Microbiome最新文献

{"title":"MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.","authors":"Annabel Cansdale, James P J Chong","doi":"10.1186/s40168-024-01949-z","DOIUrl":"10.1186/s40168-024-01949-z","url":null,"abstract":"<p><strong>Background: </strong>Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.</p><p><strong>Results: </strong>To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.</p><p><strong>Conclusions: </strong>The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569123","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}

{"title":"Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway.","authors":"Jian Gu, Zhichao Yao, Bruno Lemaitre, Zhaohui Cai, Hongyu Zhang, Xiaoxue Li","doi":"10.1186/s40168-024-01931-9","DOIUrl":"10.1186/s40168-024-01931-9","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota can facilitate host growth under nutrient-constrained conditions. However, whether this effect is limited to certain bacterial species remains largely unclear, and the relevant underlying mechanisms remain to be thoroughly investigated.</p><p><strong>Results: </strong>We found that the microbiota was required for Bactrocera dorsalis larval growth under poor dietary conditions. Monoassociation experiments revealed that Enterobacteriaceae and some Lactobacilli promoted larval growth. Among the 27 bacterial strains tested, 14 significantly promoted larval development, and the Enterobacteriaceae cloacae isolate exhibited the most obvious promoting effect. A bacterial genome-wide association study (GWAS) revealed that the vitamin B6 synthesis pathway was critical for the promotion of E. cloacae growth. Deletion of pdxA, which is responsible for vitamin B6 biosynthesis, deprived the mutant strains of larval growth-promoting function, indicating that the 4-hydroxythreonine-4-phosphate dehydrogenase(pdxA) gene was crucial for promoting larval growth in E. cloacae. Importantly, supplementation of a poor diet with vitamin B6 successfully rescued the axenic larval growth phenotype of B. dorsalis.</p><p><strong>Conclusion: </strong>Our results suggest that gut microbes promote insect larval growth by providing vitamin B6 under nutrient scarcity conditions in B. dorsalis. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569122","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}

{"title":"Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized.","authors":"Erica P Ryu, Yoshina Gautam, Diana M Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Prasad Gautam, David A Relman, Ahmed A Shibl, Jeevan Bahadur Sherchand, Aashish R Jha, Emily R Davenport","doi":"10.1186/s40168-024-01941-7","DOIUrl":"10.1186/s40168-024-01941-7","url":null,"abstract":"<p><strong>Background: </strong>Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called \"vanishing microbiomes\" potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations.</p><p><strong>Results: </strong>Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the USA within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain sources.</p><p><strong>Conclusion: </strong>Our findings demonstrate that by studying populations within Nepal, we can isolate an important role of lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576296","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}

{"title":"The gut microbiome in patients with Cushing's disease affects depression- and anxiety-like behavior in mice.","authors":"Ding Nie, Dawei Wang, Zhenhua Wang, Qiuyue Fang, Hongyun Wang, Weiyan Xie, Chuzhong Li, Yazhuo Zhang","doi":"10.1186/s40168-024-01939-1","DOIUrl":"10.1186/s40168-024-01939-1","url":null,"abstract":"<p><strong>Background: </strong>Depression and anxiety significantly impact the quality of life in individuals with Cushing's disease (CD), which originates from pituitary neuroendocrine tumors (PitNETs), yet our understanding of the underlying mechanisms is limited. There is substantial evidence linking gut microbes to depression, anxiety, and endocrinology.</p><p><strong>Results: </strong>The gut bacterial phenotype of patients with Cushing's disease was significantly different from that of the control group, and when the mice were treated with fecal bacteria from these patients, both anxiety- and depression-like behavior were significantly increased. However, this effect can be alleviated by supplementing with 2-(14, 15-epoxyeicosatrienoyl) glycerol (2-14,15-EG) which was found at reduced levels in the peripheral blood of mice treated with coprofecal bacteria from Cushing's disease. In this process, the effects of hormone levels and immune factors were not significant. In addition, in an animal model, corticosterone has been observed to affect behavioral changes in mice through gut microbiota composition, clarifying the cause-and-effect relationship between hormones, microbiota, and behavior. Finally, there was no significant difference in gut microbiome composition and its effects on mouse behavior in patients with Cushing's disease with different levels of depression and anxiety.</p><p><strong>Conclusions: </strong>In summary, this research enhances our current understanding of how gut microbes in patients with Cushing's disease contribute to depression and anxiety, offering novel insights for clinical treatment approaches. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11529176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558205","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}

{"title":"Quality traits drive the enrichment of Massilia in the rhizosphere to improve soybean oil content.","authors":"Qin Han, Guanghui Zhu, Hongmei Qiu, Mingbo Li, Jiaming Zhang, Xinying Wu, Renhao Xiao, Yan Zhang, Wei Yang, Bing Tian, Lanxi Xu, Jiayang Zhou, Yutong Li, Yueqiang Wang, Yang Bai, Xia Li","doi":"10.1186/s40168-024-01933-7","DOIUrl":"10.1186/s40168-024-01933-7","url":null,"abstract":"<p><strong>Background: </strong>Soybean seeds are rich in protein and oil. The selection of varieties that produce high-quality seeds has been one of the priorities of soybean breeding programs. However, the influence of improved seed quality on the rhizosphere microbiota and whether the microbiota is involved in determining seed quality are still unclear. Here, we analyzed the structures of the rhizospheric bacterial communities of 100 soybean varieties, including 53 landraces and 47 modern cultivars, and evaluated the interactions between seed quality traits and rhizospheric bacteria.</p><p><strong>Results: </strong>We found that rhizospheric bacterial structures differed between landraces and cultivars and that this difference was directly related to their oil content. Seven bacterial families (Sphingomonadaceae, Gemmatimonadaceae, Nocardioidaceae, Xanthobacteraceae, Chitinophagaceae, Oxalobacteraceae, and Streptomycetaceae) were obviously enriched in the rhizospheres of the high-oil cultivars. Among them, Oxalobacteraceae (Massilia) was assembled specifically by the root exudates of high-oil cultivars and was associated with the phenolic acids and flavonoids in plant phenylpropanoid biosynthetic pathways. Furthermore, we showed that Massilia affected auxin signaling or interfered with active oxygen-related metabolism. In addition, Massilia activated glycolysis pathway, thereby promoting seed oil accumulation.</p><p><strong>Conclusions: </strong>These results provide a solid theoretical basis for the breeding of revolutionary soybean cultivars with desired seed quality and optimal microbiomes and the development of new cultivation strategies for increasing the oil content of seeds. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546239","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}

{"title":"Eubacterium siraeum suppresses fat deposition via decreasing the tyrosine-mediated PI3K/AKT signaling pathway in high-fat diet-induced obesity.","authors":"Xueshuang Lai, Shuang Liu, Jian Miao, Ran Shen, Zhen Wang, Zhe Zhang, Huanfa Gong, Meng Li, Yuchun Pan, Qishan Wang","doi":"10.1186/s40168-024-01944-4","DOIUrl":"10.1186/s40168-024-01944-4","url":null,"abstract":"<p><strong>Background: </strong>Obesity in humans can lead to chronic diseases such as diabetes and cardiovascular disease. Similarly, subcutaneous fat (SCF) in pigs affects feed utilization, and excessive SCF can reduce the feed efficiency of pigs. Therefore, identifying factors that suppress fat deposition is particularly important. Numerous studies have implicated the gut microbiome in pigs' fat deposition, but research into its suppression remains scarce. The Lulai black pig (LL) is a hybrid breed derived from the Laiwu pig (LW) and the Yorkshire pig, with lower levels of SCF compared to the LW. In this study, we focused on these breeds to identify microbiota that regulate fat deposition. The key questions were: Which microbial populations reduce fat in LL pigs compared to LW pigs, and what is the underlying regulatory mechanism?</p><p><strong>Results: </strong>In this study, we identified four different microbial strains, Eubacterium siraeum, Treponema bryantii, Clostridium sp. CAG:413, and Jeotgalibaca dankookensis, prevalent in both LW and LL pigs. Blood metabolome analysis revealed 49 differential metabolites, including tanshinone IIA and royal jelly acid, known for their anti-adipogenic properties. E. siraeum was strongly correlated with these metabolites, and its genes and metabolites were enriched in pathways linked to fatty acid degradation, glycerophospholipid, and glycerolipid metabolism. In vivo mouse experiments confirmed that E. siraeum metabolites curb weight gain, reduce SCF adipocyte size, increase the number of brown adipocytes, and regulate leptin, IL-6, and insulin secretion. Finally, we found that one important pathway through which E. siraeum inhibits fat deposition is by suppressing the phosphorylation of key proteins in the PI3K/AKT signaling pathway through the reduction of tyrosine.</p><p><strong>Conclusions: </strong>We compared LW and LL pigs using fecal metagenomics, metabolomics, and blood metabolomics, identifying E. siraeum as a strain linked to fat deposition. Oral administration experiments in mice demonstrated that E. siraeum effectively inhibits fat accumulation, primarily through the suppression of the PI3K/AKT signaling pathway, a critical regulator of lipid metabolism. These findings provide a valuable theoretical basis for improving pork quality and offer insights relevant to the study of human obesity and related chronic metabolic diseases. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11526712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546238","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}

{"title":"The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections.","authors":"Ana-Belen Martin-Cuadrado, Esther Rubio-Portillo, Francesc Rosselló, Josefa Antón","doi":"10.1186/s40168-024-01921-x","DOIUrl":"10.1186/s40168-024-01921-x","url":null,"abstract":"<p><strong>Background: </strong>Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.</p><p><strong>Results: </strong>The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.</p><p><strong>Conclusion: </strong>Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546240","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}

{"title":"Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health.","authors":"Xu Xu, Renqiang Jiang, Xinling Wang, Shanshan Liu, Menghui Dong, Hancheng Mao, Xingrui Li, Ziyu Ni, Nana Lv, Xuhui Deng, Wu Xiong, Chengyuan Tao, Rong Li, Qirong Shen, Stefan Geisen","doi":"10.1186/s40168-024-01947-1","DOIUrl":"10.1186/s40168-024-01947-1","url":null,"abstract":"<p><strong>Background: </strong>Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown.</p><p><strong>Results: </strong>Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum.</p><p><strong>Conclusions: </strong>Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522303","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}

{"title":"The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III-IV periodontitis patients.","authors":"Sven Kleine Bardenhorst, Daniel Hagenfeld, Johannes Matern, Karola Prior, Inga Harks, Peter Eickholz, Katrin Lorenz, Ti-Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Yvonne Jockel-Schneider, Dag Harmsen, Benjamin Ehmke","doi":"10.1186/s40168-024-01945-3","DOIUrl":"10.1186/s40168-024-01945-3","url":null,"abstract":"<p><strong>Background: </strong>Periodontitis, a prevalent chronic inflammatory disease, offers insights into the broader landscape of chronic inflammatory conditions. The progression and treatment outcomes of periodontitis are closely related to the oral microbiota's composition. Adjunctive systemic Amoxicillin 500 mg and Metronidazole 400 mg, often prescribed thrice daily for 7 days to enhance periodontal therapy's efficacy, have lasting effects on the oral microbiome. However, the precise mechanism through which the oral microbiome influences clinical outcomes in periodontitis patients remains debated. This investigation explores the pivotal role of the oral microbiome's composition in mediating the outcomes of adjunctive systemic antibiotic treatment.</p><p><strong>Methods: </strong>Subgingival plaque samples from 10 periodontally healthy and 163 periodontitis patients from a randomized clinical trial on periodontal therapy were analyzed. Patients received either adjunctive amoxicillin/metronidazole or a placebo after mechanical periodontal treatment. Microbial samples were collected at various intervals up to 26 months post-therapy. Using topic models, we identified microbial communities associated with normobiotic and dysbiotic states, validated with 86 external and 40 internal samples. Logistic regression models evaluated the association between these microbial communities and clinical periodontitis parameters. A Directed Acyclic Graph (DAG) determined the mediating role of oral microbiota in the causal path of antibiotic treatment effects on clinical outcomes.</p><p><strong>Results: </strong>We identified clear distinctions between dysbiotic and normobiotic microbial communities, differentiating healthy from periodontitis subjects. Dysbiotic states consistently associated with below median %Pocket Probing Depth ≥ 5 mm (OR = 1.26, 95% CI [1.14-1.42]) and %Bleeding on Probing (OR = 1.09, 95% CI [1.00-1.18]). Factors like microbial response to treatment, smoking, and age were predictors of clinical attachment loss progression, whereas sex and antibiotic treatment were not. Further, we showed that the oral microbial treatment response plays a crucial role in the causal effect of antibiotic treatment on clinical treatment outcomes.</p><p><strong>Conclusions: </strong>The shift towards a normobiotic subgingival microbiome, primarily induced by adjunctive antibiotics, underscores the potential for microbiome-targeted interventions to enhance therapeutic efficacy in chronic inflammatory conditions. This study reaffirms the importance of understanding the oral microbiome's role in periodontal health and paves the way for future research exploring personalized treatment strategies based on individual microbiome profiles. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503493","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}

{"title":"A single-stranded based library preparation method for virome characterization.","authors":"Xichuan Zhai, Alex Gobbi, Witold Kot, Lukasz Krych, Dennis Sandris Nielsen, Ling Deng","doi":"10.1186/s40168-024-01935-5","DOIUrl":"10.1186/s40168-024-01935-5","url":null,"abstract":"<p><strong>Background: </strong>The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.</p><p><strong>Results: </strong>We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA + Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.</p><p><strong>Conclusion: </strong>We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503478","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}