Evidence map›Paper›PMID 39497067›Full record

ArticleBMC genomics2024

Removal of sequencing adapter contamination improves microbial genome databases.

Andrew H Moeller, Brian A Dillard, Samantha L Goldman, Madalena V F Real, Daniel D Sprockett

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Andrew H MoellerDepartment of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08540, USA. andrew.moeller@princeton.edu.
Brian A DillardDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
Samantha L GoldmanDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
Madalena V F RealDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
Daniel D SprockettDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.

Funding

Uncovering the modes and genetics of gut bacterial transmissionR35GM138284 · NIGMS · PRINCETON UNIVERSITY · PI Andrew Moeller · 2020 to 2026
$2.4M
Host-Microbe Interactions that Determine Host Traits and DiseaseT32AI145821 · NIAID · CORNELL UNIVERSITY · PI LAZZARO, BRIAN · 2020 to 2024
$1.9M
The genomics and consequences of gut bacterial adaptation to high-fat dietsR01DK139214 · NIDDK · PRINCETON UNIVERSITY · PI Andrew Moeller · 2024 to 2026
$1.3M
NIAID NIH HHS T32 AI145821NIDDK NIH HHS R01 DK139214NIGMS NIH HHS R35 GM138284
6 · The paper itself

Abstract

Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.

Indexed as

Databases, GeneticAnimalsCattleDNA ContaminationGenome, MicrobialHigh-Throughput Nucleotide SequencingHumansMiceSequence Analysis, DNASwineBacterial genomesMetagenomeMicrobial ecologyMicrobiotaSymbiosis

Identifiers

PMID39497067
PMCPMC11536531

What OpenQuestion holds

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Registered trials

None linked

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.