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ELife Apr 2024Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating...
Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating the tracking of metabolic changes over time after stress in rare cells such as hematopoietic stem cells (HSCs). Here, we aimed to identify the key metabolic enzymes that define differences in glycolytic metabolism between steady-state and stress conditions in murine HSCs and elucidate their regulatory mechanisms. Through quantitative C metabolic flux analysis of glucose metabolism using high-sensitivity glucose tracing and mathematical modeling, we found that HSCs activate the glycolytic rate-limiting enzyme phosphofructokinase (PFK) during proliferation and oxidative phosphorylation (OXPHOS) inhibition. Real-time measurement of ATP levels in single HSCs demonstrated that proliferative stress or OXPHOS inhibition led to accelerated glycolysis via increased activity of PFKFB3, the enzyme regulating an allosteric PFK activator, within seconds to meet ATP requirements. Furthermore, varying stresses differentially activated PFKFB3 via PRMT1-dependent methylation during proliferative stress and via AMPK-dependent phosphorylation during OXPHOS inhibition. Overexpression of induced HSC proliferation and promoted differentiated cell production, whereas inhibition or loss of suppressed them. This study reveals the flexible and multilayered regulation of HSC glycolytic metabolism to sustain hematopoiesis under stress and provides techniques to better understand the physiological metabolism of rare hematopoietic cells.
Topics: Animals; Mice; Adenosine Triphosphate; Anaerobiosis; Glycolysis; Hematopoiesis; Hematopoietic Stem Cells; Oxidative Phosphorylation; Phosphofructokinase-2; Phosphoric Monoester Hydrolases
PubMed: 38573813
DOI: 10.7554/eLife.87674 -
Microbiome Apr 2024The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon...
BACKGROUND
The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8).
RESULTS
To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility.
CONCLUSION
We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.
Topics: Archaea; Isotope Labeling; Oxidation-Reduction; Methane; Carbon; DNA; Anaerobiosis; Geologic Sediments; Phylogeny
PubMed: 38570877
DOI: 10.1186/s40168-024-01779-z -
Journal of the West African College of... 2024Surgical site infection (SSI) is the second most common cause of nosocomial infection, after urinary tract infection. Sequelae of SSI include increased healthcare costs...
BACKGROUND
Surgical site infection (SSI) is the second most common cause of nosocomial infection, after urinary tract infection. Sequelae of SSI include increased healthcare costs and worse patient outcomes. There is a paucity of research studies on the impact of anaerobic organisms on SSIs in Nigeria. The aim of this study was to determine the role of anaerobic bacteria in SSI encountered at the Lagos University Teaching Hospital (LUTH).
MATERIALS AND METHODS
A total of 438 patients were consecutively recruited into this study from general surgery, obstetrics and gynaecology and paediatric units of the LUTH from 1 July through 31 December 2019. Two surgical wound specimens were collected from all patients with suspected SSIs. One was for anaerobic culture using Brucella blood agar incubated in an anaerobic jar that secured anaerobiosis using the anaerobic gas pack. The other swab was used for aerobic culture on blood agar incubated on air at 37C. Identifications and antibiotic sensitivity testing were performed according to standard laboratory procedures.
RESULT
The overall incidence of SSI in the study was 12.3%. The incidence of anaerobic SSI was 1.1%. The distribution of anaerobic infections by medical specialty unit was as follows; general surgery (1.6%), obstetrics and gynaecology (0.8%) and paediatrics (0.9%). Bacteroides species was the only anaerobic isolate. The risk factors associated with the development of SSI by multiple logistic regression analysis were duration of surgery greater than 2 h (OR 1.418; 95% CI 1.834-9.286; 0.001) and NNIS risk index 2 and 3 - (OR 2.165; 95% CI 2.366-32.086; 0.001).
CONCLUSIONS
The prevalence of anaerobic SSI was 1.1%. Duration of surgery greater than 2 h and NNIS risk index 2 and 3 were independent predictors of SSI.
PubMed: 38562385
DOI: 10.4103/jwas.jwas_91_23 -
BioRxiv : the Preprint Server For... Mar 2024Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative...
BACKGROUND
Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. ) and restricts obligate anaerobes (eg. ). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism.
METHODS
Primary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or mice reconstituted with human IBD stool (Hu- ). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by (aerobic respiration-proficient) and mutant (aerobic respiration-deficient).
RESULTS
Metagenomic (16S) analysis revealed AuPhos reduced relative abundances of and increased blooms of in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) . Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1β,MCP1, RankL). Histological investigation of AuPhos-fed Px- mice showed significantly decreased colitis score in AuPhos-treated Px- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes ( , ). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine).
CONCLUSION
These findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism.
PubMed: 38559035
DOI: 10.1101/2024.03.14.584471 -
The Science of the Total Environment Jun 2024Anaerobic digestion can provide benefits not only from the perspective of renewable energy production but also in the form of fertilization effect and increased...
Anaerobic digestion can provide benefits not only from the perspective of renewable energy production but also in the form of fertilization effect and increased retention of C in soils after digestate application. This study consisted of two phases, where the first phase assessed the suitability of carbon-rich co-feedstocks for methane production via laboratory testing. The second phase assessed the balance and stability of C before and after anaerobic digestion by systematic digestate characterization, and by evaluating its carbon retention potential using a modeling approach. The results indicated that pyrolysis chars had a negligible effect on the methane production potential of cattle manure, while wheat straw expectedly increased methane production. Thus, a mixture of cattle manure and wheat straw was digested in pilot-scale leach-bed reactors and compared with undigested manure and straw. Although the total amount of C in the digestate was lower than in the untreated feedstocks, the digestion process stabilized C and was modeled to be more effective in retaining C in the soil than untreated cattle manure and wheat straw. In addition, digestion converted 23-27 % of the C into valuable methane, increasing the valorization of the total C in the feedstock. Considering anaerobic digestion processes as a strategy to optimize both carbon and nutrient valorization provides a more holistic approach to addressing climate change and improving soil health.
Topics: Manure; Methane; Fertilizers; Carbon; Anaerobiosis; Animals; Cattle; Soil; Triticum
PubMed: 38554957
DOI: 10.1016/j.scitotenv.2024.172083 -
Environment International Apr 2024Ciprofloxacin (CIP) poses a high risk of resistance development in water environments. Therefore, comprehensive effects and recovery strategies of CIP in anaerobic...
Ciprofloxacin (CIP) poses a high risk of resistance development in water environments. Therefore, comprehensive effects and recovery strategies of CIP in anaerobic ammonia oxidation (anammox) process were systematically elucidated from consortia and pure strains perspectives. The anammox consortia was not significantly affected by the stress of 10 mg L CIP, while the higher concentration (20 mg L) of CIP caused a dramatic reduction in the nitrogen removal performance of anammox system. Simultaneously, the abundances of dominant functional bacteria and corresponding genes also significantly decreased. Such inhibition could not be mitigated by the recovery strategy of adding hydrazine and hydroxylamine. Reducing nitrogen load rate from 5.1 to 1.4 kg N m d promoted the restoration of three reactors. In addition, the robustness and recovery of anammox systems was evaluated using starvation and shock strategies. Simultaneously, antibiotic resistance genes and key metabolic pathways of anammox consortia were upregulated, such as carbohydrate and energy metabolisms. In addition, 11 pure stains were isolated from the anammox system and identified through phylogenetic analysis, 40 % of which showed multidrug resistance, especially Pseudomonas. These findings provide deep insights into the responding mechanism of anammox consortia to CIP stress and promote the application of anammox process for treating wastewater containing antibiotics.
Topics: Ciprofloxacin; Anti-Bacterial Agents; Oxidation-Reduction; Ammonia; Anaerobiosis; Bioreactors; Bacteria; Microbial Consortia; Nitrogen; Wastewater
PubMed: 38554504
DOI: 10.1016/j.envint.2024.108599 -
Environmental Science & Technology Apr 2024Methane emissions present a significant environmental challenge in both natural and engineered aquatic environments. Denitrifying anaerobic methane oxidation (N-DAMO)...
Methane emissions present a significant environmental challenge in both natural and engineered aquatic environments. Denitrifying anaerobic methane oxidation (N-DAMO) has the potential for application in wastewater treatment plants. However, our understanding of the N-DAMO process is primarily based on studies conducted on environmental samples or enrichment cultures using metagenomic approaches. To gain deeper insights into N-DAMO, we used antimicrobial compounds to study the function and physiology of ' Methanoperedens nitroreducens' and ' Methylomirabilis oxyfera' in N-DAMO enrichment cultures. We explored the effects of inhibitors and antibiotics and investigated the potential application of N-DAMO in wastewater contaminated with ammonium and heavy metals. Our results showed that ' M. nitroreducens' was susceptible to puromycin and 2-bromoethanesulfonate, while the novel methanogen inhibitor 3-nitrooxypropanol had no effect on N-DAMO. Furthermore, ' M. oxyfera' was shown to be susceptible to the particulate methane monooxygenase inhibitor 1,7-octadiyne and a bacteria-suppressing antibiotic cocktail. The N-DAMO activity was not affected by ammonium concentrations below 10 mM. Finally, the N-DAMO community appeared to be remarkably resistant to lead (Pb) but susceptible to nickel (Ni) and cadmium (Cd). This study provides insights into microbial functions in N-DAMO communities, facilitating further investigation of their application in methanogenic, nitrogen-polluted water systems.
Topics: Nitrates; Wastewater; Anaerobiosis; Methane; Bacteria; Ammonium Compounds; Oxidation-Reduction; Anti-Infective Agents; Nitrites; Bioreactors; Denitrification
PubMed: 38551595
DOI: 10.1021/acs.est.3c07197 -
Nature Communications Mar 2024Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their...
Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.
Topics: Humans; Animals; Neocallimastigomycota; Turtles; Phylogeny; Anaerobiosis; Symbiosis; Mammals; Fungi
PubMed: 38548766
DOI: 10.1038/s41467-024-47047-4 -
The Science of the Total Environment May 2024Granular activated carbon (GAC), a porous carbon-based material, provides increased attachment space for functional microorganisms and enhances nitrogen removal by...
Granular activated carbon (GAC), a porous carbon-based material, provides increased attachment space for functional microorganisms and enhances nitrogen removal by facilitating extracellular electron transfer in the anammox process. This study investigates the effects of GAC on the biosynthesis of microbial extracellular secretions (MESs) and explores the roles of these secretions in anammox activities. Four lab-scale reactors were operated: two downstream UASB reactors (D1 and D2) receiving effluents from the upstream UASB reactors (U1: no-GAC, U2: yes-GAC). Our results indicate that MESs were enhanced with the addition of GAC. The effluent from U2 exhibited a 59.62 % higher amino acid content than that from U1. These secretions contributed to an increase in the nitrogen loading rate (NLR) in the downstream reactors. Specifically, NLR in D1 increased from 130.5 to 142.7 g N/m/day, and in D2, it escalated from 137.5 to 202.8 g N/m/day, likely through acting as cross-feeding substrates or vital nutrients. D2 also showed increased anammox bacterial activity, enriched Ca. Brocadia population and hao gene abundance. Furthermore, this study revealed that D2 sludge has significantly higher extracellular polymeric substances (EPS) (48.71 mg/g VSS) and a larger average granule size (1.201 ± 0.119 mm) compared to D1 sludge. Overall, GAC-stimulated MESs may have contributed to the enhanced performance of the anammox process.
Topics: Sewage; Charcoal; Anaerobic Ammonia Oxidation; Bioreactors; Bacteria; Anaerobiosis; Nitrogen; Oxidation-Reduction
PubMed: 38537814
DOI: 10.1016/j.scitotenv.2024.171980 -
Environmental Science and Pollution... Apr 2024This manuscript presents a scientometric review of recent advances in microwave pretreatment processes for sewage sludge, systematically identifying existing gaps and... (Review)
Review
This manuscript presents a scientometric review of recent advances in microwave pretreatment processes for sewage sludge, systematically identifying existing gaps and prospects. For this purpose, 1763 papers on the application of microwave technology to sludge pretreatment were retrieved from the Web of Science (WoS) using relevant keywords. These publications were then analyzed using diverse scientometric indices. The results show that research in this field encompasses applications based on the non-thermal effects of microwaves, enhanced effectiveness of anaerobic digestion (AD), and the energy balance of this pretreatment system. Overcoming existing technical challenges, such as the cleavage of extracellular polymers, reducing microwave energy consumption, understanding the non-thermal effects of microwaves, promoting AD of sludge in combination with other chemical and physical methods, and expanding the application of the technology, are the main scientific focuses. Additionally, this paper thoroughly examines both the constraints and potential of microwave pretreatment technology for wastewater treatment.
Topics: Microwaves; Sewage; Wastewater; Waste Disposal, Fluid; Anaerobiosis
PubMed: 38532216
DOI: 10.1007/s11356-024-32931-9