ISME communications最新文献

Asymmetric metabolic adaptations undermine stability in microbial syntrophy.

IF 5.1

ISME communications Pub Date : 2025-01-25 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf011

Nan Ye, Zhi-Chun Yang, Zhuang-Dong Bai

{"title":"Asymmetric metabolic adaptations undermine stability in microbial syntrophy.","authors":"Nan Ye, Zhi-Chun Yang, Zhuang-Dong Bai","doi":"10.1093/ismeco/ycaf011","DOIUrl":"10.1093/ismeco/ycaf011","url":null,"abstract":"Syntrophic interaction, driven by metabolite exchange, is widespread within microbial communities. However, co-inoculation of most auxotrophic microorganisms often fails to establish a stable metabolite exchange relationship. Here, we engineered two auxotrophic Escherichia coli strains, each dependent on the other for essential amino acid production, to investigate the dynamics of syntrophic relationships. Through invasion-from-rare experiments, we observed the rapid formation of syntrophic consortia stabilized by frequency-dependent selection, converging to a 2:1 ratio of lysine-to-arginine auxotrophs. However, laboratory evolution over 25 days revealed that syntrophic interactions were evolutionarily unstable, with cocultures collapsing as ΔL cells dominated the population. Reduced fitness in cocultures was driven by the emergence of a \"selfish\" ΔL phenotype, characterized by decreased arginine production and exploitation of lysine produced by ΔA cells. Dynamic metabolic assays revealed that metabolite production and utilization patterns strongly influenced the fitness of each strain. ΔL cells displayed metabolic plasticity, adjusting lysine utilization in response to lysine availability, which enabled them to outcompete ΔA cells. In contrast, ΔA cells lacked similar plasticity, resulting in their negative selection. These findings demonstrate that asymmetric metabolic responses and the emergence of selfish phenotypes destabilize syntrophic relationships. Our work underscores the importance of balanced metabolic exchanges for developing sustainable synthetic microbial consortia and offers insights into the evolutionary dynamics of microbial cooperation.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf011"},"PeriodicalIF":5.1,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11815887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412014","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

High ectomycorrhizal relative abundance during winter at the treeline.

IF 5.1

ISME communications Pub Date : 2025-01-25 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf010

Luis A Saona, Christian I Oporto, Pablo Villarreal, Kamila Urbina, Cristian Correa, Julian F Quintero-Galvis, Paulo Moreno-Meynard, Frida I Piper, Juliana A Vianna, Roberto F Nespolo, Francisco A Cubillos

{"title":"High ectomycorrhizal relative abundance during winter at the treeline.","authors":"Luis A Saona, Christian I Oporto, Pablo Villarreal, Kamila Urbina, Cristian Correa, Julian F Quintero-Galvis, Paulo Moreno-Meynard, Frida I Piper, Juliana A Vianna, Roberto F Nespolo, Francisco A Cubillos","doi":"10.1093/ismeco/ycaf010","DOIUrl":"10.1093/ismeco/ycaf010","url":null,"abstract":"The rhizosphere is the soil region around plant roots hosting a diverse microbial community, influencing nutrient availability and how plants react to extreme conditions. However, our understanding of the fungi biodiversity and the impact of environmental variations on this biodiversity is still in its infancy. Our study investigates fungal communities' diversity and functional traits in the rhizosphere of Nothofagus pumilio, one of the few winters deciduous treeline species in the world, forming the treeline in southern South America. At four distinct locations covering 10° latitude, we collected soil samples at treeline and 200 m below over four seasons during a single year. We employed ITS metabarcoding to elucidate fungal community structures. Our results reveal that fungal diversity was mainly determined by latitudinal variation, with higher levels during warmer seasons and lower altitudes. Interestingly, we found a marked dominance of ectomycorrhizal fungi at the treeline, particularly during the winter. In contrast, saprotrophic fungi were more abundant at lower altitudes, particularly during the warmer spring and summer seasons. These findings highlight the temporal and spatial dynamics of rhizospheric fungal communities and their potential roles in ecological processes, emphasizing the value of these communities as indicators of environmental change in high-elevation forests.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf010"},"PeriodicalIF":5.1,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11815889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412023","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

Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow.

IF 5.1

ISME communications Pub Date : 2025-01-10 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf003

Ze Ren, Wei Luo, Huirong Li, Haitao Ding, Yunlin Zhang

{"title":"Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow.","authors":"Ze Ren, Wei Luo, Huirong Li, Haitao Ding, Yunlin Zhang","doi":"10.1093/ismeco/ycaf003","DOIUrl":"10.1093/ismeco/ycaf003","url":null,"abstract":"Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf003"},"PeriodicalIF":5.1,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11765414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049174","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

Sexual reproduction during diatom bloom. 硅藻华期间有性繁殖。

IF 5.1

ISME communications Pub Date : 2025-01-07 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae169

Léa Prigent, Julien Quéré, Martin Plus, Mickael Le Gac

{"title":"Sexual reproduction during diatom bloom.","authors":"Léa Prigent, Julien Quéré, Martin Plus, Mickael Le Gac","doi":"10.1093/ismeco/ycae169","DOIUrl":"10.1093/ismeco/ycae169","url":null,"abstract":"Phytoplankton supports food webs in all aquatic ecosystems. Ecological studies highlighted the links between environmental variables and species successions in situ. However, the role of life cycle characteristics on phytoplankton community dynamics remains poorly characterized. In diatoms, sexual reproduction creates new genetic combinations and prevents excessive cell size miniaturization. It has been extensively studied in vitro but seldom in the natural environment. Here, analyzing metatranscriptomic data in the light of the expression patterns previously characterized in vitro, we identified a synchronized and transient sexual reproduction event during a bloom of the toxic diatom species Pseudo-nitzschia australis. Despite the complexity of environmental conditions encountered in situ, sexual reproduction appeared to be the strongest differential gene expression signal that occurred during the bloom. The potential link between environmental conditions and the initiation of sexual reproduction remain to be determined, but sexual reproduction probably had a major impact on the bloom dynamic.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae169"},"PeriodicalIF":5.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11749564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017585","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

Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks. 菌根树的土壤微生物碳利用效率不同：来自基质化学计量学和微生物网络的见解。

IF 5.1

ISME communications Pub Date : 2024-12-27 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae173

Jing Yu, Jingyi Yang, Lingrui Qu, Xiaoyi Huang, Yue Liu, Ping Jiang, Chao Wang

{"title":"Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks.","authors":"Jing Yu, Jingyi Yang, Lingrui Qu, Xiaoyi Huang, Yue Liu, Ping Jiang, Chao Wang","doi":"10.1093/ismeco/ycae173","DOIUrl":"10.1093/ismeco/ycae173","url":null,"abstract":"The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and 18O-H2O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial-fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae173"},"PeriodicalIF":5.1,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11742255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017587","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

Arsenic modifies the microbial community assembly of soil-root habitats in Pteris vittata. 砷改变了蜈蚣草土壤根生境的微生物群落组合。

IF 5.1

ISME communications Pub Date : 2024-12-27 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae172

Jiahui Lin, Zhongmin Dai, Mei Lei, Qian Qi, Weijun Zhou, Lena Q Ma, Randy A Dahlgren, Jianming Xu

{"title":"Arsenic modifies the microbial community assembly of soil-root habitats in Pteris vittata.","authors":"Jiahui Lin, Zhongmin Dai, Mei Lei, Qian Qi, Weijun Zhou, Lena Q Ma, Randy A Dahlgren, Jianming Xu","doi":"10.1093/ismeco/ycae172","DOIUrl":"10.1093/ismeco/ycae172","url":null,"abstract":"Pteris vittata, renowned for its ability to hyperaccumulate arsenic, presents a promising solution to the escalating issue of global soil arsenic contamination. This fern cultivates a unique underground microbial community to enhance its environmental adaptability. However, our understanding of the assembly process and the long-term ecological impacts of this community remains limited, hindering the development of effective soil remediation strategies. This study addresses this gap by investigating soil-root habitats from three geographically diverse fields comprising a gradient of arsenic contamination, complemented by a time-scale greenhouse experiment. Field investigations reveal that arsenic stress influences community assembly dynamics in the rhizosphere by enhancing processes of homogeneous selection. Greenhouse experiments further reveal that arsenic exposure alters the assembly trajectory of rhizosphere communities by promoting key microbial modules. Specifically, arsenic exposure increases the enrichment of a core taxon (i.e. Rhizobiaceae) in the rhizosphere, both in field and greenhouse settings, boosting their abundance from undetectable levels to 0.02% in the soil after phytoremediation. Notably, arsenic exposure also promotes a pathogenic group (i.e. Spirochaetaceae) in the rhizosphere, increasing their abundance from undetectable levels to 0.1% in the greenhouse. This raise concerns that warrant further investigation in future phytoremediation studies. Overall, this study elucidates the assembly dynamics of the soil microbiome following the introduction of a remediation plant and emphasizes the often-overlooked impacts on soil microbial community following phytoremediation. By probing the ecological impacts of remediation plants, this work advances a more nuanced understanding of the complex ecological implications inherent in phytoremediation processes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae172"},"PeriodicalIF":5.1,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11742257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017514","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

Litter quality modulates changes in bacterial and fungal communities during the gut transit of earthworm species of different ecological groups.

IF 5.1

ISME communications Pub Date : 2024-12-26 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae171

Huizhen Chao, Linlin Zhong, Ina Schaefer, Mingming Sun, André Junggebauer, Feng Hu, Stefan Scheu

{"title":"Litter quality modulates changes in bacterial and fungal communities during the gut transit of earthworm species of different ecological groups.","authors":"Huizhen Chao, Linlin Zhong, Ina Schaefer, Mingming Sun, André Junggebauer, Feng Hu, Stefan Scheu","doi":"10.1093/ismeco/ycae171","DOIUrl":"10.1093/ismeco/ycae171","url":null,"abstract":"Earthworms are keystone animals stimulating litter decomposition and nutrient cycling. However, earthworms comprise diverse species which live in different soil layers and consume different types of food. Microorganisms in the gut of earthworms are likely to contribute significantly to their ability to digest organic matter, but this may vary among earthworm species. Here, we analyse the effect of food (litter) quality on gut microbiota and their changes during the gut passage (from foregut to hindgut) of earthworms of different ecological groups. The endogeic (soil living) species Aporrectodea caliginosa and the anecic (litter feeding) species Lumbricus terrestris were fed with high- (rape leaves) and low-quality litter (wheat straw) in a microcosm experiment for 18 weeks. Irrespective of earthworm species, alpha diversity of bacterial and fungal communities changed little during the gut passage, with the composition and diversity of microbial communities in the gut generally resembling those in soil more than in litter. In addition, the low-quality litter supported higher alpha diversity and more complex communities than high-quality litter. Further, gut microbial communities of the anecic L. terrestris changed less during gut passage than those of the endogeic A. caliginosa, especially when fed low-quality litter. Our findings indicate that earthworm gut microbial communities are predominantly shaped by the soil they ingest, but are modulated by the quality of litter they feed on and earthworm ecological group. Overall, the results suggest that earthworms primarily influence soil microbiota by mixing and spreading microorganisms from different microhabitats through bioturbation rather than by digesting microorganisms.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae171"},"PeriodicalIF":5.1,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070062","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

Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers. 波动的营养负荷对河流中硝酸盐还原微生物的影响。

IF 5.1

ISME communications Pub Date : 2024-12-24 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae168

Shengjie Li, Rui Zhao, Shuo Wang, Yiwen Yang, Muhe Diao, Guodong Ji

{"title":"Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers.","authors":"Shengjie Li, Rui Zhao, Shuo Wang, Yiwen Yang, Muhe Diao, Guodong Ji","doi":"10.1093/ismeco/ycae168","DOIUrl":"10.1093/ismeco/ycae168","url":null,"abstract":"Rivers serve important functions for human society and are significantly impacted by anthropogenic nutrient inputs (e.g. organic and sulfur compounds). Reduced organic and sulfur compounds influence the nitrogen cycle as they are electron donors of microbial nitrate reduction. Water pollution caused by individual nutrients and the mechanisms have been studied, but how the variation in multiple nutrient loadings influences nitrate-reducing microorganisms is less understood. Two sets of microcosms were established and exposed to nitrate, along with either acetate or thiosulfate, at different times. Nutrient concentrations responded to the loading pollutant. The nutrient loading order was more important in shaping microbial community structure and microbial interactions through the exchange of growth-required substances. This indicated that upstream or historical nutrient inflows impacted current nitrate reduction by changing the seeding microbial community, highlighting the importance of river connectivity. Based on metatranscriptome analysis, although the order and type of nutrient loadings were equally important in regulating global transcriptomes, transcripts of enzymes for key metabolisms (nitrate reduction, sulfur oxidation, etc.) more actively responded to the nutrient type. The regulation of a small set of genes was sufficient to make the transition, while most transcripts were not degraded and regenerated. These insights are important for understanding the varying pollution status of rivers and for developing effective solutions, such as remediation.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae168"},"PeriodicalIF":5.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017582","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

Microcystin shapes the Microcystis phycosphere through community filtering and by influencing cross-feeding interactions. 微囊藻毒素通过群落过滤和影响交叉摄食相互作用来塑造微囊藻的藻圈。

IF 5.1

ISME communications Pub Date : 2024-12-24 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae170

Rebecca Große, Markus Heuser, Jonna E Teikari, Dinesh K Ramakrishnan, Ahmed Abdelfattah, Elke Dittmann

{"title":"Microcystin shapes the Microcystis phycosphere through community filtering and by influencing cross-feeding interactions.","authors":"Rebecca Große, Markus Heuser, Jonna E Teikari, Dinesh K Ramakrishnan, Ahmed Abdelfattah, Elke Dittmann","doi":"10.1093/ismeco/ycae170","DOIUrl":"10.1093/ismeco/ycae170","url":null,"abstract":"The cyanobacterium Microcystis causes harmful algal blooms that pose a major threat to human health and ecosystem services, particularly due to the prevalence of the potent hepatotoxin microcystin (MC). With their pronounced EPS layer, Microcystis colonies also serve as a hub for heterotrophic phycosphere bacteria. Here, we tested the hypothesis that the genotypic plasticity in its ability to produce MC influences the composition and assembly of the Microcystis phycosphere microbiome. In an analysis of individual colonies of a natural Microcystis bloom, we observed a significantly reduced richness of the community in the presence of MC biosynthesis genes. A subsequent synthetic community experiment with 21 heterotrophic bacterial strains in co-cultivation with either the wild-type strain Microcystis aeruginosa PCC 7806 or the MC-free mutant ΔmcyB revealed not only a tug-of-war between phototrophic and heterotrophic bacteria, but also a reciprocal dominance of two isolates of the genus Sphingomonas and Flavobacterium. In contrast, an Agrobacterium isolate thrived equally well in both consortia. In substrate utilization tests, Sphingomonas showed the strongest dependence on Microcystis exudates with a clear preference for the wild-type strain. Genome sequencing revealed a high potential for complementary cross-feeding, particularly for the Agrobacterium and Sphingomonas isolates but no potential for MC degradation. We postulate that strain-specific functional traits, such as the ability to perform glycolate oxidation, play a crucial role in the cross-feeding interactions, and that MC is one of the determining factors in the Microcystis phycosphere due to its interference with inorganic carbon metabolism.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae170"},"PeriodicalIF":5.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017584","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

Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer. 溃疡性结肠炎患者粪便微生物群和粪便滤液转移后的细菌和病毒组合。

IF 5.1

ISME communications Pub Date : 2024-12-23 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae167

Howard Junca, Arndt Steube, Simon Mrowietz, Johannes Stallhofer, Marius Vital, Luiz Gustavo Dos Anjos Borges, Dietmar H Pieper, Andreas Stallmach

{"title":"Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.","authors":"Howard Junca, Arndt Steube, Simon Mrowietz, Johannes Stallhofer, Marius Vital, Luiz Gustavo Dos Anjos Borges, Dietmar H Pieper, Andreas Stallmach","doi":"10.1093/ismeco/ycae167","DOIUrl":"10.1093/ismeco/ycae167","url":null,"abstract":"Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae167"},"PeriodicalIF":5.1,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017458","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