Niche-specific Features of the Intestinal Bacteroidales

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 2007 Nov 13

PMID 17993536

Citations 46

Authors

Michael J Coyne

Laurie E Comstock

Affiliations

Soon will be listed here.

Abstract

By analyzing the genomic sequences of 12 Bacteroidales species, we found that all intestinal species have numerous polysaccharide biosynthesis loci, many with promoters that we demonstrate undergo DNA inversion. This feature is not conserved in the Bacteroidales order as a whole, as oral species do not share these genetic features.

Citing Articles

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.

Jin X, Cheng A, Chanin R, Yu F, Dimas A, Jasper M Microbiome. 2025; 13(1):71.

PMID: 40059174 PMC: 11892184. DOI: 10.1186/s40168-025-02052-7.

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.

Schwartz L, Norman J, Hasan S, Adamek O, Dzuong E, Lowenstein J Biochemistry. 2024; 64(1):180-191.

PMID: 39663570 PMC: 11713874. DOI: 10.1021/acs.biochem.4c00519.

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.

Cortes-Martin A, Buttimer C, Maier J, Tobin C, Draper L, Ross R bioRxiv. 2024; .

PMID: 39605433 PMC: 11601342. DOI: 10.1101/2024.11.17.624012.

Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Wen J, Zhang H, Chu D, Chen X, Feng J, Wang Y Nucleic Acids Res. 2024; 52(21):12817-12830.

PMID: 39460615 PMC: 11602134. DOI: 10.1093/nar/gkae966.

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.

Zhang Z, Cole C, Coyne M, Lin H, Dylla N, Smith R Cell Host Microbe. 2024; 32(10):1853-1867.e5.

PMID: 39293438 PMC: 11466702. DOI: 10.1016/j.chom.2024.08.016.

References

Aduse-Opoku J, Slaney J, Hashim A, Gallagher A, Gallagher R, Rangarajan M . Identification and characterization of the capsular polysaccharide (K-antigen) locus of Porphyromonas gingivalis. Infect Immun. 2005; 74(1):449-60. PMC: 1346596. DOI: 10.1128/IAI.74.1.449-460.2006. View

Salyers A, Gupta A, Wang Y . Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol. 2004; 12(9):412-6. DOI: 10.1016/j.tim.2004.07.004. View

Chenna R, Sugawara H, Koike T, Lopez R, Gibson T, Higgins D . Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003; 31(13):3497-500. PMC: 168907. DOI: 10.1093/nar/gkg500. View

Bailey T, Elkan C . Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994; 2:28-36. View

Stappenbeck T, Hooper L, Gordon J . Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A. 2002; 99(24):15451-5. PMC: 137737. DOI: 10.1073/pnas.202604299. View

Coyne M, Tzianabos A, Mallory B, Carey V, Kasper D, Comstock L . Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis. Infect Immun. 2001; 69(7):4342-50. PMC: 98505. DOI: 10.1128/IAI.69.7.4342-4350.2001. View

Weinacht K, Roche H, Krinos C, Coyne M, Parkhill J, Comstock L . Tyrosine site-specific recombinases mediate DNA inversions affecting the expression of outer surface proteins of Bacteroides fragilis. Mol Microbiol. 2004; 53(5):1319-30. DOI: 10.1111/j.1365-2958.2004.04219.x. View

Lee S, Sabet M, Um H, Yang J, Kim H, Zhu W . Identification and characterization of the genes encoding a unique surface (S-) layer of Tannerella forsythia. Gene. 2006; 371(1):102-11. DOI: 10.1016/j.gene.2005.11.027. View

Bayley D, Rocha E, Smith C . Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol Lett. 2000; 193(1):149-54. DOI: 10.1111/j.1574-6968.2000.tb09417.x. View

10.

Roche-Hakansson H, Chatzidaki-Livanis M, Coyne M, Comstock L . Bacteroides fragilis synthesizes a DNA invertase affecting both a local and a distant region. J Bacteriol. 2006; 189(5):2119-24. PMC: 1855777. DOI: 10.1128/JB.01362-06. View

11.

Mazmanian S, Liu C, Tzianabos A, Kasper D . An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005; 122(1):107-18. DOI: 10.1016/j.cell.2005.05.007. View

12.

Krinos C, Coyne M, Weinacht K, Tzianabos A, Kasper D, Comstock L . Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature. 2001; 414(6863):555-8. DOI: 10.1038/35107092. View

13.

Xu J, Bjursell M, Himrod J, Deng S, Carmichael L, Chiang H . A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003; 299(5615):2074-6. DOI: 10.1126/science.1080029. View

14.

Coyne M, Weinacht K, Krinos C, Comstock L . Mpi recombinase globally modulates the surface architecture of a human commensal bacterium. Proc Natl Acad Sci U S A. 2003; 100(18):10446-51. PMC: 193581. DOI: 10.1073/pnas.1832655100. View

15.

Davey M, Duncan M . Enhanced biofilm formation and loss of capsule synthesis: deletion of a putative glycosyltransferase in Porphyromonas gingivalis. J Bacteriol. 2006; 188(15):5510-23. PMC: 1540017. DOI: 10.1128/JB.01685-05. View

16.

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

17.

Coyne M, Kalka-Moll W, Tzianabos A, Kasper D, Comstock L . Bacteroides fragilis NCTC9343 produces at least three distinct capsular polysaccharides: cloning, characterization, and reassignment of polysaccharide B and C biosynthesis loci. Infect Immun. 2000; 68(11):6176-81. PMC: 97696. DOI: 10.1128/IAI.68.11.6176-6181.2000. View

18.

Jenkins S, Drucker D, Hillier V, Ganguli L . Numerical taxonomy of Bacteroides and other genera of Gram-negative anaerobic rods. Microbios. 1992; 69(279):139-54. View

19.

Shoji M, Ratnayake D, Shi Y, Kadowaki T, Yamamoto K, Yoshimura F . Construction and characterization of a nonpigmented mutant of Porphyromonas gingivalis: cell surface polysaccharide as an anchorage for gingipains. Microbiology (Reading). 2002; 148(Pt 4):1183-1191. DOI: 10.1099/00221287-148-4-1183. View

20.

Fletcher C, Coyne M, Bentley D, Villa O, Comstock L . Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem. Proc Natl Acad Sci U S A. 2007; 104(7):2413-8. PMC: 1892957. DOI: 10.1073/pnas.0608797104. View