Biology subjects

Okazaki, Y.

Publications and source records attributed to Okazaki, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Genome-resolved biogeography reveals multidimensional structuring of freshwater giant viruses across global deep lakes

Giant viruses (GV) are increasingly recognized as important ecosystem regulators. While metagenomics has uncovered extensive GV diversity, the global distributions of individual species and the biogeographic processes driving the pattern remain poorly understood. Here, we reconstructed GV metagenome-assembled genomes (MAGs) from 35 globally distributed deep freshwater lakes spanning five continents, aiming to identify their biogeographic patterns. The resulting 1663 non-redundant MAGs significantly expanded the known freshwater GV diversity, with [~]84% lacking a previously reported species representative. These MAGs were grouped into cosmopolitan and geographically restricted lineages. We identified 27 cosmopolitan GV species spanning multiple viral lineages, including families of Imitervirales, Pimascovirales, and mirusviruses order Styxvirales. The cosmopolitan species were characterized by their larger genomes and expanded gene repertoires of host-interaction functions, which may facilitate interactions with diverse hosts and contribute to their global distributions. The presence of geographically restricted species and the stronger distance-decay in community similarity observed in freshwater than marine ecosystems suggest that physical connectivity between ecosystems is an important factor influencing GV dispersal. We identified 312 and 177 GV MAGs almost exclusively associated with the epilimnion and hypolimnion, respectively. This water-layer preference of individual MAGs was highly consistent across lakes, suggesting conserved vertical partitioning in association with the thermal stratification of the water column. Overall, our findings reveal that GV biogeography in deep freshwater lakes is structured by the combined influence of horizontal dispersal limitation, vertical partitioning, and lineage-specific evolutionary histories.

microbiology↗

bioRxiv2026

Integrating spatial and single-cell multi-omics analysis of induced pluripotent stem cell-derived cervical adenocarcinoma model

Human papillomavirus 18 (HPV18) preferentially infects cervical stem cell-like cells and is strongly associated with adenocarcinoma. However, the mechanisms underlying differentiation into cervical adenocarcinoma remain unclear due to the lack of appropriate experimental models. We aimed to establish a model of HPV18-associated cervical adenocarcinoma and elucidate its molecular and cellular differentiation mechanisms. HPV18 E6/E7 were introduced into induced pluripotent stem cell-derived reserve cell-like cells (iRCs) to generate tumor models. Spatial transcriptomics and single-cell multi-omics analyses were performed to integrate histological and molecular data. A distinct component (Gland_A) exhibited morphological and immunohistochemical features of cervical adenocarcinoma and was efficiently induced in iRC-18 tumors. Gland_A showed increased chromatin accessibility and elevated expression of FOXA1, FOXA2, and ALDH1A1. Analysis of clinical samples confirmed enrichment of ALDH1A1 in HPV-associated adenocarcinomas. This model recapitulates key features of HPV18-associated cervical adenocarcinoma and provides insights into its differentiation mechanisms.

cancer biology↗

bioRxiv2026

Rapid diversification of a natural Heterosigma akashiwo virus population during a host bloom

Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Most knowledge on their population genetic dynamics is derived from a small number of laboratory-based experiments, whereas patterns in nature are rarely observed. To overcome this limitation, we traced genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan, by integrating cell counting, metabarcoding, metagenomic and metatranscriptomic sequencing. Our study revealed that HaV dominated the giant virus community in most samples, with the relative abundances of up to 56%. Despite the high abundances, the HaV population exhibited a relatively low level of microdiversity but with a high pN/pS ratio compared to other giant viruses in the study site. Microdiversity increased during the early sampling period, reached a maximum at mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, possibly driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Together, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variation.

ecology↗

bioRxiv2025

Couples in the deep: dissolved organic and microbial communities in the oxygenated hypolimnion of a deep freshwater lake

The interaction between dissolved organic matter (DOM) and microbial communities is a critical yet understudied driver of biogeochemical cycling in aquatic ecosystems. Understanding these interactions is essential for elucidating the chemical and microbial dynamics that sustain ecosystem functionings. Here, we combined non-target ultra high-resolution mass spectrometry-based environmental metabolome analysis with microbiome analysis to conduct the first comprehensive investigation of DOM-microbe linkages in both the epilimnion and oxygenated hypolimnion of a deep freshwater lake throughout the stratification period, with Lake Biwa (Japan) as a model system. To facilitate interpretation of DOM-microbe networks, we developed an integrated compound category classification (IC3) framework for assigning molecular formulae (MFs) to specific compound categories. Using a compositional data analysis framework, we identified specific MFs and bacterial taxa that covaried in the hypolimnion, which exhibited substantially more complex networks than the epilimnion. These networks encompassed 1705 out of the 1755 common MFs, representing the majority of total peak intensities, underscoring stronger DOM-microbe coupling in deep waters. Hypolimnion specialist bacteria were associated with specific MFs and co-ocuuring taxa, providing environmental metabolomic evidence for substrate preference and potential symbiotic relations. Notably, more than three-fourths of these MFs in relative abundance were classified as recalcitrant, including lipid-, lignin-, tannin-like, and carboxyl-rich alicyclic molecules, suggesting the capability of hypolimnion specialists to use or produce these compounds. Our study offers the first high-resolution insights into DOM-microbe associations in a deep freshwater lake and establishes a framework for more efficient and robust analyses of such interactions.

ecology↗

bioRxiv2025

Giant viruses specific to deep oceans show persistent presence and activity

Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate deep-sea GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To investigate the global deep-sea-specific GV distribution, we compiled GV reference genomic data from the OceanDNA MAG project and other resources, and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included one GV identified in our Muroto sampling, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat. IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the deep-sea water. Using a global marine dataset, we further uncovered the widespread existence of deep-sea-specific giant viruses and characterized their unique gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.

genomics↗

bioRxiv2025

Horizontal transfer of a 180-kbp genomic fraction among the largest viral genomes

Viruses are generally considered tiny biological entities with small genomes; however, some dsDNA viruses, known as giant viruses, have large genomes that are comparable to those of small bacteria. Previous studies indicated that the genomes of giant viruses expanded from a small ancestor by a combination of gene duplication, de novo gene creation, and horizontal gene transfer (HGT). Among them, virus-to-virus HGTs are recently recognized as an important mechanism for disseminating functional genes between giant viruses. In this study, we isolated a giant virus of a member of pandoraviruses, which have the largest genome sizes reaching 2.5 Mbp. Based on the average nucleotide identity of known pandoraviruses, this new pandoravirus belongs to an existing viral species. However, its genome was approximately 200 kbp larger than those of the other strains from the same species. A genome-wide comparison identified a 180-kbp region with 168 genes missing from the other strains but found in phylogenetically distant pandoraviruses. The GC ratio and homology of the deduced amino acid sequences in this 180-kbp region suggest that the new virus horizontally acquired this region from a distantly related pandoravirus. The gene composition in the 180-kbp region further indicates that this region was already large at the time of the horizontal transfer. Our findings suggest that pandoraviruses can horizontally exchange a large portion of their genomes. This event presumably represents one mechanism for accelerating genomic evolution and gigantism in giant viruses.

microbiology↗

bioRxiv2025

Genome-wide mapping of the Galleria mellonella larvae transcription start sites during fungal infection and treatment

Using Low Quantity single strand CAGE (LQ-ssCAGE), we mapped the transcription start sites (TSS). We annotated the 5 end of the invertebrate Galleria mellonella, an upcoming and booming experimental model in infectious disease and immunology research. However, the current genome annotation of this model organism lacks annotation of the 5 end and TSS information. G. mellonella larva was infected with the fungal pathogen Madurella mycetomatis to map TSS under healthy and infection conditions. Larvae were first treated with itraconazole or ravuconazole, and then RNA-seq and LQ-ssCAGE libraries were prepared and sequenced 4, 30, and 52 hours following infection. The LQ-ssCAGE data was processed to identify CAGE transcription start site (CTSS), uni-, and bi-directional clusters. LQ-ssCAGE enabled us to precisely identify 39,410 TSS and 249 active enhancers; we assigned genomic features to the resulting TSSs and enhancers. The majority of the TSS peaks are annotated as promoter regions, while the enhancers were annotated as intergenic and genic. Furthermore, we confirmed the quality of TSS calling by promoter shapes and GC bias. Furthermore, we identified a set of super-enhancers and predicted de-novo motifs. The raw and processed data was deposited to NCBI GEO GSE282923. CTSS, TSS peaks, and enhancers coordinated are available through the ZENBU Genome browser. In this study, we reported the first atlas of TSS and active enhancers of G. mellonella.

genomics↗

bioRxiv2024

Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria

The ecological importance of virus-host interactions is unclear due to the limited ability of metagenomics to resolve virus-host pairs and the infection state of individual cells. We addressed these problems using single-cell genomics combined with published metagenomic data on lake bacterioplankton. We obtained 862 medium- to high-quality single-cell amplified genomes (SAGs) from two water layers and two seasons in Lake Biwa, Japan. We assembled 176 viral (dsDNA phage) contigs in the SAGs, and identified novel virus-host pairs including the discovery of viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. A virus was detected in 133 (15.4%) SAGs through read mapping analysis. The viral detection rate showed little variation among samples (12.1-18.1%) but significant variation in host taxonomy (4.2-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were achieved by collective infection by diverse viruses, suggesting weak density-dependent virus-host selections, presumably because of their non-persistent interactions with viruses due to their fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their co-dominance with viruses is achieved by genomic microdiversification that diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Overall, we demonstrated that virus-host interactions are highly diverse within and between host lineages, which was overlooked by metagenomics analysis, as exemplified by the CL500-11 virus, which showed extremely high read coverages in cellular and virion metagenomes, but infected < 1% of host cells. Significance statementVirus-host interactions are among the most significant driving forces of microbial biogeochemical cycles and genomic diversification. Unlike experimental conditions, bacterial cells in the natural environment are not uniformly infected by a single virus, but interact with diverse viruses under heterogeneous eco-physiological and genetic conditions. The specificity and heterogeneity of infection are the keys to understanding complex virus-host interactions and the mechanisms behind their co-existence. However, these interactions remain unclear due to the limitations of conventional metagenomic approaches. We addressed this issue by detecting viral signals from single-cell-amplified genomes of lake bacterial communities. The results revealed novel virus-host pairs and their infection rates, suggesting that viral defense strategies differ among host lineages, reflecting their ecological characteristics.

ecology↗

bioRxiv2024

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.

microbiology↗

bioRxiv2024

BCR, not TCR, repertoire diversity is associated with favorable COVID-19 prognosis

The SARS-CoV-2 pandemic has had a widespread and severe impact on society, yet there have also been instances of remarkable recovery, even in critically ill patients. In this study, we used single-cell RNA sequencing to analyze the immune responses in recovered and deceased COVID-19 patients during moderate and critical stages. The study included three unvaccinated patients from each outcome category. Although expanded T cell receptor (TCR) clones were predominantly SARS-CoV-2-specific, they represented only a small fraction of the total repertoire in all patients. In contrast, while deceased patients exhibited monoclonal B cell receptor (BCR) expansions without COVID-19 specificity, survivors demonstrated diverse and specific BCR clones. These findings suggest that neither TCR diversity nor BCR monoclonal expansions are sufficient for viral clearance and subsequent recovery. Differential gene expression analysis revealed that protein biosynthetic processes were enriched in survivors, but that potentially damaging mitochondrial ATP metabolism was activated in the deceased. This study underscores that BCR repertoire diversity, but not TCR diversity, correlates with favorable outcomes in COVID-19.

immunology↗

bioRxiv2024

Spatiotemporal dynamics revealed the dark water community of giant virus from a deep freshwater lake

Giant viruses significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about giant viruses of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment of genetic diversity. We sought to bridge this knowledge gap and overcome previous technical limitations. We subjected spatiotemporal (2 depths x 12 months) samples from Lake Biwa to metagenome-assembled genome reconstruction enhanced by long-read metagenomics. This yielded 294 giant virus metagenome-assembled genomes. Of these, 285 included previously unknown species in five orders of nucleocytoviruses and the first representatives of freshwater mirusviruses, which exhibited marked divergence between freshwater- and marine-derived lineages. Notably, 42 (14.3%) genomes were composed of single contigs with completeness values >90%, demonstrating the good performance of our long-read metagenomic assembly. Giant viruses were partitioned across water depths, with most species specific to either the sunlit epilimnion or the dark hypolimnion. Epilimnion-specific members tended to be opportunistic and to exhibit short and intense abundance peaks, in line with the fact that they regulate the surface algal blooms. During the spring bloom, mirusviruses and members of three nucleocytovirus families were among the most abundant giant viruses. In contrast, hypolimnion-specific ones including algaviruses and mirusviruses were typically more persistent in the hypolimnion throughout the water-stratified period, suggesting that they infect hosts specific to the hypolimnion and play previously unexplored ecological roles in dark water-specific microbial ecosystems.

ecology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2023

Gene transfer among viruses substantially contributes to gene gain of giant viruses

Horizontal gene transfers (HGTs) integrate all forms of life and viruses into a vast network of gene flow, which facilitates the transmission of genes beyond vertical inheritance and enhances genomic evolution. HGT is known to occur between closely related viruses. We hypothesized that there is frequent HGT among nucleocytoviruses, a group of diverse but evolutionarily related DNA viruses encoding hundreds to thousands of genes. However, the frequency of viral HGT (vHGT) has not been systematically investigated for nucleocytoviruses. We reconciled over 4,700 gene trees with a robust viral species tree that contains 195 reference viral genomes mainly from cultivation as a reference to infer evolutionary events, including gene gains (gene duplication, origination, and vHGT) and losses. The inferred evolutionary scenarios revealed that the genomes of these viruses have undergone numerous gene gain and loss events, with vHGT representing 28% to 42% of gene gain events in each viral order. By integrating the evolutionary paths of multiple viruses, our data suggest that vHGT is crucial for nucleocytovirus evolution.

evolutionary biology↗

bioRxiv2023

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics

Oxidative phosphorylation defects results in mitochondrial diseases, with cardiac involvement markedly impacting prognosis. However, the mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear, impeding the development of effective treatments. Here, we employed single-nucleus RNA sequencing (snRNA-seq) on hearts from mitochondrial cardiomyopathy (MCM) mice with cardiac-specific Ndufs6 knockdown (FS6KD). Pseudotime trajectory analysis of cardiomyocytes from early stage of female FS6KD hearts revealed dynamic cellular state transitioning from compensation to severe compromise, coincided with transient upregulation of a critical transcription factor, activating transcription factor 3 (Atf3). Genetic ablation or adeno-associated virus-mediated Atf3 knockdown in FS6KD mice effectively delayed cardiomyopathy progression in a female-specific manner. Notably, human MCM snRNA-seq revealed a similar transition, including the dynamic expression of ATF3. In conclusion, our findings highlight a fate-determining role of Atf3 in female MCM progression, providing a promising therapeutic candidate for the currently intractable disease.

cell biology↗

bioRxiv2023

A 1.5 Mb continuous endogenous viral element region in the arbuscular mycorrhizal fungus Rhizophagus irregularis

Most fungal viruses are RNA viruses and no double-stranded DNA virus that infects fungi is known to date. A recent study detected DNA polymerase genes that originated from large dsDNA viruses in the genomes of basal fungi, suggestive of the existence of dsDNA viruses capable of infecting fungi. In this study, we searched for viral infection signatures in chromosome-level genome assemblies of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We identified a continuous 1.5 Mb putative viral region on a chromosome in R. irregularis strain 4401. Phylogenetic analyses revealed that the viral region is related to viruses in the family Asfarviridae of the phylum Nucleocytoviricota. Single-copy marker genes from Nucleocytoviricota were detected as single-copy genes in the viral region. Furthermore, this viral region was absent in the genomes of four other R. irregularis strains and had fewer signals of fungal transposable elements than the other genomic regions. These results suggest a recent and single insertion of a large dsDNA viral genome in the genome of this fungal strain, providing strong evidence of the recent infection of the fungus by a dsDNA virus.

microbiology↗

bioRxiv2023

A rapid genome-wide analysis of isolated giant viruses only using MinION sequencing

Following the discovery of Acanthamoeba polyphaga mimivirus, diverse giant viruses have been isolated. However, only a small fraction of these isolates has been completely sequenced, limiting our understanding of the genomic diversity of giant viruses. MinION is a portable and low-cost long-read sequencer that can be readily used in a laboratory. Although MinION provides highly error-prone reads that require correction through additional short-read sequencing, recent studies assembled high-quality microbial genomes only using MinION sequencing. Here, we evaluated the accuracy of MinION-only genome assemblies for giant viruses by re-sequencing a prototype marseillevirus. Assembled genomes presented over 99.98% identity to the reference genome with a few gaps, demonstrating a high accuracy of the MinION-only assembly. As a proof of concept, we de novo assembled five newly isolated viruses. Average nucleotide identities to their closest known relatives suggest that the isolates represent new species of marseillevirus, pithovirus, and mimivirus. Assembly of subsampled reads demonstrated that their taxonomy and genomic composition could be analyzed at the 50x sequencing coverage. We also identified a pithovirus gene whose homologues were detected only in metagenome-derived relatives. Collectively, we propose that MinION-only assembly is an effective approach to rapidly perform a genome-wide analysis of isolated giant viruses.

microbiology↗

bioRxiv2023

Facilitative interaction networks in experimental microbial community dynamics

Understanding potential roles of facilitative interactions between species is one of the major challenges in ecology and microbiology. However, we still have limited knowledge of entangled webs of facilitative interactions in ecosystems. By compiling whole-genome shotgun metagenomic data of an experimental microbial community, we tested the hypothesis that architecture of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.

ecology↗

bioRxiv2023

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we show that community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was explained by the magnitude of gene-repertoire overlaps among bacterial species. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

microbiology↗