DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences

Bağcı, Caner; Patz, Sascha; Huson, Daniel H.

doi:10.1002/cpz1.59

Cited by 85 publications

(57 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genes with KEGG annotation were assigned into KEGG pathways. For taxonomic assignment we used the Diamond software [ 51 ]. Then, based on gene abundance, PCA, PCOA, and PLS-DA analysis were performed by our internal scripts.…”

Section: Methodsmentioning

confidence: 99%

The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors

et al. 2021

View full text Add to dashboard Cite

Background Anxiety and depression are complications in Irritable bowel syndrome (IBS) patients. In this study, we recruited 18 IBS patients with mild-modest anxiety and depression behaviors, and after the screening, we defined the FMT treatment group (n = 9) and the control group (n = 9). The IBS symptom severity scale (IBS-SSS), Hamilton Anxiety Rating Scale (HAM-A), Hamilton Depression Rating Scale (HAM-D), Irritable Bowel Syndrome Quality of Life (IBS-QOL) and Bristol stool scale (BSS) were evaluated one week before FMT (baseline), one-week-, one-month-, two-month-, and three-month-following FMT. Meanwhile, we determined the SCFAs in the patient’s feces and serum and continued the metagenomic analysis of the microorganisms in the patient’s feces. Results The results showed that the patient’s anxiety and depression behavior gradually improved with FMT treatment. Moreover, the illness and quality of life had also been relieved significantly. The content of isovaleric acid and valeric acid was significantly reduced in the FMT group compared to the Col group. Metagenomic analysis showed that FMT treatment decreased the abundance of Faecalibacterium, Eubacterium and Escherichia. From KEGG functional analysis, we confirmed that the top five abundant pathways were “bacterial chemotaxis, “flagellar assembly”, “glycine, serine and threonine metabolism”, “apoptosis”, and “bacterial invasion of epithelial cells”. Conclusions FMT treatment can effectively alleviate the anxiety and depression behaviors of IBS-D patients and reduce the IBS-SSS score, indicating that FMT can improve patients’ symptoms. The high throughput sequencing results show that Bifidobacterium and Escherichia play the most critical role in the formation and recovery of IBS-D patients. The GC/MS data indicated that faeces isovaleric acid and valeric acid might be more suitable as a metabolic indicator of IBS-D remission. Trial registration ChiCTR, ChiCTR1900024924, Registered 3 August 2019, https://www.chictr.org.cn/showproj.aspx?proj=41676.

show abstract

Section: Methodsmentioning

confidence: 99%

The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors

et al. 2021

View full text Add to dashboard Cite

show abstract

“…As with the previous command, collect all the input files you want to analyze in a folder. This protocol is suitable for estimating the quality of metagenomic bins or "metagenomeassembled genomes" (MAGs) of unknown taxonomic origin, e.g., obtained from binner programs such as MetaBat (Kang et al, 2019), MaxBin2 (Wu & Singer, 2021), and MEGAN (Bagcı, Patz, & Huson, 2021;Huson et al, 2018). In such cases, the input file is a folder containing one FASTA file per bin.…”

Section: Running Busco On Multiple Inputs Without Specifying a Lineage Datasetmentioning

confidence: 99%

BUSCO: Assessing Genomic Data Quality and Beyond

et al. 2021

View full text Add to dashboard Cite

Evaluation of the quality of genomic “data products” such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single‐copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome‐assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto‐lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO “plugin” workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto‐lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees

show abstract

“…The resulting alignment files are then "meganized" or analyzed using MEGAN (16) so as to perform taxonomic and functional binning. A detailed protocol of this simple two-step pipeline is presented in (17).…”

Section: Introductionmentioning

confidence: 99%

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis

Gautam

Felderhoff

Bağcı

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

In microbiome analysis, one main approach is to align metagenomic sequencing reads against a protein-reference database such as NCBI-nr, and then to perform taxonomic and functional binning based on the alignments. This approach is embodied, for example, in the standard DIAMOND+MEGAN analysis pipeline, which first aligns reads against NCBI-nr using DIAMOND and then performs taxonomic and functional binning using MEGAN. Here we propose the use of the AnnoTree protein database, rather than NCBI-nr, in such alignment-based analyses to determine the prokaryotic content of metagenomic samples. We demonstrate a 2-fold speedup over the usage of the prokaryotic part of NCBI-nr, and increased assignment rates, in particular, assigning twice as many reads to KEGG. In addition to binning to the NCBI taxonomy, MEGAN now also bins to the GTDB taxonomy.IMPORTANCEThe NCBI-nr database is not explicitly designed for the purpose of microbiome analysis and its increasing size makes its unwieldy and computationally expensive for this purpose. The AnnoTree protein database is only one quarter the size of the full NCBI-nr database and is explicitly designed for metagenomic analysis, and so should be supported by alignment-based pipelines.

show abstract

DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences

Cited by 85 publications

References 60 publications

The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors

The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors

BUSCO: Assessing Genomic Data Quality and Beyond

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis

Contact Info

Product

Resources

About