microViz: an R package for microbiome data visualization and statistics

Barnett, David J.M.; Arts, Ilja C. W.; Penders, John

doi:10.21105/joss.03201

Cited by 203 publications

(133 citation statements)

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“…Reads by sample were normalized using median sequencing depth. Taxonomy plots and unconstrained principal component analysis (PCA) were done at the order level using MicroViz ( Barnett et al, 2021 ), and taxa were center log-transformed using the function clr . Shannon diversity index was determined using Mothur.…”

Section: Methodsmentioning

confidence: 99%

Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

et al. 2022

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Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.

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Section: Methodsmentioning

confidence: 99%

Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

et al. 2022

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“…The R packages, phyloseq [ 27 ], microbiome [ 28 ], dplyr [ 29 ], ggplot2 [ 30 ], and microViz [ 31 ] were used for the ordination and visualization of taxonomic composition. Again, taxa present in less than 5% of samples were filtered out for all analyses.…”

Section: Methodsmentioning

confidence: 99%

“…Again, taxa present in less than 5% of samples were filtered out for all analyses. Unconstrained ordination was performed using principal component analysis (PCA) based on Aitchison distances at the genus and phylum levels [ 31 ]. Permutational multivariate analysis of variance (PERMANOVA) was used to analyse differences in overall microbiota composition between groups with and without adjusting for probiotic use as a potential covariate [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

“…Unconstrained ordination was performed using principal component analysis (PCA) based on Aitchison distances at the genus and phylum levels [ 31 ]. Permutational multivariate analysis of variance (PERMANOVA) was used to analyse differences in overall microbiota composition between groups with and without adjusting for probiotic use as a potential covariate [ 31 ]. The homogeneity of multivariate dispersions was assessed using the microViz package [ 31 ] and revealed no significant differences in dispersion.…”

Section: Methodsmentioning

confidence: 99%

“…Permutational multivariate analysis of variance (PERMANOVA) was used to analyse differences in overall microbiota composition between groups with and without adjusting for probiotic use as a potential covariate [ 31 ]. The homogeneity of multivariate dispersions was assessed using the microViz package [ 31 ] and revealed no significant differences in dispersion. The workflow of ANCOM v2.1, which accounts for the underlying compositional structure and sparseness of microbiota data, was used to identify taxa with differential abundance between controls and breast cancer patients or controls and breast cancer patients treated with adjuvant or neoadjuvant systemic therapy, respectively [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

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Intestinal Microbiota in Postmenopausal Breast Cancer Patients and Controls

Aarnoutse

Hillege

Ziemons

et al. 2021

Cancers

Self Cite

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Background: Previous preclinical and clinical research has investigated the role of intestinal microbiota in carcinogenesis. Growing evidence exists that intestinal microbiota can influence breast cancer carcinogenesis. However, the role of intestinal microbiota in breast cancer needs to be further investigated. This study aimed to identify the microbiota differences between postmenopausal breast cancer patients and controls. Patients and methods: This prospective cohort study compared the intestinal microbiota richness, diversity, and composition in postmenopausal histologically proven ER+/HER2- breast cancer patients and postmenopausal controls. Patients scheduled for (neo)adjuvant adriamycin, cyclophosphamide (AC), and docetaxel (D), or endocrine therapy (tamoxifen) were prospectively enrolled in a multicentre cohort study in the Netherlands. Patients collected a faecal sample and completed a questionnaire before starting systemic cancer treatment. Controls, enrolled from the National Dutch Breast Cancer Screening Programme, also collected a faecal sample and completed a questionnaire. Intestinal microbiota was analysed by amplicon sequencing of the 16S rRNA V4 gene region. Results: In total, 81 postmenopausal ER+/HER2- breast cancer patients and 67 postmenopausal controls were included, resulting in 148 faecal samples. Observed species richness, Shannon index, and overall microbial community structure were not significantly different between breast cancer patients and controls. There was a significant difference in overall microbial community structure between breast cancer patients scheduled for adjuvant treatment, neoadjuvant treatment, and controls at the phylum (p = 0.042) and genus levels (p = 0.015). Dialister (p = 0.001) and its corresponding family Veillonellaceae (p = 0.001) were higher in patients scheduled for adjuvant treatment, compared to patients scheduled for neoadjuvant treatment. Additional sensitivity analysis to correct for the potential confounding effect of prophylactic antibiotic use, indicated no differences in microbial community structure between patients scheduled for neoadjuvant systemic treatment, adjuvant systemic treatment, and controls at the phylum (p = 0.471) and genus levels (p = 0.124). Conclusions: Intestinal microbiota richness, diversity, and composition are not different between postmenopausal breast cancer patients and controls. The increased relative abundance of Dialister and Veillonellaceae was observed in breast cancer patients scheduled for adjuvant treatment, which might be caused by a relative decrease in other bacteria due to prophylactic antibiotic administration rather than an absolute increase.

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Ingestible Device for Gastric Fluid Sampling

Mandsberg,

Moro,

Ghavami

et al. 2024

Adv Materials Technologies

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The composition of the human gastrointestinal microbiota is linked to the health of the host, and interventions targeting intestinal microbes may thus be designed to prevent or mitigate disease. As the spatiotemporal structure and physiology impact the residing bacterial community, local sampling is gaining attention, with various ingestible sampling devices being developed to target specific sites. However, the stomach has received limited attention, despite its potential downstream influence. This work presents a simple ingestible device for gastric fluid sampling and outlines a series of characterizations to ensure device safety, reliability, and accuracy. In vitro testing determined seal effectiveness, mechanical integrity, biocompatibility, and device‐sample inertness. In situ and ex vivo testing confirmed sampling accuracy, demonstrated microbiome composition stability for at least 24 h, and differentiation of microbiota between two primates. 16S rRNA gene amplicon sequencing of samples from a porcine ingestion model showed that samples resembled post‐mortem gastric samples and differed from fecal and colonic samples. Also addressed in this study, is production scalability and shelf‐life to facilitate the safe and effective deployment of devices in clinical settings.

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microViz: an R package for microbiome data visualization and statistics

Cited by 203 publications

References 6 publications

Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

Intestinal Microbiota in Postmenopausal Breast Cancer Patients and Controls

Ingestible Device for Gastric Fluid Sampling

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