Evidence map›Paper›PMID 37855606›Full record

ArticlemSystems2023

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.

Kellie A Heom, Chatarin Wangsanuwat, Lazarina V Butkovich, Scott C Tam, Annette R Rowe, Michelle A O'Malley, Siddharth S Dey

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in mSystems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 43% of its field
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

3 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
  3. The cancer microbiome.Advances in clinical chemistry · 2025
    Review
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

7 authors at 2 institutions in 1 country.

Kellie A Heom *Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.ORCID 0009-0004-4962-9886
Chatarin Wangsanuwat *Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Lazarina V ButkovichDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Scott C TamDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
Annette R RoweBiological Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Michelle A O'MalleyDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.ORCID 0000-0002-6065-8491
Siddharth S DeyDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.
University of California, Santa Barbara · USUniversity of Cincinnati · US

Funding

A marker-free technology for mapping the epigenome of cell types in mammalian tissuesR01HG011013 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2020 to 2024
$1.8M
Understanding DNA methylation reprogramming dynamics during preimplantation development using single-cell sequencingR01HD099517 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2019 to 2023
$1.4M
NHGRI NIH HHS R01 HG011013NICHD NIH HHS R01 HD099517
6 · The paper itself

Abstract

importanceMicrobes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.

Indexed as

BacteriaRNA, RibosomalCoculture TechniquesRNA, MessengerTranscriptomeRNA, MessengerRNA, Ribosomalbacterial mRNA sequencingfungal and bacterial co-cultureslignocellulose deconstructionnon-model microbial sequencingrRNA depletion

Identifiers

PMID37855606
PMCPMC10734481
OpenAlexW4387764615

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.