TY  - JOUR
AU  - Scanlan, Pauline D.
AU  - Stensvold, Christen R.
AU  - Rajilić-Stojanović, Mirjana
AU  - Heilig, Hans G. H. J.
AU  - de Vos, Willem M.
AU  - O'Toole, Paul W.
AU  - Cotter, Paul D.
PY  - 2014
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2741
AB  - To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n=105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine.
PB  - Oxford Univ Press, Oxford
T2  - FEMS Microbiology Ecology
T1  - The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota
EP  - 330
IS  - 1
SP  - 326
VL  - 90
DO  - 10.1111/1574-6941.12396
ER  - 

@article{
author = "Scanlan, Pauline D. and Stensvold, Christen R. and Rajilić-Stojanović, Mirjana and Heilig, Hans G. H. J. and de Vos, Willem M. and O'Toole, Paul W. and Cotter, Paul D.",
year = "2014",
abstract = "To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n=105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine.",
publisher = "Oxford Univ Press, Oxford",
journal = "FEMS Microbiology Ecology",
title = "The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota",
pages = "330-326",
number = "1",
volume = "90",
doi = "10.1111/1574-6941.12396"
}

Scanlan, P. D., Stensvold, C. R., Rajilić-Stojanović, M., Heilig, H. G. H. J., de Vos, W. M., O'Toole, P. W.,& Cotter, P. D.. (2014). The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. in FEMS Microbiology Ecology
Oxford Univ Press, Oxford., 90(1), 326-330.
https://doi.org/10.1111/1574-6941.12396

Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HGHJ, de Vos WM, O'Toole PW, Cotter PD. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. in FEMS Microbiology Ecology. 2014;90(1):326-330.
doi:10.1111/1574-6941.12396 .

Scanlan, Pauline D., Stensvold, Christen R., Rajilić-Stojanović, Mirjana, Heilig, Hans G. H. J., de Vos, Willem M., O'Toole, Paul W., Cotter, Paul D., "The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota" in FEMS Microbiology Ecology, 90, no. 1 (2014):326-330,
https://doi.org/10.1111/1574-6941.12396 . .

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Heilig, Hans G. H. J.
AU  - Tims, Sebastian
AU  - Zoetendal, Erwin G.
AU  - de Vos, Willem M.
PY  - 2013
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2518
AB  - The microbiota that colonizes the human intestinal tract is complex and its structure is specific for each of us. In this study we expand the knowledge about the stability of the subject-specific microbiota and show that this ecosystem is stable in short-term intervals ( lt 1 year) but also during long periods of time ( gt 10 years). The faecal microbiota composition of five unrelated and healthy subjects was analysed using a comprehensive and highly reproducible phylogenetic microarray, the HITChip. The results show that the use of antibiotics, application of specific dietary regimes and distant travelling have limited impact on the microbiota composition. Several anaerobic genera, including Bifidobacterium and a number of genera within the Bacteroidetes and the Firmicutes phylum, exhibit significantly higher similarity than the total microbiota. Although the gut microbiota contains subject-specific species, the presence of which is preserved throughout the years, their relative abundance changes considerably. Consequently, the recently proposed enterotype status appears to be a varying characteristic of the microbiota. Our data show that the intestinal microbiota contains a core community of permanent colonizers, and that environmentally introduced changes of the microbiota throughout adulthood are primarily affecting the abundance but not the presence of specific microbial species.
PB  - Wiley, Hoboken
T2  - Environmental Microbiology
T1  - Long-term monitoring of the human intestinal microbiota composition
EP  - 1159
IS  - 4
SP  - 1146
VL  - 15
DO  - 10.1111/1462-2920.12023
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and Heilig, Hans G. H. J. and Tims, Sebastian and Zoetendal, Erwin G. and de Vos, Willem M.",
year = "2013",
abstract = "The microbiota that colonizes the human intestinal tract is complex and its structure is specific for each of us. In this study we expand the knowledge about the stability of the subject-specific microbiota and show that this ecosystem is stable in short-term intervals ( lt 1 year) but also during long periods of time ( gt 10 years). The faecal microbiota composition of five unrelated and healthy subjects was analysed using a comprehensive and highly reproducible phylogenetic microarray, the HITChip. The results show that the use of antibiotics, application of specific dietary regimes and distant travelling have limited impact on the microbiota composition. Several anaerobic genera, including Bifidobacterium and a number of genera within the Bacteroidetes and the Firmicutes phylum, exhibit significantly higher similarity than the total microbiota. Although the gut microbiota contains subject-specific species, the presence of which is preserved throughout the years, their relative abundance changes considerably. Consequently, the recently proposed enterotype status appears to be a varying characteristic of the microbiota. Our data show that the intestinal microbiota contains a core community of permanent colonizers, and that environmentally introduced changes of the microbiota throughout adulthood are primarily affecting the abundance but not the presence of specific microbial species.",
publisher = "Wiley, Hoboken",
journal = "Environmental Microbiology",
title = "Long-term monitoring of the human intestinal microbiota composition",
pages = "1159-1146",
number = "4",
volume = "15",
doi = "10.1111/1462-2920.12023"
}

Rajilić-Stojanović, M., Heilig, H. G. H. J., Tims, S., Zoetendal, E. G.,& de Vos, W. M.. (2013). Long-term monitoring of the human intestinal microbiota composition. in Environmental Microbiology
Wiley, Hoboken., 15(4), 1146-1159.
https://doi.org/10.1111/1462-2920.12023

Rajilić-Stojanović M, Heilig HGHJ, Tims S, Zoetendal EG, de Vos WM. Long-term monitoring of the human intestinal microbiota composition. in Environmental Microbiology. 2013;15(4):1146-1159.
doi:10.1111/1462-2920.12023 .

Rajilić-Stojanović, Mirjana, Heilig, Hans G. H. J., Tims, Sebastian, Zoetendal, Erwin G., de Vos, Willem M., "Long-term monitoring of the human intestinal microbiota composition" in Environmental Microbiology, 15, no. 4 (2013):1146-1159,
https://doi.org/10.1111/1462-2920.12023 . .

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Biagi, Elena
AU  - Heilig, Hans G. H. J.
AU  - Kajander, Kajsa
AU  - Kekkonen, Riina A.
AU  - Tims, Sebastian
AU  - de Vos, Willem M.
PY  - 2011
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1854
AB  - BACKGROUND & AIMS: Irritable bowel syndrome (IBS) has been associated with disruptions to the intestinal microbiota, but studies have had limited power, coverage, and depth of analysis. We aimed to define microbial populations that can be used discriminate the fecal microbiota of patients with IBS from that of healthy subjects and correlate these with IBS intestinal symptom scores. METHODS: The microbiota composition was assessed by global and deep molecular analysis of fecal samples from 62 patients with IBS patients and 46 healthy individuals (controls). We used a comprehensive and highly reproducible phylogenetic microarray in combination with quantitative polymerase chain reaction. RESULTS: The intestinal microbiota of IBS patients differed significantly (P=.0005) from that of controls. The microbiota of patients, compared with controls, had a 2-fold increased ratio of the Firmicutes to Bacteroidetes (P=.0002). This resulted from an approximately 1.5-fold increase in numbers of Dorea, Ruminococcus, and Clostridium spp (P lt .005); a 2-fold decrease in the number of Bacteroidetes (P lt .0001); a 1.5-fold decrease in numbers of Bifidobacterium and Faecalibacterium spp (P lt .05); and, when present, a 4-fold lower average number of methanogens (3.50 x 10(7) vs 8.74 x 10(6) cells/g feces; P=.003). Correlation analysis of the microbial groups and IBS symptom scores indicated the involvement of several groups of Firmicutes and Proteobacteria in the pathogenesis of IBS. CONCLUSIONS: Global and deep molecular analysis of fecal samples indicates that patients with IBS have a different composition of microbiota. This information might be used to develop better diagnostics and ultimately treatments for IBS.
PB  - W B Saunders Co-Elsevier Inc, Philadelphia
T2  - Gastroenterology
T1  - Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome
EP  - 1801
IS  - 5
SP  - 1792
VL  - 141
DO  - 10.1053/j.gastro.2011.07.043
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and Biagi, Elena and Heilig, Hans G. H. J. and Kajander, Kajsa and Kekkonen, Riina A. and Tims, Sebastian and de Vos, Willem M.",
year = "2011",
abstract = "BACKGROUND & AIMS: Irritable bowel syndrome (IBS) has been associated with disruptions to the intestinal microbiota, but studies have had limited power, coverage, and depth of analysis. We aimed to define microbial populations that can be used discriminate the fecal microbiota of patients with IBS from that of healthy subjects and correlate these with IBS intestinal symptom scores. METHODS: The microbiota composition was assessed by global and deep molecular analysis of fecal samples from 62 patients with IBS patients and 46 healthy individuals (controls). We used a comprehensive and highly reproducible phylogenetic microarray in combination with quantitative polymerase chain reaction. RESULTS: The intestinal microbiota of IBS patients differed significantly (P=.0005) from that of controls. The microbiota of patients, compared with controls, had a 2-fold increased ratio of the Firmicutes to Bacteroidetes (P=.0002). This resulted from an approximately 1.5-fold increase in numbers of Dorea, Ruminococcus, and Clostridium spp (P lt .005); a 2-fold decrease in the number of Bacteroidetes (P lt .0001); a 1.5-fold decrease in numbers of Bifidobacterium and Faecalibacterium spp (P lt .05); and, when present, a 4-fold lower average number of methanogens (3.50 x 10(7) vs 8.74 x 10(6) cells/g feces; P=.003). Correlation analysis of the microbial groups and IBS symptom scores indicated the involvement of several groups of Firmicutes and Proteobacteria in the pathogenesis of IBS. CONCLUSIONS: Global and deep molecular analysis of fecal samples indicates that patients with IBS have a different composition of microbiota. This information might be used to develop better diagnostics and ultimately treatments for IBS.",
publisher = "W B Saunders Co-Elsevier Inc, Philadelphia",
journal = "Gastroenterology",
title = "Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome",
pages = "1801-1792",
number = "5",
volume = "141",
doi = "10.1053/j.gastro.2011.07.043"
}

Rajilić-Stojanović, M., Biagi, E., Heilig, H. G. H. J., Kajander, K., Kekkonen, R. A., Tims, S.,& de Vos, W. M.. (2011). Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome. in Gastroenterology
W B Saunders Co-Elsevier Inc, Philadelphia., 141(5), 1792-1801.
https://doi.org/10.1053/j.gastro.2011.07.043

Rajilić-Stojanović M, Biagi E, Heilig HGHJ, Kajander K, Kekkonen RA, Tims S, de Vos WM. Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome. in Gastroenterology. 2011;141(5):1792-1801.
doi:10.1053/j.gastro.2011.07.043 .

Rajilić-Stojanović, Mirjana, Biagi, Elena, Heilig, Hans G. H. J., Kajander, Kajsa, Kekkonen, Riina A., Tims, Sebastian, de Vos, Willem M., "Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome" in Gastroenterology, 141, no. 5 (2011):1792-1801,
https://doi.org/10.1053/j.gastro.2011.07.043 . .

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 . .

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 . .

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 . .