Difficulty in Assigning Fungal Identity Based on DNA Sequences.
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ABSTRACT:
SUBMITTER: Ruiz ON
PROVIDER: S-EPMC8638600 | biostudies-literature | 2021 Dec
REPOSITORIES: biostudies-literature
Publications
Difficulty in Assigning Fungal Identity Based on DNA Sequences.
Ruiz Oscar N ON Radwan Osman O
Microbiology resource announcements 20211202 48
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Project description:Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important. Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew's Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments. Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match. Discussion. Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates that de novo methods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
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Project description:Most research and theory on identity integration focuses on adolescents and young adults under age 30, and relatively little is known about how identity adjusts to major life events later in life. The purpose of the present study was to operationalize and investigate identity disruption, or a loss of temporal identity integration following a disruptive life event, within the developmental context of established adulthood and midlife. We used a mixed-methods approach to examine identity disruption among 244 Afghanistan and Iraq war veterans with reintegration difficulty who participated in an expressive writing intervention. Participants completed measures of social support, posttraumatic stress disorder (PTSD) symptom severity, satisfaction with life, and reintegration difficulty at baseline right before writing, and 3 and 6 months after the expressive writing intervention. The expressive writing samples were coded for identity disruption using thematic analysis. We hypothesized that identity disruption would be associated with lower social support, more severe PTSD symptoms, lower satisfaction with life, and greater reintegration difficulty at baseline. Forty-nine percent (n = 121) of the sample indicated identity disruption in their writing samples. Identity disruption was associated with more severe PTSD symptoms, lower satisfaction with life, and greater reintegration difficulty at baseline, and with less improvement in social support. The findings suggest that identity disruption is a meaningful construct for extending the study of identity development to established adult and midlife populations, and for understanding veterans' adjustment to civilian life. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
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