Evidence map›Paper›PMID 39982577›Full record

ArticleMolecular biology reports2025

ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias.

Shrikant Bhute, Jon G Sanders, Se Jin Song, Sydney Lavoie, Austin Swafford, Caitlin Guccione, Lucas Patel, Antonio Gonzalez, Michelle G Rooks, Rob Knight and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular biology reports, 2025. 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
–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

3 citing papers in PubMed.

  1. Article
  2. Review
  3. 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

11 authors.

Shrikant BhuteCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA.
Jon G SandersCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA.
Se Jin SongCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA.
Sydney LavoiePfizer Research and Development, Cambridge, MA, USA.
Austin SwaffordCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA.
Caitlin GuccioneDepartment of Pediatrics, University of California San Diego, La Jolla, San Diego, CA, USA.
Lucas PatelDepartment of Pediatrics, University of California San Diego, La Jolla, San Diego, CA, USA.
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, San Diego, CA, USA.
Michelle G RooksPfizer Research and Development, Cambridge, MA, USA.
Rob KnightCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA.
Andrew BartkoCenter for Microbiome Innovation, University of California San Diego, La Jolla, San Diego, CA, USA. abartko@ucsd.edu.

Funding

MEDICAL SCIENTIST TRAINING PROGRAMT32GM007198 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHI, NEIL C, INSEL, PAUL A · 1985 to 2024
$29.3M
NIGMS NIH HHS T32 GM007198University of California San Diego Medical Scientist Training Program NIH/NIGMS T32GM007198
6 · The paper itself

Abstract

backgroundHost DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies.

resultsWe find that all methods that rely on differential lysis of host and microbial cells introduce substantial biases as assessed by 16 S rRNA gene amplicon profiling. However, ChIP enables 10-fold enrichment of microbial DNA while introducing less bias, sufficient to make assessment possible against background, in both pigs and humans.

conclusionsWe recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.

conclusionsWe recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.

Indexed as

Chromatin ImmunoprecipitationDNA, BacterialAnimalsGastrointestinal MicrobiomeHumansMicrobiotaRNA, Ribosomal, 16SSwineDNA, BacterialRNA, Ribosomal, 16SChromatin immunoprecipitationFrozen tissueHost depletionMicrobiome

Identifiers

PMID39982577
PMCPMC11845529

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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.