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Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

https://doi.org/10.1371/journal.pone.0148347
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Centipeda periodontii in human periodontitis
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TWARIT: An extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences
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MetaSAMS—A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
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C16S — A Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences
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Butyric Acid Effects in the Development of Periodontitis and Systemic Diseases
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β‐lactamase producing bacteria in the subgingival microflora of adult patients with periodontitis. A comparison between Spain and The Netherlands
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Antimicrobial resistance with focus on oral beta‐lactamases
inferredcites →https://doi.org/10.1038/ismej.2011.191openalex-snapshot
Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing
inferredcites →https://doi.org/10.1038/nature09944openalex-snapshot
Enterotypes of the human gut microbiome
inferredcites →https://doi.org/10.1038/nature10187openalex-snapshot
Erratum: Enterotypes of the human gut microbiome
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Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq041openalex-snapshot
Identifying biologically relevant differences between metagenomic communities
inferredcites →https://doi.org/10.1093/bioinformatics/btq608openalex-snapshot
SPHINX—an algorithm for taxonomic binning of metagenomic sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btv287openalex-snapshot
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
inferredcites →https://doi.org/10.1093/dnares/dsu013openalex-snapshot
Multiple Omics Uncovers Host–Gut Microbial Mutualism During Prebiotic Fructooligosaccharide Supplementation
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The Ribosomal Database Project (RDP)
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KEGG: Kyoto Encyclopedia of Genes and Genomes
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KEGG: Kyoto Encyclopedia of Genes and Genomes
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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
inferredcites →https://doi.org/10.1093/nar/gkr1044openalex-snapshot
IMG: the integrated microbial genomes database and comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gks497openalex-snapshot
METAGENassist: a comprehensive web server for comparative metagenomics
inferredcites →https://doi.org/10.1093/nar/gkt1099openalex-snapshot
PATRIC, the bacterial bioinformatics database and analysis resource
inferredcites →https://doi.org/10.1099/00207713-33-3-628openalex-snapshot
Centipeda periodontii gen. nov., sp. nov. from Human Periodontal Lesions
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1111/1574-6941.12228openalex-snapshot
A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome
inferredcites →https://doi.org/10.1111/j.1600-0765.1984.tb01311.xopenalex-snapshot
Salivary concentrations of steroid hormones in males and in cycling and postmenopausal females with and without periodontitis
inferredcites →https://doi.org/10.1111/jre.12031openalex-snapshot
Prevalence of β‐lactamase‐producing bacteria in human periodontitis
inferredcites →https://doi.org/10.1111/jre.12137openalex-snapshot
Effect of non‐surgical periodontal treatment on short chain fatty acid levels in gingival crevicular fluid of patients with generalized aggressive periodontitis
inferredcites →https://doi.org/10.1126/science.1198719openalex-snapshot
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
inferredcites →https://doi.org/10.1186/1471-2164-12-s3-s4openalex-snapshot
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences
inferredcites →https://doi.org/10.1186/1471-2180-12-189openalex-snapshot
A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms
inferredcites →https://doi.org/10.1186/1471-2180-12-276openalex-snapshot
Complex sputum microbial composition in patients with pulmonary tuberculosis
inferredcites →https://doi.org/10.1186/2049-2618-1-31openalex-snapshot
Community differentiation of the cutaneous microbiota in psoriasis
inferredcites →https://doi.org/10.1186/2049-2618-2-18openalex-snapshot
The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term
inferredcites →https://doi.org/10.1186/2049-2618-2-29openalex-snapshot
Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis
inferredcites →https://doi.org/10.1371/journal.pone.0095547openalex-snapshot
Gut Microbiomes of Indian Children of Varying Nutritional Status
inferredcites →https://doi.org/10.29333/ejgm/82469openalex-snapshot
Oxidative Stress in Periodontitis
inferredcites →https://doi.org/10.4103/2278-0521.134855openalex-snapshot
Non surgical management of periodontitis related halitosis among adults

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The Rice Leaf Microbiome Has a Conserved Community Structure Controlled by Complex Host-Microbe Interactions
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Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils
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Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings
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Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut
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The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions
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Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
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Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential
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Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India
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A snapshot of gut microbiota of an adult urban population from Western region of India
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Lifestyle-Induced Microbial Gradients: An Indian Perspective
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Crosstalk Between Female Gonadal Hormones and Vaginal Microbiota Across Various Phases of Women’s Gynecological Lifecycle
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Investigating the Effect of Bacilli and Lactic Acid Bacteria on Water Quality, Growth, Survival, Immune Response, and Intestinal Microbiota of Cultured Litopenaeus vannamei
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Bacteria associated with periodontal disease are also increased in health
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Additional file 1 of Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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Additional file 3 of Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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Additional file 4 of Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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Additional file 6 of Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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Additional file 8 of Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
inferred← citeshttps://doi.org/10.6084/m9.figshare.14157805openalex-snapshot
Additional file 1 of Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India
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Additional file 2 of Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India
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