The ISME JournalPub Date : 2026-04-10DOI: 10.1093/ismejo/wrag079
Mingming Du,Peipei Xue,Budiman Minasny,Ho Jun Jang,Alex McBratney
{"title":"Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.","authors":"Mingming Du,Peipei Xue,Budiman Minasny,Ho Jun Jang,Alex McBratney","doi":"10.1093/ismejo/wrag079","DOIUrl":"https://doi.org/10.1093/ismejo/wrag079","url":null,"abstract":"Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping the soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterised by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cross-niche metabolite-microbiome interactions orchestrate systemic soybean resistance to Fusarium root rot.","authors":"Qi Liu,Lang Cheng,Enxi Zhang,Li Ling,Weiyi Tan,Suwen Liang,Canwei Shu,Qibin Ma,Shuai Zhao,Jian Wei,Yingxiang Wang,Hai Nian,Yanbo Cheng,Tengxiang Lian","doi":"10.1093/ismejo/wrag080","DOIUrl":"https://doi.org/10.1093/ismejo/wrag080","url":null,"abstract":"Fusarium root rot, predominantly caused by Fusarium falciforme, poses a significant threat to soybean productivity globally. Microbiome-based strategies offer sustainable alternatives, but the mechanisms underlying multi-niche interactions remain elusive. Here, we found that a tolerant soybean cultivar (GXD2) coordinates spatially resolved metabolite signals to recruit beneficial microbes across the rhizosphere, root endosphere, and leaf endosphere. Specifically, formononetin and maltol selectively enrich Bacillus and Massilia in the rhizosphere; arctigenin and isovanillic acid recruit Bacillus and Streptomyces to the root endosphere; and flavonoids such as diosmetin attract Penicillium and Aspergillus to the leaf endosphere. Leveraging these interactions, we constructed different types of synthetic communities (SynComs) via top-down (host-selected taxa) and bottom-up (antagonist-based) strategies. Both SynComs suppressed root rot in susceptible cultivars, with foliar application of top-down SynComs significantly enhancing shoot growth. Transcriptomics revealed distinct modes of actions, that top-down SynComs activated mitogen-activated protein kinase (MAPK)-linked terpenoid and flavonoid pathways, whereas bottom-up SynComs primarily modulated host carbon-nitrogen allocation, effectively limiting pathogen resources. Our findings unveil a \"metabolite-mediated, multi-niche collaborative defense\" model, presenting a robust framework for microbiome-based disease management and paving the way toward sustainable crop protection strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identifying phenotypic and genetic traits for assessing pathogenic potential and biocontrol capacity in Burkholderia sensu lato strains.","authors":"Kirsty Agnoli,Anugraha Mathew,Stefano Gualdi,Sarah Paszti,Lionel Moulin,Annette Vergunst,Peter Mergaert,Leo Eberl","doi":"10.1093/ismejo/wrag081","DOIUrl":"https://doi.org/10.1093/ismejo/wrag081","url":null,"abstract":"In the 1990s, several Burkholderia strains were registered as biocontrol agents but later withdrawn after opportunistic infections were reported. Phylogenetic revisions now separate the group into Burkholderia sensu stricto (s.s.), including environmental and clinical strains with elevated pathogenic potential, and several newly established genera, largely presumed harmless. We analysed 76 Burkholderia sensu lato (s.l.; taxa formerly classified as Burkholderia) for pathogenic potential in a Galleria mellonella model, in vitro biocontrol activity, and phenotypic traits linked to virulence or environmental fitness. Proteolytic activity and siderophore production manifested in strains with higher pathogenic potential, whereas oxalate utilization and other environmental traits correlated with lower pathogenic potential. Whereas most pathogenic strains belonged to B. s.s., some Paraburkholderia isolates also exhibited elevated pathogenic potential. Transfer of the ornibactin biosynthetic cluster from a clinical Burkholderia strain to environmental Paraburkholderia sacchari increased pathogenic potential without affecting biocontrol activity or persistence, illustrating the fine line between safe and hazardous strains. Collectively, our results identify novel phenotypic traits and genetic markers that enable improved, strain-level evaluation of pathogenic potential and biocontrol capacity, supporting the rational selection or engineering of Burkholderia s.l. strains for safe agricultural applications.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2026-04-10DOI: 10.1093/ismejo/wrag084
Isaac Meza-Padilla,Sarit Avrani,Kirsten M Müller,Jozef I Nissimov
{"title":"A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere.","authors":"Isaac Meza-Padilla,Sarit Avrani,Kirsten M Müller,Jozef I Nissimov","doi":"10.1093/ismejo/wrag084","DOIUrl":"https://doi.org/10.1093/ismejo/wrag084","url":null,"abstract":"It has been proposed that a defining distinction between viruses and cells lies in the absence or presence of ribosomal genes, respectively. Recent studies revealing that viruses occasionally encode ribosomal proteins (RPs) have challenged this view. However, so far, only viral genomes with up to three RPs have been discovered. Here, we perform a functional genome analysis of the Microcystis jumbo phage PhiMa05 and show that it encodes six RPs, an RP acetyltransferase, and a ribosome biogenesis protein. To our knowledge, this makes PhiMa05 the first cyanophage reported to encode RPs, as well as the virus with the most comprehensive RP-coding set of the known virosphere. Evolutionary analyses suggest that these viral RP-coding genes may have been horizontally transferred from a temperate ancestor of PhiMa05 to certain members of the Vampirovibrionia, a non-photosynthetic basal lineage of Cyanobacteriota, via the integration of the viral genome. We find that four RPs, the RP acetyltransferase, and the ribosome biogenesis protein of the PhiMa05-like prophages are the only copies of those proteins that the near-complete genomes of some Vampirovibrio hosts possess. We hypothesize that such cellular organisms may depend on the PhiMa05-like prophage for protein synthesis, and hence life itself. Collectively, our results provide evidence for the existence of viruses with particularly enriched sets of RP-coding genes and indicate that, in some cases, such viral genes have been transferred to cells, potentially becoming essential for the survival of the host.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.","authors":"Hirokazu Toju,Kenta Suzuki,Martina Sánchez-Pinillos,Genta Shima,Takuya Kageyama,Ibuki Hayashi,Mikihito Noguchi,Hiroaki Fujita,Yoshiyuki Goto,Shinji Nakaoka,Masayuki Ushio,Yasunori Ichihashi,W Florian Fricke,Kenji Mizumoto,Lena Takayasu,Wataru Suda,Misako Takayasu,Masato Yamamichi,Wolfram Weckwerth","doi":"10.1093/ismejo/wrag085","DOIUrl":"https://doi.org/10.1093/ismejo/wrag085","url":null,"abstract":"Microbiomes are increasingly recognized as key to addressing global challenges in health and sustainability, as they can provide emergent biological functions unattainable with single microbial species. However, microbial communities occasionally undergo abrupt shifts in species composition despite their intrinsic steadiness, making it difficult to maintain highly functional microbiome states. Here, we outline emerging statistical frameworks that integrate ecological stability theory with empirical analyses of microbiome structure and function. Approaches inspired by the concept of \"stability landscapes\" now enable inference of how the relationship between community structure and assembly potential changes along environmental gradients. Such empirical analyses offer bird's-eye perspectives for maintaining or restoring community states with desirable microbiome functions. Moreover, identifying the attractors of microbiome dynamics facilitates forecasting of abrupt transitions into dysfunctional states (i.e., dysbiosis). Bridging classic ecological theory and empirical microbiome analyses will deepen our understanding of the principles governing species-rich community assembly, expanding the scope of microbiome-based solutions across medical, industrial, agricultural, and environmental sciences.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"278 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2026-04-09DOI: 10.1093/ismejo/wrag062
Fuyan Li,Andrew Burger,John M Eppley,David M Karl,Edward F DeLong
{"title":"Seasonality drives temporal niche partitioning of pelagic prokaryotes.","authors":"Fuyan Li,Andrew Burger,John M Eppley,David M Karl,Edward F DeLong","doi":"10.1093/ismejo/wrag062","DOIUrl":"https://doi.org/10.1093/ismejo/wrag062","url":null,"abstract":"Prokaryote seasonality is well documented in lakes, coastal areas and inland seas, yet microbial annual periodicity in diverse open ocean settings is less well characterized. Here, we report seasonality in pelagic prokaryotes from open ocean depth profiles collected over 8.5 years in the North Pacific Subtropical Gyre. At depths shallower than 150 m, we found significant annual cycling in >62% of all pelagic prokaryote taxa. Although the proportion of seasonally cycling taxa diminished at depths greater than 150 m, annual periodicity to depths of 4000 m was observed in some taxa. Even among closely related prokaryotes in the same clade, variable seasonal maxima were observed, a sub-clade-level temporal niche partitioning referred to here as seasonal ecotypes. One prevailing trend in the euphotic zone was a seasonal shift from surface water abundance maxima in winter, to spring and summer annual peaks at greater depths. In the upper mixed layer, most Prochlorococcus seasonal ecotypes had winter abundance maxima, while bacterial heterotrophs typically peaked in summer. In the euphotic subsurface, common seasonal ecotypes included Prochlorococcus having spring or summer maxima, and heterotrophic and chemolithoautotrophic prokaryotes having winter or fall maxima. At meso- and bathypelagic depths, most prokaryotes exhibited winter, spring, or fall seasonal maxima, alongside annual peaks of surface-dwelling photoautotrophs exported to the deep sea. The results indicate that seasonal ecotype annual cycling is a central feature of open ocean prokaryote communities, and suggest that subtle yet predictable seasonal niche partitioning helps drive and sustain prokaryote genetic diversification throughout the open ocean's interior.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2026-04-07DOI: 10.1093/ismejo/wrag047
Youssef Ahmiane, Carlos Lax, Sonia Béjar-González, Francisco Esteban Nicolás, Laura Camuña-Pardo, Maria José Figueras, Ana Fernández-Bravo, Victoriano Garre, Javier Capilla, Marta Sanchis
{"title":"Light restores sporulation in Rhizopus microsporus cured of its endosymbionts, unveiling their role in fitness and virulence","authors":"Youssef Ahmiane, Carlos Lax, Sonia Béjar-González, Francisco Esteban Nicolás, Laura Camuña-Pardo, Maria José Figueras, Ana Fernández-Bravo, Victoriano Garre, Javier Capilla, Marta Sanchis","doi":"10.1093/ismejo/wrag047","DOIUrl":"https://doi.org/10.1093/ismejo/wrag047","url":null,"abstract":"Rhizopus microsporus is a major cause of mucormycosis, an infection caused by Mucorales that increasingly affects immunocompromised individuals. Certain isolates of R. microsporus harbor bacterial endosymbionts that regulate key fungal functions, particularly asexual and sexual reproduction, but these effects have been explored exclusively in environmental isolates. Although some clinical isolates contain Mycetohabitans endosymbionts, their influence on fungal reproduction remains unknown. This dependence on endosymbionts for asexual spore formation in environmental isolates has established the Rhizopus-Mycetohabitans association as a model for studying fungal-bacterial endosymbiosis, but it has also constrained functional comparative studies across environmental and clinical backgrounds. We show that light exposure partially restores asexual sporulation in endosymbiont-cured environmental strains, enabling the generation of isogenic sporulating lines. Transcriptomic analyses revealed that both light and endobacteria modulate overlapping signal transduction pathways, regulating the expression of conserved genes involved in asexual development in Mucorales and other fungi. Functional assays demonstrated that asexual spores from cured strains are viable; however, the presence of endosymbionts accelerates spore formation, enhances osmotic stress tolerance, and helps maintain cell-wall integrity. Cured strains exhibit altered membrane composition, including reduced ergosterol levels, which may contribute to their resistance to macrophage phagocytosis. Despite these compensatory adaptations, cured strains showed attenuated virulence in a murine mucormycosis model, highlighting the role of bacterial endosymbionts in fungal pathogenicity. The discovery of light-induced sporulation in cured strains provides a valuable experimental framework for future comparative studies requiring asexual spores, offering new opportunities to explore the role of fungal-bacterial endosymbiosis in fungal biology and human disease.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147649165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Oxygen scavenging enables microoxic survival of the marine anammox bacterium Scalindua sp.","authors":"Satoshi Okabe,Keishi Nukada,Keitaro Horiguchi,Mamoru Oshiki","doi":"10.1093/ismejo/wrag075","DOIUrl":"https://doi.org/10.1093/ismejo/wrag075","url":null,"abstract":"Marine anammox bacteria of the genus Scalindua play a pivotal role in nitrogen loss within oceanic oxygen minimum zones (OMZs), yet their physiological resilience to oxygen exposure remains poorly characterized. Here, we show that Scalindua sp. possesses an intrinsic capacity to reduce ambient oxygen under microoxic conditions (headspace O₂ ≈ 3%), exhibiting specific oxygen reduction rates (SORRs) of ~10 nmol-O₂ min-1 mg- protein-1. Anammox activity, evidenced by 29N₂ production, resumed once dissolved oxygen (DO) declined below ~5 μM, defining the DO threshold. This oxygen-scavenging ability is likely mediated by direct oxygen reduction to water via cbb₃-type cytochrome c oxidase (CcO) and A-type flavodiiron proteins (Fdps), with minimal reactive oxygen species (ROS) generation. CcO activity increased rapidly and markedly upon nitrite addition, consistent with the immediate onset of oxygen consumption and the transcriptional induction of CcO subunit genes. Nitrite was essential for sustaining oxygen consumption, and the rapid CcO activation suggests that nitrite stimulates CcO function through an unresolved regulatory mechanism. Nitrite oxidation also supplies supplementary electrons for oxygen reduction independently of core anammox metabolism, underscoring a flexible substrate-driven detoxification mechanism that enables Scalindua sp. to cope with transient microoxia. Together, these results show that Scalindua sp. employs a multi-layered defense -moderate oxygen-reduction capacity coupled with efficient ROS detoxification- conferring high and reversible oxygen tolerance. Although laboratory conditions cannot fully replicate natural OMZ complexity, our findings indicate that this physiological flexibility reflects the potential ecological resilience of Scalindua sp. in dynamic ocean environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"52 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147585519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unique microbial communities and phylosymbiosis signals in herpetofauna.","authors":"Jiaying Li,Yuze Gao,Xuelin Zhao,Jiahao Zhu,Si Zheng,Qihan Guo,Longhui Zhao,Guocheng Shu,Yuzhou Gong,Wujie Xu,Ting Chen","doi":"10.1093/ismejo/wrag076","DOIUrl":"https://doi.org/10.1093/ismejo/wrag076","url":null,"abstract":"Microbial symbionts are closely related to the internal and external factors of their host. However, the prevalence of phylosymbiosis (the presence of host phylogenetic signal in microbial community composition) remains controversial, especially in animals collectively referred to as herpetofauna. To expand our understanding of host-microbiota interactions, we analyzed 11,697 symbiotic microbiota samples from of 337 herpetofaunal species, covering skin, oral cavity, gut, cloaca, feces, and other body sites. The composition of the microbial communities gradually changes along the digestive tract, and is host-specific in each region. Overall, herpetofauna's dominant microbial taxa (Firmicutes, Proteobacteria, Bacteroidota) are more similar to mammals than fish (which are dominated by Proteobacteria, Firmicutes, and Fusobacteriota). However, phylosymbiosis in herpetofauna is weaker than in mammals and tends to occur at higher host taxonomic levels. The strength of the phylosymbiosis signal is influenced by body site, host genetic distance, and analytical method. It indicates that phylosymbiosis exists but is not universal. The intensity and significance of this signal are influenced by host taxonomic scale, the location of the microbial communities, and the the assessment methods. These results advance our knowledge of host-microbe interactions across the Tree of Life.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147585518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.","authors":"Feilong Deng,Yanhua Han,Yunjuan Peng,Zhijian Xu,Jianbo Yang,Jinling He,Desheng Li,Guixin Dong,Peng Zhang,Hui Jiang,Jianmin Chai,Chengdong Wang,Jiangchao Zhao,Ying Li","doi":"10.1093/ismejo/wrag068","DOIUrl":"https://doi.org/10.1093/ismejo/wrag068","url":null,"abstract":"Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147585517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}