Evidence map›Paper›PMID 39840975›Full record

ArticleApplied and environmental microbiology2025

Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.

Beilei Ge, Ryan C McDonald, Qianru Yang, Kelly J Domesle, Saul Sarria, Xin Li, Chih-Hao Hsu, Karen G Jarvis, Daniel A Tadesse

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Applied and environmental microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

9 authors.

Beilei GeOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.ORCID 0000-0001-7995-7427
Ryan C McDonaldOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Qianru YangOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Kelly J DomesleOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Saul SarriaOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Xin LiOffice of Surveillance and Compliance, Center for Veterinary Medicine, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
Chih-Hao HsuOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Karen G JarvisOffice of Applied Microbiology and Technology, U.S. Food and Drug Administration, Laurel, Maryland, USA.
Daniel A TadesseOffice of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood & Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing

Indexed as

Animal FeedBacteriaFood MicrobiologyMetagenomicsMicrobiotaAnimalsCattleDNA, BacterialDogsRNA, Ribosomal, 16SSequence Analysis, DNADNA, BacterialRNA, Ribosomal, 16S16S rRNA gene amplicon sequencinganimal foodDNA extractionmicrobiomemock communitypeptide nucleic acidresistomeshotgun metagenomics

Identifiers

PMID39840975
PMCPMC11837513

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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.