Caenorhabditis elegans responses to bacteria from its natural habitats

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 27, 2016, Pages E3941-E3949

  Samuel, Buck S ^a,d   Rowedder, Holli ^a   Braendle, Christian ^b   Félix, Marie Anne ^c   Ruvkun, Gary ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b CNRS   (France)

^c ECOLE NORMALE SUPÉRIEURE   (France)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Caenorhabditis elegans; Ecology; Host microbe interactions

Indexed keywords

DNA 16S;

ACETOBACTER; ACETOBACTERACEAE; ACTINOBACTERIA; ADULT; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL VIRULENCE; BACTERIUM; BACTERIUM ISOLATION; BACTEROIDETES; CAENORHABDITIS ELEGANS; CHRYSEOBACTERIUM; CONTROLLED STUDY; ENTEROBACTER; ENTEROBACTERIACEAE; FIRMICUTES; FLAVOBACTERIACEAE; FORAGE; GLUCONOACETOBACTER; GLUCONOBACTER; LACTOBACILLUS; LACTOCOCCUS; MICROBACTERIACEAE; MICROBIAL COMMUNITY; MICROBIOME; MICROENVIRONMENT; MICROHABITAT; MOLECULAR PHYLOGENY; NONHUMAN; OXIDATIVE STRESS; POPULATION ABUNDANCE; POPULATION GROWTH; PRIORITY JOURNAL; PROMOTER REGION; PROTEOBACTERIA; PROVIDENCIA; PSEUDOMONADACEAE; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; RNA SEQUENCE; SERRATIA; SPECIES COMPOSITION; SPHINGOBACTERIUM; STENOTROPHOMONAS; XANTHOMODACEAE; XANTHOMONAS; ANIMAL; MALUS; MICROBIAL CONSORTIUM; MICROBIOLOGY; PHYSIOLOGY;

ANIMALS; CAENORHABDITIS ELEGANS; MALUS; MICROBIAL CONSORTIA;

EID: 84977263855     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1607183113     Document Type: Article

References (52)

1. McFall-Ngai M, et al. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA 110(9):3229-3236.
2. Goodrich JK, Davenport ER, Waters JL, Clark AG, Ley RE (2016) Cross-species comparisons of host genetic associations with the microbiome. Science 352(6285):532-535.
3. Arora T, Bäckhed F (2016) The gut microbiota and metabolic disease: Current understanding and future perspectives. J Intern Med doi: 10.1111/joim.12508.
4. Petersen C, Dirksen P, Schulenburg H (2015) Why we need more ecology for genetic models such as C. Elegans. Trends Genet 31(3):120-127.
5. Hillenmeyer ME, et al. (2008) The chemical genomic portrait of yeast: Uncovering a phenotype for all genes. Science 320(5874):362-365.
6. Andersen EC, et al. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat Genet 44(3):285-290.
7. Félix MA, Duveau F (2012) Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae. BMC Biol 10:59.
8. Félix MA, et al. (2013) Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest. BMC Evol Biol 13:10.
9. Frézal L, Félix MA (2015) C. Elegans outside the Petri dish. eLife 4:4.
10. Hodgkin J, Félix MA, Clark LC, Stroud D, Gravato-Nobre MJ (2013) Two Leucobacter strains exert complementary virulence on Caenorhabditis including death by wormstar formation. Curr Biol 23(21):2157-2161.
11. Troemel ER, Félix MA, Whiteman NK, Barrière A, Ausubel FM (2008) Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans. PLoS Biol 6(12):2736-2752.
12. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77(1):71-94.
13. Morran LT, Schmidt OG, Gelarden IA, Parrish RC, 2nd, Lively CM (2011) Running with the Red Queen: Host-parasite coevolution selects for biparental sex. Science 333(6039): 216-218.
14. Lemaitre B, Ausubel FM (2008) Animal models for host-pathogen interactions. Curr Opin Microbiol 11(3):249-250.
15. Masri L, et al. (2015) Host-pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biol 13(6):e1002169.
16. Darby C, Hsu JW, Ghori N, Falkow S (2002) Caenorhabditis elegans: Plague bacteria biofilm blocks food intake. Nature 417(6886):243-244.
17. Berg M, et al. (2016) Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME J doi: 10.1038/ismej.2015.253.
18. Haney CH, Samuel BS, Bush J, Ausubel FM (2015) Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants 1(6).
19. Lundberg DS, et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488(7409):86-90.
20. Leff JW, Fierer N (2013) Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 8(3):e59310.
21. Yashiro E, Spear RN, McManus PS (2011) Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere. J Appl Microbiol 110(5):1284-1296.
22. Broderick NA, Lemaitre B (2012) Gut-associated microbes of Drosophila melanogaster. Gut Microbes 3(4):307-321.
23. Wong AC, Chaston JM, Douglas AE (2013) The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. ISME J 7(10):1922-1932.
24. Dunbar TL, Yan Z, Balla KM, Smelkinson MG, Troemel ER (2012) C. Elegans detects pathogen-induced translational inhibition to activate immune signaling. Cell Host Microbe 11(4):375-386.
25. Liu Y, Samuel BS, Breen PC, Ruvkun G (2014) Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature 508(7496):406-410.
26. McEwan DL, Kirienko NV, Ausubel FM (2012) Host translational inhibition by Pseudomonas aeruginosa exotoxin A triggers an immune response in Caenorhabditis elegans. Cell Host Microbe 11(4):364-374.
27. Melo JA, Ruvkun G (2012) Inactivation of conserved C. Elegans genes engages pathogen- and xenobiotic-associated defenses. Cell 149(2):452-466.
28. Richardson CE, Kooistra T, Kim DH (2010) An essential role for XBP-1 in host protection against immune activation in C. Elegans. Nature 463(7284):1092-1095.
29. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5(7):e177.
30. Kirienko NV, Cezairliyan BO, Ausubel FM, Powell JR (2014) Pseudomonas aeruginosa PA14 pathogenesis in Caenorhabditis elegans. Methods Mol Biol 1149:653-669.
31. Tan MW, Mahajan-Miklos S, Ausubel FM (1999) Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis. Proc Natl Acad Sci USA 96(2):715-720.
32. Kirienko NV, et al. (2013) Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. Cell Host Microbe 13(4):406-416.
33. Watson E, et al. (2014) Interspecies systems biology uncovers metabolites affecting C. Elegans gene expression and life history traits. Cell 156(4):759-770.
34. MacNeil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ (2013) Diet-induced developmental acceleration independent of TOR and insulin in C. Elegans. Cell 153(1):240-252.
35. Golden JW, Riddle DL (1984) A Caenorhabditis elegans dauer-inducing pheromone and an antagonistic component of the food supply. J Chem Ecol 10(8):1265-1280.
36. Avery L, You YJ (2012) C. Elegans feeding. WormBook 1-23.
37. Benson AK, et al. (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci USA 107(44):18933-18938.
38. Roeselers G, et al. (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5(10):1595-1608.
39. Estes KA, Dunbar TL, Powell JR, Ausubel FM, Troemel ER (2010) bZIP transcription factor zip-2 mediates an early response to Pseudomonas aeruginosa infection in Caenorhabditis elegans. Proc Natl Acad Sci USA 107(5):2153-2158.
40. Irazoqui JE, et al. (2010) Distinct pathogenesis and host responses during infection of C. Elegans by P. aeruginosa and S. aureus. PLoS Pathog 6:e1000982.
41. Kim DH, et al. (2002) A conserved p38 MAP kinase pathway in Caenorhabditis elegans innate immunity. Science 297(5581):623-626.
42. Stiernagle T (2006) Maintenance of C. Elegans. WormBook 1-11.
43. Barrière A, Félix MA (2014) Isolation of C. Elegans and related nematodes. WormBook 1-19.
44. Ley RE, et al. (2008) Evolution of mammals and their gut microbes. Science 320(5883): 1647-1651.
45. Caporaso JG, et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621-1624.
46. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460-2461.
47. Caporaso JG, et al. (2010) PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics 26(2):266-267.
48. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261-5267.
49. Lozupone C, Knight R (2005) UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12):8228-8235.
50. Knights D, Costello EK, Knight R (2011) Supervised classification of human microbiota. FEMS Microbiol Rev 35(2):343-359.
51. Gilbert JA, Jansson JK, Knight R (2014) The Earth Microbiome project: Successes and aspirations. BMC Biol 12:69.
52. Félix MA, Braendle C (2010) The natural history of Caenorhabditis elegans. Curr Biol 20(22):R965-R969.