The DOI matches its Crossref record.
Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces
Open accessAbstract
For the detection of six groups of anaerobic bacteria in human feces, we designed seven new 16S rRNA-based oligonucleotide probes. This set of probes extends the current set of probes and gives more data on the composition of the human gut flora. Probes were designed for Phascolarctobacterium and relatives (Phasco741), Veillonella (Veil223), Eubacterium hallii and relatives (Ehal1469), Lachnospira and relatives (Lach571), and Eubacterium cylindroides and relatives (Ecyl387), and two probes were designed for Ruminococcus and relatives (Rbro730 and Rfla729). The hybridization conditions for the new probes were optimized for fluorescent in situ hybridization, and the probes were validated against a set of reference organisms. The probes were applied to fecal samples of 11 volunteers to enumerate their target bacterial groups. The Phasco741 and Veil223 probes both detected average numbers below 1% of the total number of bacteria as determined with the bacterial kingdom-specific Bact338 probe. The Ecyl387 probe detected about 1.4%, the Lach571 and Ehal1469 probes detected 3.8 and 3.6%, respectively, and a combination of the Rbro730 and Rfla729 probes detected 10.3%. A set of 15 probes consisting of probes previously described and those presented here were evaluated in hybridization with the fecal samples of the same volunteers. Together, the group-specific probes detected 90% of the total bacterial cells.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Revised Estimates for the Number of Human and Bacteria Cells in the Body
Sender, R., Fuchs, S., & Milo, R. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002533 · Cited by 5,425
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182
Microbiota and SCFA in lean and overweight healthy subjects
Schwiertz, A., Taras, D., Schäfer, K., Beijer, S., Bos, N. A., Donus, C., & Hardt, P. D. (2010) · Obesity · doi:10.1038/oby.2009.167 · Cited by 2,457
The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age
Mariat, D., Firmesse, O., Levenez, F., Guimarăes, V., Sokol, H., Doré, J., Corthier, G., & Furet, J.-P. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-123 · Cited by 1,755
Dowd, S. E., Callaway, T. R., Wolcott, R. D., Sun, Y., McKeehan, T., Hagevoort, R. G., & Edrington, T. S. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-125 · Cited by 1,121
“(tentative pectinoschiza) is another genus which has been poorly characterized in environments other than the rumen and has only been occasionally detected in the feces of pigs and humans [55,56].”
BackgroundBrouns, F., Bjorck, I., Frayn, K. N., Gibbs, A. L., Lang, V., Slama, G., & Wolever, T. M. S. (2005) · Nutrition Research Reviews · doi:10.1079/nrr2005100 · Cited by 1,093
Mueller, S., Saunier, K., Hanisch, C., Norin, E., Alm, L., Midtvedt, T., Cresci, A., Silvi, S., Orpianesi, C., Verdenelli, M. C., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.2.1027-1033.2006 · Cited by 1,006
Desbonnet, L., Garrett, L., Clarke, G., Bienenstock, J., & Dinan, T. G. (2008) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2008.03.009 · Cited by 952
Duncan, S. H., Belenguer, A., Holtrop, G., Johnstone, A. M., Flint, H. J., & Lobley, G. E. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02340-06 · Cited by 941
Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P., & Lochs, H. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.7.3380-3389.2005 · Cited by 894
Belenguer, A., Duncan, S. H., Calder, A. G., Holtrop, G., Louis, P., Lobley, G. E., & Flint, H. J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3593-3599.2006 · Cited by 856
Ramirez-Farias, C., Slezak, K., Fuller, Z., Duncan, A., Holtrop, G., & Louis, P. (2008) · British Journal of Nutrition · doi:10.1017/s0007114508019880 · Cited by 822
Walker, A. W., Duncan, S. H., McWilliam Leitch, E. C., Child, M. W., & Flint, H. J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.3692-3700.2005 · Cited by 796
Russell, W. R., Gratz, S. W., Duncan, S. H., Holtrop, G., Ince, J., Scobbie, L., Duncan, G., Johnstone, A. M., Lobley, G. E., Wallace, R. J., et al. (2011) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.002188 · Cited by 775
Lopez-Siles, M., Khan, T. M., Duncan, S. H., Harmsen, H. J. M., Garcia-Gil, L. J., & Flint, H. J. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06858-11 · Cited by 433
Self-citationHold, G. L., Schwiertz, A., Aminov, R. I., Blaut, M., & Flint, H. J. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.7.4320-4324.2003 · Cited by 350
Vulevic, J., Juric, A., Tzortzis, G., & Gibson, G. R. (2013) · The Journal of Nutrition · doi:10.3945/jn.112.166132 · Cited by 349
Fecal Microbiota Composition and Frailty
van Tongeren, S. P., Slaets, J. P. J., Harmsen, H. J. M., & Welling, G. W. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.10.6438-6442.2005 · Cited by 333
Self-citationSwidsinski, A. (2005) · World Journal of Gastroenterology · doi:10.3748/wjg.v11.i8.1131 · Cited by 314
Exploring the Diversity of the Bifidobacterial Population in the Human Intestinal Tract
Turroni, F., Foroni, E., Pizzetti, P., Giubellini, V., Ribbera, A., Merusi, P., Cagnasso, P., Bizzarri, B., de'Angelis, G. L., Shanahan, F., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02216-08 · Cited by 311
Selective colonization of insoluble substrates by human faecal bacteria
Leitch, E. C. M., Walker, A. W., Duncan, S. H., Holtrop, G., & Flint, H. J. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01186.x · Cited by 297
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303
Walker, A. W., Martin, J. C., Scott, P., Parkhill, J., Flint, H. J., & Scott, K. P. (2015) · Microbiome · doi:10.1186/s40168-015-0087-4 · Cited by 273
Impact of Coffee Consumption on the Gut Microbiota: A Human Volunteer Study
Jaquet, M., Rochat, I., Moulin, J., Cavin, C., & Bibiloni, R. (2009) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2009.01.011 · Cited by 232
Benus, R. F. J., van der Werf, T. S., Welling, G. W., Judd, P. A., Taylor, M. A., Harmsen, H. J. M., & Whelan, K. (2010) · British Journal Of Nutrition · doi:10.1017/s0007114510001030 · Cited by 210
Self-citationAnti-inflammatory effects of bifidobacteria by inhibition of LPS-induced NF-κB activation
Riedel, C. U. (2006) · World Journal of Gastroenterology · doi:10.3748/wjg.v12.i23.3729 · Cited by 210
Biedermann, L., Brülisauer, K., Zeitz, J., Frei, P., Scharl, M., Vavricka, S. R., Fried, M., Loessner, M. J., Rogler, G., & Schuppler, M. (2014) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000129 · Cited by 178
Human gut microbiota: Does diet matter?
Maukonen, J., & Saarela, M. (2015) · Proceedings of The Nutrition Society · doi:10.1017/s0029665114000688 · Cited by 177
LEACH, S. T., MITCHELL, H. M., ENG, W. R., ZHANG, L., & DAY, A. S. (2008) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2008.03796.x · Cited by 164
Aguilera, M., Cerdà-Cuéllar, M., & Martínez, V (2015) · Gut Microbes · doi:10.4161/19490976.2014.990790 · Cited by 162
Maukonen, J., Satokari, R., Mättö, J., Söderlund, H., Mattila-Sandholm, T., & Saarela, M. (2006) · Journal of Medical Microbiology · doi:10.1099/jmm.0.46134-0 · Cited by 156
The active human gut microbiota differs from the total microbiota
Peris-Bondia, F., Latorre, A., Artacho, A., Moya, A., & D'Auria, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022448 · Cited by 113
Grimaldi, R., Cela, D., Swann, J. R., Vulevic, J., Gibson, G. R., Tzortzis, G., & Costabile, A. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw233 · Cited by 109
Fijlstra, M., Ferdous, M., Koning, A. M., Rings, E. H. H. M., Harmsen, H. J. M., & Tissing, W. J. E. (2015) · Supportive Care in Cancer · doi:10.1007/s00520-014-2487-6 · Cited by 97
Self-citationInvolvement of Innate Immunity in the Development of Inflammatory and Autoimmune Diseases
TLASKALOVÁ-HOGENOVÁ, H., TUCKOVÁ, L., STEPÁNKOVÁ, R., HUDCOVIC, T., PALOVÁ-JELÍNKOVÁ, L., KOZÁKOVÁ, H., ROSSMANN, P., SANCHEZ, D., CINOVÁ, J., HRNČÍŘ, T., et al. (2005) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1361.122 · Cited by 68
Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients
Benus, R. F., Harmsen, H. J., Welling, G. W., Spanjersberg, R., Zijlstra, J. G., Degener, J. E., & van der Werf, T. S. (2010) · Intensive Care Medicine · doi:10.1007/s00134-010-1826-4 · Cited by 63
Self-citation
Metadata
- Authors
- Harmsen, H. J. M., Raangs, G. C., He, T., Degener, J. E., & Welling, G. W.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2002-06
- Volume
- 68
- Issue
- 6
- Pages
- 2982-2990
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W2167730457
- Cited by
- 401
- References
- 0
- FWCI
- 8.21
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
