Evidence map›Paper›PMID 31672156›Full record

ArticleGenome biology2019

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

Jon G Sanders, Sergey Nurk, Rodolfo A Salido, Jeremiah Minich, Zhenjiang Z Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D Arthur, Feng Chen and 21 more

Registry-linked trialAbstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06513026 (Milk for Diabetes Prevention), which is not on this map. Cited by 55 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
55citing papers in PubMed, 1 pooled it
–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.

NCT06513026 narecruitingnot on this mapstarted 2026, after this paper: background citation

Milk for Diabetes Prevention

TypeinterventionalSponsorAlbert Einstein College of MedicineRan2026 to 2028Enrolled40ConditionsLactose Intolerance, Lactose Intolerant, Lactase Persistence, Pre-DiabetesArmsLactose-Containing Milk, Lactose-Free Milk
3 · Its place in the literature

Who cites it

55 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  16. Environmental and Maternal Imprints on Infant Gut Metabolic Programming.bioRxiv : the preprint server for biology · 2025
    Article
  17. Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025
    Article
  18. Article
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  20. The microbiome diversifiesbioRxiv : the preprint server for biology · 2024
    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

31 authors.

Jon G SandersDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Sergey NurkCenter for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
Rodolfo A SalidoDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Jeremiah MinichDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Zhenjiang Z XuDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Qiyun ZhuDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Cameron MartinoDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Marcus FedarkoDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Timothy D ArthurDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Feng ChenIllumina, Inc., La Jolla, CA, USA.
Brigid S BolandDivision of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Greg C HumphreyDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Caitriona BrennanDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Karenina SandersDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
James GaffneyDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Kristen JepsenInstitute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
Mahdieh KhosroheidariInstitute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
Cliff GreenInstitute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
Marlon LiyanageDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Jason W DangDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Vanessa V PhelanSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Robert A QuinnSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Anton BankevichCenter for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
John T ChangDivision of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Tariq M RanaDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Douglas J ConradDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
William J SandbornDivision of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Larry SmarrDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Pieter C DorresteinDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
Pavel A PevznerDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA. robknight@ucsd.edu.ORCID 0000-0002-0975-9019

Funding

GRADUATE TRAINING PROGRAM IN BIONFORMATICST32GM008806 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, REN, BING · 2001 to 2020
$6.2M
Modeling HIV/AIDS Associated Neurological Disorders with Human Pluripotent CellsDP1DA039562 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RANA, TARIQ M · 2015 to 2020
$3.9M
Identification and Regulation of RNA Modification by HIV infection and MethamphetamineR01DA046171 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RANA, TARIQ M · 2018 to 2022
$3.1M
NIDA NIH HHS DA039562NIDA NIH HHS DA046171NIDA NIH HHS DP1 DA039562NIDA NIH HHS R01 DA046171NIGMS NIH HHS T32 GM008806NIH HHS T32GM8806
6 · The paper itself

Abstract

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.

Indexed as

Genomic LibraryHigh-Throughput Nucleotide SequencingAnimalsBenchmarkingGastrointestinal MicrobiomeHumansMetagenomicsMiceAssemblyBenchmarkBinningLeaderboard metagenomeLong reads

Identifiers

PMID31672156
PMCPMC6822431

What OpenQuestion holds

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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.