Evidence map›Paper›PMID 39021442›Full record

ArticleISME communications2024

scMicrobe PTA: near complete genomes from single bacterial cells.

Robert M Bowers, Veronica Gonzalez-Pena, Kartika Wardhani, Danielle Goudeau, Matthew James Blow, Daniel Udwary, David Klein, Albert C Vill, Ilana L Brito, Tanja Woyke and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in ISME communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. A genomic view of Earth's biomes.Nature reviews. Genetics · 2026
    Review
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Robert M BowersDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Veronica Gonzalez-PenaDepartment of Pediatrics, Stanford University, Stanford, CA, United States.
Kartika WardhaniDepartment of Pediatrics, Stanford University, Stanford, CA, United States.
Danielle GoudeauDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Matthew James BlowDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Daniel UdwaryDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
David KleinDepartment of Pediatrics, Stanford University, Stanford, CA, United States.
Albert C VillChan Zuckerberg Biohub, San Francisco, CA, United States.
Ilana L BritoChan Zuckerberg Biohub, San Francisco, CA, United States.
Tanja WoykeDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Rex R MalmstromDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Charles GawadDepartment of Pediatrics, Stanford University, Stanford, CA, United States.

Funding

Creating a Catalog of Cancer Clonotype Drug Sensitivities with Single-CellGenome SequencingDP2CA239145 · NCI · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI GAWAD, CHARLES · 2018 to 2018
$2.3M
NCI NIH HHS DP2 CA239145
6 · The paper itself

Abstract

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

Indexed as

biosynthetic gene clustersmicrobial ecologymicrobiomemicrobiome sequencingmobile genetic elementsmultiple displacement amplificationprimary template-directed amplificationsingle cell genomicsunculturable bacteriawhole genome amplification

Identifiers

PMID39021442
PMCPMC11253033

What OpenQuestion holds

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Registered trials

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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.