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At least 19 recordsLinked to original sources
PubMed1976

Co-metabolism of fluorobenzoates by natural microbial populations.

Co-metabolic degradation of monofluorobenzoates was carried out by a mixed soil population in a basal salts medium. The monofluorobenzoates did not support growth of microorganisms but were shown to be subject to ring cleavage as a result of microbial activity. Rate of ring cleavage was increased by use of the co-substrate enrichment technique using glucose as the co-substrate. Results indicate that the monofluorobenzoates were subject to an initial co-metabolic attack with glucose, providing the energy necessary for co-metabolism to proceed to a point where complete metabolism became possible.

Bacteria↗
PubMed1989

Enrichment of dibenzofuran utilizing bacteria with high co-metabolic potential towards dibenzodioxin and other anellated aromatics.

Dibenzofuran degrading bacteria were enriched from various environmental sources. A mutualistic mixed culture of strain DPO 220 and strain DPO 230 was characterized. Strain DPO 220 alone showed limited growth with dibenzofuran as sole source of carbon and energy (td greater than or equal to 4.5 h). A labile degradation product, C12H10O5, and salicylate were isolated from the culture fluid. Salicylate was found to be a central intermediate of DBF-degradation. Strain DPO 220 co-metabolized a wide range of anellated aromatics as well as heteroaromatics. High rates of co-oxidation of dibenzodioxin demonstrate analogue-enrichment to be a powerful technique for selecting enzymatic activities for otherwise non-degradable substrates.

Bacteria↗
PubMed1989

[Transformation of xenobiotics by soil microorganisms and their potential distribution].

Xenobiotics, i.e., unnaturally occurring organic substances, become transformed in soils, waters and ground water aquifers primarily by co-metabolism or by physico-chemical processes. The persistence of both xenobiotics and natural substances, i.e., time required for a 95% disappearance of the original compounds, is dependent on the chemical and physical characteristics of a compound itself (its molecular recalcitrance), on soil properties and conditions, and on the relationships of these factors. Among the specific factors which influence the persistence of individual compounds belong both natural and anthropogenic "non-physiological" characteristics and structures. Naturally occurring compounds become transformed metabolically, those with a xenobiotic character mainly co-metabolically. The degradation kinetics for both types of compounds have an exponential character, and according to a semi-logarithmic figure, it is a first order function (i.e., mineralization or transformation have a linear character). The co-metabolic processes depend closely on the concentration of the given compound in soil solution as well as on the general microbial activity. Metabolically utilizable compounds may serve microorganisms as sources of C, N, and eventually also of P and energy, after the necessary enzymes have become induced and synthetized. Co-metabolical compounds may not have these functions or microorganisms may require a long period to become adapted to them. In general, all means which support the microbial activity, may also support the co-metabolical transformations in the soil. This is especially true for aeration and manuring of soil both of which stimulate unspecifically the proliferation and activity of microorganisms, and indirectly also a co-metabolism of xenobiotics.

Bacteria↗
PubMed1989

D-xylose utilization by Saccharomyces cerevisiae.

Although it is generally accepted that Saccharomyces cerevisiae is unable to assimilate D-xylose, four strains were found to utilize xylose aerobically at different efficiencies in the presence of a mixture of substrates. The degree of D-xylose utilization by S. cerevisiae ATCC 26602 depended upon the presence of other substrates or yeast extract. The greatest amount of xylose (up to 69% over 7 d) was utilized when sugar substrates such as D-ribose were co-metabolized. Much lower degrees of utilization occurred with co-metabolism of organic acids, polyols or ethanol. A mixture of D-glucose, D-ribose, D-raffinose, glycerol and D-xylose resulted in greater xylose utilization than the presence of a single substrate and xylose. The absence of growth on a co-substrate alone did not prevent the utilization of xylose in its presence. Xylose was co-metabolized with ribose under anaerobic conditions but at a much slower rate than under aerobic conditions. When [14C]xylose was utilized in the presence of ribose under anaerobic conditions, the radioactive label was detected mainly in xylitol and not in the small amounts of ethanol produced. Under aerobic conditions the radioactive label was distributed between xylitol (91.3 +/- 0.8%), CO2 (2.6 +/- 2.3%) and biomass (1.7 +/- 0.6%). No other metabolic products were detected. Whereas most xylose was dissimilated rather than assimilated by S. cerevisiae, the organism apparently possesses a pathway which completely oxidizes xylose in the presence of another substrate.

Aerobiosis↗
PubMed2026

Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.

Microbial symbiosis underpins host adaptation, yet mechanisms of metabolic integration in holobionts remain unclear. Using metatranscriptomics, genomics, and metabolic assays, we investigated gut microbiome interactions in the European spruce bark beetle (Ips typographus). We observed metabolic complementarity among symbionts and host, forming cross-domain networks that support nutrient acquisition. Nitrogen recycling revealed strong interdependence: no single partner possessed a complete uric acid degradation pathway, but combined evidence supports a distributed pathway spanning beetle, Bacteria, and fungi. Additionally, bacterial nitrate reduction to ammonia indicates a potential nitrogen influx, making otherwise inaccessible inorganic nitrogen available to the host. Shaped by microbial interactions, symbionts also likely supply specific amino acids, while vitamin metabolism showed cross-domain co-metabolism, with Bacteria as main producers of B vitamins, while host and fungi modulated interconversion. Carbohydrate degradation was highly partitioned; bacteria target xylan and pectin, while fungi contribute to glucan breakdown. Crucially, our data provide indirect evidence that the beetle may contribute to complete cellulose degradation, highlighting an underappreciated host role in lignocellulose processing. In terms of enzymatic functional diversity, the bacteriome emerged as the most important microbiome component-an observation that contrasts with the traditional focus on fungi and underscores the need to consider bacterial contributions in insect symbioses. Despite life-stage variation, core metabolic functions remained stable. Overall, metabolic interdependence, rather than microbial composition alone, structures holobiont function. These results highlight functional redundancy and ecological resilience, emphasizing the importance of microbial cooperation and host-microbe metabolic evolution.

Bark beetle↗
PubMed1991

Degradation and mineralization of 3-chlorobiphenyl by a mixed aerobic bacterial culture.

A mixed bacterial culture obtained from polychlorinated-biphenyl-contaminated river sediments proved capable of degrading 3-chlorobiphenyl (3-CB) under aerobic laboratory conditions. Almost total mineralization of 150 mg/l of 3-CB occurred when, after 3 days of incubation, the mineral medium was supplied with benzoic acid as a carbon source. Two strains of Pseudomonas capable of degrading the substrate to 3-chlorobenzoic acid and a strain of Pseudomonas fluorescens capable of co-metabolizing this metabolite were selected from the mixed culture. A nearly stoichiometric amount of chloride, which defines the percentage of total mineralization, was eliminated during mixed culture growth.

Bacteria, Aerobic↗
PubMed1992

Degradation of phenol and phenolic compounds by Pseudomonas putida EKII.

The phenol-degrading strain Pseudomonas putida EKII was isolated from a soil enrichment culture and utilized phenol up to 10.6 mM (1.0 g.l-1) as the sole source of carbon and energy. Furthermore, cresols, chlorophenols, 3,4-dimethylphenol, and 4-chloro-m-cresol were metabolized as sole substrates by phenol-grown resting cells of strain EKII. Under conditions of cell growth, degradation of these xenobiotics was achieved only in co-metabolism with phenol. Phenol hydroxylase activity was detectable in whole cells but not in cell-free extracts. The specificity of the hydroxylating enzyme was found during transformation of cresols and chlorophenols: ortho- and meta-substituted phenols were degraded via 3-substituted catechols, while degradation of para-substituted phenols proceeded via 4-substituted catechols. In cell-free extracts of phenol-grown cells a high level of catechol 2,3-dioxygenase as well as smaller amounts of 2-hydroxymuconic semialdehyde hydrolyase and catechol 1,2-dioxygenase were detected. The ring-cleaving enzymes were characterized after partial purification by DEAE-cellulose chromatography.

Biodegradation, Environmental↗
PubMed1989

Inhibition of benzo[a]pyrene-7,8-diol formation in vitro by complex organic mixtures.

Coal-derived complex organic mixtures [COM] with boiling points greater than or equal to 370 degrees C (greater than or equal to 700 degrees F) are known to inhibit both mouse skin tumor initiation by benzo[a]pyrene [BAP], and BAP-induced bacterial mutagenesis. We have examined the effects of 5 COM, with boiling points of 149-370 degrees C (300-700 degrees F), 370-398 degrees C (700-750 degrees F), 398-426 degrees C (750-800 degrees F), 426-454 degrees C (800-850 degrees F), and greater than 454 degrees C (greater than 850 degrees F), on both the rate and the route of BAP metabolism by rat liver homogenates in vitro. When co-metabolized in 40:1 excess with BAP, all of the COM reduced the rate of BAP metabolism. The 149-370 degrees C (300-700 degrees F) COM reduced the initial rate of BAP metabolism to 34% of the rate for BAP alone, while the four higher-boiling COM reduced it to 6.3-9.3% of the rate for BAP alone. In addition, the 2 highest-boiling COM (426-454 degrees C and greater than 454 degrees C boiling points) were found to reduce the percentage of BAP metabolized to BAP-7,8-diol, in comparison to incubations using BAP alone. The 370-398 degrees C and 398-426 degrees C COM did not alter the percentage of BAP metabolized to BAP-7,8-diol, while the 149-370 degrees C COM increased it. Both the general inhibition of BAP metabolism (by all of the COM), and the specific inhibition of BAP-7,8-diol formation (by the highest-boiling COM) may play a role in the inhibition of formation of BAP-induced skin tumors by these materials.

Animals↗
PubMed1991

Transformation of 3-chlorodibenzofuran by Pseudomonas sp. HH69.

The dibenzofuran-degrading bacterial strain Pseudomonas sp. HH69 showed high oxidative activity towards 3-chlorodibenzofuran (3CDF). During the co-metabolic turnover of 3CDF large amounts of 4-chlorosalicylate and temporarily small amounts of salicylate were excreted. Simultaneously a yellow colour appeared due to the excretion of two polar products. Conversion of 3CDF by a mutant, derived from Pseudomonas sp. HH69 and defective in 2,3-dihydroxybiphenyl-1,2-dioxygenase led to the formation of equal quantities of 4'-chloro-2,2',3-trihydroxybiphenyl (4'CTHBP) and 4-chloro-2,2',3-trihydroxybiphenyl (4CTHBP). Crude extracts of the wild type transformed 4'CTHBP to 4-chlorosalicylate, whilst 4CTHBP was transformed to salicylate. Hence, we propose a non-selective initial attack on both aromatic rings of 3CDF and a degradative pathway for the resulting chlorotrihydroxybiphenyls.

Benzofurans↗
PubMed2025

A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.

Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.

Humans↗
PubMed1992

Intracellular pH and the role of D-lactate dehydrogenase in the production of metabolic end products by Leuconostoc lactis.

The kinetics of lactate dehydrogenase from Leuconostoc lactis NCW1 were studied. The pH optimum for the enzyme depended on the concentration of pyruvate used in the assay and the enzyme displayed an ordered mechanism with respect to substrate binding. The Km for pyruvate and NADH and the Vmax of the enzyme decreased 20-, 30- and 6-fold respectively as the pH decreased from 8.0 to 5.0. No activators were found and none of the intermediates of the phosphoketolase pathway tested inhibited the enzyme. ATP, ADP, GTP and NAD+ were inhibitory. The intracellular volume (Vol(in)) and intracellular pH (pH(in)) decreased as the extracellular pH (pH(ex)) decreased. Co-metabolism of citrate and glucose affected the Vol(in) but did not affect the pH(in), which decreased by 0.6 units per unit change in pH(ex); at pH 7.0, the pH(in) and pH(ex) were equal. The results suggest that pH(in) may play a role in determining the production of diacetyl and acetoin at low pH by Leuconostoc.

Adenosine Diphosphate↗
PubMed1991

Degradation of 2-methylaniline and chlorinated isomers of 2-methylaniline by Rhodococcus rhodochrous strain CTM.

Rhodococcus rhodochrous strain CTM co-metabolized 2-methylaniline and some of its chlorinated isomers in the presence of ethanol as additional carbon source. Degradation of 2-methylaniline proceeded via 3-methylcatechol, which was metabolized mainly by meta-cleavage. In the case of 3-chloro-2-methylaniline, however, only a small proportion (about 10%) was subjected to meta-cleavage; the chlorinated meta-cleavage product was accumulated in the culture fluid as a dead-end metabolite. In contrast, 4-chloro-2-methylaniline was degraded via ortho-cleavage exclusively. Enzyme assays showed the presence of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase as inducible enzymes in strain CTM. Extended cultivation of strain CTM with 2-methylaniline and 3-chloro-2-methylaniline yielded mutants, including R. rhodochrous strain CTM2, that had lost catechol 2,3-dioxygenase activity; these mutants degraded the aromatic amines exclusively via the ortho-cleavage pathway. DNA hybridization experiments using a gene probe revealed the loss of the catechol 2,3-dioxygenase gene from strain CTM2.

Aniline Compounds↗
PubMed1989

Microbiological methods for the cleanup of soil and ground water contaminated with halogenated organic compounds.

There is growing interest in the enhancement of microbial degradative activities as a means of bringing about the in situ cleanup of contaminated soils and ground water. The halogenated organic compounds are likely to be prime targets for such biotechnological processes because of their widespread utilisation and the biodegradability of many of the most commonly used compounds. The aim of this review is to consider the potential for microbiological cleanup of haloorganic-contaminated sites. The technologies available involve the provision of suitable environmental conditions to facilitate maximum biodegradation rates either in the subsurface or in on-site bioreactors. Methodologies include the supply of inorganic nutrients, the supply of oxygen gas, the addition of degradative microbial inocula and the introduction of co-metabolic substrates. The potential efficiencies and limitations of the methods are critically discussed from a microbiological viewpoint with respect to substrate degradability and population responses to supplementation.

Bacteria↗
PubMed1979

Accelerated mineralization of two organophosphate insecticides in the rhizosphere.

Numerous xenobiotic compounds, including the organophosphate insecticides O, O-diethyl-O-(2-isopropyl-6-methyl-4-pyrimidinyl) phosphorothioate (diazinon) and O, O-diethyl-O-p-nitrophenyl phosphorothioate (parathion), appear to be degraded in the soil environment by an initial cometabolic attack. Comparing the mineralization rates of radiolabeled diazinon and parathion in root-free and in rhizosphere soil, we tested our hypothesis that, because of the presence of root exudates, the rhizosphere is an especially favorable environment for such co-metabolic transformations. The insecticides were added individually at 5 mug/g to sealed flasks containing either soil permeated by the root system of a bush bean plant or identical soil without roots. Periodically, the flask atmospheres were flushed through traps and the evolved (14)CO(2) was quantitated. Bush bean plant roots without associated rhizosphere microorganisms failed to produce a significant amount of (14)CO(2). During 1 month of incubation, rhizosphere flasks mineralized 12.9 and 17.9% of the added diazinon and parathion radiocarbon, respectively, compared to 5.0 and 7.8% by the soil without roots. The mineralization of parathion but not of diazinon was stimulated in a similar manner when soil without roots was repeatedly irrigated with a root exudate produced in aseptic solution culture. Viable counts of microorganisms on soil extract agar were not significantly altered by root permeation or by root exudate treatment of the soil, leaving population selection and/or enhanced cometabolic activity as the most plausible interpretations for the observed stimulatory effects. Rhizosphere interactions may substantially shorten the predicted half-lives of some xenobiotic compounds in soil.

Bacteria↗
PubMed2026

Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.

BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed. RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT‒qPCR and ELISA. CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.

Probiotics↗
PubMed2024

Investigating the degradation potential of microbial consortia for perfluorooctane sulfonate through a functional "top-down" screening approach.

Perfluorooctane sulfonate (PFOS) is a prominent perfluorinated compound commonly found in the environment, known to pose various risks to human health. However, the removal of PFOS presents significant challenges, primarily due to the limited discovery of bacteria capable of effectively degrading PFOS. Moreover, single degradation bacteria often encounter obstacles in individual cultivation and the breakdown of complex pollutants. In contrast, microbial consortia have shown promise in pollutant degradation. This study employed a continuous enrichment method, combined with multiple co-metabolic substrates, to investigate a microbial consortium with the potential for PFOS degradation. By employing this methodology, we effectively identified a microbial consortium that demonstrated the capacity to reduce PFOS when exposed to an optimal concentration of methanol. The consortium predominantly comprised of Hyphomicrobium species (46.7%) along with unclassified microorganisms (53.0%). Over a duration of 20 days, the PFOS concentration exhibited a notable decrease of 56.7% in comparison to the initial level, while considering the exclusion of adsorption effects. Furthermore, by comparing the predicted metabolic pathways of the microbial consortium with the genome of a known chloromethane-degrading bacterium, Hyphomicrobium sp. MC1, using the KEGG database, we observed distinct variations in the metabolic pathways, suggesting the potential role of the unclassified microorganisms. These findings underscore the potential effectiveness of a "top-down" functional microbial screening approach in the degradation of stubborn pollutants.

Fluorocarbons↗