What do we mean when we refer to Bacteroidetes populations in the human gastrointestinal microbiota?

FEMS Microbiology Letters

Volumn 299, Issue 2, 2009, Pages 175-183

  Hoyles, Lesley ^a   McCartney, Anne L ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

Bacteroidaceae; Bacteroidetes; FISH; Porphyromonadaceae; Prevotellaceae; Rikenellaceae

Indexed keywords

ADULT; ARTICLE; BACTERIUM DETECTION; BACTEROIDALES; CONTROLLED STUDY; DIET; FECES ANALYSIS; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; HUMAN EXPERIMENT; INTESTINE FLORA; MALE; NONHUMAN; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PREVOTELLA; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ADULT; ANIMALS; BACTEROIDETES; COLONY COUNT, MICROBIAL; FECES; FEMALE; GASTROINTESTINAL TRACT; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; OLIGONUCLEOTIDE PROBES; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

ANIMALIA; BACTEROIDACEAE; BACTEROIDALES; BACTEROIDES; BACTEROIDETES; FIRMICUTES; PORPHYROMONADACEAE; PREVOTELLA; PREVOTELLACEAE; RIKENELLACEAE;

EID: 70349239142     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2009.01741.x     Document Type: Article

References (27)

1. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ Weightman AJ (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microb 71 : 7724 7736.
2. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microb 72 : 5734 5741.
3. Behrens S, Rühland C, Inácio J, Huber H, Fonseca Á, Spencer-Martins I, Fuchs BM Amann R (2003) In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microb 69 : 1748 1758. (Pubitemid 36314318)
4. Daims H, Brühl A, Amann R, Schleifer KH Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22 : 434 444.
5. Devillard E, McIntosh FM, Paillard D, Thomas NA, Shingfield KJ Wallace RJ (2009) Differences between human subjects in the composition of the faecal bacterial community and faecal metabolism of linoleic acid. Microbiology 155 : 513 520.
6. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obesity 32 : 1720 1724.
7. Felsenstein J (1989) PHYLIP. Phylogeny inference package. Cladistics 5 : 164 166.
8. Guo X, Xia X, Tang R, Zhou J, Zhao H Wang K (2008) Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs. Lett Appl Microbiol 47 : 367 373.
9. Huber T, Faulkner G Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 : 2317 2319.
10. Hugenholtz P Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Micr 53 : 289 293.
11. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD Gordon JI (2005) Obesity alters gut microbial ecology. P Natl Acad Sci USA 102 : 11070 11075.
12. Ley RE, Turnbaugh PJ, Klein S Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444 : 1022 1023.
13. Ley RE, Hamady M, Lozupone C et al 2008) Evolution of mammals and their gut microbes. Science 320 : 1647 1651.
14. Ludwig W, Euzéby J Whitman WB (2008) Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. Available at
15. Macfarlane GT, Macfarlane S Gibson GR (1998) Validation of three-stage continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon. Microb Ecol 35 : 180 187.
16. Manz W, Amann R, Ludwig W, Vancanneyt M Schleifer KH (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142 : 1097 1106.
17. Martín-Peláez S, Gibson GR, Martín-Orúe SM, Klinder A, Rastall RA, La Ragione RM, Woodward MJ Costabile A (2008) In vitro fermentation of carbohydrates by porcine faecal inocula and their influence on Salmonella Typhimurium growth in batch culture systems. FEMS Microbiol Ecol 66 : 608 619.
18. Nadal I, Santacruz A, Marcos A et al 2009) Shifts in clostridia, bacteroides and immunoglobulin-coating fecal bacteria associated with weight loss in obese adolescents. Int J Obes (Lond) 33 : 758 767.
19. Pouteau E, Ngyuen P, Ballèvre O Krempf M (2003) Production rates and metabolism of short-chain fatty acids in the colon and whole body using stable isotopes. P Nutr Soc 62 : 87 93.
20. Sakamoto M, Takagaki A, Matsumoto K, Kato Y, Goto K Benno Y (2009) Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces. Int J Syst Evol Microbiol 59 : 1748 1753.
21. Salminen S, Bouley C, Boutron-Ruault MC, Cummings JH, Franck A, Gibson GR, Isolauri E, Moreau MC, Roberfroid M Rowland I (1998) Functional food science and gastrointestinal physiology and function. Brit J Nutr 80 (suppl 1) : S147 S171.
22. Shkoporov AN, Khokhlova EV, Kulagina EV, Smeianov VV, Kafarskaia LI Efimov BA (2008) Application of several molecular techniques to study numerically predominant Bifidobacterium spp. and Bacteroidales order strains in the feces of healthy children. Biosci Biotech Bioch 72 : 742 748.
23. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 : 1027 1031.
24. Turnbaugh PJ, Hamady M, Yatsunenko T et al 2009) A core gut microbiome in obese and lean twins. Nature 457 : 480 484.
25. Wagner M, Horn M Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6 : 302 309.
26. Weller R, Glöckner FO Amann R (2000) 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Syst Appl Microbiol 23 : 107 114.
27. Zhang H, DiBaise JK, Zuccolo A et al 2009) Human gut microbiota in obesity and after gastric bypass. P Natl Acad Sci USA 106 : 2365 2370.