ReviewSystematic biology2015
Phylogenetics and the human microbiome.
Review in Systematic biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- The Relationship between Exposome and Microbiome.Microorganisms · 2024Review
- Analyzing microbial evolution through gene and genome phylogenies.Biostatistics (Oxford, England) · 2024Article
- A link between evolution and society fostering the UN sustainable development goals.Evolutionary applications · 2024Article
- DEPP: Deep Learning Enables Extending Species Trees using Single Genes.Systematic biology · 2023Article
- Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study.Frontiers in microbiology · 2021Article
- Captivity affects diversity, abundance, and functional pathways of gut microbiota in the northern grass lizard Takydromus septentrionalis.MicrobiologyOpen · 2020Article
- Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.Molecular ecology · 2020Article
- TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.Bioinformatics (Oxford, England) · 2019Article
- Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.PloS one · 2019Article
- Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions.Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract · 2018Review
- Article
- Rearing Room Affects the Non-dominant Chicken Cecum Microbiota, While Diet Affects the Dominant Microbiota.Frontiers in veterinary science · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.