Microbiome最新文献

{"title":"Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges.","authors":"Julie Rodriguez, Magali Cordaillat-Simmons, Nelly Badalato, Bernard Berger, Heloise Breton, Raynald de Lahondès, Mélanie Deschasaux-Tanguy, Clara Desvignes, Camille D'Humières, Stephan Kampshoff, Aonghus Lavelle, Amira Metwaly, Narciso M Quijada, Jos F M L Seegers, Austin Udocor, Hub Zwart, Emmanuelle Maguin, Joël Doré, Céline Druart","doi":"10.1186/s40168-024-01991-x","DOIUrl":"https://doi.org/10.1186/s40168-024-01991-x","url":null,"abstract":"<p><strong>Background: </strong>In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant influence on human health. This has led to the emergence of companies offering microbiome testing services. Some of these services are sold directly to the consumer via companies' websites or via medical laboratory websites.</p><p><strong>Methodology: </strong>In order to provide an overview of the consumer experience proposed by these microbiome testing services, one single faecal sample was sent to six different companies (five based in Europe and one based in the USA). Two out of the six testing kits were commercialized by medical laboratories, but without any requirement for a medical prescription. The analyses and reports received were discussed with a panel of experts (21 experts from 8 countries) during an online workshop.</p><p><strong>Results: </strong>This workshop led to the identification of several limitations and challenges related to these kits, including over-promising messages from the companies, a lack of transparency in the methodology used for the analysis and a lack of reliability of the results. The experts considered the interpretations and recommendations provided in the different reports to be premature due to the lack of robust scientific evidence and the analyses associated with the reports to be of limited clinical utility. The experts also discussed the grey areas surrounding the regulatory status of these test kits, including their positioning in the European market. The experts recommended a distinction between regulatory requirements based on the intended use or purpose of the kit: on the one hand, test kits developed to satisfy consumer curiosity, with a clear mention of this objective, and no mention of any disease or risk of disease, and on the other hand, in vitro diagnostic (IVD) CE-marked test kits, which could go deeper into the analysis and interpretation of samples, as such a report would be intended for trained healthcare professionals.</p><p><strong>Conclusions: </strong>Recommendations or actions, specific to the context of use of microbiome testing kits, are listed to improve the quality and the robustness of these test kits to meet expectations of end users (consumers, patients and healthcare professionals). The need for standardization, robust scientific evidence, qualification of microbiome-based biomarkers and a clear regulatory status in Europe are the main issues that will require attention in the near future to align laboratory development with societal needs and thus foster translation into daily health practice.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"258"},"PeriodicalIF":13.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: 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/s40168-024-01986-8","DOIUrl":"10.1186/s40168-024-01986-8","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"257"},"PeriodicalIF":13.8,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794913","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":"Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor.","authors":"Alessandra Granato, Simone Renwick, Christopher Yau, Tiffany Kong, Michelle C Daigneault, Mikael Knip, Emma Allen-Vercoe, Jayne S Danska","doi":"10.1186/s40168-024-01976-w","DOIUrl":"10.1186/s40168-024-01976-w","url":null,"abstract":"<p><strong>Background: </strong>The human gut microbiota is inoculated at birth and undergoes a process of assembly and diversification during the first few years of life. Studies in mice and humans have revealed associations between the early-life gut microbiome and future susceptibility to immune and metabolic diseases. To resolve microbe and host contributing factors to early-life development and to disease states requires experimental platforms that support reproducible, longitudinal, and high-content analyses.</p><p><strong>Results: </strong>Here, we deployed a continuous single-stage chemostat culture model of the human distal gut to study gut microbiota from 18- to 24-month-old children integrating both culture-dependent and -independent methods. Chemostat cultures recapitulated multiple aspects of the fecal microbial ecosystem enabling investigation of relationships between bacterial strains and metabolic function, as well as a resource from which we isolated and curated a diverse library of early life bacterial strains.</p><p><strong>Conclusions: </strong>We report the reproducible, longitudinal dynamics of early-life bacterial communities cultured in an advanced model of the human gut providing an experimental approach and a characterized bacterial resource to support future investigations of the human gut microbiota in early childhood.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"255"},"PeriodicalIF":13.8,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784702","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 host genotype actively shapes its microbiome across generations in laboratory mice.","authors":"Laurentiu Benga, Anna Rehm, Christina Gougoula, Philipp Westhoff, Thorsten Wachtmeister, W Peter M Benten, Eva Engelhardt, Andreas P M Weber, Karl Köhrer, Martin Sager, Stefan Janssen","doi":"10.1186/s40168-024-01954-2","DOIUrl":"10.1186/s40168-024-01954-2","url":null,"abstract":"<p><strong>Background: </strong>The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.</p><p><strong>Results: </strong>To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.</p><p><strong>Conclusions: </strong>Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"256"},"PeriodicalIF":13.8,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785302","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":"Correction: 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/s40168-024-01988-6","DOIUrl":"10.1186/s40168-024-01988-6","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"252"},"PeriodicalIF":13.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770309","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":"Dynamics of rice seed-borne bacteria from acquisition to seedling colonization.","authors":"Liying Chen, Han Bao, Jie Yang, Yan Huo, Jiabin Zhang, Rongxiang Fang, Lili Zhang","doi":"10.1186/s40168-024-01978-8","DOIUrl":"10.1186/s40168-024-01978-8","url":null,"abstract":"<p><strong>Background: </strong>Rice cultivation relies on planting grains harboring beneficial microbiota. However, the origination, distribution, and transmission dynamics of grain-borne bacteria remain unclear.</p><p><strong>Results: </strong>Using rice grain as a model system, this study investigates the primary sources, major niches in seeds, and the dynamics of community acquisition, maintenance, and transmission between generations of grain-borne bacteria. Quantitative PCR and 16S rRNA gene sequencing demonstrate rice grains acquiring bacteria primarily from the external environment during panicle heading and flowering. These bacteria concentrate between the caryopsis and glumes, establishing sizable communities in developing seeds. The dominant taxa included Pantoea, Pseudomonas, and Sphingomonas. Throughout seed development and storage, community structure remains consistent while abundance fluctuates within one order of magnitude. Upon germination under axenic conditions, seed bacteria successfully colonize shoots and roots of offspring seedlings. However, bacteria transmitted solely through internal routes fail to form comparably large communities. Analysis of taxonomic composition uncovers dramatic reshaping from seeds to seedlings, potentially reflecting functional adaptation.</p><p><strong>Conclusions: </strong>We clarify seed-borne bacterial origination, acquisition timing, seed colonization, intergenerational transmission, and seedling diversification. Our findings provide novel insights into rice seed bacterial dynamics critical for microbiome management. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"253"},"PeriodicalIF":13.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770319","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 pharmacomicrobiomics in HIV prevention, treatment, and women's health.","authors":"Erik C Swanson, Christopher M Basting, Nichole R Klatt","doi":"10.1186/s40168-024-01953-3","DOIUrl":"10.1186/s40168-024-01953-3","url":null,"abstract":"<p><p>In the absence of an effective vaccine or curative treatment for HIV, the global HIV/AIDS epidemic continues despite significant advances in treatment and prevention. Antiretroviral therapy (ART) drugs have transformed HIV from a terminal illness to a manageable chronic condition. Likewise, pre-exposure prophylaxis treatment (PrEP) has dramatically reduced transmission in some of the highest risk populations. However, quality of life and life expectancy in people living with HIV (PWH) still lag significantly behind the general population. The mechanisms that reduce the efficacy of PrEP and ART are multifaceted, but one factor that warrants additional attention is the impact of the microbiome on ART and PrEP efficacy, as well as pharmacokinetics more broadly. In this review, we assess the current state of research on the HIV-associated microbiome, how this impacts treatment efficacy, and how microbiome states can alter HIV susceptibility. We also explore how the mechanisms we propose could extend to the efficacy of other drugs and identify promising areas of research that remain understudied. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"254"},"PeriodicalIF":13.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770351","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":"Host-specific effects of Eubacterium species on Rg3-mediated modulation of osteosarcopenia in a genetically diverse mouse population.","authors":"Soyeon Hong, Bao Ngoc Nguyen, Huitae Min, Hye-Young Youn, Sowoon Choi, Emmanuel Hitayezu, Kwang-Hyun Cha, Young Tae Park, Choong-Gu Lee, GyHye Yoo, Myungsuk Kim","doi":"10.1186/s40168-024-01971-1","DOIUrl":"10.1186/s40168-024-01971-1","url":null,"abstract":"<p><strong>Background: </strong>Osteosarcopenia, characterized by the simultaneous loss of bone and muscle mass, is a serious health problem in the aging population. This study investigated the interplay between host genetics, gut microbiota, and musculoskeletal health in a mouse model of osteosarcopenia, exploring the therapeutic potential of gut microbiota modulation.</p><p><strong>Methods: </strong>We examined the effects of Rg3, a phytochemical, on osteosarcopenia and its interactions with host genetics and gut microbiota in six founder strains of the Collaborative Cross (CC) population. Subsequently, we evaluated the therapeutic potential of Eubacterium nodatum (EN) and Eubacterium ventriosum (EV), two gut microbes identified as significant correlates of Rg3-mediated osteosarcopenia improvement, in selected C57BL/6 J (B6) and 129S1/SvImJ (129S1) mouse strains.</p><p><strong>Results: </strong>Rg3 treatment altered gut microbiota composition aligned with osteosarcopenia phenotypes, which response varied depending on host genetics. This finding enabled the identification of two microbes in the Eubacterium genus, potential mediator of Rg3 effect on osteosarcopenia. Oral administration of EN and EV differentially impacted bone density, muscle mass, exercise performance, and related gene expression in a mouse strain-specific manner. In 129S1 mice, EN and EV significantly improved these parameters, effectively reversing osteosarcopenic phenotypes. Mechanistic investigations revealed that these effects were mediated through the modulation of osteoblast differentiation and protein degradation pathways. In contrast, EN and EV did not significantly improve osteosarcopenic phenotypes in B6 mice, although they did modulate mitochondrial biogenesis and microbial diversity.</p><p><strong>Conclusions: </strong>Our findings underscore the complex interplay between host genetics and the gut microbiota in osteosarcopenia and emphasize the need for personalized treatment strategies. EN and EV exhibit strain-specific therapeutic effects, suggesting that tailoring microbial interventions to individual genetic backgrounds may be crucial for optimizing treatment outcomes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"251"},"PeriodicalIF":13.8,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770326","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":"Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.","authors":"Andrea Dell'Olio, William T Scott, Silvia Taroncher-Ferrer, Nadia San Onofre, José Miguel Soriano, Josep Rubert","doi":"10.1186/s40168-024-01975-x","DOIUrl":"https://doi.org/10.1186/s40168-024-01975-x","url":null,"abstract":"<p><strong>Background: </strong>Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.</p><p><strong>Results: </strong>Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.</p><p><strong>Conclusion: </strong>We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"250"},"PeriodicalIF":13.8,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11608498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770342","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":"Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.","authors":"Lilian A Cloarec, Thomas Bacchetta, Maxime Bruto, Christophe Leboulanger, Vincent Grossi, Céline Brochier-Armanet, Jean-Pierre Flandrois, Adrian Zurmely, Cécile Bernard, Marc Troussellier, Hélène Agogué, Magali Ader, Christine Oger-Desfeux, Philippe M Oger, Adrien Vigneron, Mylène Hugoni","doi":"10.1186/s40168-024-01956-0","DOIUrl":"10.1186/s40168-024-01956-0","url":null,"abstract":"<p><strong>Background: </strong>DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.</p><p><strong>Results: </strong>Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.</p><p><strong>Conclusions: </strong>This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"249"},"PeriodicalIF":13.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11606122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751173","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}