ReviewGenome biology and evolution2019
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.
Review in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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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.
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Who cites it
47 citing papers in PubMed, 79 citations in OpenAlex.
- A Metagenome-Based Methodology to Track Genomically Recoded Strains and Assess Their Effects on Indigenous Microbes.Environmental science & technology · 2026Article
- Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.Antibiotics (Basel, Switzerland) · 2026Review
- Identification and characteristics of a novel fosfomycin glutathione transferase, FosA12, from an MDR clinical isolate ofAntimicrobial agents and chemotherapy · 2026Article
- Association of Human Gut Microbiota with Alzheimer's Disease Pathogenesis: An Exploratory Clinical Study.Brain sciences · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.bioRxiv : the preprint server for biology · 2025Article
- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- The Environmental Lifecycle of Antibiotics and Resistance Genes: Transmission Mechanisms, Challenges, and Control Strategies.Microorganisms · 2025Review
- Genomic Insights intoInternational journal of molecular sciences · 2025Article
- Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.NPJ biofilms and microbiomes · 2025Article
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.Environmental microbiology · 2025Article
- Article
- Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms.The ISME journal · 2025Article
- Profiling lateral gene transfer events in the human microbiome using WAAFLE.Nature microbiology · 2025Article
- Article
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
- On the impact of incomplete taxon sampling on the relative timing of gene transfer events.PLoS biology · 2024Article
- Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.Microbiome · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
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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.