Evaluating the use of diversity indices to distinguish between microbial communities with different traits

Feranchuk, Sergey; Belkova, Natalia; Potapova, Ulyana; Kuzmin, Dmitry A.; Беликов, С. И.

doi:10.1016/j.resmic.2018.03.004

Cited by 32 publications

(20 citation statements)

References 27 publications

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“…The filtered dataset was used for assessment of beta diversity (dissimilarity between groups) and to identify predictive microbial and clinical predictors of the structure of the microbiota. Alpha diversity richness (distinct OTUs within a sample) was assessed with the Chao1 test, while evenness (distribution of OTUs within a sample) was assessed with the Shannon and inverse Simpson measures [22]. To evaluate whether the samples clustered based upon either HLA-B27 status (for comparison of the offspring) or disease status (for comparison of the HLA-B27+ offspring to diagnosed SpA patients), the permutational analysis of variance (PERMANOVA) test was run against the distance matrix generated from the Bray Curtis measure of dissimilarity [23].…”

Section: Sequencing and Analysis Of 16s Ribosomal Dna From The Fecal ...mentioning

confidence: 99%

Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients

Stoll

DeQuattro

et al. 2022

Children

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Multiple studies have shown the microbiota to be abnormal in patients with spondyloarthritis (SpA). The purpose of this study was to explore the genetic contributions of these microbiota abnormalities. We analyzed the impact of HLA-B27 on the microbiota of children at risk for SpA and compared the microbiota of HLA-B27+ pediatric offspring of ankylosing spondylitis (AS) patients with that of HLA-B27+ children with SpA. Human DNA was obtained from the offspring for determination of HLA-B27 status and polygenic risk score (PRS). Fecal specimens were collected from both groups for sequencing of the V4 region of the 16S ribosomal RNA gene. Among the offspring of AS patients, there was slight clustering by HLA-B27 status. After adjusting for multiple comparisons, five operational taxonomic units (OTUs) representing three unique taxa distinguished the HLA-B27+ from negative children: Blautia and Coprococcus were lower in the HLA-B27+ offspring, while Faecalibacterium prausnitzii was higher. HLA-B27+ offspring without arthritis were compared to children with treatment-naïve HLA-B27+ SpA. After adjustments, clustering by diagnosis was present. A total of 21 OTUs were significantly associated with diagnosis state, including Bacteroides (higher in SpA patients) and F. prausnitzii (higher in controls). Thus, our data confirmed associations with B fragilis and F prausnitzii with juvenile SpA, and also suggest that the mechanism by which HLA-B27 is associated with SpA may not involve alterations of the microbiota.

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Section: Sequencing and Analysis Of 16s Ribosomal Dna From The Fecal ...mentioning

confidence: 99%

Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients

Stoll

DeQuattro

et al. 2022

Children

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“…The approaches used for data processing are partly based on the methods described by Feranchuk et al . [79]. The functional annotation of microbiomes was implemented using PICRUSt package [78] using a conventional pipeline, as it was described in PICRUSt documentation.…”

Section: Methodsmentioning

confidence: 99%

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities

et al. 2019

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The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.

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“…The figures below illustrating the services described are based on the surveys described in (Feranchuk et al 2018). Namely, one of the surveys presents bacterial symbionts of marine sponges in coral reefs near an Indonesian shore, as described in (Cleary et al 2018).…”

Section: Overviewmentioning

confidence: 99%

“…Estimates of the alpha-diversity adopted in the system are based on implementations from the scikit-bio package (Shannon, Simpson, Chao1, Ace, Fisher α, Gini). In addition, an alternative estimator of the Gini measure and two parametric diversity measures, as specified in (Feranchuk et al 2018), are included in the set of estimators. The rarefaction analysis uses the Python code, adapted from the scikit-bio package, and the ability to estimate the Michaelis-Menthen fit to rarefaction curves is included as an alphadiversity estimator.…”

Section: Specificationsmentioning

confidence: 99%

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Tools and a web server for data analysis and presentation in microbial ecology

et al. 2019

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The methods for data presentation are important in bioinformatics as data processing algorithms. The article describes the software package for the extensive analysis of tables with estimates of bacterial abundance levels in environmental samples. The package was designed to be executed in a distributed hardware environment, with powerful packages in Python in the backend and interactive front-end forms. Most of microbial ecology-specific functionality is implemented by the scikit-bio Python package, together with the other Python packages intended for big data analysis. Interactive visualisation tools are implemented by the D3.js software library, therefore, the software project is named D3b. The package is a suite of tools for the analysis of microbial ecology data implemented as a web-service and as a desktop application. It supports a substantial part of the graphical and analytical descriptions of microbial communities used in scientific publications. Source codes are available at github (sferanchuk/d3b_charts) and the on-line version of the system is accessible at d3b-charts.bri-shur.com.

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Evaluating the use of diversity indices to distinguish between microbial communities with different traits

Cited by 32 publications

References 27 publications

Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients

Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities

Tools and a web server for data analysis and presentation in microbial ecology

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