Microbiome Research Reports最新文献

Putative pseudolysogeny-dependent phage gene implicated in the superinfection resistance of Cutibacterium acnes 与痤疮棒状杆菌超级抗感染能力有关的假溶酶原依赖性噬菌体基因

Microbiome Research Reports Pub Date : 2024-04-18 DOI: 10.20517/mrr.2023.42

Stephanie Wottrich, Stacee Mendonca, Cameron Safarpour, Christine Nguyen, L. J. Marinelli, Stephen P. Hancock, Robert L. Modlin, J. M. Parker

{"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}

引用次数: 0

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics RapidAIM 2.0：研究人类肠道微生物组对异种生物功能反应的高通量测定法

Microbiome Research Reports Pub Date : 2024-04-03 DOI: 10.20517/mrr.2023.57

Leyuan Li, J. Mayne, Adrian Beltran, Xu Zhang, Zhibin Ning, Daniel Figeys

{"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}

引用次数: 0

MetaBIDx: a new computational approach to bacteria identification in microbiomes MetaBIDx：微生物群细菌鉴定的新计算方法

Microbiome Research Reports Pub Date : 2024-04-01 DOI: 10.20517/mrr.2024.01

Diem-Trang Pham, Vinhthuy T. Phan

{"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}

引用次数: 0

Microbiota-gut-liver-brain axis and hepatic encephalopathy 微生物群-肠-肝-脑轴与肝性脑病

Microbiome Research Reports Pub Date : 2024-01-25 DOI: 10.20517/mrr.2023.44

Haifeng Lu, Hua Zhang, Zhongwen Wu, Lanjuan Li

{"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}

引用次数: 0

Bifidobacterium longum subsp. infantis regulates Th1/Th2 balance through the JAK-STAT pathway in growing mice 长双歧杆菌亚种通过 JAK-STAT 途径调节生长期小鼠的 Th1/Th2 平衡

Microbiome Research Reports Pub Date : 2024-01-19 DOI: 10.20517/mrr.2023.64

M. Ding, Bowen Li, Haiqin Chen, R. P. Ross, Catherine Stanton, Shilong Jiang, Jianxin Zhao, Wei Chen, Bo Yang

{"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}

引用次数: 0

CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus φ13 bacteriophages 乳酸乳球菌 TP901-1 和金黄色葡萄球菌 φ13 噬菌体溶菌酶开关中的 CI:Mor 相互作用

Microbiome Research Reports Pub Date : 2024-01-19 DOI: 10.20517/mrr.2023.50

Anders K. Varming, Zhiyu Huang, Ghofran M. Hamad, K. K. Rasmussen, H. Ingmer, M. Kilstrup, Leila Lo Leggio

{"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}

引用次数: 0

The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice 人类肠道细菌 Eggerthella lenta 对非生物小鼠肠道代谢组的影响

Microbiome Research Reports Pub Date : 2024-01-18 DOI: 10.20517/mrr.2023.65

Alina Viehof, Sven-Bastiaan Haange, Theresa Streidl, Kristin Schubert, B. Engelmann, Dirk Haller, U. Rolle-Kampczyk, Martin von Bergen, T. Clavel

{"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}

引用次数: 0

Methodological recommendations for human microbiota-gut-brain axis research 人类微生物群-肠-脑轴研究方法建议

Microbiome Research Reports Pub Date : 2024-01-01 DOI: 10.20517/mrr.2023.33

Yangwen Ou, Clara Belzer, Hauke Smidt, C. de Weerth

引用次数: 0

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 肠道微生物群和饮食在结直肠癌和乳腺癌发病和发展中的作用以及这两种肿瘤之间的相互联系

Microbiome Research Reports Pub Date : 2023-11-27 DOI: 10.20517/mrr.2023.36

Sergio Ruiz-Saavedra, A. Zapico, Sonia González, N. Salazar, C. G. de los Reyes-Gavilán

{"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}

引用次数: 0

The role of microbiota in tumorigenesis, progression and treatment of bladder cancer 微生物群在膀胱癌的肿瘤发生、发展和治疗中的作用

Microbiome Research Reports Pub Date : 2023-11-20 DOI: 10.20517/mrr.2023.47

Zijing Peng, Jingming Zhuang, Bing Shen

引用次数: 0