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CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.

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Title: CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.
Authors: Avershina E; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway., Birkeland EE; Department of Pharmacy, University of Oslo, Oslo, Norway., Bucher-Johannessen C; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway., Rounge TB; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway.; Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
Source: Gut microbes [Gut Microbes] 2026 Dec 31; Vol. 18 (1), pp. 2734649. Date of Electronic Publication: 2026 Sep 21.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Taylor & Francis Country of Publication: United States NLM ID: 101495343 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1949-0984 (Electronic) Linking ISSN: 19490976 NLM ISO Abbreviation: Gut Microbes Subsets: MEDLINE
Imprint Name(s): Publication: 2015- : Philadelphia, PA : Taylor & Francis
Original Publication: Austin, Tex. : Landes Bioscience
MeSH Terms: Bacteria*/genetics , Bacteria*/classification , Bacteria*/immunology , Bacteria*/isolation & purification , Bacteria*/virology , Gastrointestinal Microbiome*/genetics , Interspersed Repetitive Sequences* , CRISPR-Cas Systems*, Plasmids/genetics ; Feces/microbiology ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; Humans ; Middle Aged ; Metagenome ; Norway ; Female ; Diet
Abstract: Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.
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Contributed Indexing: Keywords: CRISPR spacer; CRISPR-Cas; Gut microbiome; gut mobilome; mobile genetic elements; plasmid; virus
Entry Date(s): Date Created: 20260922 Date Completed: 20260922 Latest Revision: 20260924
Update Code: 20260924
PubMed Central ID: PMC13596890
DOI: 10.1080/19490976.2026.2734649
PMID: 42768305
Database: MEDLINE
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  Data: CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.
– Name: Author
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  Data: <searchLink fieldCode="AU" term="%22Avershina+E%22">Avershina E</searchLink>; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway.<br /><searchLink fieldCode="AU" term="%22Birkeland+EE%22">Birkeland EE</searchLink>; Department of Pharmacy, University of Oslo, Oslo, Norway.<br /><searchLink fieldCode="AU" term="%22Bucher-Johannessen+C%22">Bucher-Johannessen C</searchLink>; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway.<br /><searchLink fieldCode="AU" term="%22Rounge+TB%22">Rounge TB</searchLink>; Department of Pharmacy, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Oslo University Hospital, Oslo, Norway.; Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
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  Data: <searchLink fieldCode="JN" term="%22101495343%22">Gut microbes</searchLink> [Gut Microbes] 2026 Dec 31; Vol. 18 (1), pp. 2734649. <i>Date of Electronic Publication: </i>2026 Sep 21.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Taylor+%26+Francis%22">Taylor & Francis </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101495343 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1949-0984 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2219490976%22">19490976 </searchLink><i>NLM ISO Abbreviation: </i>Gut Microbes <i>Subsets: </i>MEDLINE
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  Data: <i>Publication</i>: 2015- : Philadelphia, PA : Taylor & Francis<br /><i>Original Publication</i>: Austin, Tex. : Landes Bioscience
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  Data: <searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+immunology%22">immunology</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+virology%22">virology</searchLink> <br /><searchLink fieldCode="MM" term="%22Gastrointestinal+Microbiome%22">Gastrointestinal Microbiome*</searchLink>/<searchLink fieldCode="MM" term="%22Gastrointestinal+Microbiome+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Interspersed+Repetitive+Sequences%22">Interspersed Repetitive Sequences*</searchLink> <br /><searchLink fieldCode="MM" term="%22CRISPR-Cas+Systems%22">CRISPR-Cas Systems*</searchLink><br /><searchLink fieldCode="MH" term="%22Plasmids%22">Plasmids</searchLink>/<searchLink fieldCode="MH" term="%22Plasmids+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Feces%22">Feces</searchLink>/<searchLink fieldCode="MH" term="%22Feces+microbiology%22">microbiology</searchLink> ; <searchLink fieldCode="MH" term="%22Bacteriophages%22">Bacteriophages</searchLink>/<searchLink fieldCode="MH" term="%22Bacteriophages+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Gastrointestinal+Tract%22">Gastrointestinal Tract</searchLink>/<searchLink fieldCode="MH" term="%22Gastrointestinal+Tract+microbiology%22">microbiology</searchLink> ; <searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22Middle+Aged%22">Middle Aged</searchLink> ; <searchLink fieldCode="MH" term="%22Metagenome%22">Metagenome</searchLink> ; <searchLink fieldCode="MH" term="%22Norway%22">Norway</searchLink> ; <searchLink fieldCode="MH" term="%22Female%22">Female</searchLink> ; <searchLink fieldCode="MH" term="%22Diet%22">Diet</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: <i>Keywords: </i>CRISPR spacer; CRISPR-Cas; Gut microbiome; gut mobilome; mobile genetic elements; plasmid; virus
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  Data: <i>Date Created: </i>20260922 <i>Date Completed: </i>20260922 <i>Latest Revision: </i>20260924
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        Text: English
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      – SubjectFull: Plasmids genetics
        Type: general
      – SubjectFull: Feces microbiology
        Type: general
      – SubjectFull: Bacteriophages genetics
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      – SubjectFull: Bacteria virology
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      – SubjectFull: Gastrointestinal Microbiome genetics
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      – SubjectFull: Interspersed Repetitive Sequences
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      – TitleFull: CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.
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              Text: 2026 Dec 31
              Type: published
              Y: 2026
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              Value: 1949-0984
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