The human microbiome: A hot spot of microbial horizontal gene transfer
Open accessAbstract
The human body harbors numerous microbes, and here exists a close relationship between microbes and human health. The Human Microbiome Project has generated whole genome sequences of several hundred human microbes. In this study, we identified horizontal gene transfer (HGT) events in human microbes and tried to elucidate the relationships between the gene-transferring microbes. A total of 13,514 high confidence HGT genes were identified in 308 human microbes. The horizontally transferred genes were enriched for Gene Ontology terms pertaining to catalytic functions and metabolic processes. Construction of an HGT event network suggested that the human microbes could be divided into specific communities which only partly overlap their distribution in human body. Our research suggests that human microbiome may facilitate frequent horizontal gene transfer among bacteria in human body. Awareness of HGT in human microbiome may aid our understanding of the relationship between the human microbiome and human health.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Given the widespread consumption of probiotic products and starter cultures together with fermented foods by humans and their interaction with the resident gut microbiota, there is a heightened risk of ARG transmission.
“Given the widespread consumption of probiotic products and starter cultures together with fermented foods by humans and their interaction with the resident gut microbiota, there is a heightened risk of ARG transmission (L. Liu et al., 2012).”
From Exploring the resistome of probiotics, starter cultures, and cheeses via metagenomic analysis (2025) · cites this paper as L. Liu et al., 2012
Section 2.4 says bacteria can acquire antibiotic resistance through horizontal gene transfer. But section 2.2 does not address probiotics, starter cultures, or fermented foods; it says microorganisms entering with the diet have less opportunity to transfer genes to resident gut microbes than resident microbes have to transfer genes among themselves. The paper therefore does not establish the claimed heightened risk from consuming those products. Page numbers are unavailable in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 49 · Cited by 131
- Authors
- Liu, L., Chen, X., Skogerbø, G., Zhang, P., Chen, R., He, S., & Huang, D.-W.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Chen, Runsheng
- He, Shunmin
- Huang, Da-Wei
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2012-11
- Volume
- 100
- Issue
- 5
- Pages
- 265-270
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W1991402127
- Semantic Scholar
- d007991cf69856cdeb613978eb23b42c79b05e4f
- Cited by
- 131
- References
- 49
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 7 · 2023: 11 · 2022: 14 · 2021: 20 · 2020: 11 · 2019: 12 · 2018: 7 · 2017: 13 · 2016: 7 · 2015: 3 · 2014: 5 · 2013: 5 · 2012: 1
- FWCI
- 1.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Genomics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Chinese Academy of Science Knowledge Innovation Project (KSCX2-EW-R-01-02)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- horizontal gene transfer, human microbiome, human-associated bacteria, microbial community structure, Human Microbiome Project, metabolic genes
- MeSH terms
- Genes, Bacterial, Humans, Computational Biology, Gene Transfer, Horizontal, Genomics, Metagenome, Biota, Molecular Sequence Annotation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
