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- Dillon, MR, et al.
(författare)
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Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops
- 2021
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Ingår i: PLoS computational biology. - : Public Library of Science (PLoS). - 1553-7358. ; 17:6, s. e1009056-
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Tidskriftsartikel (refereegranskat)abstract
- In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn’t work well, and what we plan to do differently in future workshops.
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- Du, Y, et al.
(författare)
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Influence of Pre-treatment Saliva Microbial Diversity and Composition on Nasopharyngeal Carcinoma Prognosis
- 2022
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Ingår i: Frontiers in cellular and infection microbiology. - : Frontiers Media SA. - 2235-2988. ; 12, s. 831409-
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Tidskriftsartikel (refereegranskat)abstract
- The human microbiome has been reported to mediate the response to anticancer therapies. However, research about the influence of the oral microbiome on nasopharyngeal carcinoma (NPC) survival is lacking. We aimed to explore the effect of oral microbiota on NPC prognosis.MethodsFour hundred eighty-two population-based NPC cases in southern China between 2010 and 2013 were followed for survival, and their saliva samples were profiled using 16s rRNA sequencing. We analyzed associations of the oral microbiome diversity with mortality from all causes and NPC.ResultsWithin- and between-community diversities of saliva were associated with mortality with an average of 5.29 years follow-up. Lower Faith’s phylogenetic diversity was related to higher all-cause mortality [adjusted hazard ratio (aHR), 1.52 (95% confidence interval (CI), 1.06–2.17)] and NPC-specific mortality [aHR, 1.57 (95% CI, 1.07–2.29)], compared with medium diversity, but higher phylogenetic diversity was not protective. The third principal coordinate (PC3) identified from principal coordinates analysis (PCoA) on Bray–Curtis distance was marginally associated with reduced all-cause mortality [aHR, 0.85 (95% CI, 0.73–1.00)], as was the first principal coordinate (PC1) from PCoA on weighted UniFrac [aHR, 0.86 (95% CI, 0.74–1.00)], but neither was associated with NPC-specific mortality. PC3 from robust principal components analysis was associated with lower all-cause and NPC-specific mortalities, with HRs of 0.72 (95% CI, 0.61–0.85) and 0.71 (95% CI, 0.60–0.85), respectively.ConclusionsOral microbiome may be an explanatory factor for NPC prognosis. Lower within-community diversity was associated with higher mortality, and certain measures of between-community diversity were related to mortality. Specifically, candidate bacteria were not related to mortality, suggesting that observed associations may be due to global patterns rather than particular pathogens.
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- Mubanga, M, et al.
(författare)
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The gut microbiome and asthma in a Swedish twin study
- 2023
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Ingår i: Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology. - 1365-2222. ; 53:11, s. 1212-1215
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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- Mubanga, M, et al.
(författare)
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The gut microbiome and asthma in a Swedish twin study
- 2023
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Ingår i: Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology. - 1365-2222.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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