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At least 19 recordsLinked to original sources
PubMed2026

Decoding microbial metabolic complementarity from individual traits to community structuring.

A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.

Bacteria↗
PubMed2026

Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.

Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remain limited, in part because the role of donor‒recipient metabolic interactions in shaping the post-FMT community remains poorly understood. Here, we leverage metagenome-scale metabolic modeling to quantify metabolic niche complementarity between donor and recipient microbiomes and predict post-FMT community composition. Using MICOM-derived metabolic models, we show that donor genomes whose metabolic flux profiles are more dissimilar from the recipient community colonize at significantly higher rates in a murine FMT model. In a human IBS trial, the same metric predicted post-FMT community composition via leave-one-out cross-validation and captured known disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to evaluate personalized donor screening, identifying super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition. Together, these results support metabolic niche complementarity as a potential determinant of post-FMT community composition and provide a mechanistic basis for evaluating donor-recipient metabolic compatibility. This framework offers a scalable approach for generating testable hypotheses for personalized donor selection.

Fecal Microbiota Transplantation↗
PubMed2006

Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters.

Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission.

Amino Acids↗
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↗
PubMed1990

Carnitine and coenzyme Q10: biochemical properties and functions, synergism and complementary action.

The mechanisms by which carnitine and coenzyme Q10 intervene in the energetic metabolism are described. In particular, the metabolic stages in which the action of carnitine is complementary to the action of coenzyme Q10 are illustrated. The synergism of the pharmacological and therapeutic actions that is found when these compounds are administered together is explained on the basis of their biochemical and metabolic complementarity.

Animals↗
PubMed2026

Metabolic niche differentiation and napA evolution stabilize partial denitrification in wastewater ecosystems.

Although partial denitrification (PD) is increasingly applied as a nitrite-supplying strategy for anammox-based nitrogen removal, the ecological distribution, metabolic specialization, and genomic determinants of stable nitrite accumulation remain poorly understood at the ecosystem scale. Here, we reconstructed 516 high-quality metagenome-assembled genomes (MAGs) using high-depth metagenomic sequencing of 107 wastewater treatment plants and classified denitrifiers according to their nitrite production or consumption capacities. Of these genomes, 23% (120 MAGs) were classified as partial denitrifiers, 41% (211 MAGs) as complete denitrifiers, and 36% (185 MAGs) as nitrite-reducing denitrifiers, revealing pronounced functional partitioning rather than dominance by complete denitrification pathways. Comparative genomics showed that partial denitrifiers possess metabolic architectures favoring rapid carbon oxidation and NADH generation while exhibiting constrained NADPH production and biosynthetic investment, thereby promoting nitrate-to-nitrite conversion but limiting subsequent nitrite reduction. Nitrite accumulation does not result from incomplete denitrification pathways but from metabolic niche differentiation. These metabolic trade-offs were further associated with the evolutionary divergence of the periplasmic nitrate reductase gene, napA, which displayed distinct sequence characteristics and genomic contexts between partial and complete denitrifiers. Integration of carbohydrate-active enzyme repertoires further revealed metabolic complementarity between partial denitrifiers and anammox bacteria, supporting efficient carbon handoff without direct substrate competition. From an engineering perspective, operating conditions that impose moderate electron limitation, such as low or fluctuating C/N ratios and intermittent carbon feeding, may selectively enrich partial denitrifiers and enhance a stable nitrite supply for PD-anammox systems. Together, these findings identify PD as a predictable ecological state shaped by genome-encoded metabolic specialization and provide a mechanistic basis for designing robust, low-carbon nitrogen-removal processes.

Anammox↗
PubMed2006

[The variants of personality maladaptation in patients with multiple sclerosis].

Thirty-four patients with multiple sclerosis (MS), aged 14-52 years, age-at-disease-onset 24,3 +/- 7,5 years, have been studied. Disease severity score measured with the Kurtzke scale (EDSS) was 3,6 +/- 1,7. Seven patients were at the exacerbation stage, 27--in remission. Personality features in context of its maladaptation were studied using a modified version of MMPI. Neurotic, psychotic and mixed types of maladaptation have been singled out. The positron emission tomography indices of metabolic brain activity by glucose metabolism rate were concurrently determined. Data on the complementarity of metabolic processes activity in frontal, temporal-parietal and limbic cortical areas with different variants of personality maladaptation and different MMPI personality profiles were obtained.

Adaptation, Psychological↗
PubMed2026

In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.

BACKGROUND: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison. RESULTS: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence. CONCLUSIONS: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.

Metabolic Networks and Pathways↗
PubMed1991

Complementarity of magnetic resonance spectroscopy, positron emission tomography and single photon emission tomography for the in vivo investigation of human cardiac metabolism and neurotransmission.

The three techniques allowing the noninvasive study of cardiac metabolism, namely magnetic resonance spectroscopy (MRS), positron emission tomography (PET) and single photon emission computed tomography (SPET), all use external detection with stable or radioactive isotopes. These techniques yield different information. PET is quantitative and very sensitive, and therefore only tracer amounts of molecules need to be injected. It allows neurotransmitters and receptors to be studied and a global view of metabolism (oxygen consumption, glucose and fatty acid utilization) to be obtained. SPET also has good sensitivity, but uses gamma-emitting isotopes of heteroatoms. Their longer half-lives allow follow-up for hours or days. MRS is based on stable elements with high (hydrogen 1, phosphorus 31, fluorine 19...) or low (carbon 13, Deuterium) natural abundance. It has very low sensitivity and only millimolar concentrations of substrates can be detected, but various parts of metabolism can be studied. The in vivo measurement of myocardial concentration of substances has many problems that are common to all three techniques (measurement of the volume, measurement of the quantity of each molecule, resolution, partial volume effect, improvement of the signal-to-noise ratio, movement of the organ). The complementarity of the techniques is illustrated by their applications to the study of cardiac metabolism. For instance, the energy metabolism can be studied by 31P-MRS, which detects the high-energy compounds ATP and phosphocreatine, and 13C-MRS yields information on the tricarboxylic acid cycle activity. PET and SPET allow the utilization of fatty acids, the normal fuels of the heart, to be studied. During ischaemia, PET with 18F-fluorodeoxyglucose (18FDG) can determine the glucose consumption and 1H-MRS shows the increase in lactic acid, reflecting anaerobic glycolysis. Comparison of the use of acetate labelled with 11C for PET or 13C for MRS shows the potentials and limitations of each technique. Myocardial perfusion can be evaluated directly with various PET tracers or indirectly with thallium 201 or various technetium-99m-labelled tracers by SPET. No MRS marker of perfusion is so far clinically available. Mainly SPET and PET are used clinically for the investigation of ischaemic heart disease as well as cardiomyopathies, but some initial results using 31P-MRS are being obtained.

Animals↗
PubMed1997

Molecular complementarity I: the complementarity theory of the origin and evolution of life.

We assert that molecular complementarity is much more widespread than is commonly acknowledged in biological systems, if not actually ubiquitous. It creates the coupling necessary for non-equilibrium systems to form. It stabilizes aggregates against degradation, thereby increasing concentrations to levels adequate to foster the formation of prebiotic systems and represents the earliest form in which natural selection was manifested. Complementarity confers on all interacting parts of such systems in formation carrying capacity. RNA or DNA are not, therefore, necessary to the emergence of life, but represent specialized forms of complementary molecules adapted specifically to information storage and transmission. Non-genetic information exists in metabolic functions and probably preceded genetic information historically. Complementarity also provides the basis for homeostasis and buffering of such systems not only in a chemical, but also in structural and temporal terms. It provides a mechanism for understanding how new, emergent properties can arise, and a basis for the self-organization of systems. We demonstrate that such aggregates can have properties not predictable from their individual components, thus providing a means for understanding how new functions emerge during evolution. Selection is for modules rather than individual components. The formation of functional sub-systems that can then be integrated as modules greatly increases the probability of the emergence of life. The result of such modular evolution alters the standard view of evolution from a tree or bush-like image to an integrated network composed of alternating periods of integration (as molecules and molecular aggregates merge) and divergence (as molecules and aggregates undergo variations). This provides a mechanism for evolution by punctuated equilibria. Molecular complementarity puts strict limits on variations, however, preventing evolution from being random. The evolutionary, physiological and embryological consequences of this view of life are outlined, and various models and experiments described that further characterize it.

Animals↗
PubMed1994

Hypoglycemia caused by selegiline, an antiparkinsonian drug: can such side effects be predicted?

Treatment with selegiline produced profound hypoglycemia in a 70-year-old man with Parkinson's disease. The hypoglycemia was accompanied by hyperinsulinemia and persisted for 1 week after selegiline was discontinued. Although this side effect of antidepressant monoamine oxidase inhibitors was well documented in 1959-1968 publications, it was not known to the manufacturer of selegiline. Effects of drugs on glucose metabolism may be predictable through a novel molecular modeling technique developed in our laboratories, which shows that glucose exhibits stereochemical complementarity to a specific site in partially unwound DNA. Selegiline and other molecules affecting glucose metabolism fit into the same DNA base sequence. It therefore should be possible to employ this technique to identify pharmaceutical agents that possess hypoglycemic or hyperglycemic effects in vivo.

Aged↗
PubMed1999

Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks.

Biological organization is based on the coherent energy transfer allowing for macromolecules to operate with high efficiency and realize computation. Computation is executed with virtually 100% efficiency via the coherent operation of molecular machines in which low-energy recognitions trigger energy-driven non-equilibrium dynamic processes. The recognition process is of quantum mechanical nature being a non-demolition measurement. It underlies the enzymatic conversion of a substrate into the product (an elementary metabolic phenomenon); the switching via separation of the direct and reverse routes in futile cycles provides the generation and complication of metabolic networks (coherence within cycles is maintained by the supramolecular organization of enzymes); the genetic level corresponding to the appearance of digital information is based on reflective arrows (catalysts realize their own self-reproduction) and operation of hypercycles. Every metabolic cycle via reciprocal regulation of both its halves can generate rhythms and spatial structures (resulting from the temporally organized depositions from the cycles). Via coherent events which percolate from the elementary submolecular level to organismic entities, self-assembly based on the molecular complementarity is realized and the dynamic informational field operating within the metabolic network is generated.

Isoenzymes↗
PubMed2006

Compositional complementarity and prebiotic ecology in the origin of life.

We hypothesize that life began not with the first self-reproducing molecule or metabolic network, but as a prebiotic ecology of co-evolving populations of macromolecular aggregates (composomes). Each composome species had a particular molecular composition resulting from molecular complementarity among environmentally available prebiotic compounds. Natural selection acted on composomal species that varied in properties and functions such as stability, catalysis, fission, fusion and selective accumulation of molecules from solution. Fission permitted molecular replication based on composition rather than linear structure, while fusion created composomal variability. Catalytic functions provided additional chemical novelty resulting eventually in autocatalytic and mutually catalytic networks within composomal species. Composomal autocatalysis and interdependence allowed the Darwinian co-evolution of content and control (metabolism). The existence of chemical interfaces within complex composomes created linear templates upon which self-reproducing molecules (such as RNA) could be synthesized, permitting the evolution of informational replication by molecular templating. Mathematical and experimental tests are proposed.

Biological Evolution↗
PubMed1997

Molecular modelling of mammalian CYP2B isoforms and their interaction with substrates, inhibitors and redox partners.

1. The construction of three-dimensional models of CYP2B isozymes from rat (CYP2B1), rabbit (CYP2B4) and man (CYP2B6), based on a multiple sequence alignment with CYP102, a unique eukaryotic-like bacterial P450 (in terms of possessing an NADPH-dependent FAD- and FMN-containing oxidoreductase redox partner) of known crystal structure, is reported. 2. The enzyme models described are shown to be consistent with experimental evidence from site-directed mutagenesis studies, antibody recognition sites and amino acid residues identified as being associated with redox partner interactions, together with the location of a key serine residue (Ser-128) likely to be involved in protein kinaseA-mediated phosphorylation. 3. A substantial number of known substrates and inhibitors of CYP2B isozymes are shown to fit the putative active sites of the enzyme models in agreement with their reported position of metabolism or mode of inhibition respectively. In particular, there is complementarity between the characteristic non-planar geometries of CYP2B substrates and key groups in the enzymes' active sites. 4. Molecular modelling of CYP2B isozymes appears to rationalize a number of the reported findings from quantitative structure-activity relationship investigations on series of CYP2B substrates and inhibitors.

Amino Acid Sequence↗
PubMed2000

Molecular modelling of human CYP2E1 by homology with the CYP102 haemoprotein domain: investigation of the interactions of substrates and inhibitors within the putative active site of the human CYP2E1 isoform.

1. The construction of a three-dimensional model of human CYP2E1 is reported. It is based on homology with the haemoprotein domain of the unusual bacterial P450, CYP102, which is of known crystal structure. 2. Interactive docking of a number of human CYP2E1 substrates is consistent with their known positions of CYP2E1-mediated metabolism, where specific interactions with key active site amino acid side-chains appear to rationalize the binding and orientation of substrate molecules. 3. Amino acid residues within the putative active site of human CYP2E1, including those associated with the binding of substrates and inhibitors, are shown to correspond with those identified by site-directed mutagenesis experiments conducted on CYP2 family isoforms, and they are known to affect substrate metabolism regioselectivity. 4. Consequently, it was found that the CYP2E1 active site exhibits complementarity with the structural characteristics of known substrates and inhibitors of this enzyme, including their relatively low molecular weights and disposition of hydrogen bond-forming groups.

Amino Acid Sequence↗
PubMed2002

Development of a combined protein and pharmacophore model for cytochrome P450 2C9.

A combined protein and pharmacophore model for cytochrome P450 2C9 (CYP2C9) has been derived using various computational chemistry techniques. A combination of pharmacophore modeling (using 31 metabolic pathways for 27 substrates), protein modeling (using the rabbit CYP2C5/3 crystal structure), and molecular orbital calculations was used to derive a model that incorporated steric, electronic, and chemical stability properties. The initial pharmacophore model (based on a subset of 17 metabolic pathways for 16 substrates) and the protein model used to construct the combined model were derived independently and showed a large degree of complementarity. The combined model is in agreement with experimental results concerning the substrates used to derive the model and with site-directed mutagenesis data available for CYP2C9. The model has been successfully used to predict the metabolism of substrates not used to construct the model, of which four examples are discussed in detail. The model has also been successful in explaining the differences in substrate specificity between CYP2C9 and CYP2C19.

Amino Acid Sequence↗
PubMed1998

Genetic engineering in mice: impact on insulin signalling and action.

The expression of a number of genes encoding key players in insulin signalling and action, including insulin, insulin receptor (IR), downstream signalling molecules such as insulin receptor substrate-1 (IRS-1) and IRS-2, glucose transporters (GLUT4, GLUT2) and important metabolic enzymes such as glucokinase, has now been altered in transgenic or knockout mice. Such mice presented with phenotypes ranging from mild defects, revealing complementarity between key molecules or pathways, to severe diabetes with ketoacidosis and early postnatal death. Insulin action could also be improved by overproduction of proteins acting at regulatory steps. The development of diabetes by combining mutations, which alone do not lead to major metabolic alterations, validated the 'diabetogenes' concept of non-insulin-dependent diabetes mellitus. Genes encoding insulin-like growth factors (IGF-I and IGF-II) and their type I receptor (IGF-IR) have also been disrupted. It appears that although IR and IGF-IR are both capable of metabolic and mitogenic signalling, they are not fully redundant. However, IR could replace IGF-IR if efficiently activated by IGF-II. Studies with cell lines lacking IR or IGF-IR lend support to such conclusions. Concerning the issues of specificity and redundancy, studies with cell lines derived from IRS-1-deficient mice showed that IRS-1 and IRS-2 are also not completely interchangeable.

Animals↗