ISME communications最新文献_第3页

Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system. 食用着色剂亮蓝色在体外简化微生物群模型系统中引起持续的功能和结构变化。

IF 5.1

ISME communications Pub Date : 2025-03-22 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf050

Victor Castañeda-Monsalve, Sven-Bastiaan Haange, Laura-Fabienne Fröhlich, Qiuguo Fu, Ulrike Rolle-Kampczyk, Martin von Bergen, Nico Jehmlich

{"title":"Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system.","authors":"Victor Castañeda-Monsalve, Sven-Bastiaan Haange, Laura-Fabienne Fröhlich, Qiuguo Fu, Ulrike Rolle-Kampczyk, Martin von Bergen, Nico Jehmlich","doi":"10.1093/ismeco/ycaf050","DOIUrl":"10.1093/ismeco/ycaf050","url":null,"abstract":"The human gut microbiota plays a vital role in maintaining host health by acting as a barrier against pathogens, supporting the immune system, and metabolizing complex carbon sources into beneficial compounds such as short-chain fatty acids. Brilliant blue E-133 (BB), is a common food dye that is not absorbed or metabolized by the body, leading to substantial exposure of the gut microbiota. Despite this, its effects on the microbiota are not well-documented. In this study, we cultivated the Simplified Human Microbiota Model (SIHUMIx) in a three-stage in vitro approach (stabilization, exposure, and recovery). Using metaproteomic and metabolomic approaches, we observed significant shifts in microbial composition, including an increase in the relative abundance of Bacteroides thetaiotaomicron and a decrease in beneficial species such as Bifidobacterium longum and Clostridium butyricum. We observed lower protein abundance in energy metabolism, metabolic end products, and particularly lactate and butyrate. Disturbance in key metabolic pathways related to energy production, stress response, and amino acid metabolism were also observed, with some pathways affected independently of bacterial abundance. These functional changes persisted during the recovery phase, indicating that the microbiota did not fully return to its pre-exposure state. Our findings suggest that BB has a lasting impact on gut microbiota structure and function, raising concerns about its widespread use in the food industry. This study underscores the need for further research into the long-term effects of food colorants on the gut microbiota and their potential health implications.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf050"},"PeriodicalIF":5.1,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813029","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

Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena. 黑麦根际微生物群氮循环行规的变化受作物生产力的驱动。

IF 5.1

ISME communications Pub Date : 2025-03-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf020

Simon Lewin, Marc Wehrhan, Sonja Wende, Michael Sommer, Steffen Kolb

{"title":"Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena.","authors":"Simon Lewin, Marc Wehrhan, Sonja Wende, Michael Sommer, Steffen Kolb","doi":"10.1093/ismeco/ycaf020","DOIUrl":"10.1093/ismeco/ycaf020","url":null,"abstract":"Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiomes at the agroecosystem scale necessitates bridging the gap to microscale structures of microbiomes. We hypothesized that differences of microbial nitrogen (N) cycle guilds in the rhizosphere of rye align with a soil catena that has been formed by tillage erosion. The rhizosphere was sampled at four sites, which captured a complete tillage erosion gradient from extremely eroded to depositional soils. The gene abundances characteristic of microbial N cycle guilds were assessed via metagenomics. The eroded sites showed the lowest plant productivity and soil mineral N availability, which was associated with an enrichment of glnA in the rhizosphere. Genes associated with dissimilatory nitrate-to-ammonium reducers and diazotrophy prevailed in the eroded soil profiles. The strongest correlations of the biomasses of rye plants along the catena with N cycle functions were observed for norBC. Thus, tillage erosion as a legacy of agricultural management aligns with substantial differences in rhizosphere microbiome functionality in N cycling. These microbiome differences were linked to plant shoot properties. Thus, the dynamics of the microbiome can be indirectly assessed by remote sensing.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf020"},"PeriodicalIF":5.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702477","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

The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River. 温度和盐度升高对博伊河异养纳米鞭毛虫微生物群落和食物选择性的影响

IF 5.1

ISME communications Pub Date : 2025-03-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf049

Lisa Boden, Dana Bludau, Guido Sieber, Aman Deep, Daria Baikova, Gwendoline M David, Una Hadžiomerović, Tom L Stach, Jens Boenigk

{"title":"The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.","authors":"Lisa Boden, Dana Bludau, Guido Sieber, Aman Deep, Daria Baikova, Gwendoline M David, Una Hadžiomerović, Tom L Stach, Jens Boenigk","doi":"10.1093/ismeco/ycaf049","DOIUrl":"10.1093/ismeco/ycaf049","url":null,"abstract":"Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf049"},"PeriodicalIF":5.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11976726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813058","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

Combined metabolomic and genomic analyses reveal phage-specific and infection stage-specific alterations to marine Roseobacter metabolism. 结合代谢组学和基因组学分析揭示了噬菌体特异性和感染阶段特异性对海洋玫瑰杆菌代谢的改变。

IF 5.1

ISME communications Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf047

Min Jin, Lanlan Cai, Longfei Lu, Meishun Yu, Rui Zhang

{"title":"Combined metabolomic and genomic analyses reveal phage-specific and infection stage-specific alterations to marine Roseobacter metabolism.","authors":"Min Jin, Lanlan Cai, Longfei Lu, Meishun Yu, Rui Zhang","doi":"10.1093/ismeco/ycaf047","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf047","url":null,"abstract":"Phages can reshape the metabolic network of hosts to support specific requirements for replication during infection. However, metabolomic profiling of phage-elicited host global metabolic alterations and the linkage of phage-encoded auxiliary metabolic genes to these alterations are understudied. In this study, the dynamics of intracellular metabolites of Dinoroseobacter shibae DFL12, a member of marine environmentally and biogeochemically relevant Roseobacter clade, in response to four distinct lytic roseophage infections were investigated. Metabolomic profiling indicated that roseophage infections significantly altered host metabolism in a phage-specific manner. Pathway enrichment analyses showed that the central carbon pathway and DNA, amino acid, and coenzyme metabolism were commonly altered by roseophages, revealing a central role of these pathways in phage replication. Furthermore, clear infection stage-specific host responses were observed, corresponding to different metabolic demands of phage replication in the early and late infection stages. Interestingly, the content of host vitamin B1, which is the essential nutrient provided by D. shibae to its symbiotic microalgae, increased in the early infection stage for most roseophages, implying that phage infection may impact the symbiosis of D. shibae with microalgae. Finally, combined metabolomic and phage genomics analyses showed that roseophages adopt different strategies to expand the host pyrimidine pool (recycling or de novo synthesis of pyrimidine nucleotides), and this difference was likely related to variation in the GC content between phage and host genomes. Collectively, these results highlight the potential importance of phage-specific and infection stage-specific host metabolic reprogramming in marine phage-host interactions, bacteria-microalgae symbiosis, and biogeochemical cycles.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf047"},"PeriodicalIF":5.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060669","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

Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil. 混合营养蓝藻是多氯联苯污染水稻土中重要的活性重氮营养菌。

IF 5.1

ISME communications Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae160

Wenbo Hu, Ying Teng, Xiaomi Wang, Yongfeng Xu, Yi Sun, Hongzhe Wang, Yanning Li, Shixiang Dai, Ming Zhong, Yongming Luo

{"title":"Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.","authors":"Wenbo Hu, Ying Teng, Xiaomi Wang, Yongfeng Xu, Yi Sun, Hongzhe Wang, Yanning Li, Shixiang Dai, Ming Zhong, Yongming Luo","doi":"10.1093/ismeco/ycae160","DOIUrl":"10.1093/ismeco/ycae160","url":null,"abstract":"Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). 15N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae160"},"PeriodicalIF":5.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671910","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

Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing. 通过rRNA基因扩增子测序进行微生物组跨结构域绝对定量的合成DNA峰值标准。

IF 5.1

ISME communications Pub Date : 2025-03-17 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf028

Dieter M Tourlousse, Yuji Sekiguchi

{"title":"Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.","authors":"Dieter M Tourlousse, Yuji Sekiguchi","doi":"10.1093/ismeco/ycaf028","DOIUrl":"10.1093/ismeco/ycaf028","url":null,"abstract":"Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of 12 unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf028"},"PeriodicalIF":5.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652469","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

Changes within the coral symbiosis underpin seasonal trophic plasticity in reef corals. 珊瑚共生关系的变化支撑着珊瑚的季节性营养可塑性。

IF 5.1

ISME communications Pub Date : 2025-03-14 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae162

Emily Chei, Inga Elizabeth Conti-Jerpe, Leonard Pons, David Michael Baker

{"title":"Changes within the coral symbiosis underpin seasonal trophic plasticity in reef corals.","authors":"Emily Chei, Inga Elizabeth Conti-Jerpe, Leonard Pons, David Michael Baker","doi":"10.1093/ismeco/ycae162","DOIUrl":"10.1093/ismeco/ycae162","url":null,"abstract":"Scleractinian corals are mixotrophic organisms that use both autotrophic and heterotrophic pathways to fulfill their metabolic needs. Corals span a spectrum of trophic strategies and vary in their dependence on associated algal symbionts, with certain species capable of increasing heterotrophic feeding to compensate for the loss of autotrophic nutrition. As this ability can improve the likelihood of survival following marine heat waves and environmental disturbance, the continued threat of global and local stressors necessitates the investigation of trophic plasticity to determine coral responses to changing conditions. Here, we examined trophic strategy shifts between wet (high temperature and light) and dry (low temperature and light) seasons for seven genera of scleractinian corals by applying a Bayesian statistical model to determine the isotopic niches of paired coral hosts and their symbionts. Using a novel index (Host Evaluation: Reliance on Symbionts), trophic strategy was evaluated along a continuum of mixotrophy for each season. Three genera exhibited significant trophic shifts and were more heterotrophic in the dry season, likely as a mechanism to compensate for decreased symbiont functioning under lower temperatures and irradiance during these months. The magnitude of trophic plasticity varied across genera, and this pattern was positively correlated with global distribution. Together, our findings substantiate taxonomic differences in nutritional flexibility and provide support for trophic plasticity as a distinguishing trait for understanding coral biogeography.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae162"},"PeriodicalIF":5.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702466","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

Use of MALDI-TOF mass spectrometry and IDBac to mine for understudied bacterial genera from the environment. 利用 MALDI-TOF 质谱仪和 IDBac 从环境中挖掘未被充分研究的细菌属。

IF 5.1

ISME communications Pub Date : 2025-03-13 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf046

Antonio Hernandez, Nyssa K Krull, Brian T Murphy

{"title":"Use of MALDI-TOF mass spectrometry and IDBac to mine for understudied bacterial genera from the environment.","authors":"Antonio Hernandez, Nyssa K Krull, Brian T Murphy","doi":"10.1093/ismeco/ycaf046","DOIUrl":"10.1093/ismeco/ycaf046","url":null,"abstract":"Bacterial natural products have greatly contributed to the global drug discovery effort. Further, the incorporation of understudied bacterial taxa into discovery pipelines remains a promising approach to supply much needed chemical diversity to this effort. Unfortunately, researchers lack rapid and efficient techniques to accomplish this. Here we present an approach that employs matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and the bioinformatics platform IDBac to perform targeted isolation of understudied bacteria from environmental samples. A dendrogram of MS protein spectra from 479 unknown bacterial isolates was seeded with spectra from 50 characterized strains that represented target understudied genera. This method was highly effective at identifying representatives from target taxa, demonstrating an 86.3% success rate when an estimated genus level cutoff was implemented in the dendrogram. Overall, this study shows the potential of MALDI-MS/IDBac to mine environmental bacterial isolate collections for target taxa in high-throughput, particularly in the absence of proprietary software. It also provides a cost-effective alternative to morphology and gene-sequencing analyses that are typically used to guide identification and prioritization strategies from large bacterial isolate collections.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf046"},"PeriodicalIF":5.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143775226","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

The infant microbiota hopscotches between community states toward maturation-longitudinal stool parameters and microbiota development in a cohort of European toddlers. 婴儿微生物群在走向成熟的群落状态之间跳跃——一组欧洲幼儿的纵向粪便参数和微生物群发育。

IF 5.1

ISME communications Pub Date : 2025-03-11 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf016

Evangelia Intze, Monika Schaubeck, Mohsen Pourjam, Klaus Neuhaus, Ilias Lagkouvardos, Thomas C A Hitch, Thomas Clavel

{"title":"The infant microbiota hopscotches between community states toward maturation-longitudinal stool parameters and microbiota development in a cohort of European toddlers.","authors":"Evangelia Intze, Monika Schaubeck, Mohsen Pourjam, Klaus Neuhaus, Ilias Lagkouvardos, Thomas C A Hitch, Thomas Clavel","doi":"10.1093/ismeco/ycaf016","DOIUrl":"10.1093/ismeco/ycaf016","url":null,"abstract":"The development of the gut microbiome is critical during early life and is associated with infant health. To test whether this development is deterministic and how it is influenced by factors such as diet and mode of birth, we studied microbiota profiles and fecal parameters of 540 European infants, fed a synbiotic or control infant formula during their first year of life, up to 36 months of age. The diversity of the microbiota gradually increased until 36 months, at which point it resembled adult community states, indicating that microbiota maturation had occurred. However, distinct gut microbiota community states were observed that differed at each stage of maturation. The distribution of infants within the communities even at 36 months was significantly influenced by early life events, with a higher prevalence of infants born by cesarean section having the immature M36-C1 community state at 36 months. The microbial community state at one time point was not predictive of the next; instead, we observed hopscotching of the infant microbiota between different community states. This work provides new longitudinal data on the infant gut microbiome in relation to diet, suggesting that ecosystem development is not deterministic, but that early life events influence the community state of an individual's gut microbiota beyond infancy.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf016"},"PeriodicalIF":5.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627017","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

Detection of rare plasmid hosts using a targeted Hi-C approach. 利用靶向Hi-C方法检测稀有质粒宿主。

IF 5.1

ISME communications Pub Date : 2025-03-09 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae161

Salvador Castañeda-Barba, Benjamin J Ridenhour, Eva M Top, Thibault Stalder

{"title":"Detection of rare plasmid hosts using a targeted Hi-C approach.","authors":"Salvador Castañeda-Barba, Benjamin J Ridenhour, Eva M Top, Thibault Stalder","doi":"10.1093/ismeco/ycae161","DOIUrl":"10.1093/ismeco/ycae161","url":null,"abstract":"Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. This is partly due to the limitations of current methods in associating a plasmid with its host in microbiomes. To address this knowledge gap, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this approach as Hi-C+. We applied Hi-C and Hi-C+ to soil microbial communities in which we mimicked increasingly rare transfer of an antimicrobial resistance plasmid from a donor to a recipient. This was achieved by inoculating agricultural soil with mixtures of known plasmid-containing and plasmid-free cells at different proportions. We demonstrated that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. Hi-C+ further improved the detection limit of Hi-C 100-fold and allowed the identification of plasmid hosts at the genus level. As a culture-independent approach, Hi-C+ will significantly improve our understanding of the range and frequency of spread of antibiotic resistance and other genes that are introduced into soil and other microbiomes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae161"},"PeriodicalIF":5.1,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756265","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