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Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions. 宿主多样性的增加限制了细菌的普遍性,但可能促进微生物之间的相互作用。
IF 6.1
ISME communications Pub Date : 2025-08-23 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf146
Iris A Holmes, José G Martínez-Fonseca, Rudolf von May, Briana A Sealey, Peter A Cerda, Maggie R Grundler, Erin P Westeen, Daniel Nondorf, Joanna G Larson, Christopher R Myers, Tory A Hendry
{"title":"Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions.","authors":"Iris A Holmes, José G Martínez-Fonseca, Rudolf von May, Briana A Sealey, Peter A Cerda, Maggie R Grundler, Erin P Westeen, Daniel Nondorf, Joanna G Larson, Christopher R Myers, Tory A Hendry","doi":"10.1093/ismeco/ycaf146","DOIUrl":"10.1093/ismeco/ycaf146","url":null,"abstract":"<p><p>Host-associated bacteria vary in the number of host species they occupy. By colonizing many host species, host generalists can have disproportionate ecological impacts and should gain an evolutionary advantage when host species availability varies. However, past work has shown that many bacterial lineages are host specific. We hypothesized that constraints on bacterial host generalism will differ depending on ecological context. To test this, we assessed patterns of diversity and specialization in the cloacal microbiomes of reptile communities from the temperate zone to the tropics, a 10-fold increase in host species richness. We found that some host-specific lineages increased in richness along with their hosts, while generalist lineages did not. Generalist lineages were able to attain their highest host prevalence when host diversity was lower. In our highest diversity host communities, we found that the successful generalists, typically Proteobacteria, were disproportionately likely to co-occur with one another across evolutionarily disparate hosts. Our data indicated that bacterial lineages may adapt to the evolutionary pressures of high diversity host communities either by specializing on hosts or by forming cohorts of co-occurring bacterial lineages. Previous research across vertebrate gut microbiomes has shown that mutually beneficial relationships between bacterial lineages are widespread. Our work further supports that finding and contextualizes it within a range of host community diversity.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf146"},"PeriodicalIF":6.1,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Anaerobic gut fungal community in ostriches (Struthio camelus). 鸵鸟肠道厌氧真菌群落。
IF 6.1
ISME communications Pub Date : 2025-08-22 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf144
Julia Vinzelj, Kathryn Nash, Adrienne L Jones, R Ty Young, Casey H Meili, Carrie J Pratt, Yan Wang, Mostafa S Elshahed, Noha H Youssef
{"title":"Anaerobic gut fungal community in ostriches (<i>Struthio camelus</i>).","authors":"Julia Vinzelj, Kathryn Nash, Adrienne L Jones, R Ty Young, Casey H Meili, Carrie J Pratt, Yan Wang, Mostafa S Elshahed, Noha H Youssef","doi":"10.1093/ismeco/ycaf144","DOIUrl":"10.1093/ismeco/ycaf144","url":null,"abstract":"<p><p>Anaerobic gut fungi (AGF; <i>Neocallimastigomycota</i>) are crucial for the degradation of plant biomass in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in nonmammalian hosts remains sparse. Here, we report on the AGF community in fecal samples of 13 domesticated ostriches. The ostrich (<i>Struthio camelus</i>) is an herbivorous, flightless, hindgut-fermenting member of the class <i>Aves</i> (birds). Illumina-based metabarcoding targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform AGF community with low alpha diversity in the fecal samples. The community was mostly comprised of sequences potentially representing two novel species in the genus <i>Piromyces,</i> and a novel genus in the <i>Neocallimastigomycota</i>. Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One <i>Piromyces</i> strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of ≈ 30Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other <i>Piromyces</i> species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class <i>Aves</i>), highlight a unique AGF community in the ostrich alimentary tract, and document the occurrence of a strong pattern of fungal-host association in ostriches, similar to previously observed patterns in AGF canonical mammalian hosts.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf144"},"PeriodicalIF":6.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization. 高性能合成微生物群落的生态设计:从理论基础到功能优化。
IF 6.1
ISME communications Pub Date : 2025-08-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf133
Zhihan Wang, Shang Wang, Qing He, Xingsheng Yang, Bo Zhao, Haihan Zhang, Ye Deng
{"title":"Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization.","authors":"Zhihan Wang, Shang Wang, Qing He, Xingsheng Yang, Bo Zhao, Haihan Zhang, Ye Deng","doi":"10.1093/ismeco/ycaf133","DOIUrl":"10.1093/ismeco/ycaf133","url":null,"abstract":"<p><p>The complexity of natural microbial communities poses significant challenges for predictive manipulation, driving the emergence of Synthetic Microbial Communities (SynComs) as tractable models for functional optimization in environmental, agricultural, and biomedical applications. While SynComs provide enhanced controllability, their rational design faces persistent challenges in achieving both functional precision and ecological stability. Here, we present a theoretical and methodological framework for engineering SynComs through the strategic integration of ecological principles, evolutionary theory, and computational innovation. By (i) ecological interaction engineering for dynamic equilibrium of cooperative and competitive relationships, (ii) hierarchical species orchestration ensuring structural integrity through keystone species governance, helper-mediated adaptation, and rare taxa preservation, (iii) evolution-guided artificial selection overcoming functional-stability trade-offs, and (iv) modular metabolic stratification for efficient resource partitioning, we demonstrate how SynComs can be programmed for predictable functionality. We further identify critical frontiers for SynCom construction and application, including: mechanistic decoding of microbial interaction networks, high-throughput culturomics for strain discovery, artificial intelligence-enabled exploitation of microbial dark matter, automated platform-assisted consortium assembly, predictive modelling of long-term community dynamics, and the development of standardized frameworks and shared databases. The theory-technology integrated paradigm establishes SynComs as programmable ecotechnologies capable of addressing global sustainability challenges through engineered ecological resilience. This synthesis provides both a conceptual roadmap and a practical toolkit for transitioning from empirical community construction to predictive ecosystem engineering.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf133"},"PeriodicalIF":6.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12373479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Temperature-driven biogeography of marine giant viruses infecting picoeukaryotes Micromonas. 海洋巨病毒感染微真核生物微单胞菌的温度驱动生物地理学研究。
IF 6.1
ISME communications Pub Date : 2025-08-14 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf137
David Demory, Hisashi Endo, Anne-Claire Baudoux, Estelle Bigeard, Nigel Grimsley, Nathalie Simon, Hiroyuki Ogata, Joshua S Weitz
{"title":"Temperature-driven biogeography of marine giant viruses infecting picoeukaryotes <i>Micromonas</i>.","authors":"David Demory, Hisashi Endo, Anne-Claire Baudoux, Estelle Bigeard, Nigel Grimsley, Nathalie Simon, Hiroyuki Ogata, Joshua S Weitz","doi":"10.1093/ismeco/ycaf137","DOIUrl":"10.1093/ismeco/ycaf137","url":null,"abstract":"<p><p>Climate shapes the biogeography of microbial and viral communities in the ocean. Among abiotic factors, temperature is one of the main drivers of microbial community distribution. However, we lack knowledge on how temperature shapes the life history traits, population dynamics, and the biogeography of marine viruses. This study integrates mathematical modeling with <i>in situ</i> observations to investigate the temperature-driven biogeography of marine viruses. We focused on prasinoviruses, a group of giant viruses that infect the picoeukaryote <i>Micromonas</i>, a widespread phytoplankton with thermotypes adapted from poles to tropics. Analyzing the Tara Oceans and Polar Circle databases, we found that temperature is the primary determinant of <i>Micromonas</i> virus (MicV) distribution in the surface ocean. Phylogenetic reconstruction of MicVs revealed that these viruses form several groups with cryophile or cryo-mesophile preferences. We applied a mechanistic model to describe temperature-driven population dynamics, allowing us to predict the global presence and absence of MicVs. The probability of lysis and the probability of infection emerged as reliable predictors of MicV distribution, indicating that temperature-driven cellular mechanisms significantly shape viral community structure and distribution in the global oceans.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf137"},"PeriodicalIF":6.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition. 不同物种组成的合成群落的比较代谢模型揭示了高阶微生物相互作用。
IF 6.1
ISME communications Pub Date : 2025-08-14 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf142
Dongyu Wang, Kristopher A Hunt, Britt Abrahamson, Zachary Flinkstrom, Xuanyu Tao, Ralph S Tanner, Kara B DeLeόn, Aifen Zhou, Jizhong Zhou, Michael J McInerney, Mari-Karoliina H Winkler, David A Stahl, Pieter Candry, Chongle Pan
{"title":"Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition.","authors":"Dongyu Wang, Kristopher A Hunt, Britt Abrahamson, Zachary Flinkstrom, Xuanyu Tao, Ralph S Tanner, Kara B DeLeόn, Aifen Zhou, Jizhong Zhou, Michael J McInerney, Mari-Karoliina H Winkler, David A Stahl, Pieter Candry, Chongle Pan","doi":"10.1093/ismeco/ycaf142","DOIUrl":"10.1093/ismeco/ycaf142","url":null,"abstract":"<p><p>Understanding how microbial interactions scale with community complexity is key to microbiome engineering and ecological theory. This study investigates emergent metabolic behaviors in controlled <i>in vitro</i> synthetic anaerobic communities of two, three, or four species: cellulolytic bacterium (<i>Ruminiclostridium cellulolyticum</i>), a hydrogenotrophic methanogen (<i>Methanospirillum hungatei</i>), an acetoclastic methanogen (<i>Methanosaeta concilii</i>), and a sulfate-reducing bacterium (<i>Desulfovibrio vulgaris</i>), representing core metabolic guilds in cellulose degradation and carbon conversion. We applied a systems biology framework combining proteogenomics, stoichiometric flux modeling, and SMETANA (Species Metabolic Coupling Analysis) to quantify syntrophic cooperation and competition across configurations. Cooperation peaked in tri-cultures and declined nonlinearly in more complex assemblies. Species roles shifted contextually. <i>Ruminiclostridium cellulolyticum</i> was the dominant donor, adjusting cellulase and hydrogenase expression by partner. <i>Methanosaeta concilii</i> became fully metabolite-dependent while enhancing methanogenesis. <i>Desulfovibrio vulgaris</i> improved syntrophic efficiency via redox and hydrogen turnover. In contrast, <i>Methanospirillum hungatei</i>'s metabolic centrality declined despite higher CH₄ output, suggesting interaction strength depends more on compatibility than richness. Reduced interactions in the four-species community stemmed from a single configuration and need further validation. This study moves beyond descriptive work by quantitatively resolving how metabolic networks rewire across defined communities. By characterizing context-dependent flux shifts at multiple layers, we provide a framework for interpreting and engineering stable, functionally interdependent microbial ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf142"},"PeriodicalIF":6.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12422100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population. 在封闭的岛屿鸟类种群中,肠道微生物群落表现出细微的空间差异。
IF 6.1
ISME communications Pub Date : 2025-08-11 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf138
Sarah F Worsley, Chuen Zhang Lee, Maaike A Versteegh, Terry Burke, Jan Komdeur, Hannah L Dugdale, David S Richardson
{"title":"Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population.","authors":"Sarah F Worsley, Chuen Zhang Lee, Maaike A Versteegh, Terry Burke, Jan Komdeur, Hannah L Dugdale, David S Richardson","doi":"10.1093/ismeco/ycaf138","DOIUrl":"10.1093/ismeco/ycaf138","url":null,"abstract":"<p><p>Environmental variation is a key factor shaping microbial communities in wild animals. However, most studies have focussed on separate populations distributed over large spatial scales. How ecological factors shape inter-individual microbiome variation within a single landscape and host population remains poorly understood. Here, we use dense sampling of individuals in a natural, closed population of Seychelles warblers (<i>Acrocephalus sechellensis</i>) on Cousin Island (<0.7 km diameter, 0.34 km<sup>2</sup> total area) to determine whether gut microbiome communities exhibit high-resolution spatial variation over fine scales (average territory area is 0.0023 km<sup>2</sup>). We identified a small but highly significant quadratic relationship between geographic distance and gut microbiome beta diversity across the island. Microbiome composition initially diverged with increasing geographic distance between territories. However, after ca. >300 m, microbiome composition became increasingly similar amongst individuals situated on different sides of the island. This relationship was robust to the effects of host relatedness, age, and sex. Further analysis showed that microbiome composition differed between individuals inhabiting coastal and inland territories. Warblers in coastal territories harboured greater abundances of marine bacteria and lower abundances of anaerobic taxa commonly linked to host metabolic health, suggesting that exposure to different environmental microbes and variation in host condition (which is lower in coastal territories) could drive spatial patterns of gut microbiome variation across the island. This work demonstrates that host-microbe interactions can be labile even at very fine spatial scales. Such variability may have implications for how species respond to anthropogenic disturbance in wild habitats.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf138"},"PeriodicalIF":6.1,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12400925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Temporal profiling of rumen and hindgut microbiota revealed enterotypes affecting the microbial interactions and assembly in the gut of dairy cows. 瘤胃和后肠微生物群的时间分析揭示了影响奶牛肠道微生物相互作用和组装的肠道类型。
IF 6.1
ISME communications Pub Date : 2025-08-02 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf130
Yangyi Hao, Youyoung Choi, Jana Seifert, Wei Wang, Ya Jing Wang, Zhijun Cao, Hongjian Yang, Le Luo Guan, Shengli Li
{"title":"Temporal profiling of rumen and hindgut microbiota revealed enterotypes affecting the microbial interactions and assembly in the gut of dairy cows.","authors":"Yangyi Hao, Youyoung Choi, Jana Seifert, Wei Wang, Ya Jing Wang, Zhijun Cao, Hongjian Yang, Le Luo Guan, Shengli Li","doi":"10.1093/ismeco/ycaf130","DOIUrl":"10.1093/ismeco/ycaf130","url":null,"abstract":"<p><p>It has been reported that rumen microbiota affects the cattle's milk-yield productivity, but the gut microbiota's contribution to the individualized performance and its associated mechanism have not been well defined. In this study, microbiota of 222 rumen and hindgut respective samples collected from 74 cows throughout the prepartum, postpartum, and peak-lactation periods were assessed using 16S rRNA gene amplicon analysis and were evaluated whether they affected inter-individual microbial interactions, assembly, functions, and contributed to host milk production and serum parameters. Prevotella-dominated (R-Prevot, n = 27) and Butyrivibrio-dominated (R-Butyri, n = 47) enterotypes were identified for rumen microbiota, and Prevotellaceae_UCG-003-dominated (H-Prevot, n = 33) and Paeniclostridium-dominated (H-Paenic, n = 41) enterotypes were identified for fecal microbiota. Positive cohesion (cooperative behaviour) was higher, while negative cohesion (competitive behavior) was lower in R-Prevot compared to R-Butyri enterotype throughout the three lactation periods. For H-Prevot enterotype, positive cohesion was higher at prepartum and peak-lactation, but lower at postpartum; and negative cohesion was lower at prepartum and postpartum with no difference detected at peak-lactation. Both deterministic and stochastic processes contributed to the rumen and hindgut microbiota assembly process with the proportion of dispersal limitation process being higher in R-Butyri than in R-Prevot, as well as in H-Prevot than in H-Paenic enterotype at peak-lactation. Additionally, the cows with R-Prevot/H-Prevot enterotypes (n = 15) had higher milk yield and lower serum non-esterified fatty acid concentration than the cows with R-Butyri/H-Paenic enterotypes (n = 29) during lactation. These findings provide evidence that enterotype could affect microbial interactions and assembly processes, as well as the cows' productivity.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf130"},"PeriodicalIF":6.1,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12376038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Probiotic paradox: bacillibactin from Bacillus velezensis drives pathogenic Vibrio alginolyticus proliferation through siderophore piracy. 益生菌悖论:来自velezensis芽孢杆菌的芽孢杆菌素通过铁噬菌盗版驱动致病性溶藻弧菌增殖。
IF 6.1
ISME communications Pub Date : 2025-08-01 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf132
Yanhua Zeng, Haimin Chen, Xiaoxiao Gong, Manwei Jiang, Ni Liu, Wen Li, Na Zhang, Hao Long, Aiyou Huang, Zhenyu Xie
{"title":"Probiotic paradox: bacillibactin from <i>Bacillus velezensis</i> drives pathogenic <i>Vibrio alginolyticus</i> proliferation through siderophore piracy.","authors":"Yanhua Zeng, Haimin Chen, Xiaoxiao Gong, Manwei Jiang, Ni Liu, Wen Li, Na Zhang, Hao Long, Aiyou Huang, Zhenyu Xie","doi":"10.1093/ismeco/ycaf132","DOIUrl":"10.1093/ismeco/ycaf132","url":null,"abstract":"<p><p>The opportunistic pathogen <i>Vibrio alginolyticus</i> dominates iron-depleted marine ecosystems, likely driven by its diverse repertoire of siderophore receptors that enable iron piracy from exogenous sources. While the ability to utilize xenosiderophores via piracy can be advantageous under iron limitation, the identities of exogenous siderophore producers interacting with <i>V. alginolyticus</i> remain poorly characterized. Here, we show that 17.0% of siderophore-producing isolates from <i>V. alginolyticus</i>-dominated mariculture systems significantly enhance the growth of <i>V. alginolyticus</i> HN08155 under iron limitation, including six <i>Bacillus</i> strains established as probiotics in aquaculture. Notably, <i>Bacillus velezensis</i> WD26-16 exhibits the strongest growth-promoting effect via catechol-type siderophore bacillibactin production. Genomic analyses demonstrate that 86.1% of marine <i>Bacillus</i> spp. in the Genome Taxonomy Database harbor conserved bacillibactin biosynthetic gene clusters, with near-complete conservation across all <i>B. velezensis</i> strains, suggesting ubiquitous siderophore-mediated interaction with <i>V. alginolyticus</i>. Exogenous bacillibactin induces distinct metabolic modulation in <i>V. alginolyticus</i>, activating pathways critical for amino acid metabolism, protein biosynthesis, and energy production to sustain proliferative demands. This metabolic adaptation is mediated by coordinated upregulation of multiple siderophore receptors (IutA, IrgA, VctA) that allows functional plasticity in xenosiderophore piracy. Co-culture experiments reveal that <i>V. alginolyticus</i> exploits bacillibactin to outcompete <i>B. velezensis</i> and achieves a 3.4-fold growth advantage compared to the monoculture. Our results uncover an ecological paradox: probiotic <i>B. velezensis</i> inadvertently enhances pathogenic <i>V. alginolyticus</i> proliferation through siderophore piracy. This iron-centric competition mechanism likely drives vibriosis outbreaks in aquaculture systems, necessitating urgent reassessment of probiotic selection criteria to avoid unintended pathogen amplification.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf132"},"PeriodicalIF":6.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics. CleanBar:用于单细胞组学拆分和池条形码的多功能解复用工具。
IF 6.1
ISME communications Pub Date : 2025-08-01 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf134
Vicente Arnau, Alicia Ortiz-Maiques, Juan Valero-Tebar, Lucas Mora-Quilis, Vaida Kurmauskaite, Lorea Campos Dopazo, Pilar Domingo-Calap, Mária Džunková
{"title":"CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.","authors":"Vicente Arnau, Alicia Ortiz-Maiques, Juan Valero-Tebar, Lucas Mora-Quilis, Vaida Kurmauskaite, Lorea Campos Dopazo, Pilar Domingo-Calap, Mária Džunková","doi":"10.1093/ismeco/ycaf134","DOIUrl":"10.1093/ismeco/ycaf134","url":null,"abstract":"<p><p>Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four <i>Klebsiella</i> strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf134"},"PeriodicalIF":6.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12376035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes. 海洋原核生物和光合真核生物的定量宏基因组学。
IF 6.1
ISME communications Pub Date : 2025-07-30 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf131
Qicheng Bei, Nathan L R Williams, Laura E Furtado, Daria Di Blasi, Jelani Williams, Vanda Brotas, Glen Tarran, Andrew P Rees, Chris Bowler, Jed A Fuhrman
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