Evidence map›Paper›PMID 41068119›Full record

ArticleNPJ biofilms and microbiomes2025

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.

Shuang Liu, Bo Feng, Zhenyang Zhang, Jian Miao, Xueshuang Lai, Wei Zhao, Qinqin Xie, Xiaowei Ye, Caiyun Cao, Pengfei Yu and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NPJ biofilms and microbiomes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Strengths and limitations ofGut microbes reports · 2026
    Review
  4. 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

16 authors.

Shuang Liu *Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Bo Feng *Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Zhenyang ZhangDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Jian MiaoDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Xueshuang LaiDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Wei ZhaoDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Qinqin XieDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Xiaowei YeDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Caiyun CaoDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Pengfei YuDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Jiabao SunDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Jianwei GuoDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Zhen WangDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Qishan WangDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Zhe ZhangDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China. zhe_zhang@zju.edu.cn.
Yuchun PanDepartment of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China. panyc@zju.edu.cn.

Funding

National Key Research and Development Program of China 2021YFD1200802,2023YFF1001100National Natural Science Foundation of China 32272832Zhejiang Provincial Natural Science Foundation of China LZ23C170003
6 · The paper itself

Abstract

The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.

Indexed as

ArchaeaBacteriaGastrointestinal MicrobiomeGenome, BacterialAnimalsInterspersed Repetitive SequencesMetagenomeMetagenomicsPhylogenySwine

Identifiers

PMID41068119
PMCPMC12511339

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.