reduced intestinal mucosal permeability and exerts a protective effect on the intestinal tract. This study lays the foundation for exploring NMN's utility in clinical research.

Glycyl Radical Enzymes and Sulfonate Metabolism in the Microbiome

Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O₂-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H₂S, a process linked to certain chronic diseases and conditions.

Impact of dietary sulfolipid-derived sulfoquinovose on gut microbiota composition and inflammatory status of colitis-prone interleukin-10-deficient mice

The interplay between diet, intestinal microbiota and host is a major factor impacting health. A diet rich in unsaturated fatty acids has been reported to stimulate the growth of Bilophila wadsworthia by increasing the proportion of the sulfonated bile acid taurocholate (TC). The taurine-induced overgrowth of B. wadsworthia promoted the development of colitis in interleukin-10-deficient (IL-10^-/-) mice. This study aimed to investigate whether intake of the sulfonates sulfoquinovosyl diacylglycerols (SQDG) with a dietary supplement or their degradation product sulfoquinovose (SQ), stimulate the growth of B. wadsworthia in a similar manner and, thereby, cause intestinal inflammation. Conventional IL-10^-/- mice were fed a diet supplemented with the SQDG-rich cyanobacterium Arthrospira platensis (Spirulina). SQ or TC were orally applied to conventional IL-10^-/- mice and gnotobiotic IL-10^-/- mice harboring a simplified human intestinal microbiota with or without B. wadsworthia. Analyses of inflammatory parameters revealed that none of the sulfonates induced severe colitis, but both, Spirulina and TC, induced expression of pro-inflammatory cytokines in cecal mucosa. Cell numbers of B. wadsworthia decreased almost two orders of magnitude by Spirulina feeding but slightly increased in gnotobiotic SQ and conventional TC mice. Changes in microbiota composition were observed in feces as a result of Spirulina or TC feeding in conventional mice. In conclusion, the dietary sulfonates SQDG and their metabolite SQ did not elicit bacteria-induced intestinal inflammation in IL-10^-/- mice and, thus, do not promote colitis.

Interindividual Differences in Human In Vitro Intestinal Microbial Conversion of Green Tea (‐)‐Epigallocatechin‐3‐ O ‐Gallate and Consequences for Activation of Nrf2 Mediated Gene Expression

Scope

An in vitro faecal incubation model combined with reporter gene assay based testing strategy is developed to characterize interindividual differences in the gut microbial conversion of (‐)‐epigallocatechin‐3‐O‐gallate (EGCG) and its consequences for potential activation of Nrf2‐mediated gene expression.

Method & Results

Anaerobic human faecal incubations are performed to characterize the microbial metabolism of EGCG including interindividual variability. EGCG derived intestinal microbial metabolite patterns show substantial interindividual differences that are correlated to relative microbial abundances determined by 16S rRNA sequencing. Results obtained show the time‐dependent formation of gallic acid, pyrogallol, phenylpropane‐2‐ols, phenyl‐γ‐valerolactones, and 5‐(3′,5′‐dihydroxyphenyl)valeric acid as the major metabolites, with substantial interindividual differences. The activity of the formed metabolites in the activation of EpRE‐mediated gene expression is tested by EpRE‐LUX reporter gene assay. In contrast to EGCG, at low micromolar concentrations, especially gallic acid, pyrogallol, and catechol induce significant activity in the EpRE‐LUX assay.

Conclusions

Given these results and taking the level of formation into account, it is concluded that especially gallic acid and pyrogallol contribute to the EpRE‐mediated beneficial effects of EGCG. The interindividual differences in the formation may result in interindividual differences in the beneficial effects of EGCG and green tea consumption.

Comparison of the gut microbiota of short-term and long-term medical workers and non-medical controls: a cross-sectional analysis

OBJECTIVES

The hospital environment has been implicated in the enrichment and exchange of pathogens and antibiotic resistance, but its potential in shaping the symbiotic microbial community of hospital staff is unclear. This study was designed to evaluate the alteration of the gut microbiome in medical workers compared to non-medical controls.

METHODS

A prospective cross-sectional cohort study was conducted in the intensive care unit (ICU) and other departments of a centre in north-eastern China. Faecal samples of 175 healthy medical workers-short-term (1-3 months) workers (n = 80) and long-term (>1 year) workers (n = 95)-and 80 healthy non-medical controls were analysed using 16S rRNA amplicon sequencing. The hospital environmental samples (n = 9) were also analysed.

RESULTS

The gut microbiomes of medical workers exhibited marked deviations in diversity and alteration in microbial composition and function. Short-term workers showed significantly higher abundances of taxa such as Lactobacillus, Butyrivibrio, Clostridiaceae, Clostridium, Ruminococcus, Dialister, Bifidobacterium, Odoribacter, and Desulfovibrio and lower abundances of Bacteroides and Blautia than the controls. Long-term workers showed higher abundances of taxa such as Dialister, Veillonella, Clostridiaceae, Clostridium, Bilophila, Desulfovibrio, Pseudomonas, and Akkermansia and lower abundances of Bacteroides and Coprococcus than the controls. The medical workers' department (ICU versus non-ICU) and position (resident doctor versus nursing staff) also impacted their gut microbiome. Compared with the non-ICU workers, workers in the ICU showed a significant increase in the abundances of Dialister, Enterobacteriaceae, Phascolarctobacterium, Pseudomonas, Veillonella, and Streptococcus and a marked depletion of Faecalibacterium, Blautia, and Coprococcus. In contrast with the nursing staff, the resident doctors showed a significant increase in Erysipelotrichaceae and Clostridium and a decrease in Bacteroides, Blautia, and Ruminococcus in the gut microbiome. Moreover, we found that the microbiota of hospital environments potentially correlated with the workers' gut microbiota.

CONCLUSIONS

Our findings demonstrated structural changes in the gut microbial community of medical workers.

Multiplexed Quantitative Assessment of the Fate of Taurine and Sulfoquinovose in the Intestinal Microbiome

(1) Introduction: Sulfonates, which can be diet- or host-derived, are a class of compounds detected in the gut, are involved in host-microbiome interactions and have several health effects. Our aim was to develop a method to quantify five of the sulfonates in the intestine and apply it in a simplified human microbiome model. These were taurine, its metabolic precursor cysteate and one of its degradation products isethionate, as well as sulfoquinovose and one of its most relevant degradation products 2,3-dihydroxy-1-propanesulfonate. (2) Methods: An extraction and sample preparation method was developed, without the need for derivatization. To detect and quantify the extracted sulfonates, a multiplexed LC-MS/MS-MRM method was established. (3) Results: The accuracy and precision of the method were within GLP-accepted parameters (www.ema.europa.eu). To apply this method in a pilot study, we spiked either taurine or sulfoquinovose into an in vitro simplified human microbiota model with and without Bilophila wadsworthia, a known sulfonate utilizer. The results revealed that only the culture with B. wadsworthia was able to degrade taurine, with isethionate as an intermediate. After spiking the communities with sulfoquinovose, the results revealed that the simplified human microbiome model was able to degrade sulfoquinovose to 2,3-dihydroxypropane-1-sulfonate, which was probably catalyzed by Escherichia coli. In the community with B. wadsworthia, the 2,3-dihydroxypropane-1-sulfonate produced was further degraded by B. wadsworthia to sulfide. (4) Conclusions: We successfully developed a method for sulfonate quantification and applied it in a first pilot study.

Effects of Low and High FODMAP Diets on Human Gastrointestinal Microbiota Composition in Adults with Intestinal Diseases: A Systematic Review

A diet high in non-digestible carbohydrates is known to promote health, in part through its effect on the gut microbiome. While substantially proven for healthy individuals, these effects are more ambiguous in subjects with intestinal diseases. At the same time, a diet low in these fermentable carbohydrates, the low FODMAP (acronym for Fermentable Oligo-, Di-, Mono-saccharides, And Polyols) diet, is gaining popularity as a treatment option for symptom relief in irritable bowel syndrome and inflammatory bowel disease. There are, however, several indications that this diet induces effects opposite to those of prebiotic supplementation, resulting in gut microbiome changes that might be detrimental. Here, we provide a systematic review of the effects of low and high FODMAP diets on human gastrointestinal microbiota composition in adults with intestinal diseases, through literature screening using the databases PubMed, Embase, and Web of Science. We summarize study findings on dietary impact in patients, including the effect on bacterial taxa and diversity. In general, similar to healthy subjects, restricting non-digestible carbohydrate intake in patients with intestinal diseases has opposite effects compared to prebiotic supplementation, causing a reduction in bifidobacteria and an increase in bacteria associated with dysbiosis. Future studies should focus on assessing whether the induced microbial changes persist over time and have adverse effects on long-term colonic health.

Review article: FODMAPS, prebiotics and gut health-the FODMAP hypothesis revisited

BACKGROUND

Restriction of dietary FODMAP intake can alleviate symptoms in patients with irritable bowel syndrome. Because many FODMAPs have prebiotic actions, there is concern that their dietary restriction leads to dysbiosis with health consequences, and their intake is being encouraged by addition to foods and via supplements.

AIMS

To examine the hazards and benefits of high and low FODMAP intake.

METHODS

Current literature was reviewed and alternative hypotheses formulated.

RESULTS

Low FODMAP intake reduces abundance of faecal Bifidobacteria without known adverse outcomes and has no effect on diversity, but the reduction in bacterial density may potentially be beneficial to gut health. Supplementary prebiotics can markedly elevate the intake of FODMAPs over levels consumed in the background diet. While this increases the abundance of Bifidobacteria, it adversely affects gut health in animal studies by inducing colonic mucosal barrier dysfunction, mucosal inflammation and visceral hypersensitivity. Rapid colonic fermentation is central to the identified mechanisms that include injury from high luminal concentrations of short-chain fatty acids and low pH, and inflammatory effects of increased endotoxin load and glycation of macromolecules. Whether these observations translate into humans requires further study. Opposing hypotheses are presented whereby excessive intake of FODMAPs might have health benefits via prebiotic effects, but might also be injurious and contribute to the apparent increase in functional intestinal disorders.

CONCLUSIONS

Reduced FODMAP intake has few deleterious effects on gut microbiota. Consequences (both positive and negative) of excessive carbohydrate fermentation in the human intestines from elevated FODMAP intake require more attention.

Changes to the gut microbiota in mice induced by infection with Toxoplasma gondii

Toxoplasma gondii (T. gondii) is a common parasite worldwide, which can cause encephalitis, enteritis and miscarriage in abortion women. This study examined the cecal microbiome of mice infected with T. gondii through analysis of 16S rRNA genes determined by Illumina sequencing. BALB/c mice were orally infected with sporulated T. gondii oocysts. Mice were killed after 13-days- and 21-days- post infection, respectively, then their cecal contents were extracted and examined to determine the composition of gut microflora by illumina sequencing of the V3 +V4 region of the 16S rRNA genes. Our results showed the alterations in the gut microbes of BALB/c mice infected with T. gondii infection, where we observed a significant shift in the relative abundance of cecal bacteria. In mice at 13 days post-infection, the relative abundance of Proteobacteria increased, along with that of harmful bacteria, such as Bilopha and Desulfovibrio. However, the abundance of Lactobacillus decreased. At 21 days post-infection, the abundance of Lactobacillus was more than that observed for the uninfected control, with harmful bacteria, such as Bilopha and Desulfovibrio being reduced. The mice at 21-days post-infection had more beneficial intestinal bacteria than the control group. Our results suggested that the gut microbiota play an important role in disease progression from acute infection to chronic infection.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

Early-Onset Preeclampsia Is Associated With Gut Microbial Alterations in Antepartum and Postpartum Women

Background: Imbalances in gut microbiota composition are linked to hypertension, host metabolic abnormalities, systemic inflammation, and other conditions. In the present study, we examined the changes of gut microbiota in women with early-onset preeclampsia (PE) and in normotensive, uncomplicated pregnant women during late pregnancy and at 1 and 6 weeks postpartum.

Methods: Gut microbiota profiles of women with PE and healthy pregnant women in the third trimester and at 1 and 6 weeks postpartum were assessed by 16S rRNA gene amplicon sequencing. Plasma levels of interleukin-6 (IL-6), intestinal fatty acid-binding protein (I-FABP), zonulin, and lipopolysaccharide (LPS) were measured in the third trimesters.

Results: At the genus level, 8 bacterial genera were significantly enriched in the antepartum samples of PE patients compared to healthy controls, of which Blautia, Ruminococcus2, Bilophila, and Fusobacterium represented the major variances in PE microbiomes. Conversely, 5 genera, including Faecalibacterium, Gemmiger, Akkermansia, Dialister, and Methanobrevibacter, were significantly depleted in antepartum PE samples. Maternal blood pressure and liver enzyme levels were positively correlated to the PE-enriched genera such as Anaerococcus, Ruminococcus2, Oribacterium, and Bilophila, while the fetal features (e.g., Apgar score and newborn birth weight) were positively correlated with PE-depleted genera and negatively correlated with PE-enriched genera. Moreover, maternal blood IL-6 level was positively associated with gut Bilophila and Oribacterium, whereas LPS level was negatively associated with Akkermansia. In terms of postpartum women, both the gut microbial composition and the PE-associated microbial alterations were highly consistent with those of the antepartum women.

Conclusion: PE diagnosed in the third trimester of pregnancy is associated with a disrupted gut microbiota composition compared with uncomplicated pregnant women, which are associated with maternal clinical features (blood pressure level and liver dysfunction) and newborn birth weight. Moreover, these antepartum alterations in gut microbiota persisted 6 weeks postpartum.

Role of Nickel in Microbial Pathogenesis

Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.

A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia

This paper describes a pathway for anaerobic bacterial metabolism of taurine (2-aminoethanesulfonate), an abundant substrate in the human intestinal microbiota, by the intestinal bacterium and opportunistic pathogen, Bilophila wadsworthia. This metabolism converts taurine to the toxic metabolite hydrogen sulfide (H₂S), an activity associated with inflammatory bowel disease and colorectal cancer. A critical enzyme in this pathway is isethionate sulfite-lyase, a member of the glycyl radical enzyme family. This enzyme catalyzes a novel, radical-based C-S bond-cleavage reaction to convert isethionate (2-hydroxyethanesulfonate) to sulfite and acetaldehyde. This discovery improves our understanding of H₂S production in the human body and may also offer new approaches for controlling intestinal H₂S production and B. wadsworthia infections.

Hydrogen sulfide (H₂S) production in the intestinal microbiota has many contributions to human health and disease. An important source of H₂S in the human gut is anaerobic respiration of sulfite released from the abundant dietary and host-derived organic sulfonate substrate in the gut, taurine (2-aminoethanesulfonate). However, the enzymes that allow intestinal bacteria to access sulfite from taurine have not yet been identified. Here we decipher the complete taurine desulfonation pathway in Bilophila wadsworthia 3.1.6 using differential proteomics, in vitro reconstruction with heterologously produced enzymes, and identification of critical intermediates. An initial deamination of taurine to sulfoacetaldehyde by a known taurine:pyruvate aminotransferase is followed, unexpectedly, by reduction of sulfoacetaldehyde to isethionate (2-hydroxyethanesulfonate) by an NADH-dependent reductase. Isethionate is then cleaved to sulfite and acetaldehyde by a previously uncharacterized glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslA). The acetaldehyde produced is oxidized to acetyl-CoA by a dehydrogenase, and the sulfite is reduced to H₂S by dissimilatory sulfite reductase. This unique GRE is also found in Desulfovibrio desulfuricans DSM642 and Desulfovibrio alaskensis G20, which use isethionate but not taurine; corresponding knockout mutants of D. alaskensis G20 did not grow with isethionate as the terminal electron acceptor. In conclusion, the novel radical-based C-S bond-cleavage reaction catalyzed by IslA diversifies the known repertoire of GRE superfamily enzymes and enables the energy metabolism of B. wadsworthia. This GRE is widely distributed in gut bacterial genomes and may represent a novel target for control of intestinal H₂S production.

Profiling of Protein Degraders in Cultures of Human Gut Microbiota

Unabsorbed proteins reach the colon and are fermented by the microbiota, yielding a variety of harmful metabolites. In the present study, a 16S rRNA gene survey identified the bacterial taxa flourishing in 11 batch fermentations with proteins and peptones as the sole fermentable substrates, inoculated with the feces of six healthy adults. Organic acids, ammonia, and indole resulting from protein breakdown and fermentation accumulated in all of the cultures. Analysis of differential abundances among time-points identified Enterobacteriaceae, Burkholderiaceae, and Desulfovibrionaceae (including Esherichia-Shigella, Sutterella, Parasutterella, and Bilophila) among the bacteria that especially in the cultures with low inoculation load. Lachnospiraceae and Ruminococcaceae also encompassed many taxa that significantly expanded, mainly in cultures inoculated with high inoculation load, and showed the strongest correlation with the production of ammonium, indole, and p-cresol. Anaerotruncus, Dorea, Oscillibacter, Eubacterium oxidoreducens, Lachnoclostridium, Paeniclostridium, and Rombutsia were among them. Other Firmicutes (e.g., Roseburia, Ruminococcus, Lachnospira, Dialister, Erysipelotrichaceae, and Streptococcaceae) and many Bacteroidetes (e.g., Barnesiellaceae, Prevotellaceae, and Rickenelliaceae) decreased. Sequences attributed to Bacteroides, unresolved at the level of species, presented opposite contributions, resulting in no significant changes in the genus. This study sheds light on the multitude of bacterial taxa putatively participating in protein catabolism in the colon. Protein fermentation was confirmed as unfavorable to health, due to both the production of toxic metabolites and the blooming of opportunistic pathogens and pro-inflammatory bacteria.

Increased Abundance of Lactobacillales in the Colon of Beta-Adrenergic Receptor Knock Out Mouse Is Associated With Increased Gut Bacterial Production of Short Chain Fatty Acids and Reduced IL17 Expression in Circulating CD4+ Immune Cells

Emerging evidence suggests an associative link between gut dysbiosis, the autonomic nervous system (ANS) and the immune system in pathophysiology of neurogenic hypertension (HTN). However, the close interplay between these three systems presents us with difficulties in deciphering the cause-effect relationship in disease. The present study utilized beta 1 and 2 adrenergic receptor knock out (AdrB1^tm1BkkAdrB2^tm1Bkk/J KO) mice to isolate the effects of reduced overall sympathetic drive on gut microbiota and systemic immune system. We observed the following: (i) Diminished beta adrenergic signaling mainly reflects in shifts in the Firmicutes phyla, with a significant increase in abundance of largely beneficial Bacilli Lactobacillales in the KO mice; (ii) This was associated with increased colonic production of beneficial short chain fatty acids (SCFAs) butyrate, acetate and propionate, confirming functional microbiota shifts in the KO mice; (iii) Dampened systemic immune responses in the KO mice reflected in reduction on circulating CD4⁺.IL17⁺ T cells and increase in young neutrophils, both previously associated with shifts in the gut microbiota. Taken together, these observations demonstrate that reduced expression of beta adrenergic receptors may lead to beneficial shifts in the gut microbiota and dampened systemic immune responses. Considering the role of both in hypertension, this suggests that dietary intervention may be a viable option for manipulation of blood pressure via correcting gut dysbiosis.

Poisoning with Soman, an Organophosphorus Nerve Agent, Alters Fecal Bacterial Biota and Urine Metabolites: a Case for Novel Signatures for Asymptomatic Nerve Agent Exposure

The experimental pathophysiology of organophosphorus (OP) chemical exposure has been extensively reported. Here, we describe an altered fecal bacterial biota and urine metabolome following intoxication with soman, a lipophilic G class chemical warfare nerve agent. Nonanesthetized Sprague-Dawley male rats were subcutaneously administered soman at 0.8 (subseizurogenic) or 1.0 (seizurogenic) of the 50% lethal dose (LD₅₀) and evaluated for signs of toxicity. Animals were stratified based on seizing activity to evaluate effects of soman exposure on fecal bacterial biota and urine metabolites. Soman exposure reshaped fecal bacterial biota by altering Facklamia, Rhizobium, Bilophila, Enterobacter, and Morganella genera of the Firmicutes and Proteobacteria phyla, some of which are known to hydrolyze OP chemicals. However, analogous changes were not observed in the bacterial biota of the ileum, which remained the same irrespective of dose or seizing status of animals after soman intoxication. However, at 75 days after soman exposure, the bacterial biota stabilized and no differences were observed between groups. Interestingly, in considering just the seizing status of animals, we found that the urine metabolomes were markedly different. Leukotriene C₄, kynurenic acid, 5-hydroxyindoleacetic acid, norepinephrine, and aldosterone were excreted at much higher rates at 72 h in seizing animals, consistent with early multiorgan involvement during soman poisoning. These findings demonstrate the feasibility of using the dysbiosis of fecal bacterial biota in combination with urine metabolome alterations as forensic evidence for presymptomatic OP exposure temporally to enable administration of neuroprotective therapies of the future.IMPORTANCE The paucity of assays to determine physiologically relevant OP exposure presents an opportunity to explore the use of fecal bacteria as sentinels in combination with urine to assess changes in the exposed host. Recent advances in sequencing technologies and computational approaches have enabled researchers to survey large community-level changes of gut bacterial biota and metabolomic changes in various biospecimens. Here, we profiled changes in fecal bacterial biota and urine metabolome following a chemical warfare nerve agent exposure. The significance of this work is a proof of concept that the fecal bacterial biota and urine metabolites are two separate biospecimens rich in surrogate indicators suitable for monitoring OP exposure. The larger value of such an approach is that assays developed on the basis of these observations can be deployed in any setting with moderate clinical chemistry and microbiology capability. This can enable estimation of the affected radius as well as screening, triage, or ruling out of suspected cases of exposures in mass casualty scenarios, transportation accidents involving hazardous materials, refugee movements, humanitarian missions, and training settings when coupled to an established and validated decision tree with clinical features.

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo

Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes

Wheat bran fibers are considered beneficial to human health through their impact on gut microbiota composition and activity. Here, we assessed the prebiotic potential of selected bran fractions by performing a series of fecal slurry anaerobic fermentation experiments using aleurone as well as total, ultrafine, and soluble wheat bran (swb) as carbon sources. By combining amplicon-based community profiling with a fluorescent in situ hybridization (FISH) approach, we found that incubation conditions favor the growth of Proteobacteria such as Escherichia and Bilophila. These effects were countered in all but one [total wheat bran (twb)] fermentation experiments. Growth of Bifidobacterium species was stimulated after fermentation using ultrafine, soluble, and twb, in the latter two as part of a general increase in bacterial load. Both ultrafine and swb fermentation resulted in a trade-off between Bifidobacterium and Bilophila, as previously observed in human dietary supplementation studies looking at the effect of inulin-type fructans on the human gut microbiota. Aleurone selectively stimulated growth of Dorea and butyrate-producing Roseburia. All fermentation experiments induced enhanced gas production; increased butyrate concentrations were only observed following soluble bran incubation. Our results open perspectives for the development of aleurone as a complementary prebiotic selectively targeting colon butyrate producers.

Diet and microbiota linked in health and disease

Diet has shaped microbiota profiles through human evolution.

Enrichment of sulfidogenic bacteria from the human intestinal tract

Hydrogen sulfide is formed in the human intestinal tract as the end product of the anaerobic microbial degradation of sulfur compounds present in mucus, bile or proteins. Since human gut microbial sulfur metabolism has been poorly characterized, we aimed to identify and isolate the microorganisms involved in sulfide formation. Fresh fecal samples from one healthy donor and one diagnosed with irritable bowel syndrome were used as inocula for enrichments that were supplemented with sulfate or sulfite as electron acceptors in combination with different electron donors. After two transfers, cultures with high sulfide production were selected and the phylogenetic composition of the enriched microbial communities was determined. Sulfite respiration and cysteine degradation were the dominant sulfidogenic processes, and the most abundant bacteria enriched belonged to Bilophila and Clostridium cluster XIVa. Different isolates were obtained and remarkably included a novel sulfite reducer, designated strain 2C. Strain 2C belongs to the Veillonellaceae family of Firmicutes phylum and showed limited (91%) 16S rRNA gene sequence similarity with that of known Sporomusa species and hence may represent a novel genus. This study indicates that bacteria that utilize sulfite and organic sulfur compounds rather than merely sulfate are relevant for human intestinal sulfur metabolism.

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota

OBJECTIVE

Contrary to the long-standing prerequisite of inducing selective (ie, bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterisation of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (gas chromatography mass spectrometry) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and faecal metabolites profiles.

DESIGN

Faecal samples collected during a double-blind, randomised, cross-over intervention study set up to assess the effect of inulin consumption on stool frequency in healthy adults with mild constipation were analysed. Faecal microbiota composition and metabolite profiles were linked to the study's clinical outcome as well as to quality-of-life measurements recorded.

RESULTS

While faecal metabolite profiles were not significantly altered by inulin consumption, our analyses did detect a modest effect on global microbiota composition and specific inulin-induced changes in relative abundances of Anaerostipes, Bilophila and Bifidobacterium were identified. The observed decrease in Bilophila abundances following inulin consumption was associated with both softer stools and a favourable change in constipation-specific quality-of-life measures.

CONCLUSIONS

Ecosystem-wide analysis of the effect of a dietary intervention with prebiotic inulin-type fructans on the colon microbiota revealed that this effect is specifically associated with three genera, one of which (Bilophila) representing a promising novel target for mechanistic research.

TRIAL REGISTRATION NUMBER

NCT02548247.

A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice

BACKGROUND

Bilophila wadsworthia is a major member of sulfidogenic bacteria in human gut, it was originally recovered from different clinical specimens of intra-abdominal infections and recently was reported potentially linked to different chronic metabolic disorders. However, there is still insufficient understanding on its detailed function and mechanism to date.

METHODS

A B. wadsworthia strain was isolated from fresh feces of a latent autoimmune diabetes in adults patient and we investigated its pathogenicity by oral administration to specific-pathogen-free mice. Tissue samples and serum were collected after sacrifice. Stool samples were collected at different time points to profile the gut microbiota.

RESULTS

Bilophila wadsworthia infection resulted in the reduction of body weight and fat mass, apparent hepatosplenomegaly and elevated serum inflammatory factors, including serum amyloid A and interleukin-6, while without significant change of the overall gut microbiota structure.

CONCLUSIONS

These results demonstrated that higher amount of B. wadsworthia caused systemic inflammatory response in SPF mice, which adds new evidence to the pathogenicity of this bacterium and implied its potential role to the chronic inflammation related metabolic diseases like diabetes.

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent

Host mucin is the main constituent of the mucus layer that covers the gut epithelium of the host, and an important source of glycans for the bacteria colonising the intestine. Akkermansia muciniphila is a mucin-degrading bacterium, abundant in the human gut, that is able to produce acetate and propionate during this degradation process. A. muciniphila has been correlated with human health in previous studies, but a mechanistic explanation is lacking. In this study, the main site of colonisation was characterised alongside additional conditions, such as differences in colon pH, prebiotic supplementation and variable mucin supply. To overcome the limitations of in vivo studies concerning variations in mucin availability and difficult access to proximal regions of the colon, a dynamic in vitro gut model (SHIME) was used. In this model, A. muciniphila was found to colonise the distal colon compartment more abundantly than the proximal colon ((±8 log copies/ml compared to ±4 log copies/ml) and the preference for the distal compartment was found to be pH-dependent. The addition of mucin caused a specific increase of A. muciniphila (±4.5 log increase over two days), far exceeding the response of other bacteria present, together with an increase in propionate. These findings suggest that colonisation and mucin degradation by A. muciniphila is dependent on pH and the concentration of mucin. Our results revealed the preference of A. muciniphila for the distal colon environment due to its higher pH and uncovered the quick and stable response of A. muciniphila to mucin supplementation.

Energetics of pathogenic bacteria and opportunities for drug development

The emergence and spread of drug-resistant pathogens and our inability to develop new antimicrobials to overcome resistance has inspired scientists to consider new targets for drug development. Cellular bioenergetics is an area showing promise for the development of new antimicrobials, particularly in the discovery of new anti-tuberculosis drugs where several new compounds have entered clinical trials. In this review, we have examined the bioenergetics of various bacterial pathogens, highlighting the versatility of electron donor and acceptor utilisation and the modularity of electron transport chain components in bacteria. In addition to re-examining classical concepts, we explore new literature that reveals the intricacies of pathogen energetics, for example, how Salmonella enterica and Campylobacter jejuni exploit host and microbiota to derive powerful electron donors and sinks; the strategies Mycobacterium tuberculosis and Pseudomonas aeruginosa use to persist in lung tissues; and the importance of sodium energetics and electron bifurcation in the chemiosmotic anaerobe Fusobacterium nucleatum. A combination of physiological, biochemical, and pharmacological data suggests that, in addition to the clinically-approved target F1Fo-ATP synthase, NADH dehydrogenase type II, succinate dehydrogenase, hydrogenase, cytochrome bd oxidase, and menaquinone biosynthesis pathways are particularly promising next-generation drug targets. The realisation of cellular energetics as a rich target space for the development of new antimicrobials will be dependent upon gaining increased understanding of the energetic processes utilised by pathogens in host environments and the ability to design bacterial-specific inhibitors of these processes.

Host hydrogen rather than that produced by the pathogen is important for Salmonella enterica serovar Typhimurium virulence

Salmonella enterica serovar Typhimurium utilizes molecular hydrogen as a substrate in various respiratory pathways, via H2-uptake enzymes termed Hya, Hyb, and Hyd. A different hydrogenase, the hydrogen-evolving Hyc enzyme, removes excess reductant during fermentative growth. Virulence phenotypes conferred by mutations in hyc genes, either alone or in combination with mutations in the H2-uptake enzyme genes, are addressed. Anaerobically grown ΔhycB or ΔhycC single-deletion strains were more sensitive to acid than the wild-type strain, but the Δhyc strains were like the virulent parent strain with respect to both mouse morbidity and mortality and in organ burden numbers. Even fecal-recovery numbers for both mutant strains at several time points prior to the animals succumbing to salmonellosis were like those seen with the parent. Neither hydrogen uptake nor evolution of the gas was detected in a hydrogenase quadruple-mutant strain containing deletions in the hya, hyb, hyd, and hyc genes. As previously described, a strain lacking all H2-uptake ability was severely attenuated in its virulence characteristics, and the quadruple-mutant strain had the same (greatly attenuated) phenotype. While H2 levels were greatly reduced in ceca of mice treated with antibiotics, both the ΔhycB and ΔhycC strains were still like the parent in their ability to cause typhoid salmonellosis. It seems that the level of H2 produced by the pathogen (through formate hydrogen lyase [FHL] and Hyc) is insignificant in terms of providing respiratory reductant to facilitate either organ colonization or contributions to gut growth leading to pathogenesis.

Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats

The global prevalence of Fe deficiency is high and a common corrective strategy is oral Fe supplementation, which may affect the commensal gut microbiota and gastrointestinal health. The aim of the present study was to investigate the impact of different dietary Fe concentrations on the gut microbiota and gut health of rats inoculated with human faecal microbiota. Rats (8 weeks old, n 40) were divided into five (n 8 each) groups and fed diets differing only in Fe concentration during an Fe-depletion period (12 weeks) and an Fe-repletion period (4 weeks) as follows: (1) Fe-sufficient diet throughout the study period; (2) Fe-sufficient diet followed by 70 mg Fe/kg diet; (3) Fe-depleted diet throughout the study period; (4) Fe-depleted diet followed by 35 mg Fe/kg diet; (5) Fe-depleted diet followed by 70 mg Fe/kg diet. Faecal and caecal samples were analysed for gut microbiota composition (quantitative PCR and pyrosequencing) and bacterial metabolites (HPLC), and intestinal tissue samples were investigated histologically. Fe depletion did not significantly alter dominant populations of the gut microbiota and did not induce Fe-deficiency anaemia in the studied rats. Provision of the 35 mg Fe/kg diet after feeding an Fe-deficient diet significantly increased the abundance of dominant bacterial groups such as Bacteroides spp. and Clostridium cluster IV members compared with that of an Fe-deficient diet. Fe supplementation increased gut microbial butyrate concentration 6-fold compared with Fe depletion and did not affect histological colitis scores. The present results suggest that Fe supplementation enhances the concentration of beneficial gut microbiota metabolites and thus may contribute to gut health.

Biogenic hydrogen and methane production from Chlorella vulgaris and Dunaliella tertiolecta biomass

BACKGROUND

Microalgae are a promising feedstock for biofuel and bioenergy production due to their high photosynthetic efficiencies, high growth rates and no need for external organic carbon supply. In this study, utilization of Chlorella vulgaris (a fresh water microalga) and Dunaliella tertiolecta (a marine microalga) biomass was tested as a feedstock for anaerobic H2 and CH4 production.

RESULTS

Anaerobic serum bottle assays were conducted at 37°C with enrichment cultures derived from municipal anaerobic digester sludge. Low levels of H2 were produced by anaerobic enrichment cultures, but H2 was subsequently consumed even in the presence of 2-bromoethanesulfonic acid, an inhibitor of methanogens. Without inoculation, algal biomass still produced H2 due to the activities of satellite bacteria associated with algal cultures. CH4 was produced from both types of biomass with anaerobic enrichments. Polymerase chain reaction-denaturing gradient gel electrophoresis profiling indicated the presence of H2-producing and H2-consuming bacteria in the anaerobic enrichment cultures and the presence of H2-producing bacteria among the satellite bacteria in both sources of algal biomass.

CONCLUSIONS

H2 production by the satellite bacteria was comparable from D. tertiolecta (12.6 ml H2/g volatile solids (VS)) and from C. vulgaris (10.8 ml H2/g VS), whereas CH4 production was significantly higher from C. vulgaris (286 ml/g VS) than from D. tertiolecta (24 ml/g VS). The high salinity of the D. tertiolecta slurry, prohibitive to methanogens, was the probable reason for lower CH4 production.

Tungsten and molybdenum regulation of formate dehydrogenase expression in Desulfovibrio vulgaris Hildenborough

Formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. In this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of Desulfovibrio vulgaris Hildenborough, with lactate, formate, or hydrogen as electron donors. Using Western blot analysis, quantitative real-time PCR, activity-stained gels, and protein purification, we show that a metal-dependent regulatory mechanism is present, resulting in the dimeric FdhAB protein being the main enzyme present in cells grown in the presence of tungsten and the trimeric FdhABC₃ protein being the main enzyme in cells grown in the presence of molybdenum. The putatively membrane-associated formate dehydrogenase is detected only at low levels after growth with tungsten. Purification of the three enzymes and metal analysis shows that FdhABC₃ specifically incorporates Mo, whereas FdhAB can incorporate both metals. The FdhAB enzyme has a much higher catalytic efficiency than the other two. Since sulfate reducers are likely to experience high sulfide concentrations that may result in low Mo bioavailability, the ability to use W is likely to constitute a selective advantage.

Reductive stress in microbes: implications for understanding Mycobacterium tuberculosis disease and persistence

Mycobacterium tuberculosis (Mtb) is a remarkably successful pathogen that is capable of persisting in host tissues for decades without causing disease. Years after initial infection, the bacilli may resume growth, the outcome of which is active tuberculosis (TB). In order to establish infection, resist host defences and re-emerge, Mtb must coordinate its metabolism with the in vivo environmental conditions and nutrient availability within the primary site of infection, the lung. Maintaining metabolic homeostasis for an intracellular pathogen such as Mtb requires a carefully orchestrated series of oxidation-reduction reactions, which, if unbalanced, generate oxidative or reductive stress. The importance of oxidative stress in microbial pathogenesis has been appreciated and well studied over the past several decades. However, the role of its counterpart, reductive stress, has been largely ignored. Reductive stress is defined as an aberrant increase in reducing equivalents, the magnitude and identity of which is determined by host carbon source utilisation and influenced by the presence of host-generated gases (e.g. NO, CO, O(2) and CO(2)). This increased reductive power must be dissipated for bacterial survival. To recycle reducing equivalents, microbes have evolved unique electron 'sinks' that are distinct for their particular environmental niche. In this review, we describe the specific mechanisms that some microbes have evolved to dispel reductive stress. The intention of this review is to introduce the concept of reductive stress, in tuberculosis research in particular, in the hope of stimulating new avenues of investigation.

Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia

Mycobacteria are a group of obligate aerobes that require oxygen for growth, but paradoxically have the ability to survive and metabolize under hypoxia. The mechanisms responsible for this metabolic plasticity are unknown. Here, we report on the adaptation of Mycobacterium smegmatis to slow growth rate and hypoxia using carbon-limited continuous culture. When M. smegmatis is switched from a 4.6 h to a 69 h doubling time at a constant oxygen saturation of 50%, the cells respond through the down regulation of respiratory chain components and the F₁F_o-ATP synthase, consistent with the cells lower demand for energy at a reduced growth rate. This was paralleled by an up regulation of molecular machinery that allowed more efficient energy generation (i.e. Complex I) and the use of alternative electron donors (e.g. hydrogenases and primary dehydrogenases) to maintain the flow of reducing equivalents to the electron transport chain during conditions of severe energy limitation. A hydrogenase mutant showed a 40% reduction in growth yield highlighting the importance of this enzyme in adaptation to low energy supply. Slow growing cells at 50% oxygen saturation subjected to hypoxia (0.6% oxygen saturation) responded by switching on oxygen scavenging cytochrome bd, proton-translocating cytochrome bc₁-aa₃ supercomplex, another putative hydrogenase, and by substituting NAD⁺-dependent enzymes with ferredoxin-dependent enzymes thus highlighting a new pattern of mycobacterial adaptation to hypoxia. The expression of ferredoxins and a hydrogenase provides a potential conduit for disposing of and transferring electrons in the absence of exogenous electron acceptors. The use of ferredoxin-dependent enzymes would allow the cell to maintain a high carbon flux through its central carbon metabolism independent of the NAD⁺/NADH ratio. These data demonstrate the remarkable metabolic plasticity of the mycobacterial cell and provide a new framework for understanding their ability to survive under low energy conditions and hypoxia.

Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals

The production of hydrogen sulphide, an end product of metabolism by the sulphate-reducing bacteria (SRB) has been cited as a potential aetiological agent in gastrointestinal disease. Quantitative PCR (Q-PCR) assays to enumerate desulfovibrios from two gastrointestinal disease groups: colorectal cancer (CRC) n=27 and polypectomized individuals (PP) n=27, and two healthy control groups, elderly (H1) n=8 and young adults (H2) n=30 was performed. Analysis of Desulfovibrio sp. diversity using the dissimilarity sulphite reductase (dsrAB) gene as a molecular marker was also undertaken. Q-PCR detected Desulfovibrio sp. in all samples and no significant difference was observed for PP, H1, H2 with gene copy numbers of Desulfovibrio sp. averaging at 10(6) g(-1) of faeces. Significantly reduced numbers of Desulfovibrio sp. were observed for CRC (10(5) g(-1)) compared with both PP and H2 groups (P<0.05). Diversity analysis indicated that a low Desulfovibrio sp. diversity and the predominance of Desulfovibrio piger was a feature of both healthy and disease groups. In addition, a dsrAB gene sequence distantly related to a Gram-positive SRB was also recovered, highlighting the importance of cultivation-independent techniques for furthering our understanding of the diversity of the human gastrointestinal ecosystem.