Biology subjects

Gounot, J.-S.

Publications and source records attributed to Gounot, J.-S..

8 recordsLinked to original sources

bioRxiv2026

GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

Despite being important ecological modulators of the gut microbiome, bacteriophage diversity and function remain under-characterized. We show that short-read metagenomic surveys can miss even globally highly prevalent viral family-level clusters (VFCs), that can be readily assembled and characterized with long-read metagenomic data from a relatively small cohort (n=109). While gut Bacteroidota phages have been the prevailing focus in the literature, we show that highly prevalent gut phage families frequently have Firmicutes hosts (termed GuFi phages), with broad host ranges verified using proximity-ligation (Hi-C) sequencing data. High-throughput sequencing of virus-like particles from fecal samples detected frequent enrichment of GuFi phages across samples, revealing their under-appreciated impact on the gut microbiome. We report the first in vitro induction and imaging of members of prevalent GuFi clades including the candidate orders Heliusvirales, Astravirales (VFC 2) and Suryavirales (VFC 4). Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease.

microbiology↗

bioRxiv2025

High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome

While metagenomic studies can highlight strain-level diversity within microbial communities, the diversity obtained is often incomplete. Moreover, their utility for phenotypic characterizations remains hampered without the subjacent, systematic isolation procedures required with traditional culturomics. In this work, we examined the capabilities of a commercially available high-throughput single-cell dispensing solution to selectively target and isolate diverse strains of a genus of interest, Bifidobacterium, from fecal samples. The general performance of the single-cell dispenser was first assessed, revealing a low doublet frequency of 11.5% and an ability to preserve global genus diversity when a mixed culture of Bifidobacterium was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin (BSM-MUP), and the length of incubation were found to be critical in determining isolation success. Leveraging these results, we obtained a total of 622 viable isolates from five Singaporean fecal samples, among which [~]98.7% were bifidobacteria. Whole-genome sequencing of 96 isolates revealed six different Bifidobacterium species with both inter- and intra-subject lineage diversity, and the majority of the assemblies were not previously captured using metagenomic sequencing. Our findings validate the ability of high-throughput culturomics to recover diverse, novel bacterial strains and open up the possibility to robustly interrogate their functional characteristics, advancing our understanding of important microbiomes. IMPORTANCEThe field of microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from their multicellular environment is crucial for advancing microbiome research and healthcare development. Given the time- and cost-inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted organism, covering both species and strain diversities. This generalizable and scalable method allows for the high-throughput recovery of microbes with little optimization needed for novel targets, providing a fundamental step in improving the culturomic framework to complement metagenomic approaches and enable isolate-level functional studies of important microbiomes.

microbiology↗

bioRxiv2025

Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites

While skin microbiome studies have increasingly highlighted its importance in health and disease, our understanding of inter-individual heterogeneity in structure and function remains limited, impacting the ability to develop microbiome-based stratification and therapeutics. Powered by comprehensive skin microbiome characterization in a multi-ethnic population-based cohort (>3,550 shotgun metagenomes across 18 sampling sites), we established significant undescribed inter-individual heterogeneity and the extensive prevalence of distinct microbial configurations (17 species-resolution dermotypes) in seven out of nine body sites. Combining functional in silico and in vitro studies revealed insights into how these dermotypes assemble as a function of niche-dependent microbial interactions (e.g. hypoxia-dependent inhibition of S. hominis by S. epidermidis/M. luteus) and metabolic resource utilization (e.g. differential galactose and histidine metabolism). Integration of demographic, skin physiological, and behavioral data further identified >30 significant associations with host attributes. Cross-site analysis revealed remarkable coordination across disparate skin regions (predictive AUC-ROC>0.8) and bilateral consistency (Pearson {pi}>0.95), emphasizing the role of specific microbial and host factors in shaping dermotypes. Finally, we provide multiple lines of evidence that dermotype states impact the risk for skin discomfort (e.g. irritation, itch) and diseases (e.g. eczema), that when combined with our highly accurate dermotype classifiers (AUC-ROC>0.98), provide a new paradigm for understanding skin microbiome function and stratifying patients in the context of skin and other diseases.

genomics↗

bioRxiv2024

Floria: Fast and accurate strain haplotyping in metagenomes

Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial strain genomes from microbiomes remains a key challenge. We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read metagenome sequencing data, based on minimum error correction (MEC) read clustering and a strain-preserving network flow model. Floria can function as a standalone haplotyping method, outputting alleles and reads that co-occur on the same strain, as well as an end-to-end read-to-assembly pipeline (Floria-PL) for strain-level assembly. Benchmarking evaluations on synthetic metagenomes showed that Floria is > 3x faster and recovers 21% more strain content than base-level assembly methods (Strainberry), while being over an order of magnitude faster when only phasing is required. Applying Floria to a set of 109 deeply sequenced nanopore metagenomes took <20 minutes on average per sample, and identified several species that have consistent strain heterogeneity. Applying Florias short-read haplotyping to a longitudinal gut metagenomics dataset revealed a dynamic multi-strain Anaerostipes hadrus community with frequent strain loss and emergence events over 636 days. With Floria, accurate haplotyping of metagenomic datasets takes mere minutes on standard workstations, paving the way for extensive strain-level metagenomic analyses. AvailabilityFloria is available at https://github.com/bluenote-1577/floria, and the Floria-PL pipeline is available at https://github.com/jsgounot/Floria_analysis_workflow.

bioinformatics↗

bioRxiv2023

Comparison of tet(X4)-containing contigs from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacteriaceae strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analysed. A metagenomic sequencing (MS) dataset of the same samples was mined for contigs that harboured the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and catD (also annotated as estT) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in two out of 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. Contig sequences are relatively short ([~]14-33 kb) but show high similarity to the respective plasmid sequences of the isolates. The frequent co-occurrence of florR and catD with tet(X4) corroborates the hypothesis that the transmission of tet(X4) may have originated from the veterinary sector. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism have a low abundance. Further optimisation is required if MS is to be utilised in antibiotic resistance surveillance.

microbiology↗

bioRxiv2022

Contrasting genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations

The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of the Kluyveromyces lactis yeast species, a well-known species for its involvement in dairy processes but also present in natural environments. Using a combination of short and long-read sequencing strategies, we investigated the genomic variability of 41 Kluyveromyces lactis isolates and found that the overall genetic diversity of this species is very high ({pi} = 2.9 x 10-2) compared to other species such as Saccharomyces cerevisiae ({pi} = 3 x 10-3). However, the domesticated dairy population shows a reduced level of diversity ({pi} = 7 x 10-4), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results also highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.

genomics↗

bioRxiv2019

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to explore an uncharacterized yeast species, Brettanomyces bruxellensis, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared to S. cerevisiae. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.

genomics↗

bioRxiv2017

High-quality de novo genome assembly of the Dekkera bruxellensis UMY321 yeast isolate using Nanopore MinION sequencing

Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is evidently to obtain the complete sequence and high quality assembly of a reference genome. Here, we completely sequenced and assembled a reference genome of the non-conventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.

genomics↗