Microbial Metabolism Research Articles

Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.

The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.

Integrated virtual screening and MD simulation study to discover potential inhibitors of mycobacterial electron transfer flavoprotein oxidoreductase.

Tuberculosis (TB) continues to be a major global health burden, with high incidence and mortality rates, compounded by the emergence and spread of drug-resistant strains. The limitations of current TB medications and the urgent need for new drugs targeting drug-resistant strains, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB, underscore the pressing demand for innovative anti-TB drugs that can shorten treatment duration. This has led to a focus on targeting energy metabolism of Mycobacterium tuberculosis (Mtb) as a promising approach for drug discovery. This study focused on repurposing drugs against the crucial mycobacterial protein, electron transfer flavoprotein oxidoreductase (EtfD), integral to utilizing fatty acids and cholesterol as a carbon source during infection. The research adopted an integrative approach, starting with virtual screening of approved drugs from the ZINC20 database against EtfD, followed by molecular docking, and concluding with molecular dynamics (MD) simulations. Diacerein, levonadifloxacin, and gatifloxacin were identified as promising candidates for repurposing against TB based on their strong binding affinity, stability, and interactions with EtfD. ADMET analysis and anti-TB sensitivity predictions assessed their pharmacokinetic and therapeutic potential. Diacerein and levonadifloxacin, previously unexplored in anti-tuberculous therapy, along with gatifloxacin, known for its efficacy in drug-resistant TB, have broad-spectrum antimicrobial properties and favorable pharmacokinetic profiles, suggesting potential as alternatives to current TB treatments, especially against resistant strains. This study underscores the efficacy of computational drug repurposing, highlighting bacterial energy metabolism and lipid catabolism as fruitful targets. Further research is necessary to validate the clinical suitability and efficacy of diacerein, levonadifloxacin, and gatifloxacin, potentially enhancing the arsenal against global TB.

Carbon fate and potential carbon metabolism effects during in-situ cyanobacterial inhibition by artemisinin sustained-release algaecides.

Carbon pools and microbial carbon metabolism can be significantly altered due to the diverse organic matter properties and low pH characteristics of artemisinin sustained-release algaecides (ASAs). These effects have still not been systematically studied, leading to uncertainty in the application of ASAs for cyanobacterial management in natural waters. This study assessed the effects of ASAs on carbon fate, carbon metabolism and potential ecological impacts during in-situ cyanobacterial inhibition. In the initial phase of ASAs-induced cyanobacterial inhibition (2-10 days), the carbon pool underwent significant changes due to the increased proportion of C4 plant-derived organic matter (97%), humification level (FI =0.9-1.5), and inorganic carbon concentration (TIC = 80-110mg/L). The cyanobacterial apoptosis triggered by ASAs produced particulate organic carbon, which provided a bioavailable carbon source for bacterial metabolism. ASAs enhanced the connection between bacteria and the carbon pool, as well as their carbon metabolism capabilities, by increasing the relative abundance of Proteobacteria (33.1%-37.3%), bacterial diversity, the proportion of Alphaproteobacteria and Betaproteobacteria (19.3%-29.5%) involved in carbon metabolism, and the complexity of the environment-bacteria co-occurrence network. These effects contributed to maintaining long-term ecosystem stability and resistance to cyanobacterial proliferation. Our findings elucidate the influence of bacterial carbon metabolism by ASAs as one of an important mechanism for achieving cyanobacterial inhibition in natural water, and emphasize the important role of bacteria in maintaining ecological stability during in situ cyanobacterial management.

Gut microbial metabolism of bile acids modifies the effect of Mediterranean diet interventions on cardiometabolic risk in a randomized controlled trial

ABSTRACT Bile acids (BAs) undergo extensive microbial metabolism in the gut and exert hormone-like functions on physiological processes underlying metabolic risk. However, the extent to which gut BA profiles predict cardiometabolic risk and explain individual responses to dietary interventions in humans is still unclear. In the DIRECT-PLUS Trial, we conducted a multi-omics analysis of 284 participants randomized into three groups: healthy dietary guidelines and two Mediterranean diet (MedDiet) groups. We longitudinally measured 44 fecal BAs using liquid chromatography-mass spectrometry, the gut microbiome through shotgun metagenomic sequencing, and body adiposity and serum lipids at baseline, 6, and 18 months. Fecal levels of 14 BAs, such as lithocholic acid and ursodeoxycholic acid, were prospectively associated with body mass index (BMI) and serum lipid profiles (false discovery rate [q]<0.05). Baseline fecal BA levels significantly modified the beneficial effects of the MedDiet; for example, BMI reduction induced by MedDiet interventions was more pronounced in individuals with lower 12-dehydrocholic acid levels (q-interaction <0.001). We confirmed that the gut microbiome is a major modifier of the secondary BA pool in humans. Furthermore, the association of fecal BAs with body adiposity and serum lipids varied significantly in individuals with different abundances of gut microbes carrying BA metabolism enzymes, e.g. several Ruminococcus spp. In summary, our study identifies novel predictive biomarkers for cardiometabolic risk and offers new mechanistic insights to guide personalized dietary interventions.

Influence of intestinal microbiota on the metabolism of main cardiotropic drugs

The intestinal microbiota is one of the most important pathogenetic links in the development of cardiovascular diseases. Every year the world scientific community finds new interactions at the level of signaling molecules, metabolites and microorganisms, identifying more and more patterns and cause-and-effect relationships which indicate the commonality of the intestinal microbiota (GM) and cardiovascular diseases. The state of the host's intestinal community, its qualitative and quantitative composition, directly and indirectly affects the fundamental pathogenetic mechanisms of the development of cardiovascular diseases. Despite the fact that there are scientifically based methods of treatment, cardiovascular diseases remain the leading cause of death in the world. This phenomenon is partly due to wide variations in individual response to cardiovascular drugs. The pharmacological effects of cardiotropic drugs are quite different even within groups of patients comparable in age and gender. Every year intestinal microbiota is more and more evident to be responsible for this intraspecific variability. Gut microbes influence drug metabolism in several pharmacokinetic ways, and conversely, drugs can have significant effects on the microbiome and therefore pharmacodynamic processes. Drugs can alter the gut microenvironment and microbial metabolism, influence bacterial growth, thereby changing the composition and functions of the microbial community. One of the most important functions of GM, related to “intestinal-cardiovascular system”, is participation in the metabolism of major cardiotropic medications, such as digoxin, statins, ezetimibe, antithrombotic drugs, calcium channel blockers (CCBs), beta blockers (BB), gliflozins and inhibitors of the renin-angiotensin-aldosterone system (RAAS).

Fusarium spp. in Metalworking Fluid Systems: Companions Forever

Water-miscible metalworking fluids (MWFs) are utilized in a variety of metal removal and forming operations. For end-use, formulation concentrates are diluted in water, creating conditions conducive to microbial growth and metabolism, possibly compromising the fluid’s integrity and mechanically obstructing filters or piping systems. Metalworking machines offer additional habitats on surfaces that are in permanent or temporary contact with MWFs. For that reason, biocides have been incorporated into concentrates for years, but legal constraints will restrain their use in the future. While bacterial contamination of MWFs is well documented, fungal contamination is often overseen and infrequently reported in the literature. In this study, we report fungal prevalence in in-use MWFs sampled worldwide over 10 years, and we are convinced that the presence of fungi is the norm rather than the exception. In addition, we evaluated the inhibitory effect of fungicides on fungal growth, sporulation and spore viability using traditional culture-dependent methods and flow cytometry. In essence, we show that the effectiveness of these fungicides is limited and dependent on the chemical construction of the fluid. We think that the ecology created by water-diluted MWFs is of higher importance than the anti-fungal activity of single components.

Cellulose-Based Transparent Edible Antibacterial Oxygen-Barrier Coating for Long-Term Fruit Preservation.

Long-term preservation of fresh fruit and vegetables without a cold chain is a great challenge to food security because fruits and vegetables are highly vulnerable to poor storage conditions. Fruit spoilage is a complex biochemical process that involves many factors, including microbial reproduction, oxidation, metabolism, and H2O evaporation. Only the synergy of the multiple spoilage inhibition methods can achieve long-term freshness preservation. Herein, a multifunctional cellulose-based preservation coating with antibacterial, oxygen/water vapor barrier, and antioxidant properties is proposed, which is based on cellulose microgel (CMG) and prepared using multi-component composites with montmorillonite (MMT), cationic cellulose derivative (Cell-P+), and L-ascorbic acid (Vc). It has good wetting properties on fruits with different surfaces. This method can successfully preserve the long-term freshness of various fruits. This highly transparent, edible, and washable multifunctional cellulose-based fruit preservation coating can improve the quality of agricultural products, extend the shelf life of food, and reduce the cost of cold-chain transportation.

Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut–Liver Axis

Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 108 CFU/g) (PF) and water (1.0 × 108 CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota–gut–liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut–liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.

Perspective on the Coevolutionary Role of Host and Gut Microbiota in Polyphenol Health Effects: Metabotypes and Precision Health.

"Personalized nutrition" aims to establish nutritional strategies to improve health outcomes for non-responders. However, it is utopian since most people share similar nutritional requirements. "Precision health," encompassing lifestyles, may be more fitting. Dietary (poly)phenols are "healthy" but non-nutritional molecules (thus, we can live without them). The gut microbiota influences (poly)phenol effects, producing metabolites with different activity than their precursors. Furthermore, producing distinctive metabolites, like urolithins, lunularin, and equol, leads to the term "polyphenol-related gut microbiota metabotypes," grouping individuals based on a genuine microbial metabolism of ellagic acid, resveratrol, and isoflavones, respectively. Additionally, (poly)phenols exert prebiotic-like effects through their antimicrobial activities, typically reducing microbial diversity and modulating microbiota functionality by impacting its composition and transcriptomics. Since the gut microbiota perceives (poly)phenols as a threat, (poly)phenol effects are mostly a consequence of microbiota adaptation through differential (poly)phenol metabolism (e.g., distinctive reductions, dehydroxylations, etc.). This viewpoint is less prosaic than considering (poly)phenols as essential nutritional players in human health, yet underscores their health significance in a coevolutionary partnership with the gut microbiota. In the perspective on the gut microbiota and (poly)phenols interplay, microbiota metabotypes could arbiter health effects. An innovative aspect is also emphasized: modulating the interacting microbial networks without altering the composition.

An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.

Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows. The results indicated that the proportions of highly heritable subsets (h2 ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn2+ transport) (P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942). Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows actively modulate their rumen microbiota through SNP variants to regulate their own lactation performance. Video Abstract.

Unveiling the Antibacterial Mechanism of Gold Nanoparticles by Analyzing Bacterial Metabolism at the Molecular Level.

The threat of drug-resistant bacteria is challenging, and it is urgent to explore new antibiotics. Gold nanoparticles (AuNPs) are known to be a group of promising antibacterial agents for replacing conventional antibiotics. Nevertheless, their antibacterial mechanism remains to be elucidated. Herein, we directly observed the interaction between antibacterial AuNPs and bacteria at the molecular level using neutral desorption extractive electrospray ionization mass spectrometry (ND-EESI-MS). We monitored and analyzed the dynamic changes of bacterial metabolites in real time after AuNP treatment. Ten substances representing 3 major metabolic pathways, including protein and nucleic acid synthesis, energy metabolism, and quorum sensing, were identified, indicating that AuNPs may exert antibacterial effects through multiple mechanisms influencing bacterial metabolism and communication. This study deepens the understanding of the antibacterial mechanism of AuNPs and is insightful for designing and screening new antibacterial agents.

Comprehensive analysis of the metabolism of core microorganisms in polyphenolic compound formation during the acetic acid fermentation stage of millet vinegar.

Polyphenolic compounds in millet vinegar are crucial functional substances, but the mechanisms underlying their formation and metabolism remain unclear. Acetic acid fermentation (AAF) represents the most active microbial metabolism stage and is pivotal for forming polyphenolic compounds. This study comprehensively analyzed the role of the microbiome in polyphenolic compound production and metabolism during AAF. Changing patterns were observed in both the microbiome and polyphenolic monomer compounds during AAF of millet vinegar. Lactobacillus harbinensis (0.624-0.454%) was identified as the dominant species in the pre-AAF stage, exhibiting a significant positive correlation with caffeic acid, kaempferic acid and kaempferolide (P < 0.05). Lactobacillus harbinensis-mediated polyphenolic compound metabolism was further confirmed through genomic analysis and pure culture fermentation techniques. Lactobacillus harbinensis encodes enzymes such as carbohydrate hydrolases, glycosidases and cellulases, which promote the release and metabolism of polyphenolic compounds from grain hulls. This study confirmed that L. harbinensis, as a core microorganism in millet vinegar fermentation, can significantly augment the content of total phenols and specific polyphenolic compounds. These findings provide valuable insights for optimizing millet vinegar production. © 2024 Society of Chemical Industry.

Organic matter processing by heterotrophic bacterioplankton in a large tropical river: Relating elemental composition and potential carbon mineralization.

River hydrology shapes the sources, concentration, and stoichiometry of organic matter within drainage basins. However, our understanding of how the microbes process dissolved organic matter (DOM) and recycle nutrients in tropical rivers needs to be improved. This study explores the relationships between elemental DOM composition (carbon/nitrogen/phosphorus: C/N/P), C and N uptake, and C mineralization by autochthonous bacterioplankton in the Usumacinta River, one of the most important fluvial systems in Mexico. Our study investigated changes in the composition and concentration of DOM and evaluated carbon dioxide (CO2)production rates (C-CO2) through laboratory experiments. We compared three sites representing the middle and lower river basins, including their transitional zones, during the rainy and dry seasons. After incubation (120 h at 25°C), the DOM decreased between 25% and 89% of C content. Notably, the initial high proportion of C in DOM in samples from the middle-forested zone and the transition led to elevated C-CO2 rates (>10 mg l-1 day-1), in contrast to the lower initial C proportion and subsequent C-CO2 rates (<7 mg l-1 day-1) in the lower river basin. We also found that dissolved organic carbon uptake and NO3- and NH4+ production were higher during the dry season than in the rainy season. The low water flow in the river during the dry season accentuated the differences in elemental composition and microbial processing of DOM among the sites, while the high water flow of the rainy season homogenized these factors. Our findings indicate that microbial metabolism operates with reduced efficiency in C-rich environments like forests, particularly when faced with high C/N and C/P ratios in DOM. This study highlights the influence of the tropical hydrological regime (rainy and dry seasons) and the longitudinal changes in the river basin (middle and lower) topography and land cover on microbial metabolism by constraining DOM characteristics, emphasizing the crucial role of elemental ratios in river DOM processing.

Bone loss with aging is independent of gut microbiome in mice

Emerging evidence suggests a significant role of gut microbiome in bone health. Aging is well recognized as a crucial factor influencing the gut microbiome. In this study, we investigated whether age-dependent microbial change contributes to age-related bone loss in CB6F1 mice. The bone phenotype of 24-month-old germ-free (GF) mice was indistinguishable compared to their littermates colonized by fecal transplant at 1-month-old. Moreover, bone loss from 3 to 24-month-old was comparable between GF and specific pathogen-free (SPF) mice. Thus, GF mice were not protected from age-related bone loss. 16S rRNA gene sequencing of fecal samples from 3-month and 24-month-old SPF males indicated an age-dependent microbial shift with an alteration in energy and nutrient metabolism potential. An integrative analysis of 16S predicted metagenome function and LC-MS fecal metabolome revealed an enrichment of protein and amino acid biosynthesis pathways in aged mice. Microbial S-adenosyl methionine metabolism was increased in the aged mice, which has previously been associated with the host aging process. Collectively, aging caused microbial taxonomic and functional alteration in mice. To demonstrate the functional importance of young and old microbiome to bone, we colonized GF mice with fecal microbiome from 3-month or 24-month-old SPF donor mice for 1 and 8 months. The effect of microbial colonization on bone phenotypes was independent of the microbiome donors’ age. In conclusion, our study indicates age-related bone loss occurs independent of gut microbiome.

Pre-ADMET studies of 5-(3',4'-dihydroxyphenyl)-γ-valerolactone, the bioactive intestinal metabolite of proanthocyanidins.

5-(3',4'-Dihydroxyphenyl)-γ-valerolactone (VL) is a bioactive metabolite resulting from the gut microbial metabolism of proanthocyanidins and flavonoids, known for its health-promoting effects, including antidiabetic and anti-inflammatory activities. Although VL has been observed in different in vivo studies, its pre-absorption, distribution, metabolism, excretion, toxicity (ADMET)properties have rarely been investigated. This study aims to address this gap by evaluating the pre-ADMET properties of VL for the first time. Also, the understanding of these properties is significant for correlating the encountered activities to this metabolite. In vitro absorption studies revealed that VL is rapidly metabolized and absorbed as its sulfate phase II conjugate (valerolactone sulfate), which enters systemic circulation and mildly activates the Breast Cancer Resistance Protein efflux transporter. In human S9 liver fraction, a mixture of liver enzymes used to simulate in vivo liver metabolism, VL is metabolized into glucuronic phase II conjugates (valerolactone glucuronide 1 [VLG1] and 2 [VLG2]) with a half-life of 8.72 min and an 80% conversion rate. In human liver microsomes, VL is metabolized at a slower rate (half-life of 23.08 min), suggesting that oxidative metabolism is secondary. Additionally, VL did not activate the pregnane X receptor or inhibit Cytochrome P3A4 (CYP3A4) and Cytochrome P1A2(CYP1A2) enzymes, indicating no risk of herb-drug interactions with coadministered prescription drugs.

CNSC-38. INFLUENCE OF AGE, IMMUNOREGULATORY IDO, AND IMMUNOTHERAPY ON THE MICROBIOME IN MICE WITH AN EXPERIMENTAL BRAIN TUMOR

Abstract OBJECTIVE This study aimed to determine how IDO and subject age impact the gut microbiome and microbial metabolites during immunotherapy for glioblastoma (GBM). METHODS Serum and colon contents were collected from young 16-20- or older adult 92-118-week-old wild-type (WT; C57BL/6), IDO knockout (IDOKO), and IDO enzyme null (H350A) mice analyzed for 16S rRNA gut microbiome composition and microbial-derived aromatic amino acid metabolites via LC/MS/MS. Fecal samples from young 7-8 or older adult 81-85 week-old WT mice with intracranial GL261 brain tumors treated with or without brain radiation (RT) and PD-1 mAb were also analyzed. RESULTS Young and old IDOKO and H350A mice demonstrated a unique gut microbiome signature with an elevated abundance of Bifidobacterium and Helicobacter (p&amp;lt;0.05) and a reduced abundance of Ventriosum and Sireaum compared to WT mice (p&amp;lt;0.001). Prevotellaceae, Muribaculum, Alistipes, Enterohabdus, Clostridia, and Akkermansia were different in IDOKO and H350A mice compared to WT - but only in old mice. Serum aryl-lactates including phenyllactate, indolelacatate, and 4-hydroxyphenyllactate were increased in IDOKO mice compared to WT and H350A mice (p&amp;lt;0.001) – again, only in old mice. Older adult WT mice with GL261 showed lower fecal aryl-lactates compared to younger counterparts. Treatment with RT + PD-1 mAb decreased phenyllactate levels in old but not young mice with GL261 (p&amp;lt;0.05). CONCLUSIONS There are IDO enzyme- and non-enzyme-dependent effects on gut microbiota composition and bioactive microbial aromatic amino acid metabolites. These data warrant further investigation into how microbial metabolism affects immunotherapy efficacy and brain tumor survival across the lifespan.

Microbial metabolism disrupts cytokine activity to impact host immune response

Host-pathogen interactions are shaped by the metabolic status of both the host and pathogen. The host must regulate metabolism to fuel the immune response, while the pathogen must extract metabolic resources from the host to enable its own survival. In this study, we focus on the metabolic interactions of Mycobacterium abscessus with Drosophila melanogaster. We identify MAB_1132c as an asparagine transporter required for pathogenicity in M. abscessus. We show that this requirement is specifically associated with damage to the host: flies infected with MAB_1132c knockout bacteria, or with wild-type bacteria grown in asparagine-restricted conditions, are longer lived without showing a significant change in bacterial load. This is associated with a reduction in the host innate immune response, demonstrated by the decreased transcription of antimicrobial peptides as well as a significant reduction in the ability of the infection to disrupt systemic insulin signaling. Much of the increase in host survival during infection with asparagine-limited M. abscessus can be attributed to alterations in unpaired cytokine signaling. This demonstrates that asparagine transport in M. abscessus prior to infection is not required for replicative fitness in vivo but does significantly influence the interaction with the host immune responses.

Revealing the size effect mechanisms of micro(nano)plastics on nitrogen removal performance of constructed wetland

Micro(nano)plastics (MPs) in aquatic environments can disrupt wastewater treatment, particularly nitrogen removal in constructed wetlands (CWs). However, their broader effects on microbial and plant nitrogen metabolism remain unclear. This study investigated the effects of different-sized MPs (4 mm, 100 µm, and 100 nm) on nitrogen transformation in CWs. Results revealed that 4 mm- and 100 µm-MPs did not significantly affect total nitrogen (TN) removal, although 100 µm-MPs significantly increased leaf antioxidant enzyme activities and reduced plant uptake of nitrogen by 12.95 % (p < 0.05). In contrast, 100 nm-MPs decreased the TN removal efficiency by 7.97 % via inhibiting both nitrification and denitrification, since 100 nm-MPs penetrated cell membranes, disrupted reactive oxygen species balance, and reduced bacterial viability, thus suppressing microbial nitrogen degradation by 8.07 % (p < 0.05). Additionally, 100 nm-MPs significantly inhibited plant growth and reduced plant nitrogen uptake by 16.05 % (p < 0.05). Furthermore, 100 µm-MPs increased the abundance of nitrifiers but reduced denitrifiers and functional genes, whereas 100 nm-MPs reduced the abundance of both nitrifiers and denitrifiers along with their functional genes (p < 0.05). These findings highlight the need to improve waste management to mitigate the adverse effects of MPs on nitrogen removal.

Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave

Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave’s Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.

Aldehyde-based Activation of C2α-lactylthiamin Diphosphate Decarboxylation on Bacterial 1-deoxy-d-xylulose 5-phosphate Synthase.

1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate (donor substrate) and d-glyceraldehyde 3-phosphate (d-GAP, acceptor substrate) in bacterial central metabolism. DXPS uses a ligand-gated mechanism in which binding of a small molecule "trigger" activates the first enzyme-bound intermediate, C2α-lactylThDP (LThDP), to form the reactive carbanion via LThDP decarboxylation. d-GAP is the natural acceptor substrate for DXPS and also serves a role as a trigger to induce LThDP decarboxylation in the gated step. Additionally, we have shown that O2 and d-glyceraldehyde (d-GA) can induce LThDP decarboxylation. We hypothesize this ligand-gated mechanism poises DXPS to sense and respond to cellular cues in metabolic remodeling during bacterial adaptation. Here we sought to characterize features of small molecule inducers of LThDP decarboxylation. Using a combination of CD, NMR and biochemical methods, we demonstrate that the α-hydroxy aldehyde moiety of d-GAP is sufficient to induce LThDP decarboxylation en route to DXP formation. A variety of aliphatic aldehydes also induce LThDP decarboxylation. The study highlights the capacity of DXPS to respond to different molecular cues, lending support to potential multifunctionality of DXPS and its metabolic regulation by this mechanism.