Biology subjects

Sunagawa, S.

Publications and source records attributed to Sunagawa, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. Here, we implement a scalable, cultivation-independent framework to identify 724 genomically discrete and ecologically cohesive subspecies across 270 species in the global ocean microbiome. Their diversification is underpinned by gene-specific, nucleotide-level selection on the core genomic backbone and by variable restructuring of gene content, both of which proceed in a subspecies-specific manner. In over half of the species tested, subspecies were significantly associated with distinct environmental conditions, most frequently temperature. This coupling of genomic discreteness and ecological cohesiveness positions these subspecies as biologically meaningful units, a fundamental level at which ecological and evolutionary processes jointly drive divergence and structure microbial diversity in the oceans.

ecology↗

bioRxiv2026

The Ocean Microbiomics Database reveals thermal niches and projected pressure on marine microbes in a warming ocean

Temperature is a key driver of ocean microbial community structure, yet its role in shaping global distributions and their response to warming remains unclear due to fragmented studies, inconsistent methods, and limited environmental context. We present the Ocean Microbiomics Database (OMDB) containing 274,282 genomes forming 31,058 species-level clusters, searchable at https://omdb.microbiomics.io. We show surface temperature is predicted from community composition, driven by thermal niche partitioning among congeneric taxa. Using these thermal niches to model present-day distributions globally, we find that projected warming results in microbial richness declining faster than relative abundance, with losses concentrated at high latitudes and among poorly characterized lineages. Resolving 5,891 species into four thermal clusters reveals ecological structure correlated with genome streamlining, protein thermostability, and marker-gene physicochemistry, enabling prediction of a microorganism's abundance-maximizing temperature directly from its coding sequence. This positions OMDB as a platform spanning molecular traits to global ecology, offering a genome-resolved foundation for understanding how temperature, shown to be a primary driver of ocean microbial life, will continue to shape it as the ocean warms.

microbiology↗

bioRxiv2026

Comprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry

The acquisition of sufficient nitrogen for growth, as well as the disposal of highly toxic nitrogen-containing degradation products, represent serious metabolic challenges in all multicellular organisms and microbial ecosystems. Understanding these processes requires a broadly applicable system to accurately quantify the concentration of a wide spectrum of biological amines and inorganic nitrogen-containing compounds. To date, this has been challenging due to limited specificity, selectivity, breadth and/or sensitivity of assays. Here we present a simple, optimized method based on liquid chromatography and high-resolution mass spectrometry, with an accompanying analysis pipeline, for the accurate quantification of more than 30 of these compounds, including ammonia. We demonstrate the effectiveness of this method in quantifying relevant nitrogen-containing compounds in mouse and human gut content, bacterial cultures, algal symbiosis in a cnidarian and freshwater ecosystem samples. As a proof-of-concept, we applied the method to study the influence of the gut microbiome on cecal nitrogen distribution in mice with different gnotobiotic microbiomes. This revealed a profound influence of gut microbiota composition on amino acid, ammonia, and amine concentrations in the upper large intestine. Overall, we provide a broadly applicable approach that can be used across microbial ecology fields to generate novel insights into the biology of nitrogen assimilation, exchange, and disposal.

microbiology↗

bioRxiv2026

Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential

Biological nitrogen fixation sustains productivity across Earths ecosystems, yet the diversity, distribution and ecological drivers of nitrogen-fixing prokaryotes (diazotrophs) remain incompletely resolved. Here we screened approximately 40 billion genes to generate a catalogue of 21,157 diazotroph genomes. Using this catalogue, we quantified diazotroph diversity and abundance across 9,163 metagenomes spanning diverse environments. Diazotrophy was distributed across the prokaryotic tree of life, but both gene diversity and metagenomic abundance were dominated by heterotrophic lineages. Freshwater and sedimentary ecosystems emerged as major reservoirs of nitrogen-fixation potential beyond the environments that have historically anchored the field. Diazotroph-rich assemblages were associated with nitrogen and phosphorus limitation together with carbohydrate-rich metabolic regimes, revealing distinct nutrient and energy niches for cyanobacterial and heterotrophic diazotrophs. Together, this framework unifies disparate views of diazotroph diversity, abundance and ecology, providing a foundation for improved prediction of biological nitrogen fixation across Earths ecosystems.

microbiology↗

bioRxiv2026

Biphasic bacterial community assembly predicted from generalized first principles of monoculture growth and inferred species interactions

Microbial communities occur in all habitats, yet how individual growth on available nutrients scales to community assembly remains poorly understood. This gap stems largely from the unknown effects of species interactions. These interactions arise because individual populations both consume and transform primary substrates into metabolites exploitable by others, and because parasitic and predatory mechanisms can release cellular building blocks that enable nutrient reuse. Here, we present a mathematical framework that predicts community growth and compositional succession from monoculture growth kinetics, resource availability, and species interaction parameters. To parametrize species interactions, we use a simulated-annealing optimization algorithm to search parameter space for sets that minimize the difference between modeled community growth and experimental time series from soil microcosms inoculated with defined communities of 20 or 21 soil isolates, with or without an opportunistic bacteriovorous member. The optimized interaction parameter sets were then used to predict growth dynamics in an independent 21-member community and in species drop-out communities. We find that community development is biphasic: an initial phase dominated by competition for primary resources driven by inherent strain growth kinetics, followed by a phase governed by cross-feeding and biomass formation on released byproducts. Paired metatranscriptomic analysis corroborated predicted shifts in individual growth states and revealed metabolic repurposing associated with the sudden renewed availability of metabolites and cellular building blocks. Model simulations that excluded species interactions reproduced only one-fifth of the observed community biomass, highlighting the importance of cross-feeding for soil community growth. Overall, models that integrate monoculture growth kinetics with inferred species interactions can predict the dynamics of medium-complexity communities from starting inocula even when environmental nutrient composition is largely unknown.

microbiology↗

bioRxiv2026

The ultrasmall ocean microbiome: a reservoir of microbial diversity and nitrogen fixation.

Marine microbiology has long considered ultrasmall (<0.2 {micro}m) size fractions as virus-dominated, yet emerging evidence suggests potential prokaryotic activity with implications for global biogeochemical cycles. Here, we present the first comprehensive genome-resolved survey of this fraction, built on 4,058 metagenome-assembled genomes (MAGs) representing 1,152 species across Bacteria (90.7%) and Archaea (9.3%), dominated by Pseudomonadota, Bacteroidota, and Nanoarchaeota. Over 490 non-redundant MAGs occurred exclusively in the ultrasmall fraction, with 66.8% representing novel taxa, particularly abundant in Arctic surface waters. Beyond known ultrasmall organisms (e.g., DPANN archaea and Patescibacteria), which show expected genomic and metabolic reduction, functional annotation revealed diverse metabolic potential across nitrogen, sulfur, and carbon cycling. Focusing on nitrogen fixation, we identified 13 non-cyanobacterial diazotroph species with complete nitrogenase operons spanning four bacterial classes. These resolved into two ecotypes: cosmopolitan low-abundance taxa, and Arctic ultrasmall-restricted strains reaching up to 16.7% relative abundance. Two lineages (50-400-T64 and Novosphingobium) showed ultrasmall exclusive bipolar distributions across Arctic and Southern Oceans. Beyond nitrogen fixation, these diazotrophs encoded pathways for denitrification, DNRA, sulfur oxidation, and carbon fixation. Our findings reveal an overlooked reservoir of microbial diversity including diazotrophs in the ultrasmall ocean microbiome, with significant implications for polar nitrogen budgets and global biogeochemical models.

microbiology↗

bioRxiv2026

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

Coral reefs are among the most diverse ecosystems on Earth, yet the diversity and structure of their associated microeukaryotic communities remain poorly resolved. We characterized reef-associated eukaryomes across 113 reefs spanning the Pacific Ocean using more than 6,300 samples from corals, seawater, and sediments during the Tara Pacific expedition. We identified [~]121,000 eukaryotic ASVs, revealing one of Earths largest undocumented reservoirs of eukaryotic diversity; over 80% of the recovered diversity was previously undetected in global ocean surveys and fewer than 2% of sequences matched reference databases. Reef habitats supported highly distinct communities, with sediments and seawater harboring 20-40-fold higher richness than corals. Unexpectedly, coral-associated communities across 29 host lineages were consistently dominated by small metazoans, particularly demosponges and maxillopods, identifying these taxa as pervasive and previously unrecognized components of coral eukaryomes alongside Apicomplexa. Across the Pacific, eukaryome composition was strongly structured by environmental gradients, with thermal stress emerging as the primary driver of community turnover. Together, these results identify coral reefs as a globally important reservoir of hidden eukaryotic diversity and reveal the reef eukaryome as a sensitive indicator of ecosystem reorganization under climate change.

systems biology↗

bioRxiv2026

Conserved bacterial genes for biosynthesis of the algal morphogen thallusin span land and sea

Bacterial signals control the development of marine algae, yet the molecular basis of these cross-kingdom interactions remains largely unknown. Thallusin is the paradigmatic case: isolated in 2005, it induces rhizoid and cell wall formation in the green seaweed Ulva at picomolar concentrations, but its biosynthesis has remained elusive for two decades. Comparative genomics across five bacterial phyla identifies a conserved set of genes - the eustigmatophyte bacterial operon (ebo) - as determinants of thallusin biosynthesis. Isotope labeling, heterologous expression, and gene deletion in Stieleria maiorica show that the aromatic scaffold derives from a cyclitol precursor and L-aspartate, with subsequent prenylation and cyclization. Searching 124,295 prokaryotic genomes identifies producers in eleven bacterial lineages, including soil cyanobacteria, establishing thallusin as a widespread cross-kingdom signal reaching beyond the ocean.

microbiology↗

bioRxiv2026

Meiotic pairing through barcode-like satellite DNA repeats

During meiosis, chromosomes must find, pair, and synapse with their homologous partners in the crowded milieu of the nucleus1. Although homology detection is generally attributed to recombination, pairing and synapsis can occur in its absence2-10, suggesting alternate mechanisms that discriminate between homologous and non-homologous chromosomes. In many eukaryotes, tandem repeats known as satellite DNA facilitate inter-chromosomal associations11. Notably, their non-uniform distribution across chromosomes gives rise to homologue-specific satellite DNA barcodes12-14, which have been speculated to enable meiotic pairing15-18. However, satellite DNA function remains actively debated since these repeats cannot be manipulated in most model organisms. Here, we use satellite DNA deletion, duplication, and translocation strains that are unique to Drosophila to demonstrate that repeat mismatches perturb meiotic pairing, particularly at centromeres and pericentromeres. In the absence of satellite DNA homology, pairing is antagonized by the HORMAD protein, Mad2, while a Pachytene checkpoint 2 (Pch2)-dependent meiotic delay restores pairing. Remarkably, pairing defects are also observed in the progeny of D. melanogaster natural populations that have diverged in their satellite DNA content. Finally, compromised meiotic pairing is strongly correlated with mid-oogenesis cell death, a quality control mechanism that likely culls defective oocytes to prevent chromosome mis-segregation and aneuploidy. These findings resolve a long-standing debate on satellite DNA functionality by demonstrating a barcode-like role in homology detection. We propose that this repeat-based pairing mechanism exerts an underappreciated selective pressure, constraining the divergence of rapidly evolving satellite DNA within interbreeding natural populations.

genetics↗

bioRxiv2025

The glycine betaine-cobalamin feedback loop drives cross-feeding between marine bacteria and algae

Heterotrophic bacteria supply cobalt-containing cobalamin (Cbl) to marine microalgae, which in return provide organic substrates. Such metabolic cross-feeding can regulate the species composition of prolific marine plankton and biofilms. Algal-produced glycine betaine (GB) can be catabolized by bacteria using a Cbl-dependent demethylase (MtgBCD). Yet, GBs impact on bacterial Cbl production during cross-feeding, and its control by cobalt scarcity remains elusive. Here, we demonstrate that Phaeobacter inhibens bacteria boost their Cbl production 25-fold when grown in monocultures with GB compared to glucose. During co-cultivation, P. inhibens satisfied the Cbl requirements of Gephyrocapsa huxleyi algae. Transcriptomic analysis of mono- and co-cultures revealed co-expression of mtgBCD and gbcAB genes encoding Cbl-dependent and -independent GB demethylases, respectively. Distinct growth defects of deletion mutants indicate that P. inhibens switches from Cbl-dependent to -independent GB demethylation under cobalt limitation, involving a Cbl riboswitch. Our findings suggest a positive feedback loop in which algal GB release stimulates the bacterial supply of Cbl. We predict the breakdown of this interaction under naturally occurring cobalt limitation which potentially contributes to the transient nature of algal blooms. Comparative genomics indicate that this mechanism is widespread in Rhodobacterales and other abundant marine Alphaproteobacteria, underscoring its pivotal role in global ocean productivity.

microbiology↗

bioRxiv2025

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from equator to poles, are a pervasive macroecological pattern, yet their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed layer microbiomes exhibited diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) showed no latitudinal diversity structuring. Taxonomic resolution revealed that the mixed layer LDG was underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibited distinct or contrasting LDGs. Diversity structuring also varied by seasons and regions, governed by temperature and nutrient availability. Together, these findings highlight that within the ocean microbiome, LDGs are not universal, but lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.

microbiology↗

bioRxiv2025

Transcriptomic profiles of single-copy marker genes enable predicting bacterial growth states in microbial communities

Studying microbial community dynamics is fundamental to better understand ecosystem stability, resilience and environmental change. Community composition changes with the growth of individual members, yet current methods to estimate microbial growth in communities face substantial limitations. For example, genome sequence-based estimates of maximum growth rates may not reflect growth patterns in the natural environment well, and metagenomic in situ growth prediction requires the availability of reference genomes and shows limited accuracy for slow-growing bacteria. Gene expression data provide an information-rich readout of community activity that could reflect growth, however, cross-species comparisons in community settings remain challenging. An approach using expression signatures of universal, single-copy marker genes provides independence from reference genomes and may thereby enable comparability across species. Here, we present a transcriptomic, marker gene-based growth classifier that predicts the growth states of bacterial strains from different phyla cultivated in diverse conditions. We demonstrate its application in vivo in gnotobiotic mice carrying the same bacterial strains, and in a more complex synthetic community, where predicted growth states align with reported growth inhibition induced by systemic inflammatory response. This approach offers a new method for predicting bacterial growth states across species, with potential for broad application in the study of microbial growth dynamics at the whole community level.

microbiology↗

bioRxiv2025

The JEDI marker as a universal measure of planetary biodiversity

Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hindering our capacity to document Earths biota and track its change. Here, we propose the Joint, cellular life-Encompassing DIversity (JEDI) marker as a simple, effective and quantitative measure to assess and monitor biodiversity. The JEDI marker is a ribosomal RNA gene fragment that can be amplified from all domains of life using a single pair of PCR primers. We demonstrate the applicability and effectiveness of this approach for assessing biodiversity across ecological and biological scales, from holobionts to diverse ecosystems. In addition, we provide an automated bioinformatic workflow to support the standardised and reproducible analysis of the JEDI marker in future studies. While this approach is not free from trade-offs, we argue that its advantages outweigh its limitations by providing a unique, operational and scalable solution that builds on established infrastructure to integrate the microbial majority into biodiversity assessments and provide fundamental insights into organismal dynamics and associations across domains of life. Thus, the JEDI marker approach addresses the urgent need for a universal and standardised framework to effectively measure and monitor biodiversity at planetary scales in an era of profound global change.

ecology↗

bioRxiv2025

Uncovering Cas9 PAM diversity through metagenomic mining and machine learning

Recognition of protospacer adjacent motifs (PAMs) is crucial for target site recognition by CRISPR-Cas systems. In genome editing applications, the requirement for specific PAM sequences at the target locus imposes substantial constraints, driving efforts to search for novel Cas9 orthologs with extended or alternative PAM compatibilities. Here, we present CRISPR-PAMdb, a comprehensive and publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial and archaeal genomes and PAM profiles from 7.4 million phage and plasmid sequences. Through spacer-protospacer alignment, we inferred consensus PAM preferences for 8,003 unique Cas9 clusters. To extend PAM discovery beyond traditional alignment-based approaches, we developed CICERO, a machine learning model predicting PAM preferences directly from Cas9 protein sequences. Built on the ESM2 protein language model and trained on the CRISPR-PAMdb database, CICERO achieved an average accuracy of 0.68 on test data and 0.75 on experimentally validated Cas9 orthologs. For Cas9 clusters where alignment-based predictions were infeasible, CICERO generated PAM profiles for an additional 50,308 Cas9 proteins, including 17,453 high-confidence predictions with accuracies above 0.86. CRISPR-PAMdb, alongside CICERO models, enables large-scale exploration of PAM diversity across Cas9 proteins, accelerating design of next-generation CRISPR-Cas9 tools for precise genome engineering.

synthetic biology↗

bioRxiv2025

The natural diversity of E. coli transporter-dependent capsules

Serotyping of bacteria using genomic information (in silico serotyping) has increasingly replaced serology. However, the E. coli capsule serotyping system has been largely abandoned since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution, and epidemiology. To address this, we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed >37,000 E. coli genomes, cataloging 85 transporter-dependent capsule types (K-types), including 55 novel ones. We leveraged this catalog to develop an in silico serotyping tool, kTYPr, and applied it to curated sets of >25,000 E. coli genomes and metagenome-assembled genomes spanning diverse environmental and clinical sources. We found novel K-types enriched in under-sampled environments and associated with E. coli disease. This research expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.

microbiology↗

bioRxiv2025

Unveiling the hidden biodiversity of microbial chemoreceptor genes in the rare biosphere

Chemoreception plays a central role in microbial adaptability, influencing both community structure and interactions with the environment. However, many chemosensitive microorganisms occur at low abundances in natural ecosystems, which has limited their detection and study using conventional metagenomic sequencing. Here, we employed a custom-designed target capture sequencing approach--encompassing all known chemoreceptor genes from both cultured and uncultured microorganisms--to uncover and characterize the vast chemosensory potential and biodiversity within the rarest fractions of the microbiome. Compared to standard environmental sequencing methods, our approach enhanced the detection of chemoreceptor (CR) genes and their associated sensing domains by orders of magnitude across diverse environments, including the rhizosphere, phyllosphere, soil, aquatic ecosystems, the human gut, and bovine rumen. This enabled the identification of thousands of low-abundance chemosensitive microorganisms that remained undetectable using conventional sequencing approaches, including known plant pathogens and symbionts. Phylogenetic analysis of the most divergent CR genes revealed evidence for novel chemosensitive species, potentially representing new bacterial phyla and classes. Our study provides a new perspective on the chemoreception capabilities of environmental microbes and opens new avenues for discovering and characterizing novel microbial sensing mechanisms.

microbiology↗

bioRxiv2025

Altered kinematics and muscle activities during half squats in people with ankle sprain history

Regardless of the high recurrence rate, copers manage the damage after a sprain. Copers do not experience ankle instability and continue their daily activities. However, it is unclear whether copers can use movement strategies similar to people without an ankle sprain. Identifying movement strategies can improve efficacy and prevent unwanted effects during training. Therefore, we aimed to compare the kinematics and muscular activities of the lower limbs during half squats and gait between copers and healthy controls. Ten copers (7 men, 3 women; age = 21.6 {+/-} 1.1 years) and 10 controls (6 men, 4 women; age = 22.5 {+/-} 2.8 years) were included in the cross-sectional study. We compared angles of the thigh, shank, and foot calculated from inertial measurement units and muscle activities of the biceps femoris long head, rectus femoris, gastrocnemius, and tibialis anterior between copers and controls during half squats and gait. For half squats, copers demonstrated thigh restriction with an effect size of 0.67-1.35, whereas we observed no significant differences in the shank and foot angles in the descending phase. Copers demonstrated less activity with an effect size of 0.61-1.58 in all four muscles. Copers showed lower activities of the rectus femoris and tibialis anterior during the same period of thigh restriction. For gait, there were no significant differences in lower limb angles and muscle activities between copers and controls. Copers may restrict thigh rotation unintentionally, leading to less muscle activity during half squats. Removing unconscious restrictions using sensor-based quantitative feedback can enable copers to obtain more efficient training. Our results suggest that assessing the limb movements of copers is important for efficient training, even if they do not experience instability to continue with their daily activities.

physiology↗

bioRxiv2025

DMB labelling for detection and analysis of capsular polysaccharides

Bacterial capsules are major virulence factors enabling systemic infection by undermining innate and adaptive immunity. Capsular polysaccharides are also the antigen in some of the most successful antibacterial vaccines - including the pneumococcal, neisserial and Hib conjugate vaccines. However, it remains exceptionally challenging to study capsules, primarily due to their high chemical diversity and the limited methods available for their detection and analysis. We describe a robust biochemical method for detection and analysis of ABC transporter-dependent capsular polysaccharides, a major class of capsules that are associated with extraintestinal pathogenic Escherichia coli (ExPEC). The method involves release and fluorescent tagging of polysaccharides from the cell surface. Anion exchange chromatography of labelled samples reveals the presence, relative abundance, and length-distribution of these diverse polysaccharide antigens. The method provides a modern approach to detecting the capsule phenotype, bridging a critical gap left by the decline of serotyping assays. It will enhance our understanding of fundamental capsule biology and advance the development of capsule-targeting vaccines.

biochemistry↗