MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

Thang, Mike W.C.; Chua, Xin-Yi; Price, Gareth; Gorse, D.; Field, Matthew A.

doi:10.12688/f1000research.18866.2

Cited by 15 publications

(5 citation statements)

References 31 publications

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“…Of a total of 254 KEGG pathways, 40 pathways (16 for metabolism, 7 for genetic information processing, 3 for environmental information processing, and 8 for cellular processes) were selected for discrimination among the Pre, 2 wk, 8 wk, and Donor groups using the LEfSe (linear discriminant analysis effect size, LDA > 2.5) algorithm through the Huttenhower galaxy server. 37 Although significant hits were not confirmed in the pathways, the abundances of individual predicted metagenomes in the recipients shifted toward the compositions of the donors (Wilcoxon signed-rank test, p > 0.05, Figure 4A ). Additionally, while the proportion of oxidative phosphorylation was found to be low in the Pre group, the group was shown to contain a higher abundance of ntpG, ntpI, atpD, ntpB, ppaC and hydA genes (which belong to the oxidative phosphorylation pathway) than the other groups (Wilcoxon signed-rank test, p > 0.05, Figure 4B ).…”

Section: Resultsmentioning

confidence: 92%

Alterations and Prediction of Functional Profiles of Gut Microbiota After Fecal Microbiota Transplantation for Iranian Recurrent Clostridioides difficile Infection with Underlying Inflammatory Bowel Disease: A Pilot Study

Azimirad¹,

Jo²,

Kim³

et al. 2022

JIR

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Background and Purpose: Fecal microbiota transplantation (FMT) has emerged for the therapeutic treatment of recurrent Clostridioides difficile infection (rCDI) with concurrent inflammatory bowel disease (IBD). As the first Iranian population cohort, we examined how gut microbiota and their functional profiles change in Iranian rCDI patients with underlying IBD before and after FMT. Patients and Methods: FMT was performed to eight IBD patients via colonoscopy. Profiles of gut microbiota from donors and recipients were investigated using 16S rRNA gene sequence analysis. Results: Patients experienced no IBD flare-ups or other adverse effects, and all recovered to full health. Moreover, all rCDI patients lacked the Bacteroidetes present in donor samples. After FMT, the proportion of Bacteroidetes increased until a normal range was achieved. More specifically, the relative abundance of Prevotella was found to increase significantly following FMT. Prevotella was also found to correlate negatively with inflammation metrics, suggesting that Prevotella may be a key factor for resolving CDI and IBD. Gut microbiota diversity was found to increase following FMT, while dysbiosis decreased. However, the similarity of microbial communities of host and recipients did not increase, and wide variation in the extent of donor stool engraftment indicated that the gut bacterial communities of recipients do not shift towards those of donors. Conclusion: FMT leads to significant alterations of the community structure of gut bacteria in rCDI patients with IBD. The change in relative abundance of Proteobacteria and bacterial diversity indicated that FMT promotes recovery from intestinal permeability and inflammation in rCDI patients. Moreover, strong negative correlation between Prevotella and inflammation index, and decreased dysbiosis index advocate that the improvement of CDI is possibly due to gut microbiome alteration. Collectively, our findings show that FMT would be a promising therapy to help reprogram the gut microbiome of Iranian rCDI patients with IBD.

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Section: Resultsmentioning

confidence: 92%

Alterations and Prediction of Functional Profiles of Gut Microbiota After Fecal Microbiota Transplantation for Iranian Recurrent Clostridioides difficile Infection with Underlying Inflammatory Bowel Disease: A Pilot Study

Azimirad¹,

Jo²,

Kim³

et al. 2022

JIR

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“…Workflows hosted on Galaxy instances partially solve installation issues by providing a ready-to-use platform for performing analyses. Indeed, several Galaxy workflows that are used for different purposes have been published in the last decade [48][49][50][51], but only a few of them address bacterial pathogens [52] and cover their complete characterisation. Thus, workflows hosted on Sciensano Galaxy (https://galaxy.sciensano.be/ (accessed on 10 November 2022)) for the characterisation of Neisseria meningitidis, Shiga toxin-producing Escherichia coli and Mycobacterium tuberculosis were published [1,6,53].…”

Section: Discussionmentioning

confidence: 99%

A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data

et al. 2022

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The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogenetic clustering and sequence typing. Workflow was tested using a collection of 22 in-house sequences of Salmonella enterica isolates belonging to a local outbreak, coupled with a collection of 182 Salmonella genomes publicly available. No errors were reported during the execution period, and all genomes were analysed. The bioinformatics workflow can be tailored to other pathogens of interest and is freely available for academic and non-profit use as an uploadable file to the Galaxy platform.

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“…Microbiome differential analysis was performed using a modified version of MetaDE-Galaxy [38]. In short, raw reads were run through fastqc for quality control, Trimmomatic [39] for adapter trimming and low quality base removal, QIIME [40] for Operational Taxonomic Units (OTUs) generation, and BLAST [41] for OTU identification.…”

Section: Bioinformatics and Statistical Analysismentioning

confidence: 99%

Administration of Hookworm Excretory/Secretory Proteins Improves Glucose Tolerance in a Mouse Model of Type 2 Diabetes

et al. 2022

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Diabetes is recognised as the world’s fastest growing chronic condition globally. Helminth infections have been shown to be associated with a lower prevalence of type 2 diabetes (T2D), in part due to their ability to induce a type 2 immune response. Therefore, to understand the molecular mechanisms that underlie the development of T2D-induced insulin resistance, we treated mice fed on normal or diabetes-promoting diets with excretory/secretory products (ES) from the gastrointestinal helminth Nippostrongylus brasiliensis. We demonstrated that treatment with crude ES products from adult worms (AES) or infective third-stage larvae (L3ES) from N. brasiliensis improved glucose tolerance and attenuated body weight gain in mice fed on a high glycaemic index diet. N. brasiliensis ES administration to mice was associated with a type 2 immune response measured by increased eosinophils and IL-5 in peripheral tissues but not IL-4, and with a decrease in the level of IL-6 in adipose tissue and corresponding increase in IL-6 levels in the liver. Moreover, treatment with AES or L3ES was associated with significant changes in the community composition of the gut microbiota at the phylum and order levels. These data highlight a role for N. brasiliensis ES in modulating the immune response associated with T2D, and suggest that N. brasiliensis ES contain molecules with therapeutic potential for treating metabolic syndrome and T2D.

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MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

Cited by 15 publications

References 31 publications

Alterations and Prediction of Functional Profiles of Gut Microbiota After Fecal Microbiota Transplantation for Iranian Recurrent Clostridioides difficile Infection with Underlying Inflammatory Bowel Disease: A Pilot Study

Alterations and Prediction of Functional Profiles of Gut Microbiota After Fecal Microbiota Transplantation for Iranian Recurrent Clostridioides difficile Infection with Underlying Inflammatory Bowel Disease: A Pilot Study

A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data

Administration of Hookworm Excretory/Secretory Proteins Improves Glucose Tolerance in a Mouse Model of Type 2 Diabetes

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