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Applied and Environmental Microbiology, May 2000, p. 2263-2266, Vol. 66, No. 5
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization

Abdelghani Sghir,1,* Genevieve Gramet,1 Antonia Suau,1 Violaine Rochet,1 Philippe Pochart,2 and Joel Dore1

Institut National de Recherche Agronomique, Unité d'Ecologie et Physiologie du Système Digestif, Domaine de Vilvert, 78352 Jouy-en-Josas,1 and Conservatoire National des Arts et Métiers, 75141 Paris,2 France

Received 21 October 1999/Accepted 22 February 2000


    ABSTRACT
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To investigate the population structure of the predominant phylogenetic groups within the human adult fecal microbiota, a new oligonucleotide probe designated S-G-Clept-1240-a-A-18 was designed, validated, and used with a set of five 16S rRNA-targeted oligonucleotide probes. Application of the six probes to fecal samples from 27 human adults showed additivity of 70% of the total 16S rRNA detected by the bacterial domain probe. The Bacteroides group-specific probe accounted for 37% ± 16% of the total rRNA, while the enteric group probe accounted for less than 1%. Clostridium leptum subgroup and Clostridium coccoides group-specific probes accounted for 16% ± 7% and 14% ± 6%, respectively, while Bifidobacterium and Lactobacillus groups made up less than 2%.


    TEXT
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The presence of an extremely complex microbial population adapted to live within the human host must have a significant impact on human health. Knowledge concerning numbers and species of bacteria found in the human colon is important because it provides an index of the metabolic potential of the colonic microbiota. Early work analyzing the colonic microbiota has focussed on enumeration and identification of numerically predominant cultivable species (4, 6, 14). Nevertheless, evidence has accumulated indicating that a significant fraction of the microbiota can escape cultivation (4, 13, 19, 21).

In recent years, there has been an increasing effort to describe complex environments by using genetic tools (2, 16, 18). Regarding the human intestinal gut microbiota, the rRNA approach has been used to study specific groups of bacteria by using various molecular techniques (5, 10, 12, 19, 20, 23). None of these techniques provided thorough quantitative information on the different microbial groups and their contribution in terms of activity to the whole microbial community.

In the present study, we describe the use of a set of six 16S rRNA-targeted oligonucleotide probes and quantitative dot blot hybridization technique for analyzing the human adult fecal microbiota composition from frozen fecal samples.

Probe design included a search of target and nontarget group complementarity by using the rRNA database (containing 10,700 aligned sequences as of September 1999) (11). A computer-assisted specificity control of the different probes was performed with the check probe function available from the Ribosomal Database Project facility (11). Based on human fecal rDNA sequence analysis (19), probe Clept1240 was designed to target the Clostridium leptum subgroup, which is presented in Table 1 and corresponds to the semiconserved region between nucleotides 1240 and 1257 (Escherichia coli consensus numbering). Probes specific for the Bifidobacterium group (Bif1412), Bacteroides group (Bacto1080), enteric group (Enter1432), Clostridium coccoides group (Erec482), and C. leptum subgroup (Clept1240) were used in conjunction with Lactobacillus group probe (Lacto722) to assess RNA proportions of these populations with respect to the total microbiota as determined by using the bacterial domain probe (Bact338) (see Table 2 for probe sequences).

                              
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  		TABLE 1.   Partial nucleotide sequence of the region between nucleotides 1240 and 1257 of the 16S rRNA (E. coli numbering) from various bacterial species showing the target region for the Clept1240 (underlined)a


                              
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  		TABLE 2.   16S rRNA targeted oligonucleotide probes and experimental wash temperatures of buffer under experimental conditionsa

RNA extraction and dot blot hybridization were performed as previously described by Stahl et al. (18) and modified by Doré et al. (3). The 16S rRNA-targeted oligonucleotide probes and the corresponding washing temperatures used in this study are listed in Table 2. The specificity of each probe was experimentally tested against RNA extracts from strains representing 46 different bacterial species. All probes hybridized to their corresponding target bacteria and did not cross hybridize with any of the nontarget microorganisms.

The following 46 reference species were used for dot blot hybridization: Actinomyces naeslundii (ATCC 12104), Bacteroides vulgatus (ATCC 8482), Bacteroides fragilis (ATCC 25285), Bacteroides eggerthii (ATCC 27754), Bacteroides uniformis (ATCC 8492), Bacteroides putredinis (ATCC 29800), Bifidobacterium adolescentis (ATCC 15703), Bifidobacterium pseudolongum (ATCC 25526), Bifidobacterium dentium (ATCC 15423), Bifidobacterium infantis (ATCC 15697), Bifidobacterium longum (ATCC 15707), Clostridium perfringens (ATCC 13124), Clostridium beijerinckii (ATCC 25752), Clostridium butyricum (ATCC 43755), Clostridium putrificum (ATCC 25784), Clostridium coccoides (ATCC 29236), Clostridium nexile (ATCC 27757), Clostridium absonum (ATCC 27555), Clostridium bifermentans (ATCC 638), Clostridium clostridiiforme (ATCC 25537), Coprococcus eutactus (ATCC 27759), Escherichia coli (ATCC 11775), Eubacterium siraeum (ATCC 29066), Eubacterium tenue (ATCC 25553), Eubacterium ventriosum (ATCC 27560), Enterococcus faecalis (CIP 76117), Enterococcus faecium (CIP 54.32), Fusobacterium prausnitzii (ATCC 27766), Klebsiella pneumoniae (CIP 54.45), Lactobacillus acidophilus (ATCC 4356), Lactobacillus fermentum (ATCC 14931), Lactobacillus reuteri (ATCC 23272), Leuconostoc lactis (ATCC 19256), Propionibacterium acnes (ATCC 6919), Proteus mirabilis (CIP 54.15), Pseudomonas aeruginosa (CIP 102240), Ruminococcus hansenii (ATCC 27752), Ruminococcus flavefaciens (ATCC 19208), Ruminococcus gnavus (ATCC 29149), Ruminococcus productus (ATCC 27340), Salmonella paratyphoides (CIP 54.136), Serratia marcescens (CIP 67.55), Staphylococcus aureus (CIP 65.15), Streptococcus bovis (ATCC 33317), Streptococcus sanguinis (ATCC 10556), and Streptococcus intermedius (ATCC 27335).

Fresh fecal samples were collected from 27 healthy human adults (13 males and 14 females). The individuals were 20 to 45 years old and received unrestricted western-type diets. They had not received antibiotic therapy during the preceding 6 months and were free of known metabolic or gastrointestinal diseases, including diabetes, ulcerative colitis, Crohn's disease, peptic ulcers, and cancer. The collected samples were immediately frozen and stored at -20°C for future analysis.

Dilution series of control RNA (4 to 500 ng) from pure cultures and triplicates of 250 ng of total RNA extracted from frozen fecal samples were blotted and hybridized as described previously by Doré et al. (3). Quantification of hybridization signals on dot blots was achieved by using radio imaging with the Instant Imager (Packard Instruments). All quantitative rRNA measurements were standardized by using rRNA extracts from pure cultures of B. vulgatus (ATCC 8482), B. longum (ATCC 15707), E. coli (Boehringer Mannheim rRNA standards), F. prausnitzii (ATCC 27760), L. acidophilus (ATCC 4356), and R. productus (ATCC 27340). The universal probe was used for normalizing rRNA concentrations. Results are expressed as percent of total bacterial 16S rRNA that is detected by the Bact338 and are given as means ± standard deviations from triplicate measurements.

Total Bacteroides and enteric group rRNAs accounted for 37% ± 16% and 1% of total bacterial rRNA, respectively. Low-guanine-plus-cytosine-content gram-positive organisms, including those of the genera Lactobacillus, Streptococcus, and Enterococcus, accounted for by using Lacto722 comprised up to 1% of the total 16S rRNA. Clostridium, Eubacterium, Peptostreptococcus, Ruminococcus, and Fusobacterium speciestargeted using both Erec482 and Clept1240 represented 16% ± 7% and 14% ± 6% of the total bacterial rRNA, respectively. The Bifidobacterium group represented less than 1% of the total. Thus, by using a panel of six probes, an average of 70% of all bacterial 16S rRNA was accounted for in the present study (Table 3).

                              
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  		TABLE 3.   Ribosomal RNA indexes of 27 individuals measured by quantitative dot blot hybridization by using the Bact338 as reference compared to Bacto1080, Clept1240, Erec482, Bif1412, Enter1432, and Lacto722

Our observations are consistent with previous work using molecular techniques for studying human adult fecal microbiota. Franks et al. (5) developed and applied six 16S rRNA-targeted probes for major species and groups of anaerobic intestinal bacteria to enumerate bacterial populations in fresh feces of healthy human volunteers by using a fluorescent in situ hybridization (FISH) technique. They accounted for two-thirds (64%) of the total fecal microbiota. A direct comparison with our results by using quantitative dot blot hybridization is difficult since probe specificity was different and the dot blot hybridization technique measures proportions of rRNA representing numbers as well as activities of the different groups of bacteria, while the fluorescent in situ hybridization technique measures the number of cells containing a sufficient number of ribosome to be detected.

A B. fragilis group-specific probe and a Bacteroides distasonis species-specific probe used in combination accounted for 20% of the fecal flora in the study conducted by Franks et al. (5). Our Bacto1080 probe is broader in target and encompasses the Bacteroides, Prevotella, and Porphyromonas subgroups, hence the 37% accounted for.

The C. coccoides phylogenetic group did not account for more than 16% of the total bacterial 16S rRNA. The same probe, Erec482, was used in the study conducted by Franks et al. (5), and target cells accounted for 29% of the microbiota. They also used a probe called Lowgc2P which is specific for an uncultivated group of gram-positive bacteria within the C. leptum subgroup. Its target represented 12% of the total human fecal microbiota. This result was in accordance with the 1 to 10% proportion of the total human fecal 16S rDNA detected with this probe in the study conducted by Wilson and Blitchington (21). Our novel Clept1240 probe is broader in terms of specificity and accounted for 14% of the total 16S rRNA.

Regarding the group Bifidobacterium, which was represented by less than 1% total bacterial rRNA, on average (0 to 5%), the proportion appears lower than that obtained by Langendijk et al. (10) (5%) or by Franks et al. (5) (3%). This discrepancy can, in part, be explained by the use of probes targeting different sequence region of the 16S rRNA molecule. Moreover, after thriving in their respective ecological niches, suboptimal physicochemical conditions encountered in fecal matter, such as loss of contact with the mucosa or depletion of their preferred energy substrates, would yield lower rRNA contents. The same hypothesis can explain the occurrence of low levels of enteric group rRNA, since the ecological niche of organisms in this group is the cecum. In their study using pyxigraphic sampling (15), Marteau et al. (P. Marteau, P. Pochart, J. Doré, A. Bernalier, G. Corthier, and J. C. Rambaud, unpublished data) showed that facultative anaerobes, which represented 35% of the total viable counts in the cecum, did not exceed 1% of the total in feces.

Lactobacilli have complex nutritional requirements such as amino acids, peptides, nucleic acid derivatives, vitamins, salts, fatty acid esters, and fermentable carbohydrates for growth (7). Some of these complex nutrients are probably in very low supply in the colon due to their degradation and absorption in the small intestine, hence the minor contribution of this group.

The estimation of methodological congruence based on the analysis of the fecal microbiota from the same subjects with the same probe panel by using both techniques will prove most valuable in the future.

Interindividual variations in microbiota composition were noticed in our study, but no striking differences between males and females emerged. The Bacteroides group was the most variable with a rRNA index varying between 7 and 74%. The C. leptum subgroup varied between 6 and 39%, and the C. coccoides group varied between 7 and 28% of total bacterial rRNA. This data is consistent with previous work, indicating that each individual harbors his or her own unique microbial community (6, 12).

Considering that many fastidious microorganisms not only require selective media, but also many days for growth, the use of oligonucleotide probes targeting 16S rRNA provides a direct and quantitative estimate of the microbial community without culture-based enumeration and identification. The selectivity of oligonucleotide probes and the ease with which they can be generated make them ideally suited for monitoring the growth dynamics of these microorganisms under different dietary conditions and for tracking probiotics in the gut. Moreover, the use of species-specific probes will enable us to identify and quantify major microbial species directly in the gut. This will help in the design of preventive nutrition strategies aiming to modulate human colonic bacterial populations towards a balanced and healthy microbiota.


    ACKNOWLEDGMENTS

We thank R. I. Mackie for his suggestions and comments during the preparation of the manuscript, Michele Serezat for assistance with culturing control microorganisms, and Philippe Beaumatin for RNA extraction.

This work was funded, in part, by grants from the Bureau des Ressources Génétiques and the European Union FLAIR program under project number CT97-3035.


    FOOTNOTES

* Corresponding author. Mailing address: Genoscope, 2, rue Gaston Crémieux, BP 5706, 91057 Evry Cedex, France. Phone: 01 60 87 25 31. Fax: 01 60 87 25 14. E-mail: sghir{at}genoscope.cns.fr.


    REFERENCES
Top
Abstract
Text
References

1. Alm, E. W., D. B. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62:3557-3559[Medline].
2. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 2:762-770.
3. Doré, J., A. Sghir, G. Hannequart-Gramet, G. Corthier, and P. Pochart. 1998. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 1:65-71.
4. Finegold, S. M., V. L. Sutter, and G. E. Mathisen. 1983. Normal indigenous intestinal flora, p. 3-31. In D. J. Hentges (ed.), Human intestinal microbiota in health and disease. Academic Press, New York, N.Y.
5. Franks, A. H., H. J. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut, and G. W. Welling. 1998. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 9:3336-3345.
6. Holdeman, L. V., I. J. Good, and W. E. Moore. 1976. Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress. Appl. Environ. Microbiol. 3:359-375.
7. Kandler, O., and N. Weiss. 1986. Regular nonspring Gram-positive rods, p. 1418-1434. In P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 2. The Williams and Wilkins Co., Baltimore, Md.
8. Kaufmann, P., A. Pfefferkorn, M. Teuber, and L. Meile. 1997. Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. Appl. Environ. Microbiol. 63:1268-1273[Abstract].
9. Kimura, K., A. L. McCartney, M. A. McConnell, and G. W. Tannock. 1997. Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains. Appl. Environ. Microbiol. 9:3394-3398.
10. Langendijk, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 8:3069-3075.
11. Maidak, B. L., J. R. Cole, G. L. Timothy, T. P. Charles, Jr., R. S. Paul, M. S. Jason, G. M. Garrity, L. Bing, G. J. Olsen, S. Pramanik, T. M. Schmidt, and J. M. Tiedje. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:173-174[Abstract/Free Full Text].
12. McCartney, A. L., W. Wenzhi, and G. W. Tannock. 1996. Molecular analysis of the composition of the bifidobacterial and Lactobacillus microbiota of humans. Appl. Environ. Microbiol. 12:4608-4613.
13. Moore, W. E., E. P. Cato, and L. V. Holdeman. 1978. Some current concepts in intestinal bacteriology. Am. J. Clin. Nutr. 31(Suppl. 10):S33-S42[Abstract].
14. Moore, W. E., and L. H. Moore. 1995. Intestinal floras of populations that have a high risk of colon cancer. Appl. Environ. Microbiol. 61:3202-3207[Abstract].
15. Pochart, P., F. Léman, B. Flourié, P. Pellier, I. Goderel, and J. C. Rambaud. 1993. Pyxigraphic sampling to enumerate methanogens and anaerobes in the right colon of healthy humans. Gastroenterology 108:1281-1285.
16. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 4:1241-1248.
17. Sghir, A., D. Antonopoulos, and R. I. Mackie. 1998. Design and evaluation of a Lactobacillus group-specific ribosomal RNA-targeted hybridization probe and its application to the study of intestinal microecology in pigs. Syst. Appl. Microbiol. 2:291-296.
18. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 5:1079-1084.
19. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. Gibson, M. D. Collins, and J. Doré. 1999. Direct rDNA community analysis reveals a myriad of novel bacterial lineages within the human gut. Appl. Environ. Microbiol. 65:4799-4807[Abstract/Free Full Text].
20. Wang, R. F., W. W. Cao, and C. E. Cerniglia. 1996. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl. Environ. Microbiol. 4:1242-1247.
21. Wilson, K. H., and R. B. Blitchington. 1996. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 7:2273-2278.
22. Zheng, D., E. W. Alm, D. A. Stahl, and L. Raskin. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 12:4504-4513.
23. Zoetendal, E. G., A. D. Akkermans, and W. M. De Vos. 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 10:3854-3859.

Applied and Environmental Microbiology, May 2000, p. 2263-2266, Vol. 66, No. 5
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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  • Louis, P., Duncan, S. H., McCrae, S. I., Millar, J., Jackson, M. S., Flint, H. J. (2004). Restricted Distribution of the Butyrate Kinase Pathway among Butyrate-Producing Bacteria from the Human Colon. J. Bacteriol. 186: 2099-2106 [Abstract] [Full Text]  
  • Simpson, P. J., Ross, R. P., Fitzgerald, G. F., Stanton, C. (2004). Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. Int. J. Syst. Evol. Microbiol. 54: 401-406 [Abstract] [Full Text]  
  • Smith, A. H., Mackie, R. I. (2004). Effect of Condensed Tannins on Bacterial Diversity and Metabolic Activity in the Rat Gastrointestinal Tract. Appl. Environ. Microbiol. 70: 1104-1115 [Abstract] [Full Text]  
  • Zoetendal, E. G., Collier, C. T., Koike, S., Mackie, R. I., Gaskins, H. R. (2004). Molecular Ecological Analysis of the Gastrointestinal Microbiota: A Review. J. Nutr. 134: 465-472 [Abstract] [Full Text]  
  • Mai, V., Katki, H. A., Harmsen, H., Gallaher, D., Schatzkin, A., Baer, D. J., Clevidence, B. (2004). Effects of a Controlled Diet and Black Tea Drinking on the Fecal Microflora Composition and the Fecal Bile Acid Profile of Human Volunteers in a Double-Blinded Randomized Feeding Study. J. Nutr. 134: 473-478 [Abstract] [Full Text]  
  • Tamboli, C P, Neut, C, Desreumaux, P, Colombel, J F (2004). Dysbiosis in inflammatory bowel disease. Gut 53: 1-4 [Abstract] [Full Text]  
  • Hopkins, M. J., Englyst, H. N., Macfarlane, S., Furrie, E., Macfarlane, G. T., McBain, A. J. (2003). Degradation of Cross-Linked and Non-Cross-Linked Arabinoxylans by the Intestinal Microbiota in Children. Appl. Environ. Microbiol. 69: 6354-6360 [Abstract] [Full Text]  
  • Temmerman, R., Masco, L., Vanhoutte, T., Huys, G., Swings, J. (2003). Development and Validation of a Nested-PCR-Denaturing Gradient Gel Electrophoresis Method for Taxonomic Characterization of Bifidobacterial Communities. Appl. Environ. Microbiol. 69: 6380-6385 [Abstract] [Full Text]  
  • Zabarovsky, E. R., Petrenko, L., Protopopov, A., Vorontsova, O., Kutsenko, A. S., Zhao, Y., Kilosanidze, G., Zabarovska, V., Rakhmanaliev, E., Pettersson, B., Kashuba, V. I., Ljungqvist, O., Norin, E., Midtvedt, T., Mollby, R., Winberg, G., Ernberg, I. (2003). Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems. Nucleic Acids Res 31: e95-e95 [Abstract] [Full Text]  
  • Hopkins, M. J., Macfarlane, G. T. (2003). Nondigestible Oligosaccharides Enhance Bacterial Colonization Resistance against Clostridium difficile In Vitro. Appl. Environ. Microbiol. 69: 1920-1927 [Abstract] [Full Text]  
  • Walter, J., Heng, N. C. K., Hammes, W. P., Loach, D. M., Tannock, G. W., Hertel, C. (2003). Identification of Lactobacillus reuteri Genes Specifically Induced in the Mouse Gastrointestinal Tract. Appl. Environ. Microbiol. 69: 2044-2051 [Abstract] [Full Text]  
  • Seksik, P, Rigottier-Gois, L, Gramet, G, Sutren, M, Pochart, P, Marteau, P, Jian, R, Dore, J (2003). Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 52: 237-242 [Abstract] [Full Text]  
  • Malinen, E., Kassinen, A., Rinttila, T., Palva, A. (2003). Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria. Microbiology 149: 269-277 [Abstract] [Full Text]  
  • Stebbings, S., Munro, K., Simon, M. A., Tannock, G., Highton, J., Harmsen, H., Welling, G., Seksik, P., Dore, J., Grame, G., Tilsala-Timisjarvi, A. (2002). Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis. Rheumatology (Oxford) 41: 1395-1401 [Abstract] [Full Text]  
  • Matsuki, T., Watanabe, K., Fujimoto, J., Miyamoto, Y., Takada, T., Matsumoto, K., Oyaizu, H., Tanaka, R. (2002). Development of 16S rRNA-Gene-Targeted Group-Specific Primers for the Detection and Identification of Predominant Bacteria in Human Feces. Appl. Environ. Microbiol. 68: 5445-5451 [Abstract] [Full Text]  
  • Deplancke, B., Vidal, O., Ganessunker, D., Donovan, S. M, Mackie, R. I, Gaskins, H R. (2002). Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition. Am. J. Clin. Nutr. 76: 1117-1125 [Abstract] [Full Text]  
  • Harmsen, H. J. M., Raangs, G. C., He, T., Degener, J. E., Welling, G. W. (2002). Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces. Appl. Environ. Microbiol. 68: 2982-2990 [Abstract] [Full Text]  
  • Requena, T., Burton, J., Matsuki, T., Munro, K., Simon, M. A., Tanaka, R., Watanabe, K., Tannock, G. W. (2002). Identification, Detection, and Enumeration of Human Bifidobacterium Species by PCR Targeting the Transaldolase Gene. Appl. Environ. Microbiol. 68: 2420-2427 [Abstract] [Full Text]  
  • HOPKINS, M.J., MACFARLANE, G.T. (2002). Changes in predominant bacterial populations in human faeces with age and with Clostridium difficile infection. J Med Microbiol 51: 448-454 [Abstract] [Full Text]  
  • Heilig, H. G.H.J., Zoetendal, E. G., Vaughan, E. E., Marteau, P., Akkermans, A. D.L., de Vos, W. M. (2002). Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA. Appl. Environ. Microbiol. 68: 114-123 [Abstract] [Full Text]  
  • Marteau, P., Pochart, P., Dore, J., Bera-Maillet, C., Bernalier, A., Corthier, G. (2001). Comparative Study of Bacterial Groups within the Human Cecal and Fecal Microbiota. Appl. Environ. Microbiol. 67: 4939-4942 [Abstract] [Full Text]  
  • Walter, J., Hertel, C., Tannock, G. W., Lis, C. M., Munro, K., Hammes, W. P. (2001). Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella Species in Human Feces by Using Group-Specific PCR Primers and Denaturing Gradient Gel Electrophoresis. Appl. Environ. Microbiol. 67: 2578-2585 [Abstract] [Full Text]  
  • Hopkins, M J, Sharp, R, Macfarlane, G T (2001). Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48: 198-205 [Abstract] [Full Text]  
  • SHARP, R., FISHBAIN, S., MACFARLANE, G.T. (2001). Effect of short-chain carbohydrates on human intestinal bifidobacteria and Escherichia coli in vitro. J Med Microbiol 50: 152-160 [Abstract] [Full Text]  

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