ArticleScientific reports2018
Impact of sequencing depth on the characterization of the microbiome and resistome.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
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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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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
120 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.Heart failure reviews · 2022Pooled it
- Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.Environmental health perspectives · 2026Trial
- Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles.NPJ biofilms and microbiomes · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Gut Microbiome Dysbiosis in Metabolic Syndrome: Current Evidence and Emerging Perspectives.Nutrients · 2026Review
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.Animal microbiome · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting.The ISME journal · 2026Article
- Impact of reducing metagenomic sequencing depth on phenotypic prediction accuracy of feed intake and average daily gain in beef cattle.Journal of animal science · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Microbial community characterization in semi-hydroponic systems of Starbor kale (Current research in microbial sciences · 2026Article
- Different DNA input amounts and library preparation kits yield comparable resistome characterization using target-enriched metagenomic sequencing.Frontiers in microbiology · 2026Article
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Impact of Organic and Conventional Husbandry Systems on the Gut Microbiome and Resistome in Pigs.Microorganisms · 2025Article
- Can Metagenomic Analyses Be Used Effectively in Safe Food Production?Food science & nutrition · 2025Review
- Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.Microbiology (Reading, England) · 2025Article
- Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.World journal of cardiology · 2025Review
60 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.
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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.