CeMbio - The Caenorhabditis elegans Microbiome Resource

Abstract

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.

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References 87

1. 1.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

2. 2.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

3. 3.
   Global phenotypic characterization of bacteria · 2009

   No notice
4. 4.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

5. 5.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

6. 6.
   FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments · 2010

   No notice
7. 7.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

8. 8.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

9. 9.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

10. 10.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

11. 11.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

12. 12.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

13. 13.
    phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data · 2013

    No notice
14. 14.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

15. 15.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

16. 16.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

17. 17.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

18. 18.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

19. 19.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

20. 20.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

21. 21.
    A method for high throughput determination of viable bacteria cell counts in 96-well plates · 2012

    No notice
22. 22.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

23. 23.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

24. 24.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

25. 25.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

26. 26.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

27. 27.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

28. 28.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

29. 29.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

30. 30.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

31. 31.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

32. 32.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

33. 33.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

34. 34.
    Accelerated Profile HMM Searches · 2011

    No notice
35. 35.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

36. 36.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

37. 37.
    Prodigal: prokaryotic gene recognition and translation initiation site identification · 2010

    No notice
38. 38.
    C. elegans outside the Petri dish · 2015

    No notice
39. 39.
    LoRDEC: accurate and efficient long read error correction · 2014

    No notice
40. 40.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

41. 41.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

42. 42.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

43. 43.
    Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 · 2014

    No notice
44. 44.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

45. 45.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

46. 46.
    The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model · 2016

    No notice
47. 47.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

48. 48.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

49. 49.
    Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans · 2016

    No notice
50. 50.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

51. 51.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

52. 52.
    Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation · 2016

    Corrected
53. 53.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

54. 54.
    Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine · 2017

    No notice
55. 55.
    Caenorhabditis elegans as a Model for Microbiome Research · 2017

    No notice
56. 56.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

57. 57.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

58. 58.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

59. 59.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

60. 60.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

61. 61.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

62. 62.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

63. 63.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

64. 64.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

65. 65.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

66. 66.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

67. 67.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

68. 68.
    SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells · 2019

    No notice
69. 69.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

70. 70.
    GToTree: a user-friendly workflow for phylogenomics · 2019

    No notice
71. 71.
    Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation · 2017

    No notice
72. 72.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

73. 73.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

74. 74.
    Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads · 2017

    No notice
75. 75.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

76. 76.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

77. 77.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

78. 78.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

79. 79.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

80. 80.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

81. 81.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

82. 82.
    gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models · 2021

    No notice
83. 83.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

84. 84.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

85. 85.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

86. 86.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

87. 87.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

Cited by papers we hold 5

• Glycosylated N‑Acyl Phosphoethanolamines as Bacterial Food-Dependent Signaling Molecules in Caenorhabditis Nematodes · 2025
  Not checked
• Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide. · 2021
  Not checked
• Interspecies bacterial competition regulates community assembly in the C. elegans intestine · 2021
  No notice
• Host microbiota can facilitate pathogen infection · 2021
  No notice
• The relationship between the gut microbiome and host gene expression: a review · 2020
  No notice

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