Smidt, Hauke

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orcid::0000-0002-6138-5026
  • Smidt, Hauke (5)
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Author's Bibliography

High temporal and inter-individual variation detected in the human ileal microbiota

Booijink, Carien C. G. M.; El-Aidy, Sahar; Rajilić-Stojanović, Mirjana; Heilig, Hans G. H. J.; Troost, Freddy J.; Smidt, Hauke; Kleerebezem, Michiel; de Vos, Willem M.; Zoetendal, Erwin G.

(Wiley, Hoboken, 2010)

TY  - JOUR
AU  - Booijink, Carien C. G. M.
AU  - El-Aidy, Sahar
AU  - Rajilić-Stojanović, Mirjana
AU  - Heilig, Hans G. H. J.
AU  - Troost, Freddy J.
AU  - Smidt, Hauke
AU  - Kleerebezem, Michiel
AU  - de Vos, Willem M.
AU  - Zoetendal, Erwin G.
PY  - 2010
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1735
AB  - P gt The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 107-108 bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9-28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.
PB  - Wiley, Hoboken
T2  - Environmental Microbiology
T1  - High temporal and inter-individual variation detected in the human ileal microbiota
EP  - 3227
IS  - 12
SP  - 3213
VL  - 12
DO  - 10.1111/j.1462-2920.2010.02294.x
ER  - 
@article{
author = "Booijink, Carien C. G. M. and El-Aidy, Sahar and Rajilić-Stojanović, Mirjana and Heilig, Hans G. H. J. and Troost, Freddy J. and Smidt, Hauke and Kleerebezem, Michiel and de Vos, Willem M. and Zoetendal, Erwin G.",
year = "2010",
abstract = "P gt The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 107-108 bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9-28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.",
publisher = "Wiley, Hoboken",
journal = "Environmental Microbiology",
title = "High temporal and inter-individual variation detected in the human ileal microbiota",
pages = "3227-3213",
number = "12",
volume = "12",
doi = "10.1111/j.1462-2920.2010.02294.x"
}
Booijink, C. C. G. M., El-Aidy, S., Rajilić-Stojanović, M., Heilig, H. G. H. J., Troost, F. J., Smidt, H., Kleerebezem, M., de Vos, W. M.,& Zoetendal, E. G.. (2010). High temporal and inter-individual variation detected in the human ileal microbiota. in Environmental Microbiology
Wiley, Hoboken., 12(12), 3213-3227.
https://doi.org/10.1111/j.1462-2920.2010.02294.x
Booijink CCGM, El-Aidy S, Rajilić-Stojanović M, Heilig HGHJ, Troost FJ, Smidt H, Kleerebezem M, de Vos WM, Zoetendal EG. High temporal and inter-individual variation detected in the human ileal microbiota. in Environmental Microbiology. 2010;12(12):3213-3227.
doi:10.1111/j.1462-2920.2010.02294.x .
Booijink, Carien C. G. M., El-Aidy, Sahar, Rajilić-Stojanović, Mirjana, Heilig, Hans G. H. J., Troost, Freddy J., Smidt, Hauke, Kleerebezem, Michiel, de Vos, Willem M., Zoetendal, Erwin G., "High temporal and inter-individual variation detected in the human ileal microbiota" in Environmental Microbiology, 12, no. 12 (2010):3213-3227,
https://doi.org/10.1111/j.1462-2920.2010.02294.x . .
9
263
187
240

Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

Rajilić-Stojanović, Mirjana; Maathuis, Annet; Heilig, Hans G. H. J.; Venema, Koen; de Vos, Willem M.; Smidt, Hauke

(Microbiology Soc, London, 2010)

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Maathuis, Annet
AU  - Heilig, Hans G. H. J.
AU  - Venema, Koen
AU  - de Vos, Willem M.
AU  - Smidt, Hauke
PY  - 2010
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1720
AB  - A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large intestine (TIM-2). This revealed that propagation of mixed faecal donations for the production of standardized inocula has only a limited effect on the microbiota composition, with slight changes observed mainly within the Firmicutes. Adversely, significant shifts in several major groups of intestinal microbiota were observed after inoculation of the in vitro model. Hierarchical cluster analysis was able to show that samples taken throughout the inoculum preparation grouped with microbiota profiles observed for faecal samples of healthy adults. In contrast, the TIM-2 microbiota was distinct. While members of the Bacteroidetes and some groups within the Bacilli were increased in TIM-2 microbiota, a strong reduction in the relative abundance of other microbial groups, including Bifidobacterium spp., Streptococcus spp., and Clostridium clusters IV and XlVa, was observed. The changes detected with the HITChip could be confirmed using denaturing gradient gel electrophoresis (DGGE) of SSU rRNA amplicons.
PB  - Microbiology Soc, London
T2  - Microbiology-Sgm
T1  - Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis
EP  - 3281
SP  - 3270
VL  - 156
DO  - 10.1099/mic.0.042044-0
ER  - 
@article{
author = "Rajilić-Stojanović, Mirjana and Maathuis, Annet and Heilig, Hans G. H. J. and Venema, Koen and de Vos, Willem M. and Smidt, Hauke",
year = "2010",
abstract = "A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large intestine (TIM-2). This revealed that propagation of mixed faecal donations for the production of standardized inocula has only a limited effect on the microbiota composition, with slight changes observed mainly within the Firmicutes. Adversely, significant shifts in several major groups of intestinal microbiota were observed after inoculation of the in vitro model. Hierarchical cluster analysis was able to show that samples taken throughout the inoculum preparation grouped with microbiota profiles observed for faecal samples of healthy adults. In contrast, the TIM-2 microbiota was distinct. While members of the Bacteroidetes and some groups within the Bacilli were increased in TIM-2 microbiota, a strong reduction in the relative abundance of other microbial groups, including Bifidobacterium spp., Streptococcus spp., and Clostridium clusters IV and XlVa, was observed. The changes detected with the HITChip could be confirmed using denaturing gradient gel electrophoresis (DGGE) of SSU rRNA amplicons.",
publisher = "Microbiology Soc, London",
journal = "Microbiology-Sgm",
title = "Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis",
pages = "3281-3270",
volume = "156",
doi = "10.1099/mic.0.042044-0"
}
Rajilić-Stojanović, M., Maathuis, A., Heilig, H. G. H. J., Venema, K., de Vos, W. M.,& Smidt, H.. (2010). Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis. in Microbiology-Sgm
Microbiology Soc, London., 156, 3270-3281.
https://doi.org/10.1099/mic.0.042044-0
Rajilić-Stojanović M, Maathuis A, Heilig HGHJ, Venema K, de Vos WM, Smidt H. Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis. in Microbiology-Sgm. 2010;156:3270-3281.
doi:10.1099/mic.0.042044-0 .
Rajilić-Stojanović, Mirjana, Maathuis, Annet, Heilig, Hans G. H. J., Venema, Koen, de Vos, Willem M., Smidt, Hauke, "Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis" in Microbiology-Sgm, 156 (2010):3270-3281,
https://doi.org/10.1099/mic.0.042044-0 . .
78
60
74

Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing

Kovatcheva-Datchary, Petia; Egert, Markus; Maathuis, Annet; Rajilić-Stojanović, Mirjana; de Graaf, Albert A.; Smidt, Hauke; de Vos, Willem M.; Venema, Koen

(Wiley-Blackwell, Malden, 2009)

TY  - JOUR
AU  - Kovatcheva-Datchary, Petia
AU  - Egert, Markus
AU  - Maathuis, Annet
AU  - Rajilić-Stojanović, Mirjana
AU  - de Graaf, Albert A.
AU  - Smidt, Hauke
AU  - de Vos, Willem M.
AU  - Venema, Koen
PY  - 2009
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1487
AB  - Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l(-1) of [U-(13)C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain.
PB  - Wiley-Blackwell, Malden
T2  - Environmental Microbiology
T1  - Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing
EP  - 926
IS  - 4
SP  - 914
VL  - 11
DO  - 10.1111/j.1462-2920.2008.01815.x
ER  - 
@article{
author = "Kovatcheva-Datchary, Petia and Egert, Markus and Maathuis, Annet and Rajilić-Stojanović, Mirjana and de Graaf, Albert A. and Smidt, Hauke and de Vos, Willem M. and Venema, Koen",
year = "2009",
abstract = "Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l(-1) of [U-(13)C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain.",
publisher = "Wiley-Blackwell, Malden",
journal = "Environmental Microbiology",
title = "Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing",
pages = "926-914",
number = "4",
volume = "11",
doi = "10.1111/j.1462-2920.2008.01815.x"
}
Kovatcheva-Datchary, P., Egert, M., Maathuis, A., Rajilić-Stojanović, M., de Graaf, A. A., Smidt, H., de Vos, W. M.,& Venema, K.. (2009). Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. in Environmental Microbiology
Wiley-Blackwell, Malden., 11(4), 914-926.
https://doi.org/10.1111/j.1462-2920.2008.01815.x
Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilić-Stojanović M, de Graaf AA, Smidt H, de Vos WM, Venema K. Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. in Environmental Microbiology. 2009;11(4):914-926.
doi:10.1111/j.1462-2920.2008.01815.x .
Kovatcheva-Datchary, Petia, Egert, Markus, Maathuis, Annet, Rajilić-Stojanović, Mirjana, de Graaf, Albert A., Smidt, Hauke, de Vos, Willem M., Venema, Koen, "Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing" in Environmental Microbiology, 11, no. 4 (2009):914-926,
https://doi.org/10.1111/j.1462-2920.2008.01815.x . .
165
130
136

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

Rajilić-Stojanović, Mirjana; Heilig, Hans G. H. J.; Molenaar, Douwe; Kajander, Kajsa; Surakka, Anu; Smidt, Hauke; de Vos, Willem M.

(Wiley-Blackwell Publishing, Inc, Malden, 2009)

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Heilig, Hans G. H. J.
AU  - Molenaar, Douwe
AU  - Kajander, Kajsa
AU  - Surakka, Anu
AU  - Smidt, Hauke
AU  - de Vos, Willem M.
PY  - 2009
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1439
AB  - P gt In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota - referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes ( lt  98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose-response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.
PB  - Wiley-Blackwell Publishing, Inc, Malden
T2  - Environmental Microbiology
T1  - Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults
EP  - 1751
IS  - 7
SP  - 1736
VL  - 11
DO  - 10.1111/j.1462-2920.2009.01900.x
ER  - 
@article{
author = "Rajilić-Stojanović, Mirjana and Heilig, Hans G. H. J. and Molenaar, Douwe and Kajander, Kajsa and Surakka, Anu and Smidt, Hauke and de Vos, Willem M.",
year = "2009",
abstract = "P gt In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota - referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes ( lt  98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose-response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.",
publisher = "Wiley-Blackwell Publishing, Inc, Malden",
journal = "Environmental Microbiology",
title = "Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults",
pages = "1751-1736",
number = "7",
volume = "11",
doi = "10.1111/j.1462-2920.2009.01900.x"
}
Rajilić-Stojanović, M., Heilig, H. G. H. J., Molenaar, D., Kajander, K., Surakka, A., Smidt, H.,& de Vos, W. M.. (2009). Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. in Environmental Microbiology
Wiley-Blackwell Publishing, Inc, Malden., 11(7), 1736-1751.
https://doi.org/10.1111/j.1462-2920.2009.01900.x
Rajilić-Stojanović M, Heilig HGHJ, Molenaar D, Kajander K, Surakka A, Smidt H, de Vos WM. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. in Environmental Microbiology. 2009;11(7):1736-1751.
doi:10.1111/j.1462-2920.2009.01900.x .
Rajilić-Stojanović, Mirjana, Heilig, Hans G. H. J., Molenaar, Douwe, Kajander, Kajsa, Surakka, Anu, Smidt, Hauke, de Vos, Willem M., "Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults" in Environmental Microbiology, 11, no. 7 (2009):1736-1751,
https://doi.org/10.1111/j.1462-2920.2009.01900.x . .
26
405
329
387

Diversity of the human gastrointestinal tract microbiota revisited

Rajilić-Stojanović, Mirjana; Smidt, Hauke; de Vos, Willem M.

(Wiley, Hoboken, 2007)

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Smidt, Hauke
AU  - de Vos, Willem M.
PY  - 2007
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1163
AB  - Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
PB  - Wiley, Hoboken
T2  - Environmental Microbiology
T1  - Diversity of the human gastrointestinal tract microbiota revisited
EP  - 2136
IS  - 9
SP  - 2125
VL  - 9
DO  - 10.1111/j.1462-2920.2007.01369.x
ER  - 
@article{
author = "Rajilić-Stojanović, Mirjana and Smidt, Hauke and de Vos, Willem M.",
year = "2007",
abstract = "Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.",
publisher = "Wiley, Hoboken",
journal = "Environmental Microbiology",
title = "Diversity of the human gastrointestinal tract microbiota revisited",
pages = "2136-2125",
number = "9",
volume = "9",
doi = "10.1111/j.1462-2920.2007.01369.x"
}
Rajilić-Stojanović, M., Smidt, H.,& de Vos, W. M.. (2007). Diversity of the human gastrointestinal tract microbiota revisited. in Environmental Microbiology
Wiley, Hoboken., 9(9), 2125-2136.
https://doi.org/10.1111/j.1462-2920.2007.01369.x
Rajilić-Stojanović M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. in Environmental Microbiology. 2007;9(9):2125-2136.
doi:10.1111/j.1462-2920.2007.01369.x .
Rajilić-Stojanović, Mirjana, Smidt, Hauke, de Vos, Willem M., "Diversity of the human gastrointestinal tract microbiota revisited" in Environmental Microbiology, 9, no. 9 (2007):2125-2136,
https://doi.org/10.1111/j.1462-2920.2007.01369.x . .
12
448
358
420