SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Volant, Stevenn; Lechat, Pierre; Woringer, Perrine; Motreff, Laurence; Malabat, Christophe; Kennedy, Seán; Ghozlane, Amine

doi:10.21203/rs.2.23213/v1

Cited by 4 publications

(5 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After removing reads containing incorrect primer or barcode sequences and sequences with more than one ambiguous base, we recovered from 42 samples a total of 8.075.384 reads (192.271 reads on average). The bioinformatics analysis was performed as previously described (Volant et al, 2020). Briefly, amplicons were clustered into operational taxonomic units (OTU) with VSEARCH (v1.4) and aligned against the SILVA database.…”

Section: Star Methodsmentioning

confidence: 99%

Distinct systemic and mucosal immune responses to SARS-CoV-2

Smith

Gonçalves

Charbit

et al. 2021

Preprint

View full text Add to dashboard Cite

Coordinated local mucosal and systemic immune responses following SARS-CoV-2 infection protect against COVID-19 pathologies or fail leading to severe clinical outcomes. To understand this process, we performed an integrated analysis of SARS-CoV-2 spike-specific antibodies, cytokines, viral load and 16S bacterial communities in paired nasopharyngeal swabs and plasma samples from a cohort of clinically distinct COVID-19 patients during acute infection. Plasma viral load was associated with systemic inflammatory cytokines that were elevated in severe COVID-19, and also with spike-specific neutralizing antibodies. In contrast, nasopharyngeal viral load correlated with SARS-CoV-2 humoral responses but inversely with interferon responses, the latter associating with protective microbial communities. Potential pathogenic microrganisms, often implicated in secondary respiratory infections, were associated with mucosal inflammation and elevated in severe COVID-19. Our results demonstrate distinct tissue compartmentalization of SARS-CoV-2 immune responses and highlight a role for the nasopharyngeal microbiome in regulating local and systemic immunity that determines COVID-19 clinical outcomes.

show abstract

Section: Star Methodsmentioning

confidence: 99%

Distinct systemic and mucosal immune responses to SARS-CoV-2

Smith

Gonçalves

Charbit

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Using 16S rDNA MiSeq sequencing, we further characterized the microbiota composition of cecal samples pooled from chickens control and those that received 1 % SM at 15 and 21 days old. The SHAMAN pipeline ( Volant et al., 2020 ) was used to analyse amplicons from the microbial community. The samples consisted of 511,389 amplicons, with a median length of 403 bp.…”

Section: Resultsmentioning

confidence: 99%

“…Sequence processing and taxonomic assignments were performed using the SHAMAN pipeline ( Volant et al., 2020 ). 511,389 amplicons were recovered from the 16S rDNA region.…”

Section: Methodsmentioning

confidence: 99%

Stevia as a natural additive on gut health and cecal microbiota in broilers

Medeot,

Nilson,

Miazzo

et al. 2023

Veterinary and Animal Science

View full text Add to dashboard Cite

“…We used the shiny application for metagenomic analysis server (SHAMAN, [ 28 ]) for graphical visualizations, comparisons using Principal coordinate analysis, and differential abundance analysis (based on the DESeq2 package) [ 29 , 30 ]. Other figures were generated using in-house scripts with R. Heatmaps were generated using the pheatmap package (Version 1.0.12), Venn diagrams were produced using the VennDiagram package (Version 1.6.20) and intra-class correlation (ICC) analyses were performed using the psych package (Version 1.9.12.31).…”

Section: Methodsmentioning

confidence: 99%

The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota

2020

View full text Add to dashboard Cite

An increasing body of evidence highlights the role of fecal microbiota in various human diseases. However, more than two-thirds of fecal bacteria cannot be cultivated by routine laboratory techniques. Thus, physicians and scientists use DNA sequencing and statistical tools to identify associations between bacterial subgroup abundances and disease. However, discrepancies between studies weaken these results. In the present study, we focus on biases that might account for these discrepancies. First, three different DNA extraction methods (G’NOME, QIAGEN, and PROMEGA) were compared with regard to their efficiency, i.e., the quality and quantity of DNA recovered from feces of 10 healthy volunteers. Then, the impact of the DNA extraction method on the bacteria identification and quantification was evaluated using our published cohort of sample subjected to both 16S rRNA sequencing and whole metagenome sequencing (WMS). WMS taxonomical assignation employed the universal marker genes profiler mOTU-v2, which is considered the gold standard. The three standard pipelines for 16S RNA analysis (MALT and MEGAN6, QIIME1, and DADA2) were applied for comparison. Taken together, our results indicate that the G’NOME-based method was optimal in terms of quantity and quality of DNA extracts. 16S rRNA sequence-based identification of abundant bacteria genera showed acceptable congruence with WMS sequencing, with the DADA2 pipeline yielding the highest congruent levels. However, for low abundance genera (<0.5% of the total abundance) two pipelines and/or validation by quantitative polymerase chain reaction (qPCR) or WMS are required. Hence, 16S rRNA sequencing for bacteria identification and quantification in clinical and translational studies should be limited to diagnostic purposes in well-characterized and abundant genera. Additional techniques are warranted for low abundant genera, such as WMS, qPCR, or the use of two bio-informatics pipelines.

show abstract

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Cited by 4 publications

References 0 publications

Distinct systemic and mucosal immune responses to SARS-CoV-2

Distinct systemic and mucosal immune responses to SARS-CoV-2

Stevia as a natural additive on gut health and cecal microbiota in broilers

The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota

Contact Info

Product

Resources

About