Genome- and Toxicology-Based Safety Assessment of Probiotic Akkermansia muciniphila ONE Isolated from Humans
Open accessAbstract
In this study, the genome of Akkermansia muciniphila ONE (designated AKK ONE) was sequenced, assembled, and analyzed. In addition, the safety of this strain was further evaluated by toxicological studies. The results showed that the AKK ONE genome is contained on a single chromosome with a total length of 2,817,524 bp and an average GC content of 55.48%. In total, 2411, 1131, 1168, 1745, and 1402 genes were annotated to the NR, GO, KEGG, COG, and SwissProt database, respectively. Potential resistance genes, adeF, tetW, ANT(3″)-IIa, and aadA1 were detected. AKK ONE was sensitive to ampicillin, ceftriaxone, cefotaxime, meropenem, tetracycline, and chloramphenicol and resistant to moxifloxacin. No potential virulence-related genes were detected. The PathogenFinder database analysis showed that AKK ONE was a non-potential human pathogen. This strain had good gastroenteric fluid tolerance and a weak ability to colonize the gut. No test item-related adverse effects were observed in the acute and subchronic toxicity test. AKK ONE did not display mutagenic activity either. This strain did not change the hematological and clinical biochemical parameters of mice. The weights of the organs were not affected by AKK ONE treatment. These results support that AKK ONE is safe for use as a probiotic at a dose of 8.28 × 109 CFU/kg bw/day.
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Genomic risk screening can be accelerated using AI algorithms such as DeepMicro, CARD, ResFinder, and machine-learning models identifying specific tRNAs that distinguish safe probiotics from dangerous intestinal pathogens.
“Thus, genomic risk screening can be accelerated through rapid identification using artificial intelligence (AI) algorithms (in particular, DeepMicro, which analyzes sequencing data at high speed to identify bacterial species and potential pathogens with greater speed and accuracy than cultivation-based methods); identification of ARG and virulence detection (for example, using a big data platform”
From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [165]
The Introduction describes genome-based safety assessment as fast, and Methods §2.3 reports using CARD and ResFinder to predict resistance genes. The paper does not describe DeepMicro, AI-accelerated screening, or machine-learning models that use specific tRNAs to distinguish probiotics from intestinal pathogens. It also cautions in the Introduction that genome-based safety assessment alone is not very reliable. (LLM, conf=0.88)
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Current Concepts in Probiotic Safety and Efficacy
Churin, A. A., Sokolyanskaya, L. O., Lukina, A. P., & Karnachuk, O. V. (2026) · Nutrients · doi:10.3390/nu18040696 · Cited by 31 · see citing works
“…genes and virulence factors at the genomic level); and prediction based on a machine learning model with the identification of specific tRNAs that distinguish safe probiotics against dangerous intestinal pathogens, which helps to carry out screening at an early stage [156,165,166].”
Lu, W., Zha, B., Lyu, J., LingHu, C., Chen, J., Deng, S., Zhang, X., Li, L., & Wang, G. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1500886 · Cited by 4 · see citing works
- Authors
- Lv, N., Wang, C., Zhou, H., Ma, X., Yu, X., & Ren, D.
- Affiliations
- Jilin Agricultural University (CN)
- East China University of Science and Technology (CN)
- Corresponding author
- Ren, Dayong
- Venue
- Foods
- Publisher
- MDPI AG
- Published
- 2024-06-24
- Volume
- 13
- Issue
- 13
- Pages
- 1979
- ISSN
- 2304-8158 (ISSN-L)
- PMC
- PMC11241434
- OpenAlex
- W4399977591
- Cited by
- 12
- References
- 35
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 4
- FWCI
- 2.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Foods (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Natural Science Foundation of China (32172189, 20200402068NC)
- key R&D project of Jilin Provincial Department of Science and Technology (32172189, 20200402068NC)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Agricultural and Biological Sciences › Food Science › Agricultural safety and regulations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- Akkermansia muciniphila, probiotic safety, antimicrobial resistance genes, antibiotic susceptibility, virulence genes, intestinal colonization, acute toxicity, subchronic toxicity, mutagenicity
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