Biology subjects

Bittar, F.

Publications and source records attributed to Bittar, F..

5 recordsLinked to original sources

bioRxiv2026

Bacterial NDH-1 is a key gut target of metformin mediating its antidiabetic effects

Metformin is the first-line therapy for type 2 diabetes, yet the mechanisms underlying its glucose-lowering effects remain incompletely understood. Increasing evidence implicates gut microbiota as an important mediator of metformin action, but the bacterial targets of the drug remain poorly defined. Here, we identify bacterial NADH oxidoreductase (NDH-1), the homolog of mitochondrial complex I, as a key target of metformin. Metformin inhibited bacterial growth at millimolar concentrations and, at subinhibitory concentrations, markedly impaired carbohydrate fermentation in Escherichia coli and other NDH-1-containing bacteria. Supplementation with nicotinic acid and Mg2+; restored fermentation, whereas pyruvate bypassed the metabolic defect, implicating impaired NAD+; regeneration and disruption of metabolism upstream of pyruvate formation. Genetic analysis further established NDH-1 dependence: metformin failed to inhibit fermentation in an E. coli delta-nuoF mutant lacking functional NDH-1 but retained activity in an NDH-2-deficient delta-ndh strain. Molecular docking predicted metformin binding within the NDH-1 quinone-binding region, proximal to conserved residues involved in quinone reduction. Consistent with this mechanism, Staphylococcus aureus, which lacks NDH-1, was not affected in carbohydrate fermentation, while several gut-associated probiotic and short-chain fatty acid-producing bacteria, including Lactobacillus, Bifidobacterium, and Akkermansia muciniphila, lacked detectable NDH-1 homologs, suggesting intrinsic resistance to this metabolic effect of metformin. These findings identify bacterial NDH-1 as a metabolic target of metformin and provide a mechanistic framework for its effects on the gut microbiota. Selective inhibition of NDH-1-dependent bacteria could alter microbial substrate utilization and ecological interactions in the intestine, potentially contributing to the microbiome-mediated component of metformin's antidiabetic effects.

microbiology↗

bioRxiv2026

Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield?

The Candidate Phyla Radiation (CPR) consists of microorganisms with highly reduced genomes and limited metabolic capabilities, including the inability to synthesize nucleotides and amino acids. Previous studies revealed an unexpected abundance of antimicrobial resistance-related genes in CPR genomes, with methyltransferases (MTs) accounting for up to 47.34% of detected resistance determinants. Here, we investigated the distribution, diversity, and potential functions of MTs across 12,552 CPR genomes, focusing on their roles in antimicrobial resistance and restriction-modification (R-M) systems. Sequence similarity searches were performed using BLASTp, followed by domain validation with the NCBI Conserved Domain Database (CDD). Putative restriction endonucleases (REs) associated with these systems were also identified and analyzed. We detected 20,232 resistance-associated MTs, 7,391 hsdM-like MTs, and 4,737 REs, revealing a high prevalence of putatively functional MTs relative to REs across CPR genomes. Functional CPR MTs and REs displayed extensive sequence divergence from known bacterial homologs and exhibited greater domain diversity and functional complexity than their bacterial counterparts. Selected high-confidence MT candidates were heterologously expressed in Escherichia coli BL21 and characterized using BIOLOG phenotypic assays and antimicrobial susceptibility testing. Transformed strains showed enhanced utilization of methyl pyruvate as a carbon source, whereas no significant antimicrobial resistance phenotype was detected. Collectively, these findings suggest that CPR-encoded MTs are primarily associated with R-M systems, supporting defense against foreign DNA and facilitating nucleotide scavenging rather than direct antimicrobial resistance. This study provides new insights into the adaptive strategies of CPR bacteria and the multifunctional roles of MTs in metabolically streamlined microorganisms. ImportanceCandidate Phyla Radiation (CPR) microorganisms represent a major fraction of Earths microbial diversity, yet their biology remains poorly understood. We show that CPR genomes contain large numbers of methyltransferases and associated restriction enzymes, suggesting the existence of a specialized DNA-processing system. Because CPR organisms have highly reduced metabolic capabilities, this system may help them recover valuable nucleotides from external DNA while simultaneously protecting their genomes from foreign genetic material. We also found that CPR enzymes are highly distinct from those described in other bacteria and display remarkable functional diversity, highlighting the unique evolutionary trajectories of these microorganisms. By providing the first large-scale characterization of these enzymes in CPR, our study offers new insights into how these widespread microbes survive, acquire resources, and interact with their environment, expanding our understanding of microbial diversity and adaptation.

genomics↗

bioRxiv2025

Global lessons from antibiotic resistance: metformin-hydrolyzing genes in transposable elements, a new threat for type II diabetic patients?

Metformin drug, widely used to treat type II diabetic patients, is a major pharmaceutical pollutant of wastewater and rivers. This environmental exposure has driven the evolution of bacteria, such as Aminobacter and Pseudomonas, to degrade metformin via a Ni{superscript 2}-dependent metformin hydrolase complex (MfmAB). Here we decipher the mechanism of acquisition and horizontal transfer of the mfmAB genes, initially mobilized from Aminobacter chromosomes to Pseudomonas conjugative plasmids via common transposable elements (IS1182 and IS3/IS6 elements) in composite transposons, carrying also other genes involved in guanylurea and biguanides degradation (guuH and bguH). These mobile elements, historically involved in acquisition of antibiotic-resistant genes from the environment before clonal expansion in clinical settings, now threaten to co-select for both metformin-degrading and antibiotic resistance genes in contaminated waters. This represents a global threat for diabetic patients with concurrent infections that should be urgently added in the roadmap of research in the context of One Health.

microbiology↗

bioRxiv2021

Adapted protocol for Saccharibacteria co-cultivation: two new members join the club of Candidate Phyla radiation

The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, Candidate Phyla Radiation or CPR have been recognised as representing a large proportion of the microbial kingdom (> 26%). CPR are characterised by their obligate symbiotic or exo-parasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the co-culture of CPR with a suitable bacterial host. Based on various sputa, we tried to purify CPR (Saccharibacteria members) and to cultivate them with pure hosts. This protocol was monitored by real-time PCR quantification using a specific system for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in co-culturing and sequencing a complete genome of two new Saccharibacteria species: Candidatus Minimicrobia naudis and Candidatus Minimicrobia vallesae. In addition, we noticed a decrease in the Ct number of Saccharibacteria, and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members and, in the future, their currently unknown characteristics may be revealed. IMPORTANCEIn this study, the first real-time PCR system has been developed. This technique is able to quantify specifically Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol subsequently facilitates studying the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.

microbiology↗

bioRxiv2021

Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new unique branch, thanks to the intensive application of metagenomics and advances of sequencing technologies. Despite their ultra-small size, reduced genome and metabolic pathways which mainly depend on symbiotic/exo-parasitic relationship with their bacterial host, CPR microbes are abundant and ubiquitous in almost all environments and are consequently survivors in highly competitive circumstances within microbial communities. They have been eventually identified by 16S rRNA analysis and represent more than 26% of microbial diversity. CPR microbes were able to survive in this context, although their defence mechanisms and phenotypic characteristic remain, however, poorly explored. Here, we conducted a thorough in-silico analysis on 4,062 CPR genomes to test whether these ultrasmall microorganisms might encode for antibiotic resistance (AR)-like enzymes. We used an adapted AR screening criteria with an exhaustive consensus database and complementary steps conferring their resistance functions. We conclude by reporting the surprising discovery of rich reservoir of divergent AR-like genes (n= 30,545 HITs, mean=7.5 HITs/genome [0-41] encoding for 89 AR enzymes, distributed across the 13 CPR phyla, and associated with 14 different chemical classes of antimicrobials. However, most HITs found (93.6%) were linked to glycopeptide, beta-lactams, macrolide-lincosamide-streptogramin, tetracycline and aminoglycoside resistance. Moreover, a distinct AR profile was discerned between the microgenomates group and Candidatus Parcubacteria, and between each of them and other CPR phyla. CPR cells seem to be active players during microbial competitive interactions and are well-equipped for the microbial combat in different habitats, supporting their natural survival/persistence and continued existence.

microbiology↗