Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
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Summary
Genes that are associated with overall gut prevalence, with a preference for the gut over other body sites, and with the gut in Crohn’s disease versus health are found, and many of these findings have biological plausibility based on existing literature.
- Type
- preprint
- Published
- 2017-09-16
- Cited by
- 33
- References
- 106
- Access
- Open access
- OpenAlex
- https://openalex.org/W2755485784
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:51954690
Keywords
Biology, Microbiome, Phylogenetic tree, Phylogenetics, Firmicutes
References
- Recurrent Clostridium difficile infection.
- Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data
- Structure, Function and Diversity of the Healthy Human Microbiome
- Regulatory and functional co‐operation of flagella and type 1 pili in adhesive and invasive abilities of AIEC strain LF82 isolated from a patient with Crohn's disease
- Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test.
- phytools: an R package for phylogenetic comparative biology (and other things)
- No Vacancy: How beneficial microbes cooperate with immunity to provide colonization resistance to pathogens
- Proteobacteria: microbial signature of dysbiosis in gut microbiota.
- fitdistrplus: An R Package for Fitting Distributions
- Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides
- Statistical significance for genomewide studies
- FIGfams: yet another set of protein families
- Clostridium difficile-associated enteric disease
- The Bayesian Lasso
- Patterns of Gene Flow Define Species of Thermophilic Archaea
- PATRIC, the bacterial bioinformatics database and analysis resource
- Persistent infection with Crohn’s disease-associated adherent-invasive Escherichia coli leads to chronic inflammation and intestinal fibrosis
- Generalized linear mixed models for phylogenetic analyses of community structure
- Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Cited by
- Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
- Methods for phylogenetic analysis of microbiome data
- The Glutaminase-Dependent Acid Resistance System: Qualitative and Quantitative Assays and Analysis of Its Distribution in Enteric Bacteria
- Computational Structural Biology: Successes, Future Directions, and Challenges
- New insights from uncultivated genomes of the global human gut microbiome
- phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
- Drug resistant gut bacteria mimic a host mechanism for anticancer drug clearance
- Population Genetics in the Human Microbiome.
- The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health
- Correlation and association analyses in microbiome study integrating multiomics in health and disease.
- Tree-aggregated predictive modeling of microbiome data
- phylogenize: a web tool to identify microbial genes underlying environment associations
- The assessment of leading traits in the taxonomy of the Bacillus cereus group
- Mechanisms underlying gut microbiota–host interactions in insects
- Horizontal gene transfer and adaptive evolution in bacteria
- Parallel Expansion and Divergence of an Adhesin Family in Pathogenic Yeasts Including Candida auris
- Strain identification and quantitative analysis in microbial communities.
- A primer and discussion on DNA-based microbiome data and related bioinformatics analyses
- Targeting microbiota in dietary obesity management: a systematic review on randomized control trials in adults
- Integrating phylogenetic and functional data in microbiome studies
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