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PubMed2026

Hydrogen-supported biodefluorination of unsaturated perfluorinated carboxylic acids.

PFMeUPA (i.e., (E)-perfluoro(4-methylpent-2-enoic acid) is a unsaturated perfluorohexanoic acid wtih emerging concern due to its potential to cause developmental toxicity. Here, we investigate the sustainable biological treatment of PFMeUPA under anoxic conditions by delineating batch degradation potential and continuous-flow reactor dynamics using hydrogen (H2) as the sole electron donor. In batch assays inoculated with anaerobic digestion sludge, an enriched hydrogenotrophic consortium achieved near-complete removal of 50 μM PFMeUPA over 90-days with a stoichiometric release of 125 μM fluoride (F-), representing a 26% defluorination extent that corresponds to the cleavage of two C-F bonds per molecule. The continuous-flow H₂-based membrane biofilm reactor (MBfR) harboring this enriched anaerobic biofilm was operated for 130 days, achieving 100% removal of 5 μM PFMeUPA and 20% of defluorination at a hydraulic retention time (HRT) = 6 h. Transformation product identification using high-resolution mass spectrometry suggests dominance of reductive defluorination and a shift toward hydrogenated byproducts at later stages. Metagenomic results indicate the enrichment of microbial taxa including Hydrogenophaga (hp_bin.22) and and Azonexus (hp_bin.19) genomes, which carry genes for hydrogen metabolism (hoxH) and fluoride efflux pumps (crcB). This work demonstrates the feasibility of hydrogen-supported biological treatment for unsaturated perfluorinated carboxylic acids from contaminated water. SYNOPSIS: We demonstrate reductive defluorination of branched PFAS by a H2-fed biofilm, with co-occurring hydrogenase and fluoride exporter genes in Hydrogenophaga and Azonexus as potential biodefluorination biomarkers.

Hydrogenotrophic biodefluorination↗
PubMed2025

Genetics of Anorexia Nervosa: Translation to Future Personalized Therapies.

Anorexia nervosa (AN) is a debilitating and often refractory eating disorder that is unique among psychiatric disorders insofar as nutrition is key to recovery. Treatment options and efficacy are limited with no approved medications for AN. Genetic studies are clarifying the etiology of AN, with the goal of eventually informing the development of innovative personalized pharmacologic, nutritional, microbial, and behavioral interventions. We present the current state of genome-wide and epigenome-wide association studies, gut microbiome research, and functional genomics investigations and discuss translating this knowledge into clinical practice.

Humans↗
PubMed2026

A prolonged hydrothermal past at Santorini Caldera revealed by sedimentary trace metal and microbial signatures.

Hydrothermal systems in volcanic calderas are critical in signalling volcanic unrest, forming ore deposits, and sustaining chemosynthetic microorganisms. Analysis of a ~3500-year sequence of sediments collected from the Santorini caldera, Greece, during International Ocean Discovery Program (IODP) Expedition 398 reveals the behaviour of a prolonged paleo-hydrothermal system. Sediment geochemical and metagenomic data record vigorous hydrothermal activity and metal fluxes for ~1100 years, within a 2270-year window between two major eruptions. Sediment hydrothermally-derived trace metals are significantly enriched over background (~200-fold for As and Hg, and 10-50-fold for Mn, Sb, Mo, and V), with long-term metal fluxes (9 t yr-1 As, 2.5 t yr-1 Cu, 7 kg yr-1 Ag) comparable to fluxes from present-day geothermal fields in the Taupo Volcanic Zone. Metagenomic analysis identifies elevated metal resistance genes-signals of microbial adaptation to heightened hydrothermal stressors. Here we integrate geological and genomic evidence to decipher the paleoenvironmental and biogeochemical history of the past hydrothermal system at Santorini caldera.

Geologic Sediments↗
PubMed2005

Saline Systems: a research journal bridging gene systems and ecosystems.

Saline Systems addresses the publication needs of scientists conducting basic and applied research on coastal and inland saline environments and their flora and fauna. The journal covers research at all levels, from individual genes to whole genomes and entire ecosystems. Rapid progress in the molecular biology and microbial ecology of halotolerant and halophilic organisms and the sensitivity of many saline environments warrants an online journal with fast turnaround times. Many saline environments are threatened and the need for an Open Access journal to address the dissemination and sharing of knowledge on their conservation and management is compelling. Saline Systems provides an interdisciplinary forum for scientists working within all of the relevant fields.

Editorial↗
PubMed2006

RNA Silencing in the struggle against disease.

Numerous acquired and hereditary diseases are caused by aberrant cellular or microbial gene expression. As a result of sequencing of the human genome and the genomes of various human pathogens, researchers have gained access to a large number of genes with residual functions. For functional validation of unknown genes, their functions can be specifically inhibited by antisense nucleic acids or small interfering RNAs (siRNAs) and the consequences of the functional loss, that is, the resulting phenotypes, can be analyzed. While antisense nucleic acids block the translation stoichiometrically by docking on the mRNA, siRNAs induce a highly effective cellular mechanism that causes catalytic destruction of several mRNA molecules by a single siRNA molecule. This mechanism, called RNA interference (RNAi), is only intrinsic to eukaryotic cells. Consequently, only eukaryotic target validation is pushed by RNAi whereas time-consuming conventional knockout techniques or the less efficient antisense strategies have to be applied for prokaryotic target validation. We succeeded in triggering gene silencing by siRNA in prokaryotic cells. This opens promising perspectives regarding validation of prokaryotic gene functions.

Genome, Bacterial↗
PubMed2026

A Comprehensive Review on the Biosynthesis of Tropane Alkaloids.

Tropane alkaloids (TA) constitute a class of plant specialized metabolites with important pharmaceutical applications, including the anticholinergic agents hyoscyamine and scopolamine and the local anesthetic cocaine. Over the past decade, advances in genomics, structural biology, and synthetic biology have substantially revised our understanding of TA biosynthesis, leading to the identification of numerous key biosynthetic enzymes and evolutionary mechanisms. This review comprehensively summarizes current knowledge of TA biosynthesis from precursor formation to structurally diverse end products. We describe the pathway from putrescine to tropinone, the stereoselective metabolic branching mediated by Tropinone Reductases, and the downstream biosynthesis of medicinal tropane alkaloids, calystegines, and cocaine. Particular emphasis is placed on recent discoveries concerning catalytic mechanisms, structural determinants of substrate specificity, metabolic compartmentalization, and the convergent evolution of TA biosynthesis in Solanaceae and Erythroxylaceae. We further integrate advances in genomics, evolutionary biology, and metabolic engineering to highlight emerging strategies for microbial production and pathway redesign. By providing a comprehensive synthesis of recent progress and critical perspectives on unresolved questions, this review offers an updated framework for understanding TA biosynthesis and supports future research in plant specialized metabolism, synthetic biology, and natural product engineering.

Tropanes↗
PubMed1994

[Genomic DNA fingerprinting of arbekacin-resistant MRSA by pulsed-field gel electrophoresis].

We surveyed 387 clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) obtained from 26 hospitals isolated in 1993 to determine whether they became resistant to arbekacin (ABK). Twenty-five ABK-resistant MRSA (6.5%) were isolated from 9 hospitals. Analysis of genomic DNA fingerprinting by pulsed-field gel electrophoresis was used to confirm the classification by resistance patterns, phage typing and other biological characters. After digestion with endonuclease SmaI, two or three types of restriction patterns were found in ABK-resistant MRSA isolated from each hospital. We concluded that ABK-resistant MRSA may spread through nosocomial MRSA infections.

Aminoglycosides↗
PubMed2005

Genome-wide screen identifies genes whose inactivation confer resistance to cisplatin in Saccharomyces cerevisiae.

To identify novel genes that mediate cellular resistance to cisplatin, we have screened the collection of Saccharomyces cerevisiae deletion strains. We have found reproducibly 22 genes/open reading frames (ORF), which when deleted, confer resistance to cisplatin at a concentration that is lethal to wild-type cells. Complementation of individual deletion strains with the corresponding wild-type gene abolished cisplatin resistance, confirming that specific gene deletions caused the resistance. Twenty of the genes/ORFs identified have not been previously linked to cisplatin resistance and belong to several distinct functional groups. Major functional groups encode proteins involved in nucleotide metabolism, mRNA catabolism, RNA-polymerase-II-dependent gene regulation and vacuolar transport systems. In addition, proteins that function in ubiquitination, sphingolipid biogenesis, cyclic AMP-dependent signaling, DNA repair, and genome stability are also associated with cisplatin resistance. More than half of the identified genes are known to have sequences or functional homology to mammalian counterparts. Some deletion strains are cross-resistant to selected cytotoxic agents whereas hypersensitive to others. The sensitivity of certain resistant strains to other cytotoxic agents suggests that our findings may point to particular drug combinations that can overcome resistance caused by inactivation of specific genes.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2003

Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems.

We have developed a new type of microarray, restriction site tagged (RST), for example NotI, microarrays. In this approach only sequences surrounding specific restriction sites (i.e. NotI linking clones) were used for generating microarrays. DNA was labeled using a new procedure, NotI representation, where only sequences surrounding NotI sites were labeled. Due to these modifications, the sensitivity of RST microarrays increases several hundred-fold compared to that of ordinary genomic microarrays. In a pilot experiment we have produced NotI microarrays from Gram-positive and Gram-negative bacteria and have shown that even closely related Escherichia coli strains can be easily discriminated using this technique. For example, two E.coli strains, K12 and R2, differ by less than 0.1% in their 16S rRNA sequences and thus the 16S rRNA sequence would not easily discriminate between these strains. However, these strains showed distinctly different hybridization patterns with NotI microarrays. The same technique can be adapted to other restriction enzymes as well. This type of microarray opens the possibility not only for studies of the normal flora of the gut but also for any problem where quantitative and qualitative analysis of microbial (or large viral) genomes is needed.

Bacteria↗
PubMed2026

Prevalence and Genomic Characterization of mcr-Positive Enterobacteriaceae in Retail Meat in Thailand Following the Colistin Ban.

This study aimed to investigate the prevalence and characteristics of mcr-positive Enterobacteriaceae in retail meat in Thailand following the national ban on prophylactic colistin use in food producing animals. A total of 152 meat samples (103 chicken and 49 pork) were collected from supermarkets and open markets between July and September 2023. Samples were screened for mcr-1 to mcr-5 using multiplex PCR. None of the samples from supermarkets tested positive, whereas mcr genes were detected in 15.4% (6/39) and 13.3% (4/30) of chicken and pork samples, respectively, from open markets, with mcr-1 and/or mcr-3 identified. A total of 21 isolates were recovered from PCR-positive samples (11 from chicken and 10 from pork). Escherichia coli was the predominant species (n = 19), followed by Klebsiella pneumoniae (n = 2). All mcr-positive isolates exhibited multidrug resistance. Whole-genome sequencing was performed for 19 non-clonal isolates. One K. pneumoniae strain from a pork sample co-harbored mcr-1 and mcr-8, representing the first report of this combination in the animal sector in Thailand. In addition, virulence-associated genes, including adhesion factors, toxins, and iron acquisition systems, were identified in selected isolates. Core genome SNP-based phylogenetic analysis revealed substantial genomic diversity among the isolates, suggesting relatedness to strains reported prior to the colistin ban. These findings indicate that retail meat from open markets may serve as an important route for the transmission of mcr-positive bacteria in Thailand and highlight the urgent need to incorporate systematic retail meat surveillance into national antimicrobial resistance monitoring programs.

Animals↗
PubMed2025

Clinical carbapenem-resistant Enterobacterales in a University Hospital in Dakar, Senegal: genomic insights into Enterobacter hormaechei ST182 strains carrying blaNDM-5 and blaOXA-48 genes .

Senegal has witnessed the emergence and spread of carbapenem-resistant Enterobacterales (CRE), which often cause deadly infections. Accordingly, this study aimed to determine the antimicrobial susceptibility and prevalence of carbapenemases, as well as to perform a whole-genome sequence analysis of clinical CRE isolates from a university hospital in Dakar, Senegal. MALDI-TOF MS and VITEK2 systems were used for bacterial identification and antimicrobial susceptibility testing (AST). Carbapenemase- and cephalosporinase-encoding genes were screened using simplex end-point polymerase chain reaction. Whole-genome sequencing (WGS) was performed using the Illumina MiSeq platform. The CRE isolates were resistant to almost all the 34 antimicrobials tested. Nevertheless, colistin and amikacin remained active, with susceptibility rates of 96% and 71%, respectively. Only the carbapenemase genes blaOXA-48 (53.8%; 15/28) and blaNDM (35.7%; 10/28) and the cephalosporinase gene blaCMY-1 (25%; 7/28) were identified. In this context, two extensively drug-resistant Enterobacter hormaechei isolates were subjected to WGS analysis. These isolates were assigned as sequence type (ST) 182 and carried several genes related to antimicrobial resistance (AMR), metal tolerance, and virulence. An IncL/M plasmid with 61,054 bp in length was identified as carrying the blaOXA-48 gene, whereas an IncFIB(pECLA)/IncFII(pECLA)/IncX3 mutireplicon plasmid with 217,745 bp in length was detected as harboring the blaNDM-5 gene and other genes related to AMR and metal tolerance. Our study presents the first landscape of clinical CRE circulating in Senegal, along with additional genomic analysis of E. hormaechei ST182 strains, which could be useful for mitigating the burden associated with CRE in this country.IMPORTANCEThe investigation of global critical priority CRE isolates has become crucial to reduce morbidity and mortality associated with AMR. This study revealed that colistin and amikacin can be considered good alternatives for treating CRE-associated infections in Dakar. In addition, the genomic approach revealed that the CRE isolates carried both a wide resistome and virulome. Moreover, the abundance of horizontal gene transfer regions in the genomes suggests the great implications of mobile genetic elements in the spread of AMR in Dakar. Furthermore, this study reported the complete sequences of chromosomes and blaOXA-48 and blaNDM-5-carrying plasmids. Our findings are of great importance because complete genome sequences are still rarely characterized in the West African region. Finally, this study highlights the importance of strengthening genomic surveillance of CRE in sub-Saharan African countries to mitigate the burden associated with these pathogens.

Senegal↗
PubMed2026

Proteobacteria with chemosynthetic potential are highly prevalent in the gills of Hypoplectrus reef fishes.

Fishes host a diverse microbiome in their gills, but a broad characterization of this microbiome at the metagenomic level is lacking. Here, we apply genome-resolved metagenomics to the gills of the hamlets (Hypoplectrus spp), a group of reef fishes from the Greater Caribbean. The analysis of 353 gill samples from 15 hamlet species collected at eight locations over 13 years revealed a stark contrast between the gill microbiota and reef water microbial communities, indicating a distinct and specific gill microbiome. A total of 70 gill-associated metagenome-assembled genomes (MAGs) were recovered. These MAGs belong to 17 lineages, most of which are novel. They relate to known fish gill pathogens, fish gut microbes, free-living and biofilm-associated taxa, indicating that the gill microbiome was assembled from a collection of distinct eco-evolutionary trajectories. The MAGs harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. One lineage in the Burkholderiaceae family was outstandingly prevalent across fish host species, sampling locations and years. Its genome encoded complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. To the best of our knowledge, this is the first line of evidence that fishes may host sulfur-oxidizing chemosynthetic bacteria in their gills. The functional significance of this chemosynthetic potential for the fish host or other members of the gill microbiome remains to be established. The high prevalence of this lineage allowed to build a pangenome. It revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), which parallels the phylogenomic pattern observed in the hamlets. Overall, our findings point to complex fish host-microbe and microbe-microbe eco-evolutionary interactions in the gills that may influence fish physiology, homeostasis and immune response.

Animals↗
PubMed2002

First insight into the genome of an uncultivated crenarchaeote from soil.

Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.

Crenarchaeota↗
PubMed2026

Molecular characterization of pESI-like megaplasmids in Salmonella Infantis from poultry in Lebanon.

UNLABELLED: Salmonella enterica serovar Infantis has emerged as a globally disseminated multidrug-resistant (MDR) pathogen, largely driven by the spread of the plasmid of emerging Salmonella Infantis (pESI)-like megaplasmid. In our study, we investigated the prevalence, antimicrobial resistance (AMR) phenotypes, and genomic features of S. Infantis isolates collected from poultry farms in Lebanon. A total of 72 isolates were recovered during a nationwide surveillance effort, among which 67 (93%) were MDR based on antimicrobial susceptibility testing (disk diffusion and broth microdilution) results, including resistance to critically important agents such as quinolones, and highly important classes such as tetracyclines and sulfonamides. Whole-genome sequencing was performed on 19 isolates selected through a stratified approach to encompass all identified AMR phenotypes; this analysis revealed a conserved pESI-like backbone together with MDR-associated determinants, including sul1, tet(A), and aadA. Plasmid marker analysis confirmed the presence of pESI in the majority of isolates, with plasmid-associated genes (ardA and trbA) and replicon markers (IncP and IncFIB(pN55391)) among the most prevalent. Comparative plasmid alignments with representative pESI sequences from Italy, Turkey, and the United States revealed strong conservation of the backbone alongside regional variation in AMR gene content. These findings highlight the role of poultry production systems in Lebanon as reservoirs for pESI-like megaplasmids and MDR S. Infantis, underscoring the zoonotic and public health risks posed at the human-animal-environment interface. Strengthened surveillance, antimicrobial stewardship, and biosecurity interventions are urgently needed to mitigate the spread of MDR S. Infantis within agriculture and beyond. IMPORTANCE: The emergence of plasmid of emerging Salmonella Infantis (pESI)-like megaplasmids has transformed Salmonella Infantis into a globally distributed multidrug-resistant (MDR) clone with the capacity to persist in livestock and disseminate resistance genes across ecological boundaries. Our study provides the first genomic characterization of pESI-positive S. Infantis from poultry farms in Lebanon, a region with high antimicrobial usage and limited stewardship frameworks. By integrating phenotypic susceptibility testing and whole-genome sequencing, we demonstrate that Lebanese isolates harbor conserved pESI-like backbone markers together with antimicrobial resistance determinants, aligning them with internationally circulating lineages. Comparative analysis with isolates from Italy, Turkey, and the United States highlights both the evolutionary stability and geographic diversity of pESI. These findings emphasize the urgent need for integrated surveillance and stewardship strategies to curb the spread of MDR S. Infantis and reduce the zoonotic risk at the human-animal-environment interface.

Animals↗
PubMed2003

Microarrays for bacterial detection and microbial community analysis.

Several types of microarrays have recently been developed and evaluated for bacterial detection and microbial community analysis. These studies demonstrated that specific, sensitive and quantitative detection could be obtained with both functional gene arrays and community genome arrays. Although single-base mismatch can be differentiated with phylogenetic oligonucleotide arrays, reliable specific detection at the single-base level is still problematic. Microarray-based hybridization approaches are also useful for defining genome diversity and bacterial relatedness. However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial detection and community analysis.

Bacteria↗
PubMed2026

Identification and in-depth characterization of clinical isolates of Peribacillus frigoritolerans.

UNLABELLED: Peribacillus frigoritolerans is a bacterial species commonly found in the environment and used as a plant-growth promoter and biocontrol agent in agriculture. Recent evidence has proven that Peribacillus spp. are also able to cause severe infections in humans, thus emerging as new human pathogens. In this study, for the first time, 10 P. frigoritolerans strains were isolated from human samples (both superficial and sterile deep body sites) and characterized in terms of morphology, lifestyle, genetics, and virulence. The molecular identification by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing was inconclusive, while whole-genome sequencing was effective in properly identifying isolates within the species P. frigoritolerans. The pangenome analysis provided an overview of the virulence potential of P. frigoritolerans, revealing the presence of genes involved in antibiotic resistance and toxin/exoenzyme production. Phenotypically, the strains displayed different features and behaviors, indicating strain-specific properties and high intra-species variability. A part of the strains exhibited virulence factors, being able to swim and swarm, form biofilms, and produce enzymes and toxins. Antibiotic susceptibility testing revealed resistance to ampicillin for all strains and resistance to erythromycin and clindamycin for some of them. Antimicrobial activity against Gram-positive bacteria and fungi was demonstrated, further corroborating the presence of putative bacteriocin/antimicrobial peptide-encoding genes. An association between the overall virulence potential and infection site/severity was hypothesized. Altogether, these findings highlight the extreme diversity within the species, reveal the strain-dependent pathogenic potential of P. frigoritolerans, and support its role as a candidate human pathogen. IMPORTANCE: This study provides insights into the infectious role of Peribacillus frigoritolerans, an almost unknown bacterial species with agrobiotechnological potential but no history of human infections. This is the first report of P. frigoritolerans isolation from human clinical samples. Ten P. frigorit-olerans strains were herein characterized for their morphology, lifestyle, genetics, and virulence, highlighting an extreme intra-species variability and the potential to act as pathogens in humans. Importantly, this study points out the need for unconventional methods for proper identification of this species, since traditional techniques result inconclusive. Resistance to commonly prescribed antibiotics was also evidenced, confirming the importance of antimicrobial testing on clinical iso-lates. This study lays the foundation for a more in-depth characterization of Peribacillus spp. in the clinical context.

Humans↗
PubMed2006

Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulsed field gel electrophoresis.

Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.

Capsid↗
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↗