Stephanie Wottrich, Stacee Mendonca, Cameron Safarpour, Christine Nguyen, L. J. Marinelli, Stephen P. Hancock, Robert L. Modlin, J. M. Parker
Objectives: Cutibacterium acnes , formerly Propionibacterium acnes , is a bacterial species characterized by tenacious acne-contributing pathogenic strains. Therefore, bacteriophage therapy has become an attractive treatment route to circumvent issues such as evolved bacterial antibiotic resistance. However, medical and commercial use of phage therapy for C. acnes has been elusive, necessitating ongoing exploration of phage characteristics that confer bactericidal capacity. Methods: A novel phage (Aquarius) was isolated and analyzed. Testing included genomic sequencing and annotation, electron microscopy, patch testing, reinfection assays, and qPCR to confirm pseudolysogeny and putative superinfection exclusion (SIE) protein expression. Results: Given a superinfection-resistant phenotype was observed, reinfection assays and patch tests were performed, which confirmed the re-cultured bacteria were resistant to superinfection. Subsequent qPCR indicated pseudolysogeny was a concomitantly present phenomenon. Phage genomic analysis identified the presence of a conserved gene (gp41 ) with a product containing Ltp family-like protein signatures which may contribute to phage-mediated bacterial superinfection resistance (SIR) in a pseudolysogeny-dependent manner. qPCR was performed to analyze and roughly quantify gp41 activity, and mRNA expression was high during infection, implicating a role for the protein during the phage life cycle. Conclusions: This study confirms that C. acnes bacteria are capable of harboring phage pseudolysogens and suggests that this phenomenon plays a role in bacterial SIR. This mechanism may be conferred by the expression of phage proteins while the phage persists within the host in the pseudolysogenic state. This parameter must be considered in future endeavors for efficacious application of C. acnes phage-based therapeutics.
目的：痤疮丙酸杆菌（Cutibacterium acnes）的前身是痤疮丙酸杆菌（Propionibacterium acnes），是一种以顽固的痤疮致病菌株为特征的细菌。因此，噬菌体疗法已成为一种极具吸引力的治疗方法，可规避细菌进化出的抗生素耐药性等问题。然而，噬菌体疗法对痤疮丙酸杆菌的医疗和商业用途一直难以实现，因此有必要不断探索噬菌体赋予杀菌能力的特性。方法：分离并分析了一种新型噬菌体（Aquarius）。测试包括基因组测序和注释、电子显微镜、斑块测试、再感染试验和 qPCR，以确认假溶原和推测的超级感染排除（SIE）蛋白表达。结果：由于观察到了抗超级感染表型，因此进行了再感染试验和斑块测试，结果证实再培养的细菌具有抗超级感染能力。随后的 qPCR 显示假溶原现象同时存在。噬菌体基因组分析确定了一个保守基因（gp41）的存在，其产物含有类似 Ltp 家族的蛋白质特征，可能以假溶原依赖的方式促成了噬菌体介导的细菌超级感染抗性（SIR）。结论：这项研究证实了痤疮丙酸杆菌能够携带噬菌体假溶原，并表明这种现象在细菌 SIR 中发挥了作用。当噬菌体以假溶原状态存在于宿主体内时，噬菌体蛋白的表达可能会赋予这种机制。未来在有效应用痤疮噬菌体疗法时必须考虑这一参数。
{"title":"Putative pseudolysogeny-dependent phage gene implicated in the superinfection resistance of Cutibacterium acnes","authors":"Stephanie Wottrich, Stacee Mendonca, Cameron Safarpour, Christine Nguyen, L. J. Marinelli, Stephen P. Hancock, Robert L. Modlin, J. M. Parker","doi":"10.20517/mrr.2023.42","DOIUrl":"https://doi.org/10.20517/mrr.2023.42","url":null,"abstract":"Objectives: Cutibacterium acnes , formerly Propionibacterium acnes , is a bacterial species characterized by tenacious acne-contributing pathogenic strains. Therefore, bacteriophage therapy has become an attractive treatment route to circumvent issues such as evolved bacterial antibiotic resistance. However, medical and commercial use of phage therapy for C. acnes has been elusive, necessitating ongoing exploration of phage characteristics that confer bactericidal capacity.\u0000 Methods: A novel phage (Aquarius) was isolated and analyzed. Testing included genomic sequencing and annotation, electron microscopy, patch testing, reinfection assays, and qPCR to confirm pseudolysogeny and putative superinfection exclusion (SIE) protein expression.\u0000 Results: Given a superinfection-resistant phenotype was observed, reinfection assays and patch tests were performed, which confirmed the re-cultured bacteria were resistant to superinfection. Subsequent qPCR indicated pseudolysogeny was a concomitantly present phenomenon. Phage genomic analysis identified the presence of a conserved gene (gp41 ) with a product containing Ltp family-like protein signatures which may contribute to phage-mediated bacterial superinfection resistance (SIR) in a pseudolysogeny-dependent manner. qPCR was performed to analyze and roughly quantify gp41 activity, and mRNA expression was high during infection, implicating a role for the protein during the phage life cycle.\u0000 Conclusions: This study confirms that C. acnes bacteria are capable of harboring phage pseudolysogens and suggests that this phenomenon plays a role in bacterial SIR. This mechanism may be conferred by the expression of phage proteins while the phage persists within the host in the pseudolysogenic state. This parameter must be considered in future endeavors for efficacious application of C. acnes phage-based therapeutics.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":" 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140686876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leyuan Li, J. Mayne, Adrian Beltran, Xu Zhang, Zhibin Ning, Daniel Figeys
Aim: Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol. Methods: To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on ex vivo individual human gut microbiomes biobanked with five different workflows. Results: We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, in vitro culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose. Conclusions: Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.
{"title":"RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics","authors":"Leyuan Li, J. Mayne, Adrian Beltran, Xu Zhang, Zhibin Ning, Daniel Figeys","doi":"10.20517/mrr.2023.57","DOIUrl":"https://doi.org/10.20517/mrr.2023.57","url":null,"abstract":"Aim: Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol.\u0000 Methods: To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on ex vivo individual human gut microbiomes biobanked with five different workflows.\u0000 Results: We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, in vitro culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose.\u0000 Conclusions: Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"20 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140747347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objectives: This study introduces MetaBIDx, a computational method designed to enhance species prediction in metagenomic environments. The method addresses the challenge of accurate species identification in complex microbiomes, which is due to the large number of generated reads and the ever-expanding number of bacterial genomes. Bacterial identification is essential for disease diagnosis and tracing outbreaks associated with microbial infections. Methods: MetaBIDx utilizes a modified Bloom filter for efficient indexing of reference genomes and incorporates a novel strategy for reducing false positives by clustering species based on their genomic coverages by identified reads. The approach was evaluated and compared with several well-established tools across various datasets. Precision, recall, and F1-score were used to quantify the accuracy of species prediction. Results: MetaBIDx demonstrated superior performance compared to other tools, especially in terms of precision and F1-score. The application of clustering based on approximate coverages significantly improved precision in species identification, effectively minimizing false positives. We further demonstrated that other methods can also benefit from our approach to removing false positives by clustering species based on approximate coverages. Conclusion: With a novel approach to reducing false positives and the effective use of a modified Bloom filter to index species, MetaBIDx represents an advancement in metagenomic analysis. The findings suggest that the proposed approach could also benefit other metagenomic tools, indicating its potential for broader application in the field. The study lays the groundwork for future improvements in computational efficiency and the expansion of microbial databases.
研究目的本研究介绍了一种旨在提高元基因组环境中物种预测能力的计算方法--MetaBIDx。该方法解决了在复杂微生物组中准确识别物种的难题，这是由于生成的读数数量庞大，细菌基因组的数量也在不断扩大。细菌鉴定对于疾病诊断和追踪与微生物感染相关的疫情爆发至关重要。方法MetaBIDx 利用改进的布鲁姆过滤器对参考基因组进行有效索引，并采用一种新颖的策略，根据已识别读数的基因组覆盖率对物种进行聚类，从而减少假阳性。在各种数据集上对该方法进行了评估，并与几种成熟的工具进行了比较。精确度、召回率和 F1 分数被用来量化物种预测的准确性。结果显示与其他工具相比，MetaBIDx 表现出更优越的性能，尤其是在精确度和 F1 分数方面。基于近似覆盖率的聚类应用大大提高了物种识别的精确度，有效地减少了误报。我们进一步证明，通过基于近似覆盖率对物种进行聚类来消除误报，其他方法也能从中受益。结论MetaBIDx 采用新颖的方法来减少误报，并有效利用改进的布鲁姆过滤器来索引物种，是元基因组分析的一大进步。研究结果表明，所提出的方法也能使其他元基因组工具受益，这表明它有可能在该领域得到更广泛的应用。这项研究为未来提高计算效率和扩展微生物数据库奠定了基础。
{"title":"MetaBIDx: a new computational approach to bacteria identification in microbiomes","authors":"Diem-Trang Pham, Vinhthuy T. Phan","doi":"10.20517/mrr.2024.01","DOIUrl":"https://doi.org/10.20517/mrr.2024.01","url":null,"abstract":"Objectives: This study introduces MetaBIDx, a computational method designed to enhance species prediction in metagenomic environments. The method addresses the challenge of accurate species identification in complex microbiomes, which is due to the large number of generated reads and the ever-expanding number of bacterial genomes. Bacterial identification is essential for disease diagnosis and tracing outbreaks associated with microbial infections.\u0000 Methods: MetaBIDx utilizes a modified Bloom filter for efficient indexing of reference genomes and incorporates a novel strategy for reducing false positives by clustering species based on their genomic coverages by identified reads. The approach was evaluated and compared with several well-established tools across various datasets. Precision, recall, and F1-score were used to quantify the accuracy of species prediction.\u0000 Results: MetaBIDx demonstrated superior performance compared to other tools, especially in terms of precision and F1-score. The application of clustering based on approximate coverages significantly improved precision in species identification, effectively minimizing false positives. We further demonstrated that other methods can also benefit from our approach to removing false positives by clustering species based on approximate coverages.\u0000 Conclusion: With a novel approach to reducing false positives and the effective use of a modified Bloom filter to index species, MetaBIDx represents an advancement in metagenomic analysis. The findings suggest that the proposed approach could also benefit other metagenomic tools, indicating its potential for broader application in the field. The study lays the groundwork for future improvements in computational efficiency and the expansion of microbial databases.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"551 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140759427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hepatic encephalopathy (HE) is a clinical manifestation of neurological and psychiatric abnormalities that are caused by complications of liver dysfunction including hyperammonemia, hyperuricemia, and portal hypertension. Accumulating evidence suggests that HE could be reversed through therapeutic modifications of gut microbiota. Multiple preclinical and clinical studies have indicated that gut microbiome affects the physiological function of the liver, such as the regulation of metabolism, secretion, and immunity, through the gut-liver crosstalk. In addition, gut microbiota also influences the brain through the gut-brain crosstalk, altering its physiological functions including the regulation of the immune, neuroendocrine, and vagal pathways. Thus, key molecules that are involved in the microbiota-gut-liver-brain axis might be able to serve as clinical biomarkers for early diagnosis of HE, and could be effective therapeutic targets for clinical interventions. In this review, we summarize the pathophysiology of HE and further propose approaches modulating the microbiota-gut-liver-brain axis in order to provide a comprehensive understanding of the prevention and potential clinical treatment for HE with a microbiota-targeted therapy.
肝性脑病（HE）是由高氨血症、高尿酸血症和门静脉高压症等肝功能异常并发症引起的神经和精神异常的临床表现。越来越多的证据表明，通过治疗性改变肠道微生物群可以逆转肝性脑病。多项临床前和临床研究表明，肠道微生物群会通过肠道-肝脏串联影响肝脏的生理功能，如调节代谢、分泌和免疫。此外，肠道微生物群还通过肠道-大脑串联影响大脑，改变其生理功能，包括调节免疫、神经内分泌和迷走神经通路。因此，参与微生物群-肠道-肝脏-大脑轴的关键分子可能可以作为早期诊断 HE 的临床生物标志物，也可能成为临床干预的有效治疗靶点。在这篇综述中，我们总结了 HE 的病理生理学，并进一步提出了调节微生物群-肠-肝-脑轴的方法，以便全面了解微生物群靶向疗法对 HE 的预防和潜在临床治疗。
{"title":"Microbiota-gut-liver-brain axis and hepatic encephalopathy","authors":"Haifeng Lu, Hua Zhang, Zhongwen Wu, Lanjuan Li","doi":"10.20517/mrr.2023.44","DOIUrl":"https://doi.org/10.20517/mrr.2023.44","url":null,"abstract":"Hepatic encephalopathy (HE) is a clinical manifestation of neurological and psychiatric abnormalities that are caused by complications of liver dysfunction including hyperammonemia, hyperuricemia, and portal hypertension. Accumulating evidence suggests that HE could be reversed through therapeutic modifications of gut microbiota. Multiple preclinical and clinical studies have indicated that gut microbiome affects the physiological function of the liver, such as the regulation of metabolism, secretion, and immunity, through the gut-liver crosstalk. In addition, gut microbiota also influences the brain through the gut-brain crosstalk, altering its physiological functions including the regulation of the immune, neuroendocrine, and vagal pathways. Thus, key molecules that are involved in the microbiota-gut-liver-brain axis might be able to serve as clinical biomarkers for early diagnosis of HE, and could be effective therapeutic targets for clinical interventions. In this review, we summarize the pathophysiology of HE and further propose approaches modulating the microbiota-gut-liver-brain axis in order to provide a comprehensive understanding of the prevention and potential clinical treatment for HE with a microbiota-targeted therapy.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"16 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139597316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Ding, Bowen Li, Haiqin Chen, R. P. Ross, Catherine Stanton, Shilong Jiang, Jianxin Zhao, Wei Chen, Bo Yang
Objectives: Bifidobacterium longum subsp. infantis is a dominant bacterium in infant gut, which plays a critical role in maintaining the health and development of infants. This study investigated the abilities of eight different strains of B. longum subsp. infantis to regulate the T helper (Th)1/Th2 balance. Methods: Eight B . longum subsp. infantis strains, including I2MI (FJSWXI2MIM1), I4MI [FJSWXI4MI (CCFM1270)], I4MNI (FJSWXI4MNIM1), I5TI (FJSWXI5TIM1), I6TI (FJSWXI6TIM1), I8TI [FJSWXI8TI (CCFM1271)], I10TI [FJSWXI10TI (CCFM1272)], and B6MNI [BJSWXB6MNIM1 (CCFM1269)], were gavaged to BALB/C pups in both female (n = 8) and male (n = 8) mice starting from 1 to 3 weeks old (1 × 109 CFU/day/mice). Selected immune cells were assessed by immunofluorescence and flow cytometry. Cytokines and immunoglobulins were determined by ELISA. Bacterial and bifidobacterial communities were determined by 16S rRNA gene sequencing and bifidobacterial groEL sequencing. Results: B . longum subsp. infantis I4MI and I8TI were shown to increase the ration of colonic IgG2a/IgE in male mice (P < 0.05). B6MNI was demonstrated to significantly increase the levels of colonic IFN-γ and IgG2a, as well as the ratio of IgG2a/IgE in female mice (P < 0.05). It was also shown to significantly increase the ratio of colonic IgG2a/IgE (P < 0.05) and reduce the level of colonic IL-4 in male mice (P < 0.05). Furthermore, B6MNI was demonstrated to regulate colonic JAK/STAT pathway in both male and female mice. I4MI, I5TI, and B6MNI were shown to increase the relative abundance of Bifidobacterium and B. longum subsp. infantis in both male and female mice, whereas I8TI was only shown to increase the relative abundance of Bifidobacterium and B. longum subsp. infantis in male mice (P < 0.05). Conclusion: These results indicated supplementation with B. longum subsp. infantis in early infancy may regulate the Th1/Th2 immune balance, which may prevent the development of related diseases.
{"title":"Bifidobacterium longum subsp. infantis regulates Th1/Th2 balance through the JAK-STAT pathway in growing mice","authors":"M. Ding, Bowen Li, Haiqin Chen, R. P. Ross, Catherine Stanton, Shilong Jiang, Jianxin Zhao, Wei Chen, Bo Yang","doi":"10.20517/mrr.2023.64","DOIUrl":"https://doi.org/10.20517/mrr.2023.64","url":null,"abstract":"Objectives: Bifidobacterium longum subsp. infantis is a dominant bacterium in infant gut, which plays a critical role in maintaining the health and development of infants. This study investigated the abilities of eight different strains of B. longum subsp. infantis to regulate the T helper (Th)1/Th2 balance.\u0000 Methods: Eight B . longum subsp. infantis strains, including I2MI (FJSWXI2MIM1), I4MI [FJSWXI4MI (CCFM1270)], I4MNI (FJSWXI4MNIM1), I5TI (FJSWXI5TIM1), I6TI (FJSWXI6TIM1), I8TI [FJSWXI8TI (CCFM1271)], I10TI [FJSWXI10TI (CCFM1272)], and B6MNI [BJSWXB6MNIM1 (CCFM1269)], were gavaged to BALB/C pups in both female (n = 8) and male (n = 8) mice starting from 1 to 3 weeks old (1 × 109 CFU/day/mice). Selected immune cells were assessed by immunofluorescence and flow cytometry. Cytokines and immunoglobulins were determined by ELISA. Bacterial and bifidobacterial communities were determined by 16S rRNA gene sequencing and bifidobacterial groEL sequencing.\u0000 Results: B . longum subsp. infantis I4MI and I8TI were shown to increase the ration of colonic IgG2a/IgE in male mice (P < 0.05). B6MNI was demonstrated to significantly increase the levels of colonic IFN-γ and IgG2a, as well as the ratio of IgG2a/IgE in female mice (P < 0.05). It was also shown to significantly increase the ratio of colonic IgG2a/IgE (P < 0.05) and reduce the level of colonic IL-4 in male mice (P < 0.05). Furthermore, B6MNI was demonstrated to regulate colonic JAK/STAT pathway in both male and female mice. I4MI, I5TI, and B6MNI were shown to increase the relative abundance of Bifidobacterium and B. longum subsp. infantis in both male and female mice, whereas I8TI was only shown to increase the relative abundance of Bifidobacterium and B. longum subsp. infantis in male mice (P < 0.05).\u0000 Conclusion: These results indicated supplementation with B. longum subsp. infantis in early infancy may regulate the Th1/Th2 immune balance, which may prevent the development of related diseases.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"44 22","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139611924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anders K. Varming, Zhiyu Huang, Ghofran M. Hamad, K. K. Rasmussen, H. Ingmer, M. Kilstrup, Leila Lo Leggio
Aim: To structurally characterize in detail the interactions between the phage repressor (CI) and the antirepressor (Mor) in the lysis-lysogeny switches of two Gram-positive bacteriophages, the lactococcal TP901-1 and staphylococcal φ13. Methods: We use crystallographic structure determination, computational structural modeling, and analysis, as well as biochemical methods, to elucidate similarities and differences in the CI:Mor interactions for the two genetic switches. Results: By comparing a newly determined and other available crystal structures for the N-terminal domain of CI (CI-NTD), we show that the CI interface involved in Mor binding undergoes structural changes upon binding in TP901-1. Most importantly, we show experimentally for the first time the direct interaction between CI and Mor for φ13, and model computationally the interaction interface. The computational modeling supports similar side chain rearrangements in TP901-1 and φ13. Conclusion: This study ascertains experimentally that, like in the TP901-1 lysogeny switch, staphylococcal φ13 CI and Mor interact with each other. The structural basis of the interaction of φ13 CI and Mor was computationally modeled and is similar to the interaction demonstrated experimentally between TP901-1 CI-NTD and Mor, likely involving similar rearrangement of residue side chains during the formation of the complex. The study identifies one CI residue, Glu69, which unusually interacts primarily through its aliphatic chain with an aromatic residue on Mor after changing its conformation compared to the un-complexed structure. This and other residues at the interface are suggested for investigation in future studies.
目的：从结构上详细描述乳球菌 TP901-1 和葡萄球菌 φ13 这两种革兰氏阳性噬菌体的溶解-溶原转换过程中噬菌体抑制因子（CI）和抗抑制因子（Mor）之间的相互作用。方法：我们利用晶体学结构测定、计算结构建模和分析以及生物化学方法来阐明两种基因开关中 CI:Mor 相互作用的异同。结果：通过比较新测定的 CI N 端结构域（CI-NTD）晶体结构和其他现有晶体结构，我们发现与 Mor 结合的 CI 接口在与 TP901-1 结合时发生了结构变化。最重要的是，我们首次在实验中展示了 CI 与 Mor φ13 的直接相互作用，并对相互作用界面进行了计算建模。计算模型支持 TP901-1 和 φ13 中类似的侧链重排。结论本研究通过实验证实，与 TP901-1 溶菌酶开关一样，葡萄球菌φ13 CI 和 Mor 也相互影响。对φ13 CI 和 Mor 相互作用的结构基础进行了计算建模，它与实验证明的 TP901-1 CI-NTD 和 Mor 之间的相互作用相似，可能涉及复合物形成过程中残基侧链的类似重排。研究发现了一个 CI 残基（Glu69），与未形成复合物的结构相比，该残基在改变构象后主要通过其脂肪族链与 Mor 上的一个芳香族残基异常地相互作用。建议在今后的研究中对这个残基和界面上的其他残基进行调查。
{"title":"CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages","authors":"Anders K. Varming, Zhiyu Huang, Ghofran M. Hamad, K. K. Rasmussen, H. Ingmer, M. Kilstrup, Leila Lo Leggio","doi":"10.20517/mrr.2023.50","DOIUrl":"https://doi.org/10.20517/mrr.2023.50","url":null,"abstract":"Aim: To structurally characterize in detail the interactions between the phage repressor (CI) and the antirepressor (Mor) in the lysis-lysogeny switches of two Gram-positive bacteriophages, the lactococcal TP901-1 and staphylococcal φ13.\u0000 Methods: We use crystallographic structure determination, computational structural modeling, and analysis, as well as biochemical methods, to elucidate similarities and differences in the CI:Mor interactions for the two genetic switches.\u0000 Results: By comparing a newly determined and other available crystal structures for the N-terminal domain of CI (CI-NTD), we show that the CI interface involved in Mor binding undergoes structural changes upon binding in TP901-1. Most importantly, we show experimentally for the first time the direct interaction between CI and Mor for φ13, and model computationally the interaction interface. The computational modeling supports similar side chain rearrangements in TP901-1 and φ13.\u0000 Conclusion: This study ascertains experimentally that, like in the TP901-1 lysogeny switch, staphylococcal φ13 CI and Mor interact with each other. The structural basis of the interaction of φ13 CI and Mor was computationally modeled and is similar to the interaction demonstrated experimentally between TP901-1 CI-NTD and Mor, likely involving similar rearrangement of residue side chains during the formation of the complex. The study identifies one CI residue, Glu69, which unusually interacts primarily through its aliphatic chain with an aromatic residue on Mor after changing its conformation compared to the un-complexed structure. This and other residues at the interface are suggested for investigation in future studies.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"17 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139612427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alina Viehof, Sven-Bastiaan Haange, Theresa Streidl, Kristin Schubert, B. Engelmann, Dirk Haller, U. Rolle-Kampczyk, Martin von Bergen, T. Clavel
The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta ) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis , but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.
{"title":"The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice","authors":"Alina Viehof, Sven-Bastiaan Haange, Theresa Streidl, Kristin Schubert, B. Engelmann, Dirk Haller, U. Rolle-Kampczyk, Martin von Bergen, T. Clavel","doi":"10.20517/mrr.2023.65","DOIUrl":"https://doi.org/10.20517/mrr.2023.65","url":null,"abstract":"The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta ) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis , but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"106 32","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139614486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yangwen Ou, Clara Belzer, Hauke Smidt, C. de Weerth
Observational studies have determined numerous correlations between sequence-based gut microbiota data and human mental traits. However, these associations are often inconsistent across studies. This inconsistency is one of the reasons that mechanistic validation studies of the observed correlations are lagging, making it difficult to establish causal associations. The absence of consistent study findings may partially be due to the lack of clear guidelines for identifying confounders of relations between complex microbial communities and mental conditions. Gut microbial complexity also impedes deciphering microbiota-host relations by using a single analytical approach. The aim of the current review is to help solve these problems by providing methodological recommendations for future human microbiota-gut-brain axis research on the selection of confounders, the use of integrative biostatistical methods, and the steps needed to translate correlative findings into causal conclusions.
{"title":"Methodological recommendations for human microbiota-gut-brain axis research","authors":"Yangwen Ou, Clara Belzer, Hauke Smidt, C. de Weerth","doi":"10.20517/mrr.2023.33","DOIUrl":"https://doi.org/10.20517/mrr.2023.33","url":null,"abstract":"Observational studies have determined numerous correlations between sequence-based gut microbiota data and human mental traits. However, these associations are often inconsistent across studies. This inconsistency is one of the reasons that mechanistic validation studies of the observed correlations are lagging, making it difficult to establish causal associations. The absence of consistent study findings may partially be due to the lack of clear guidelines for identifying confounders of relations between complex microbial communities and mental conditions. Gut microbial complexity also impedes deciphering microbiota-host relations by using a single analytical approach. The aim of the current review is to help solve these problems by providing methodological recommendations for future human microbiota-gut-brain axis research on the selection of confounders, the use of integrative biostatistical methods, and the steps needed to translate correlative findings into causal conclusions.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"15 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139129642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sergio Ruiz-Saavedra, A. Zapico, Sonia González, N. Salazar, C. G. de los Reyes-Gavilán
Colorectal cancer (CRC) is among the leading causes of mortality in adults of both sexes worldwide, while breast cancer (BC) is among the leading causes of death in women. In addition to age, gender, and genetic predisposition, environmental and lifestyle factors exert a strong influence. Global diet, including alcohol consumption, is one of the most important modifiable factors affecting the risk of CRC and BC. Western dietary patterns promoting high intakes of xenobiotics from food processing and ethanol have been associated with increased cancer risk, whereas the Mediterranean diet, generally leading to a higher intake of polyphenols and fibre, has been associated with a protective effect. Gut dysbiosis is a common feature in CRC, where the usual microbiota is progressively replaced by opportunistic pathogens and the gut metabolome is altered. The relationship between microbiota and BC has been less studied. The estrobolome is the collection of genes from intestinal bacteria that can metabolize oestrogens. In a dysbiosis condition, microbial deconjugating enzymes can reactivate conjugated-deactivated oestrogens, increasing the risk of BC. In contrast, intestinal microorganisms can increase the biological activity and bioavailability of dietary phytochemicals through diverse microbial metabolic transformations, potentiating their anticancer activity. Members of the intestinal microbiota can increase the toxicity of xenobiotics through metabolic transformations. However, most of the microorganisms involved in diet-microbiota interactions remain poorly characterized. Here, we provide an overview of the associations between microbiota and diet in BC and CRC, considering the diverse types and heterogeneity of these cancers and their relationship between them and with gut microbiota.
结肠直肠癌（CRC）是导致全球男女成人死亡的主要原因之一，而乳腺癌（BC）则是导致女性死亡的主要原因之一。除了年龄、性别和遗传易感性外，环境和生活方式因素也有很大影响。全球饮食（包括饮酒）是影响儿童癌症和乳腺癌发病风险的最重要的可改变因素之一。西方饮食模式提倡从食品加工和乙醇中摄入大量的异生物素，这与癌症风险的增加有关，而地中海饮食通常导致摄入更多的多酚类物质和纤维，具有保护作用。肠道菌群失调是 CRC 的常见特征，通常的微生物群会逐渐被机会性病原体取代，肠道代谢组也会发生改变。微生物群与 BC 之间关系的研究较少。雌激素代谢组是能够代谢雌激素的肠道细菌基因的集合。在菌群失调的情况下，微生物解酵素可重新激活共轭失活雌激素，从而增加 BC 的风险。相反，肠道微生物可通过各种微生物代谢转化提高膳食植物化学物质的生物活性和生物利用率，从而增强其抗癌活性。肠道微生物群成员可通过代谢转化增加异种生物的毒性。然而，大多数参与饮食-微生物群相互作用的微生物仍然特征不清。考虑到 BC 和 CRC 癌症的不同类型和异质性，以及它们之间的关系和与肠道微生物群的关系，我们在此概述了 BC 和 CRC 中微生物群与饮食之间的关系。
{"title":"Role of the intestinal microbiota and diet in the onset and progression of colorectal and breast cancers and the interconnection between both types of tumours","authors":"Sergio Ruiz-Saavedra, A. Zapico, Sonia González, N. Salazar, C. G. de los Reyes-Gavilán","doi":"10.20517/mrr.2023.36","DOIUrl":"https://doi.org/10.20517/mrr.2023.36","url":null,"abstract":"Colorectal cancer (CRC) is among the leading causes of mortality in adults of both sexes worldwide, while breast cancer (BC) is among the leading causes of death in women. In addition to age, gender, and genetic predisposition, environmental and lifestyle factors exert a strong influence. Global diet, including alcohol consumption, is one of the most important modifiable factors affecting the risk of CRC and BC. Western dietary patterns promoting high intakes of xenobiotics from food processing and ethanol have been associated with increased cancer risk, whereas the Mediterranean diet, generally leading to a higher intake of polyphenols and fibre, has been associated with a protective effect. Gut dysbiosis is a common feature in CRC, where the usual microbiota is progressively replaced by opportunistic pathogens and the gut metabolome is altered. The relationship between microbiota and BC has been less studied. The estrobolome is the collection of genes from intestinal bacteria that can metabolize oestrogens. In a dysbiosis condition, microbial deconjugating enzymes can reactivate conjugated-deactivated oestrogens, increasing the risk of BC. In contrast, intestinal microorganisms can increase the biological activity and bioavailability of dietary phytochemicals through diverse microbial metabolic transformations, potentiating their anticancer activity. Members of the intestinal microbiota can increase the toxicity of xenobiotics through metabolic transformations. However, most of the microorganisms involved in diet-microbiota interactions remain poorly characterized. Here, we provide an overview of the associations between microbiota and diet in BC and CRC, considering the diverse types and heterogeneity of these cancers and their relationship between them and with gut microbiota.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"44 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139228908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
For decades, the urinary system was regarded as a sterile environment due to the absence of any bacterial growth in clinical standard urine cultures from healthy individuals. However, a diverse array of microbes colonizes the urinary system in small quantities, exhibiting a variable compositional signature influenced by differences in sex, age, and pathological state. Increasing pieces of evidence suggest microbiota exists in tumor tissue and plays a crucial role in tumor microenvironment based on research in multiple cancer models. Current studies about microbiota and bladder cancer have preliminarily characterized the bladder cancer-related microbiota, but how the microbiota influences the biological behavior of bladder cancer remains unclarified. This review summarizes the characteristics of microbiota in bladder cancer, aims to propose possible mechanisms that microbiota acts in tumorigenesis and progression of bladder cancer based on advances in gut microbiota, and discusses the potential clinical application of microbiota in bladder cancer.
{"title":"The role of microbiota in tumorigenesis, progression and treatment of bladder cancer","authors":"Zijing Peng, Jingming Zhuang, Bing Shen","doi":"10.20517/mrr.2023.47","DOIUrl":"https://doi.org/10.20517/mrr.2023.47","url":null,"abstract":"For decades, the urinary system was regarded as a sterile environment due to the absence of any bacterial growth in clinical standard urine cultures from healthy individuals. However, a diverse array of microbes colonizes the urinary system in small quantities, exhibiting a variable compositional signature influenced by differences in sex, age, and pathological state. Increasing pieces of evidence suggest microbiota exists in tumor tissue and plays a crucial role in tumor microenvironment based on research in multiple cancer models. Current studies about microbiota and bladder cancer have preliminarily characterized the bladder cancer-related microbiota, but how the microbiota influences the biological behavior of bladder cancer remains unclarified. This review summarizes the characteristics of microbiota in bladder cancer, aims to propose possible mechanisms that microbiota acts in tumorigenesis and progression of bladder cancer based on advances in gut microbiota, and discusses the potential clinical application of microbiota in bladder cancer.","PeriodicalId":507408,"journal":{"name":"Microbiome Research Reports","volume":"125 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139256889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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