ISME Journal最新文献_第10页

Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function. 肠道微生物群失调会通过结肠吲哚和 LBP/HTR2B 介导的巨噬细胞功能来恶化色氨酸的免疫调节作用。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae166

Lili Jiang, Youling Hao, Dandan Han, Wenjian Dong, Aoyu Yang, Zhiyuan Sun, Yao Ge, Shuai Duan, Xiuwen Zhang, Zhaolai Dai

{"title":"Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.","authors":"Lili Jiang, Youling Hao, Dandan Han, Wenjian Dong, Aoyu Yang, Zhiyuan Sun, Yao Ge, Shuai Duan, Xiuwen Zhang, Zhaolai Dai","doi":"10.1093/ismejo/wrae166","DOIUrl":"10.1093/ismejo/wrae166","url":null,"abstract":"Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation of Trp-enriched gut microbiota to recipient mice subject to antibiotic pre-exposure and DSS treatment alleviated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor 2B (HTR2B) in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities. 布拉氏酵母菌通过益生菌群落中的代谢相互作用增强抗炎效应因子和 AhR 激活。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae212

Karl Alex Hedin, Mohammad H Mirhakkak, Troels Holger Vaaben, Carmen Sands, Mikael Pedersen, Adam Baker, Ruben Vazquez-Uribe, Sascha Schäuble, Gianni Panagiotou, Anja Wellejus, Morten Otto Alexander Sommer

{"title":"Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities.","authors":"Karl Alex Hedin, Mohammad H Mirhakkak, Troels Holger Vaaben, Carmen Sands, Mikael Pedersen, Adam Baker, Ruben Vazquez-Uribe, Sascha Schäuble, Gianni Panagiotou, Anja Wellejus, Morten Otto Alexander Sommer","doi":"10.1093/ismejo/wrae212","DOIUrl":"10.1093/ismejo/wrae212","url":null,"abstract":"Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified two strains that demonstrated a synergistic relationship with S. boulardii in pairwise co-cultivation. Furthermore, we computationally predicted cooperative communities with symbiotic relationships between S. boulardii and these bacteria. Experimental validation of 28 communities highlighted the role of S. boulardii as a key player in microbial communities, significantly boosting the community's cell number and production of anti-inflammatory effectors, thereby affirming its essential role in improving symbiotic dynamics. Based on our observation, one defined community significantly activated the aryl hydrocarbon receptor-a key regulator of immune response-280-fold more effectively than the community without S. boulardii. This study underscores the potential of microbial communities for the design of more effective probiotic formulations.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Conditions for the spread of CRISPR-Cas immune systems into bacterial populations. CRISPR-Cas免疫系统在细菌种群中传播的条件。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae108

Josie F K Elliott, David V McLeod, Tiffany B Taylor, Edze R Westra, Sylvain Gandon, Bridget N J Watson

{"title":"Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.","authors":"Josie F K Elliott, David V McLeod, Tiffany B Taylor, Edze R Westra, Sylvain Gandon, Bridget N J Watson","doi":"10.1093/ismejo/wrae108","DOIUrl":"10.1093/ismejo/wrae108","url":null,"abstract":"Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}_{Delta }$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11285788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Dispersal of microbes from grassland fire smoke to soils. 修正：微生物从草原火灾烟雾扩散到土壤。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae232

引用次数: 0

Diversity alone does not reliably indicate the healthiness of an animal microbiome. 仅凭多样性并不能可靠地说明动物微生物群的健康状况。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae133

Claire E Williams, Tobin J Hammer, Candace L Williams

引用次数: 0

Strategies for tailoring functional microbial synthetic communities. 定制功能性微生物合成群落的策略。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae049

Jiayi Jing, Paolina Garbeva, Jos M Raaijmakers, Marnix H Medema

{"title":"Strategies for tailoring functional microbial synthetic communities.","authors":"Jiayi Jing, Paolina Garbeva, Jos M Raaijmakers, Marnix H Medema","doi":"10.1093/ismejo/wrae049","DOIUrl":"10.1093/ismejo/wrae049","url":null,"abstract":"Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11008692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change. 全球变化下海洋 Synechococcus 元素配比的蛋白质组特征调控。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae046

Nathan S Garcia, Mingyu Du, Michele Guindani, Matthew R McIlvin, Dawn M Moran, Mak A Saito, Adam C Martiny

{"title":"Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change.","authors":"Nathan S Garcia, Mingyu Du, Michele Guindani, Matthew R McIlvin, Dawn M Moran, Mak A Saito, Adam C Martiny","doi":"10.1093/ismejo/wrae046","DOIUrl":"10.1093/ismejo/wrae046","url":null,"abstract":"Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the \"translation-compensation hypothesis\" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11020310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","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-dependent trophic associations modulate soil bacterial communities along latitudinal gradients. 与温度相关的营养关联沿着纬度梯度调节土壤细菌群落。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae145

Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu

{"title":"Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients.","authors":"Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu","doi":"10.1093/ismejo/wrae145","DOIUrl":"10.1093/ismejo/wrae145","url":null,"abstract":"Understanding the environmental and biological mechanisms shaping latitudinal patterns in microbial diversity is challenging in the field of ecology. Although multiple hypotheses have been proposed to explain these patterns, a consensus has rarely been reached. Here, we conducted a large-scale field survey and microcosm experiments to investigate how environmental heterogeneity and putative trophic interactions (exerted by protist-bacteria associations and T4-like virus-bacteria associations) affect soil bacterial communities along a latitudinal gradient. We found that the microbial latitudinal diversity was kingdom dependent, showing decreasing, clumped, and increasing trends in bacteria, protists, and T4-like viruses, respectively. Climatic and edaphic drivers played predominant roles in structuring the bacterial communities; the intensity of the climatic effect increased sharply from 30°N to 32°N, whereas the intensity of the edaphic effect remained stable. Biotic associations were also essential in shaping the bacterial communities, with protist-bacteria associations showing a quadratic distribution, whereas virus-bacteria associations were significant only at high latitudes. The microcosm experiments further revealed that the temperature component, which is affiliated with climate conditions, is the primary regulator of trophic associations along the latitudinal gradient. Overall, our study highlights a previously underestimated mechanism of how the putative biotic interactions influence bacterial communities and their response to environmental gradients.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback. 一氧化二氮对甲烷生成的抑制是一种未被充分重视的温室气体排放反馈。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae027

Yongchao Yin, Fadime Kara-Murdoch, Robert W Murdoch, Jun Yan, Gao Chen, Yongchao Xie, Yanchen Sun, Frank E Löffler

{"title":"Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback.","authors":"Yongchao Yin, Fadime Kara-Murdoch, Robert W Murdoch, Jun Yan, Gao Chen, Yongchao Xie, Yanchen Sun, Frank E Löffler","doi":"10.1093/ismejo/wrae027","DOIUrl":"10.1093/ismejo/wrae027","url":null,"abstract":"Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25 μM, followed by hydrogenotrophic (KI, 60-90 μM) and methylotrophic (KI, 110-130 μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles. 大规模单病毒基因组学揭示了河水病毒隐藏的多样性和多样化的基因特征。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae124

Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama

{"title":"Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.","authors":"Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama","doi":"10.1093/ismejo/wrae124","DOIUrl":"10.1093/ismejo/wrae124","url":null,"abstract":"Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0