Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances

mBio

Volumn 3, Issue 1, 2012, Pages 1-11

  Williams, Brent L ^a   Hornig, Mady ^a   Parekh, Tanmay ^a   Ian Lipkin, W ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ANTIGEN; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M; RNA 16S; BACTERIAL DNA; BACTERIUM ANTIBODY; RIBOSOME DNA;

ALCALIGENACEAE; ANTIGEN ANTIBODY REACTION; ARTICLE; AUTISM; BACTERIAL COUNT; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM ISOLATE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; GASTROINTESTINAL SYMPTOM; GENE SEQUENCE; GENOTYPE; HUMAN; HUMAN TISSUE; IMMUNE RESPONSE; INTESTINE BIOPSY; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SCHOOL CHILD; SUTTERELLA; SUTTERELLA STERCORICANIS; SUTTERELLA WADSWORTHENSIS; WESTERN BLOTTING; BACTERIAL LOAD; BETAPROTEOBACTERIA; BIOPSY; BLOOD; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FEMALE; GASTROINTESTINAL DISEASE; GENETICS; INTESTINE MUCOSA; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY;

ALCALIGENACEAE; SUTTERELLA; SUTTERELLA STERCORICANIS; SUTTERELLA WADSWORTHENSIS;

ANTIBODIES, BACTERIAL; AUTISTIC DISORDER; BACTERIAL LOAD; BACTERIOLOGICAL TECHNIQUES; BETAPROTEOBACTERIA; BIOPSY; BLOTTING, WESTERN; CHILD; CHILD, PRESCHOOL; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FEMALE; GASTROINTESTINAL DISEASES; HUMANS; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M; INTESTINAL MUCOSA; MALE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84857874680     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00261-11     Document Type: Article

References (45)

1. Buie T, et al. 2010. Evaluation, diagnosis, and treatment of gastrointestinal disorders in individuals with ASDs: a consensus report. Pediatrics 125(Suppl. 1):S1-S18.
2. Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA. 2011. Gastrointestinal flora and gastrointestinal status in children with autism- comparisons to typical children and correlation with autism severity. BMC Gastroenterol. 11:22.
3. White JF. 2003. Intestinal pathophysiology in autism. Exp. Biol. Med. (Maywood) 228:639-649.
4. Horvath K, Papadimitriou JC, Rabsztyn A, Drachenberg C, Tildon JT. 1999. Gastrointestinal abnormalities in children with autistic disorder. J. Pediatr. 135:559-563.
5. Ashwood P, Wills S, Van de Water J. 2006. The immune response in autism: a new frontier for autism research. J. Leukoc. Biol. 80:1-15.
6. Enstrom AM, Onore CE, van de Water JA, Ashwood P. 2010. Differential monocyte responses to TLR ligands in children with autism spectrum disorders. Brain Behav. Immun. 24:64-71.
7. Jyonouchi H, Geng L, Ruby A, Zimmerman-Bier B. 2005. Dysregulated innate immune responses in young children with autism spectrum disorders: their relationship to gastrointestinal symptoms and dietary intervention. Neuropsychobiology 51:77-85.
8. D'Eufemia P, et al. 1996. Abnormal intestinal permeability in children with autism. Acta Paediatr. 85:1076-1079.
9. de Magistris L, et al. 2010. Alterations of the intestinal barrier in patients with autism spectrum disorders and in their first-degree relatives. J. Pedi-atr. Gastroenterol. Nutr. 51:418-424.
10. Williams BL, et al. 2011. Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. PLoS One 6:e24585.
11. Finegold SM, et al. 2002. Gastrointestinal microflora studies in late-onset autism. Clin. Infect. Dis. 35:S6-S16.
12. Song Y, Liu C, Finegold SM. 2004. Real-time PCR quantitation of clos-tridia in feces of autistic children. Appl. Environ. Microbiol. 70: 6459-6465.
13. Parracho HM, Bingham MO, Gibson GR, McCartney AL. 2005. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J. Med. Microbiol. 54:987-991.
14. Wang L, et al. 2011. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl. Environ. Microbiol. 77:6718-6721.
15. Finegold SM, et al. 2010. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16:444-453.
16. O'Hara AM, Shanahan F. 2006. The gut flora as a forgotten organ. EMBO Rep. 7:688-693.
17. Macpherson AJ, Harris NL. 2004. Interactions between commensal intestinal bacteria and the immune system. Nat. Rev. Immunol. 4:478-485.
18. Heijtz RD, et al. 2011. Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. U. S. A. 108:3047-3052.
19. Vollaard EJ, Clasener HA. 1994. Colonization resistance. Antimicrob. Agents Chemother. 38:409-414.
20. Busse HJ, Auling G. 2005. Family III. Alcaligenaceae, p 647-653. In Brenner DJ, Krieg NR, Staley JT (ed), Bergey's manual of systematic bacteriology, vol 2, part C. The Proteobacteria. Springer-Verlag, New York, NY.
21. Wexler HM. 2005. Genus VIII. Sutterella, p 682-683.
22. Brenner DJ, Krieg NR, Staley JT (ed), Bergey's manual of systematic bacteriology, vol 2, part C. The Proteobacteria. Springer-Verlag, New York, NY.
23. Wexler HM, et al. 1996. Sutterella wadsworthensis gen. nov., sp. nov., bile-resistant microaerophilic Campylobacter gracilis-like clinical isolates. Int. J. Syst. Bacteriol. 46:252-258.
24. Molitoris E, Wexler HM, Finegold SM. 1997. Sources and antimicrobial susceptibilities of Campylobacter gracilis and Sutterella wadsworthensis. Clin. Infect. Dis. 25(Suppl. 2):S264-S265.
25. Mangin I, et al. 2004. Molecular inventory of faecal microflora in patients with Crohn's disease. FEMS Microbiol. Ecol. 50:25-36.
26. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ. 2006. Differences between tissue-associated intestinal micro-floras of patients with Crohn's disease and ulcerative colitis. J. Clin. Mi-crobiol. 44:4136-4141.
27. Stackebrandt E, Goebel BM. 1994. A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
28. Walker AW, et al. 2011. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 11:7.
29. Durso LM, et al. 2010. Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl. Environ. Microbiol. 76:4858-4862.
30. Li M, et al. 2008. Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl. Acad. Sci. U. S. A. 105:2117-2122.
31. Engberg J, On SL, Harrington CS, Gerner-Smidt P. 2000. Prevalence of Campylobacter, Arcobacter, Helicobacter, and Sutterella spp. in human fecal samples as estimated by a reevaluation of isolation methods for cam-pylobacters. J. Clin. Microbiol. 38:286-291.
32. Sakon H, Nagai F, Morotomi M, Tanaka R. 2008. Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 58:970-975.
33. Greetham HL, et al. 2004. Sutterella stercoricanis sp. nov., isolated from canine faeces. Int. J. Syst. Evol. Microbiol. 54:1581-1584.
34. Hong PY, Croix JA, Greenberg E, Gaskins HR, Mackie RI. 2011. Pyrosequencing-based analysis of the mucosal microbiota in healthy in-dividuals reveals ubiquitous bacterial groups and micro-heterogeneity. PLoS One 6:e25042.
35. Arumugam M, et al. 2011. Enterotypes of the human gut microbiome. Nature 473:174-180.
36. Mavin S, et al. 2011. Interpretation criteria in western blot diagnosis of Lyme borreliosis. Br. J. Biomed. Sci. 68:5-10.
37. Adams RJ, et al. 2008. IgG antibodies against common gut bacteria are more diagnostic for Crohn's disease than IgG against mannan or flagellin. Am. J. Gastroenterol. 103:386-396.
38. Hornig M, et al. 2008. Lack of association between measles virus vaccine and autism with enteropathy: a case-control study. PLoS One 3:e3140.
39. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
40. Frank DN, et al. 2007. Molecular-phylogenetic characterization of mi-crobial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U. S. A. 104:13780-13785.
41. Schloss PD, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
42. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
43. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
44. Jukes T, Cantor C. 1969. Evolution of protein molecules. Academic Press, New York, NY.
45. Chun J, et al. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57:2259-2261.