Background: The prevalence of hyperuricaemia (HUA), a metabolic disorder characterized by elevated levels of uric acid, is on the rise and is frequently associated with renal injury. Gut microbiota and gut-derived uremic toxins are critical mediators in the gut-kidney axis that can cause damage to kidney function. Gut dysbiosis has been implicated in various kidney diseases. However, the role and underlying mechanism of the gut microbiota in HUA-induced renal injury remain unknown.
Results: A HUA rat model was first established by knocking out the uricase (UOX). HUA rats exhibited apparent renal dysfunction, renal tubular injury, fibrosis, NLRP3 inflammasome activation, and impaired intestinal barrier functions. Analysis of 16S rRNA sequencing and functional prediction data revealed an abnormal gut microbiota profile and activation of pathways associated with uremic toxin production. A metabolomic analysis showed evident accumulation of gut-derived uremic toxins in the kidneys of HUA rats. Furthermore, faecal microbiota transplantation (FMT) was performed to confirm the effects of HUA-induced gut dysbiosis on renal injury. Mice recolonized with HUA microbiota exhibited severe renal injury and impaired intestinal barrier functions following renal ischemia/reperfusion (I/R) surgery. Notably, in NLRP3-knockout (NLRP3-/-) I/R mice, the deleterious effects of the HUA microbiota on renal injury and the intestinal barrier were eliminated.
Conclusion: Our results demonstrate that HUA-induced gut dysbiosis contributes to the development of renal injury, possibly by promoting the production of gut-derived uremic toxins and subsequently activating the NLRP3 inflammasome. Our data suggest a potential therapeutic strategy for the treatment of renal diseases by targeting the gut microbiota and the NLRP3 inflammasome. Video Abstract.
{"title":"Gut microbiota dysbiosis in hyperuricaemia promotes renal injury through the activation of NLRP3 inflammasome.","authors":"Xinghong Zhou, Shuai Ji, Liqian Chen, Xiaoyu Liu, Yijian Deng, Yanting You, Ming Wang, Qiuxing He, Baizhao Peng, Ying Yang, Xiaohu Chen, Hiu Yee Kwan, Lin Zhou, Jieyu Chen, Xiaoshan Zhao","doi":"10.1186/s40168-024-01826-9","DOIUrl":"10.1186/s40168-024-01826-9","url":null,"abstract":"<p><strong>Background: </strong>The prevalence of hyperuricaemia (HUA), a metabolic disorder characterized by elevated levels of uric acid, is on the rise and is frequently associated with renal injury. Gut microbiota and gut-derived uremic toxins are critical mediators in the gut-kidney axis that can cause damage to kidney function. Gut dysbiosis has been implicated in various kidney diseases. However, the role and underlying mechanism of the gut microbiota in HUA-induced renal injury remain unknown.</p><p><strong>Results: </strong>A HUA rat model was first established by knocking out the uricase (UOX). HUA rats exhibited apparent renal dysfunction, renal tubular injury, fibrosis, NLRP3 inflammasome activation, and impaired intestinal barrier functions. Analysis of 16S rRNA sequencing and functional prediction data revealed an abnormal gut microbiota profile and activation of pathways associated with uremic toxin production. A metabolomic analysis showed evident accumulation of gut-derived uremic toxins in the kidneys of HUA rats. Furthermore, faecal microbiota transplantation (FMT) was performed to confirm the effects of HUA-induced gut dysbiosis on renal injury. Mice recolonized with HUA microbiota exhibited severe renal injury and impaired intestinal barrier functions following renal ischemia/reperfusion (I/R) surgery. Notably, in NLRP3-knockout (NLRP3<sup>-/-</sup>) I/R mice, the deleterious effects of the HUA microbiota on renal injury and the intestinal barrier were eliminated.</p><p><strong>Conclusion: </strong>Our results demonstrate that HUA-induced gut dysbiosis contributes to the development of renal injury, possibly by promoting the production of gut-derived uremic toxins and subsequently activating the NLRP3 inflammasome. Our data suggest a potential therapeutic strategy for the treatment of renal diseases by targeting the gut microbiota and the NLRP3 inflammasome. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11191305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-21DOI: 10.1186/s40168-024-01825-w
Jason M Brenchley, Sergio Serrano-Villar
Background: Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV.
Results: Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents.
Conclusions: Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.
背景:尽管微生物群与艾滋病发病机制有着广泛的联系,但大多数研究,尤其是那些使用全微观技术的研究,在很大程度上都是相关性的,主要是作为产生假设的基础。此外,大多数研究侧重于描述细菌成分的分类组成,往往忽略了微生物组的其他层面。人们对微生物群影响 HIV 免疫反应的复杂机制仍然知之甚少。对肠道微生物群的干预性研究提供了一个强大的工具来检验我们是否能利用微生物群来改善 HIV 感染者的健康状况:在此,我们回顾了肠道微生物群在 HIV/SIV 疾病进展中的多方面作用及其作为治疗靶点的潜力。我们探讨了肠道微生物菌群失调与全身炎症之间复杂的相互作用,强调了基于微生物组的疗法为艾滋病治疗开辟新途径的潜力。其中包括探索益生菌、益生元、粪便微生物群移植和有针对性的饮食调整的疗效。我们还讨论了这一研究领域固有的挑战,如诱导长期微生物组改变的难度和研究设计的复杂性,包括益生菌菌株的变化、FMT 的供体选择、抗生素调节方案以及将研究结果转化为临床实践的障碍。最后,我们推测了这一快速发展领域的未来方向,强调需要更细致地了解微生物组-免疫相互作用、开发基于微生物组的个性化疗法以及应用新技术鉴定潜在的治疗药物:我们的综述强调了肠道微生物组在 HIV/SIV 疾病中的重要性及其作为创新治疗策略靶点的潜力。
{"title":"From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy.","authors":"Jason M Brenchley, Sergio Serrano-Villar","doi":"10.1186/s40168-024-01825-w","DOIUrl":"10.1186/s40168-024-01825-w","url":null,"abstract":"<p><strong>Background: </strong>Although the microbiota has been extensively associated with HIV pathogenesis, the majority of studies, particularly those using omics techniques, are largely correlative and serve primarily as a basis for hypothesis generation. Furthermore, most have focused on characterizing the taxonomic composition of the bacterial component, often overlooking other levels of the microbiome. The intricate mechanisms by which the microbiota influences immune responses to HIV are still poorly understood. Interventional studies on gut microbiota provide a powerful tool to test the hypothesis of whether we can harness the microbiota to improve health outcomes in people with HIV.</p><p><strong>Results: </strong>Here, we review the multifaceted role of the gut microbiome in HIV/SIV disease progression and its potential as a therapeutic target. We explore the complex interplay between gut microbial dysbiosis and systemic inflammation, highlighting the potential for microbiome-based therapeutics to open new avenues in HIV management. These include exploring the efficacy of probiotics, prebiotics, fecal microbiota transplantation, and targeted dietary modifications. We also address the challenges inherent in this research area, such as the difficulty in inducing long-lasting microbiome alterations and the complexities of study designs, including variations in probiotic strains, donor selection for FMT, antibiotic conditioning regimens, and the hurdles in translating findings into clinical practice. Finally, we speculate on future directions for this rapidly evolving field, emphasizing the need for a more granular understanding of microbiome-immune interactions, the development of personalized microbiome-based therapies, and the application of novel technologies to identify potential therapeutic agents.</p><p><strong>Conclusions: </strong>Our review underscores the importance of the gut microbiome in HIV/SIV disease and its potential as a target for innovative therapeutic strategies.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11193286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-21DOI: 10.1186/s40168-024-01850-9
Heather Armstrong, Mandana Rahbari, Heekuk Park, David Sharon, Aducio Thiesen, Naomi Hotte, Ning Sun, Hussain Syed, Hiatem Abofayed, Weiwei Wang, Karen Madsen, Eytan Wine, Andrew Mason
{"title":"Correction: \"Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10-/- mouse model of inflammatory bowel disease\".","authors":"Heather Armstrong, Mandana Rahbari, Heekuk Park, David Sharon, Aducio Thiesen, Naomi Hotte, Ning Sun, Hussain Syed, Hiatem Abofayed, Weiwei Wang, Karen Madsen, Eytan Wine, Andrew Mason","doi":"10.1186/s40168-024-01850-9","DOIUrl":"10.1186/s40168-024-01850-9","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11191143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-21DOI: 10.1186/s40168-024-01828-7
Eric Armstrong, Anke Hemmerling, Steve Miller, Sanja Huibner, Maria Kulikova, Emily Crawford, Gloria R Castañeda, Bryan Coburn, Craig R Cohen, Rupert Kaul
Background: Bacterial vaginosis (BV) increases HIV acquisition risk, potentially by eliciting genital inflammation. After BV treatment, the vaginal administration of LACTIN-V, a live biotherapeutic containing the Lactobacillus crispatus strain CTV-05, reduced BV recurrence and vaginal inflammation; however, 3 months after product cessation, CTV-05 colonization was only sustained in 48% of participants.
Results: This nested sub-study in 32 participants receiving LACTIN-V finds that 72% (23/32) demonstrate clinically relevant colonization (CTV-05 absolute abundance > 106 CFU/mL) during at least one visit while 28% (9/32) of women demonstrate colonization resistance, even during product administration. Immediately prior to LACTIN-V administration, the colonization-resistant group exhibited elevated vaginal microbiota diversity. During LACTIN-V administration, colonization resistance was associated with elevated vaginal markers of epithelial disruption and reduced chemokines, possibly due to elevated absolute abundance of BV-associated species and reduced L. crispatus. Colonization permissive women were stratified into sustained and transient colonization groups (31% and 41% of participants, respectively) based on CTV-05 colonization after cessation of product administration. These groups also exhibited distinct genital immune profiles during LACTIN-V administration.
Conclusions: The genital immune impact of LACTIN-V may be contingent on the CTV-05 colonization phenotype, which is in turn partially dependent on the success of BV clearance prior to LACTIN-V administration.
{"title":"Vaginal Lactobacillus crispatus persistence following application of a live biotherapeutic product: colonization phenotypes and genital immune impact.","authors":"Eric Armstrong, Anke Hemmerling, Steve Miller, Sanja Huibner, Maria Kulikova, Emily Crawford, Gloria R Castañeda, Bryan Coburn, Craig R Cohen, Rupert Kaul","doi":"10.1186/s40168-024-01828-7","DOIUrl":"10.1186/s40168-024-01828-7","url":null,"abstract":"<p><strong>Background: </strong>Bacterial vaginosis (BV) increases HIV acquisition risk, potentially by eliciting genital inflammation. After BV treatment, the vaginal administration of LACTIN-V, a live biotherapeutic containing the Lactobacillus crispatus strain CTV-05, reduced BV recurrence and vaginal inflammation; however, 3 months after product cessation, CTV-05 colonization was only sustained in 48% of participants.</p><p><strong>Results: </strong>This nested sub-study in 32 participants receiving LACTIN-V finds that 72% (23/32) demonstrate clinically relevant colonization (CTV-05 absolute abundance > 10<sup>6</sup> CFU/mL) during at least one visit while 28% (9/32) of women demonstrate colonization resistance, even during product administration. Immediately prior to LACTIN-V administration, the colonization-resistant group exhibited elevated vaginal microbiota diversity. During LACTIN-V administration, colonization resistance was associated with elevated vaginal markers of epithelial disruption and reduced chemokines, possibly due to elevated absolute abundance of BV-associated species and reduced L. crispatus. Colonization permissive women were stratified into sustained and transient colonization groups (31% and 41% of participants, respectively) based on CTV-05 colonization after cessation of product administration. These groups also exhibited distinct genital immune profiles during LACTIN-V administration.</p><p><strong>Conclusions: </strong>The genital immune impact of LACTIN-V may be contingent on the CTV-05 colonization phenotype, which is in turn partially dependent on the success of BV clearance prior to LACTIN-V administration.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11191164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-17DOI: 10.1186/s40168-024-01829-6
Suresh C Bokoliya, Jordan Russell, Yair Dorsett, Hunter Panier, Vijender Singh, Lauren Daddi, Hanshu Yuan, Liv R. Dedon, Zhongmao Liu, Yuqi Zhou, Zefang Min, J. R. Barson, Jonathan Covault, J. Bubier, Yanjiao Zhou
{"title":"Short-chain fatty acid valerate reduces voluntary alcohol intake in male mice","authors":"Suresh C Bokoliya, Jordan Russell, Yair Dorsett, Hunter Panier, Vijender Singh, Lauren Daddi, Hanshu Yuan, Liv R. Dedon, Zhongmao Liu, Yuqi Zhou, Zefang Min, J. R. Barson, Jonathan Covault, J. Bubier, Yanjiao Zhou","doi":"10.1186/s40168-024-01829-6","DOIUrl":"https://doi.org/10.1186/s40168-024-01829-6","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":15.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141335059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-14DOI: 10.1186/s40168-024-01815-y
Marius Trøseid, Susanne Dam Nielsen, Ivan Vujkovic-Cvijin
Background: Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency.
Results: PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid.
Conclusions: Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
背景:尽管采用了现代抗逆转录病毒疗法(ART),但艾滋病毒感染者(PLWH)患炎症性并发症(包括心血管疾病)的相对风险仍在增加。除了传统的风险因素和与艾滋病相关的风险因素(如合并感染、抗逆转录病毒疗法毒性和既往免疫缺陷)外,肠道微生物组可能是几个驱动因素之一:结果:即使在调整了包括性偏好在内的已知混杂因素后,艾滋病毒感染者的肠道微生物组仍然发生了改变。与艾滋病相关的微生物群与心脏代谢合并症有关,并与心血管疾病相关的微生物群特征相似,尤其是生成短链脂肪酸(SCFA)的能力降低。迄今为止,个体间的巨大差异一直是应用微生物群谱进行风险分层的障碍。这篇综述涵盖了我们对 PLWH 肠道微生物组和合并症的最新认识和最新进展,特别关注心脏代谢合并症和炎症。它全面概述了与 HIV 相关和与合并症相关的菌群失调、微生物转运和微生物群衍生代谢产物。它还包含了对 PLWH 进行的研究的最新数据,这些数据涉及与合并症和潜在肠道微生物群改变相关的循环代谢物,包括 SCFA 丙酸盐、组氨酸类似物咪唑丙酸盐和保护性代谢物吲哚-3-丙酸的循环水平:尽管最近取得了一些进展,但肠道微生物组和相关代谢物尚未被确定为生物标志物或治疗靶标。这篇综述为将该领域推向临床实践所需的未来研究指明了方向,包括精准医疗的前景和陷阱。视频摘要。
{"title":"Gut microbiome and cardiometabolic comorbidities in people living with HIV.","authors":"Marius Trøseid, Susanne Dam Nielsen, Ivan Vujkovic-Cvijin","doi":"10.1186/s40168-024-01815-y","DOIUrl":"10.1186/s40168-024-01815-y","url":null,"abstract":"<p><strong>Background: </strong>Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency.</p><p><strong>Results: </strong>PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid.</p><p><strong>Conclusions: </strong>Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-14DOI: 10.1186/s40168-024-01824-x
Li Tian, Guimei Fang, Guijie Li, Liguan Li, Tong Zhang, Yanping Mao
Background: Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.
Results: The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.
Conclusions: The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.
{"title":"Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human.","authors":"Li Tian, Guimei Fang, Guijie Li, Liguan Li, Tong Zhang, Yanping Mao","doi":"10.1186/s40168-024-01824-x","DOIUrl":"10.1186/s40168-024-01824-x","url":null,"abstract":"<p><strong>Background: </strong>Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.</p><p><strong>Results: </strong>The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.</p><p><strong>Conclusions: </strong>The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":15.5,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11179227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-10DOI: 10.1186/s40168-024-01845-6
Denise P Silva, Helena D M Villela, Henrique F Santos, Gustavo A S Duarte, José Roberto Ribeiro, Angela M Ghizelini, Caren L S Vilela, Phillipe M Rosado, Carolline S Fazolato, Erika P Santoro, Flavia L Carmo, Dalton S Ximenes, Adriana U Soriano, Caio T C C Rachid, Rebecca L Vega Thurber, Raquel S Peixoto
{"title":"Correction: Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.","authors":"Denise P Silva, Helena D M Villela, Henrique F Santos, Gustavo A S Duarte, José Roberto Ribeiro, Angela M Ghizelini, Caren L S Vilela, Phillipe M Rosado, Carolline S Fazolato, Erika P Santoro, Flavia L Carmo, Dalton S Ximenes, Adriana U Soriano, Caio T C C Rachid, Rebecca L Vega Thurber, Raquel S Peixoto","doi":"10.1186/s40168-024-01845-6","DOIUrl":"10.1186/s40168-024-01845-6","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":15.5,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11163705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.1186/s40168-024-01806-z
Ke Zhang, Chong He, Lei Wang, Langda Suo, Mengmeng Guo, Jiazhong Guo, Ting Zhang, Yangbin Xu, Yu Lei, Gongwei Liu, Quan Qian, Yunrui Mao, Peter Kalds, Yujiang Wu, Awang Cuoji, Yuxin Yang, Daniel Brugger, Shangquan Gan, Meili Wang, Xiaolong Wang, Fangqing Zhao, Yulin Chen
Background: Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.
Results: A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.
Conclusions: By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.
{"title":"Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization.","authors":"Ke Zhang, Chong He, Lei Wang, Langda Suo, Mengmeng Guo, Jiazhong Guo, Ting Zhang, Yangbin Xu, Yu Lei, Gongwei Liu, Quan Qian, Yunrui Mao, Peter Kalds, Yujiang Wu, Awang Cuoji, Yuxin Yang, Daniel Brugger, Shangquan Gan, Meili Wang, Xiaolong Wang, Fangqing Zhao, Yulin Chen","doi":"10.1186/s40168-024-01806-z","DOIUrl":"10.1186/s40168-024-01806-z","url":null,"abstract":"<p><strong>Background: </strong>Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.</p><p><strong>Results: </strong>A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.</p><p><strong>Conclusions: </strong>By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":15.5,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}