Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments Article Swipe
Jingqiu Liao
,
Xiaodong Guo
,
Shaoting Li
,
Sai Manohar Balu Anupoju
,
Rachel A. Cheng
,
Daniel L. Weller
,
Genevieve Sullivan
,
Hailong Zhang
,
Xiangyu Deng
,
Martin Wiedmann
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s43705-023-00293-x
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s43705-023-00293-x
Comprehending bacterial genomic variation linked to distinct environments can yield novel insights into mechanisms underlying differential adaptation and transmission of microbes across environments. Gaining such insights is particularly crucial for pathogens as it benefits public health surveillance. However, the understanding of bacterial genomic variation is limited by a scarcity of investigations in genomic variation coupled with different ecological contexts. To address this limitation, we focused on Listeria, an important bacterial genus for food safety that includes the human pathogen L. monocytogenes, and analyzed a large-scale genomic dataset collected by us from natural and food-associated environments across the United States. Through comparative genomics analyses on 449 isolates from the soil and 390 isolates from agricultural water and produce processing facilities representing L. monocytogenes, L. seeligeri, L. innocua, and L. welshimeri, we find that the genomic profiles strongly differ by environments within each species. This is supported by the environment-associated subclades and differential presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. Core genomes of Listeria species are also strongly associated with environments and can accurately predict isolation sources at the lineage level in L. monocytogenes using machine learning. We find that the large environment-associated genomic variation in Listeria appears to be jointly driven by soil property, climate, land use, and accompanying bacterial species, chiefly representing Actinobacteria and Proteobacteria. Collectively, our data suggest that populations of Listeria species have genetically adapted to different environments, which may limit their transmission from natural to food-associated environments.
Related Topics
Concepts
Biology
Genomics
Comparative genomics
Genome
Listeria
Domestication
Metagenomics
Evolutionary biology
Listeria monocytogenes
Actinobacteria
Genetics
Bacterial genome size
Gene
Bacteria
16S ribosomal RNA
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s43705-023-00293-x
- https://www.nature.com/articles/s43705-023-00293-x.pdf
- OA Status
- gold
- Cited By
- 17
- References
- 63
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4385999809
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4385999809Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s43705-023-00293-xDigital Object Identifier
- Title
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Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environmentsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
-
2023-08-19Full publication date if available
- Authors
-
Jingqiu Liao, Xiaodong Guo, Shaoting Li, Sai Manohar Balu Anupoju, Rachel A. Cheng, Daniel L. Weller, Genevieve Sullivan, Hailong Zhang, Xiangyu Deng, Martin WiedmannList of authors in order
- Landing page
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https://doi.org/10.1038/s43705-023-00293-xPublisher landing page
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https://www.nature.com/articles/s43705-023-00293-x.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.nature.com/articles/s43705-023-00293-x.pdfDirect OA link when available
- Concepts
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Biology, Genomics, Comparative genomics, Genome, Listeria, Domestication, Metagenomics, Evolutionary biology, Listeria monocytogenes, Actinobacteria, Genetics, Bacterial genome size, Gene, Bacteria, 16S ribosomal RNATop concepts (fields/topics) attached by OpenAlex
- Cited by
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17Total citation count in OpenAlex
- Citations by year (recent)
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2025: 10, 2024: 6, 2023: 1Per-year citation counts (last 5 years)
- References (count)
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63Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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