Search Results (102)

In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)—including Crohn’s disease and ulcerative colitis—being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen’s role in gut health and identify novel therapeutic targets. Full article

This study addresses the microbial corrosion of cement-based materials in coastal urban sewer networks, systematically investigating the kinetic mechanisms of sulfur biogeochemical cycling under seawater infiltration conditions. Through dynamic monitoring of sulfide concentrations and environmental parameter variations in anaerobic pipelines, a multiphase coupled kinetic model integrating liquid-phase, gas-phase, and biofilm metabolic processes was developed. The results demonstrate that moderate salinity enhances the activity of sulfate-reducing bacteria (SRB) and accelerates sulfate reduction rates, whereas excessive sulfide accumulation inhibits SRB activity. At 35 °C, the mathematical model coefficient “a” for sulfate reduction in the reactor with 3 g/L salinity was significantly higher than those in reactors with 19 g/L and 35 g/L salinities, with no significant difference observed between the latter two. Overall, high sulfate concentrations do not act as limiting factors for sulfide oxidation under anaerobic conditions; instead, they enhance the reaction within specific concentration ranges. The refined kinetic model enables prediction of sulfur speciation in tropical coastal urban sewer pipelines, providing a scientific basis for corrosion risk assessment. Full article

Background: Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. Methods: Using untargeted mass spectrometry-based metabolomics and 16S sequencing of human stool, we investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs—amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson’s disease (PD)—and healthy controls (HC). Results: We discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and gut dysbiosis in NDDs. DHPS was downregulated in AD, ALS, and PD, while bacteria involved in DHPS metabolism, Eubacterium and Desulfovibrio, were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS, suggesting a potential role in DHPS metabolism. A catabolic product of DHPS is hydrogen sulfide, and when in excess, it is known to promote inflammation, oxidative stress, mitochondrial damage, and gut dysbiosis, known hallmarks of NDDs. Conclusions: These findings suggest that cryptic sulfur metabolism via DHPS is a potential missing link in our current understanding of gut dysbiosis associated with NDD onset and progression. As this was a hypothesis generating study, more work is needed to elucidate the role of DHPS in gut dysbiosis and neurodegenerative diseases. Full article

Sulfur cycling is a fundamental biogeochemical process, yet its microbial underpinnings in environments like the Isinuka sulfur pool remain poorly understood. Using high-throughput Illumina 16S rRNA sequencing and PICRUSt-based functional inference, we analyzed bacterial diversity and metabolic potential in sediment and water samples. Sediments, characterized by high sulfide/sulfate/thiosulfate, salinity, alkalinity, and organic matter content under anoxic conditions, supported diverse sulfur-reducing and organic-degrading bacteria, primarily from the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. In contrast, the anoxic water column harbored a less diverse community dominated by α-, γ-, and β-Proteobacteria, including Thiocapsa and Lutimaribacter. Sulfur oxidation genes (soxABCXYZ, sqr) were abundant in water, while sulfate reduction genes (dsrAB, aprAB, and sat/met3) were concentrated in sediments. Core microbiome analysis identified Thiocapsa, Lutimaribacter, and Delftia as functional keystones, integrating sulfur oxidation and nutrient recycling. Sediments supported dissimilatory sulfate-reducing bacteria (unclassified Desulfobacteraceae, Desulfosarcina, Desulfococcus, Desulfotignum, and Desulfobacter), while water samples were enriched in sulfur-oxidizing bacteria like Thiocapsa. Metabolic profiling revealed extensive sulfur, nitrogen, and carbon cycling pathways, with sulfur autotrophic denitrification and anoxygenic photosynthesis coupling sulfur–nitrogen and sulfur–carbon cycles. This study provides key theoretical insights into the microbial dynamics in sulfur-rich environments, highlighting their roles in biogeochemical cycling and potential applications in environmental management. Full article

Although the bioleaching of secondary copper sulfides has been industrialized for decades, the application of chalcopyrite bioleaching remains under development because of its low leaching rate. The effect of contact microbes on chalcopyrite leaching is still unclear due to the technical challenges in separating the contact (sessile micro-organisms) and the non-contact (planktonic micro-organisms) processes. Chalcopyrite bioleaching experiments were conducted using a novel device that stabilizes the redox potential and distinguishs between the microbial contact and non-contact effects. The contribution of the microbial “contact mechanism” in chalcopyrite leaching was quantified considering different redox potentials, compared to the “non-contact mechanism”. Based on the copper leaching kinetics and morphology of the leaching residue, it was demonstrated that the leaching rate of chalcopyrite was significantly influenced by the redox potential (850 mV > 650 mV > 750 mV), from 6.30% to 14.02% in 8 days leaching time. At each redox potential, the chalcopyrite leaching rate was 9.3%–30.6% higher with the presence of sessile microbes than without sessile microbes. Analysis of the leached chalcopyrite surface using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectrometry (XPS) revealed the formation of polysulfide and elemental sulfur at the surface. While the contacted sulfur oxidized the microbes, here, the Acidithiobacillus caldus preferred sessile at the chalcopyrite surface rather than Leptospirillum ferriphilum. Sulfur-oxidizing bacteria reduced the elemental sulfur content at the leach residue surface, thus playing an important role in degrading the sulfur passivation layer. In chalcopyrite bioleaching, the “contact mechanism” was primarily explained by sulfur-oxidizing bacteria promoting chalcopyrite oxidation through the removal of sulfur intermediates, while the “non-contact mechanism” was explained by ferrous-oxidizing microbes influencing the redox potential. Full article

Tannic acid (TA), a prevalent polyphenolic contaminant in industrial effluents, significantly inhibits microbial activity in anaerobic digestion, thereby diminishing wastewater treatment efficiency. In this study, a sulfidized nano zero-valent iron (S-nZVI) composite incorporated into sludge biochar (SB), abbreviated as SB-S-nZVI, was synthesized via a one-step hydrothermal method. The composite’s adsorption capacity for TA and its impact on anaerobic digestion were systematically evaluated. Experimental results showed that SB-S-nZVI achieved a TA removal efficiency of 99.31% under optimal conditions (S/Fe = 0.05, dosage = 0.3 g·L⁻¹), with a maximum adsorption capacity of 337.08 mg·g⁻¹. In anaerobic digestion, the addition of 0.03 g·L⁻¹ SB-S-nZVI enhanced chemical oxygen demand (COD) removal by 3.32%, increased specific methanogenic activity by 62.66%, and improved the microbial community composition, particularly enriching hydrolytic bacteria (Georgenia) and methanogenic archaea (Methanosaeta). The mechanistic analysis revealed that the FeS protective layer of SB-S-nZVI inhibited nano zero-valent iron oxidation and facilitated chemisorption-driven TA removal. This study presents an innovative approach for the integrated treatment of TA-contaminated wastewater by combining adsorption, degradation, and energy recovery. Full article

Microbial corrosion poses a significant threat to architectural heritage worldwide. This study used metagenomics to investigate microbial diversity and taxonomic groups present in the door walls of the Ji family’s residential houses, as well as their biological functions and chemical cycles. Taxonomic annotation revealed the predominant microbial taxa associated with wall corrosion, shedding light on their potential impact on structural integrity. Moreover, analyzing the metabolites and pathways present in these microbial communities allows for a thorough understanding of their functional capabilities. Our results revealed that areas with significant damage (dwelling bad door (DBD) and dwelling bad wall (DBW)) exhibited a higher microbial diversity compared to undamaged areas (dwelling good door (DGD) and dwelling good wall (DGW)), with variations in the occurrence of archaeal and bacterial species. The presence of bacteria was found to be connected with impaired function in DBW, whereas changes in the community patterns of Sphingobium and Sphingomonas, as well as a decrease in Cercospora proportion and an increase in Fusarium proportion, were correlated with damage in DBD. Both the Entner–Doudoroff (ED) route and sulfide oxidation processes were observed in both damaged locations (DBD and DBW). However, significant nitrogen-cycling mechanisms, including dissimilatory nitrate reduction to ammonium, were only found in DBW. Furthermore, DBD specifically detected the shift from methyl mercaptan (MMPA) to methyl mercaptan (MeSH). This research highlights the intricate interplay between microbial communities and the physical deterioration of residential structures, emphasizing the importance of understanding microbial ecology in mitigating such issues. Full article

Background: Fusobacterium nucleatum is a pathobiont that plays a dual role as both a commensal and a pathogen. The oral cavity typically harbors this anaerobic, Gram-negative bacterium. At the same time, it is closely linked to colorectal cancer due to its potential involvement in tumor progression and resistance to chemotherapy. The mechanism by which it transforms from a commensal to a pathogen remains unknown. For this reason, we investigated the role of oxidative status as an initiatory factor in changing the bacterium’s pathogenicity profile. Methods: A clinical strain of F. nucleatum subsp. animalis biofilm was exposed to different oxidative stress levels through varying subinhibitory amounts of H₂O₂. Subsequently, we investigated the bacterium’s behavior in vitro by infecting the HT-29 cell line. We evaluated bacterial colonization, volatile sulfur compounds production, and the infected cell’s oxidative status by analyzing HMOX1, pri-miRNA 155, and 146a gene expression. Results: The bacterial colonization rate, dimethyl sulfide production, and pri-miRNA 155 levels all increased when stressed bacteria were used, suggesting a predominant pathogenic function of these strains. Conclusions: The response of F. nucleatum to different oxidative conditions could potentially explain the increase in its pathogenic traits and the existence of environmental factors that may trigger the bacterium’s pathogenicity and virulence. Full article

Better quality and odor of silage and normal microbial fermentation metabolism are mostly dependent on an appropriate moisture content. The purpose of this study was to determine the effects of different moisture content gradients (50, 60, 70, and 80%) on the bacterial community, odor, and quality of alfalfa silage at 60 days by using gas chromatography–mass spectrometry (GC–MS) and electronic nose, with six replicates per group. The results showed that there were significant differences in odor response intensity among all groups, among which the 80% group had the strongest reaction to terpenoids, sulfides, and nitrogen oxides. Similarly, the different volatile organic compounds (VOCs) were mainly terpenoids, alcohols, and ketones, such as pine, camphor, and menthol (e.g., carlin and levomenthol). The dominant bacterium was Enterococcus with higher fiber, pH, and ammonia nitrogen (NH₃-N) content but poorer quality and odor (p < 0.05). The differential VOCs in the 60% group were mainly heterocyclics, esters, and phenols with fruity, floral, and sweet odors such as 2-butylthiophene and acorone. Pediococcus and Lactiplantibacillus were the dominant bacteria, with higher crude protein (CP), water-soluble carbohydrates (WSC), and lactic acid (LA) contents, as well as better quality and odor (p < 0.05). The biosynthesis of terpenoids and steroids, biosynthesis of secondary metabolites, and biosynthesis of phenylpropanoids were the main metabolic pathways of differential VOCs. In conclusion, regulating moisture content can alter bacterial community and metabolites, which will encourage fermentation and enhance alfalfa silage quality and odor. Full article

Autotrophic sulfur-oxidizing bacteria can play a key role in the metal bioleaching from low-grade sulfide-containing ores. The most commonly used bioleaching group is presented with acidophilic bacteria of the order Acidithiobacillales. We studied the diversity of bacteria in the arsenopyrite gold-bearing ore and also discovered a wide distribution of neutrophilic non-thermophilic bacteria Thermithiobacillus plumbiphilus in this ore, as well as its drainage and flotation concentrate. For the first time, T. plumbiphilus was isolated from the natural arsenic-containing mineral material. The first description of complete genome for the species T. plumbiphilus was also carried out and discovered genes providing the As resistance. Culturing the isolated strain T. plumbiphilus AAFK confirmed the found bacterial resistance to arsenite and cocadylate during the effective thiosulfate oxidation. Experiments on the arsenopyrite bioleaching showed that T. plumbiphilus AAFK can be used as an auxiliary bacterial culture capable of oxidizing reduced / intermediate sulfur compounds. The genetic basis of the T. plumbiphilus AAFK resistance to the arsenic compounds is discussed; the mechanisms are similar with the ones known for acidophilic thiobacilli. The biofilm formation is shown for the first time for T. plumbiphilus; presumably, it could provide some protection and immobilization of the cells. Structures of the T. plumbiphilus AAFK cells and their production of outer membrane vesicles are described and discussed. Full article

Microbiota-derived hydrogen sulfide (H₂S) plays a crucial role in modulating the gut–brain axis, with significant implications for neurodegenerative diseases such as Alzheimer’s and Parkinson’s. H₂S is produced by sulfate-reducing bacteria in the gut and acts as a critical signaling molecule influencing brain health via various pathways, including regulating inflammation, oxidative stress, and immune responses. H₂S maintains gut barrier integrity at physiological levels and prevents systemic inflammation, which could impact neuroinflammation. However, as H₂S has a dual role or a Janus face, excessive H₂S production, often resulting from gut dysbiosis, can compromise the intestinal barrier and exacerbate neurodegenerative processes by promoting neuroinflammation and glial cell dysfunction. This imbalance is linked to the early pathogenesis of Alzheimer’s and Parkinson’s diseases, where the overproduction of H₂S exacerbates beta-amyloid deposition, tau hyperphosphorylation, and alpha-synuclein aggregation, driving neuroinflammatory responses and neuronal damage. Targeting gut microbiota to restore H₂S homeostasis through dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation presents a promising therapeutic approach. By rebalancing the microbiota-derived H₂S, these strategies may mitigate neurodegeneration and offer novel treatments for Alzheimer’s and Parkinson’s diseases, underscoring the critical role of the gut–brain axis in maintaining central nervous system health. Full article

Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Recent advancements in high-throughput omics techniques have enhanced our understanding of the human microbiome’s role in the development of CVDs. Although the relationship between the gut microbiome and CVDs has attracted considerable research attention and has been rapidly evolving in recent years, the role of the oral microbiome remains less understood, with most prior studies focusing on periodontitis-related pathogens. In this review, we summarized previously reported associations between the oral microbiome and CVD, highlighting known CVD-associated taxa such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We also discussed the interactions between the oral and gut microbes. The potential mechanisms by which the oral microbiota can influence CVD development include oral and systemic inflammation, immune responses, cytokine release, translocation of oral bacteria into the bloodstream, and the impact of microbial-related products such as microbial metabolites (e.g., short-chain fatty acids [SCFAs], trimethylamine oxide [TMAO], hydrogen sulfide [H₂S], nitric oxide [NO]) and specific toxins (e.g., lipopolysaccharide [LPS], leukotoxin [LtxA]). The processes driven by these mechanisms may contribute to atherosclerosis, endothelial dysfunction, and other cardiovascular pathologies. Integrated multi-omics methodologies, along with large-scale longitudinal population studies and intervention studies, will facilitate a deeper understanding of the metabolic and functional roles of the oral microbiome in cardiovascular health. This fundamental knowledge will support the development of targeted interventions and effective therapies to prevent or reduce the progression from cardiovascular risk to clinical CVD events. Full article

The intricate relationship between hydrogen sulfide (H₂S), gut microbiota, and sirtuins (SIRTs) can be seen as a paradigm axis in maintaining cellular homeostasis, modulating oxidative stress, and promoting mitochondrial health, which together play a pivotal role in aging and neurodegenerative diseases. H₂S, a gasotransmitter synthesized endogenously and by specific gut microbiota, acts as a potent modulator of mitochondrial function and oxidative stress, protecting against cellular damage. Through sulfate-reducing bacteria, gut microbiota influences systemic H₂S levels, creating a link between gut health and metabolic processes. Dysbiosis, or an imbalance in microbial populations, can alter H₂S production, impair mitochondrial function, increase oxidative stress, and heighten inflammation, all contributing factors in neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Sirtuins, particularly SIRT1 and SIRT3, are NAD⁺-dependent deacetylases that regulate mitochondrial biogenesis, antioxidant defense, and inflammation. H₂S enhances sirtuin activity through post-translational modifications, such as sulfhydration, which activate sirtuin pathways essential for mitigating oxidative damage, reducing inflammation, and promoting cellular longevity. SIRT1, for example, deacetylates NF-κB, reducing pro-inflammatory cytokine expression, while SIRT3 modulates key mitochondrial enzymes to improve energy metabolism and detoxify reactive oxygen species (ROS). This synergy between H₂S and sirtuins is profoundly influenced by the gut microbiota, which modulates systemic H₂S levels and, in turn, impacts sirtuin activation. The gut microbiota–H₂S–sirtuin axis is also essential in regulating neuroinflammation, which plays a central role in the pathogenesis of neurodegenerative diseases. Pharmacological interventions, including H₂S donors and sirtuin-activating compounds (STACs), promise to improve these pathways synergistically, providing a novel therapeutic approach for neurodegenerative conditions. This suggests that maintaining gut microbiota diversity and promoting optimal H₂S levels can have far-reaching effects on brain health. Full article

Against the backdrop of the increasing copper demand in a low-carbon economy, this work statistically forecasted the distribution of China’s copper tailings for the first time, and then characterized them as finely crushed and low-grade mining solid wastes containing copper mainly in the form of chalcopyrite, bornite, covelline, enargite and chalcocite based on available research data. China is the globally leading refined copper producer and consumer, where the typical commercial-scale bioleaching of copper tailings is conducted in the Dexing, Zijinshan and Jinchuan mining regions. And these leaching processes were compared in this study. Widely used chemolithoautotrophic and mesophilic bacteria are Acidithiobacillus, Leptospirillum, Acidiphilium, Alicyclobacillus and Thiobacillus with varied metal resistance. They can be used to treat copper sulfide tailings such as pyrite, chalcopyrite, enargite, chalcocite, bornite and covellite under sufficient dissolved oxygen from 1.5 to 4.1 mg/L and pH values ranging from 0.5 to 7.2. Moderate thermophiles (Acidithiobacillus caldus, Acidimicrobium, Acidiplasma, Ferroplasma and Sulfobacillus) and extreme thermophilic archaea (Acidianus, Metallosphaera, Sulfurococcus and Sulfolobus) are dominant in leaching systems with operating temperatures higher than 40 °C. However, these species are vulnerable to high pulp density and heavy metals. Heterotrophic Acidiphilium multivorum, Ferrimicrobium, Thermoplasma and fungi use organic carbon as energy to treat copper oxides (malachite, chrysocolla and azurite) and weathered sulfides (bornite, chalcocite, digenite and covellite) under a wide pH range and high pulp density. We also compared autotrophs in a planktonic state or biofilm to treat different metal sulfides using various sulfur-cycling enzymes involved in the polysulfide or thiosulfate pathways against fungi that produce various organic acids to chelate copper from oxides. Finally, we recommended a bioinformatic analysis of functional genes involved in Fe/S oxidization and C/N metabolism, as well as advanced representation that can create new possibilities for the development of high-efficiency leaching microorganisms and insight into the mechanisms of bioleaching desired metals from complex and low-grade copper tailings. Full article

Acid mine drainage (AMD) pollutes natural waters, but some impacted systems show natural attenuation. We sought to identify the biogeochemical mechanisms responsible for the natural attenuation of AMD. We hypothesized that biogenic sulfide-mediated iron reduction is one mechanism and tested this in an experimental model system. We found sulfate reduction occurred under acidic conditions and identified a suite of sulfate-reducing bacteria (SRB) belonging to the groups Desulfotomaculum, Desulfobacter, Desulfovibrio, and Desulfobulbus. Iron reduction was not detected in microcosms when iron-reducing bacteria or SRB were selectively inhibited. SRB also did not reduce iron enzymatically. Rather, the biogenic sulfide produced by SRB was found to be responsible for the reduction of iron at low pH. Addition of organic substrates and nutrients stimulated iron reduction and increased the pH. X-ray diffraction and an electron microprobe analysis revealed that the polycrystalline, black precipitate from SRB bioactive samples exhibited a greater diversity of iron chalcogenide minerals with reduced iron oxidation states, and minerals incorporating multiple metals compared to abiotic controls. The implication of this study is that iron reduction mediated by biogenic sulfide may be more significant than previously thought in acidic environments. This study not only describes an additional mechanism by which SRB attenuate AMD, which has practical implications for AMD-impacted sites, but also provides a link between the biogeochemical cycling of iron and sulfur. Full article