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  - 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 . .

TY  - JOUR
AU  - Kajander, Kajsa
AU  - Myllyluoma, E.
AU  - Rajilić-Stojanović, Mirjana
AU  - Kyronpalo, S.
AU  - Rasmussen, M.
AU  - Jarvenpaa, S.
AU  - Zoetendal, Erwin G.
AU  - de Vos, Willem M.
AU  - Vapaatalo, H.
AU  - Korpela, R.
PY  - 2008
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1269
AB  - Background Irritable bowel syndrome is the most common diagnosis in gastroenterology. Trials suggest certain probiotics to be beneficial. Aim To investigate the effects of multispecies probiotic supplementation (Lactobacillus rhamnosus GG, L. rhamnosus Lc705, Propionibacterium freudenreichii ssp. shermanii JS and Bifidobacterium animalis ssp. lactis Bb 12) on abdominal symptoms, quality of life, intestinal microbiota and inflammatory markers in irritable bowel syndrome. Methods Eighty-six irritable bowel syndrome patients (Rome 11 criteria) participated in this randomized, placebo-controlled 5-month intervention. Patients were randomized to receive daily either multispecies probiotic supplementation or placebo. Irritable bowel syndrome symptoms, quality of life, microarray-based intestinal microbiota stability (n = 20), serum cytokines and sensitive C-reactive protein were monitored. Results The composite irritable bowel syndrome score had at 5 months decreased 14 points (95% CI: -19 to -9) from baseline with the multispecies probiotic vs. three points (95% CI: -8 to 1) with placebo (P = 0.0083). Especially, distension and abdominal pain were affected. A stabilization of the microbiota was observed, as the microbiota similarity index increased with the probiotic supplementation (1.9 +/- 3.1), while it decreased with placebo (-2.9 +/- 1.7). No differences were seen in C-reactive protein. Conclusions This multispecies probiotic seems to be an effective and safe option to alleviate symptoms of irritable bowel syndrome, and to stabilize the intestinal microbiota.
PB  - Wiley, Hoboken
T2  - Alimentary Pharmacology & Therapeutics
T1  - Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota
EP  - 57
IS  - 1
SP  - 48
VL  - 27
DO  - 10.1111/j.1365-2036.2007.03542.x
ER  - 

@article{
author = "Kajander, Kajsa and Myllyluoma, E. and Rajilić-Stojanović, Mirjana and Kyronpalo, S. and Rasmussen, M. and Jarvenpaa, S. and Zoetendal, Erwin G. and de Vos, Willem M. and Vapaatalo, H. and Korpela, R.",
year = "2008",
abstract = "Background Irritable bowel syndrome is the most common diagnosis in gastroenterology. Trials suggest certain probiotics to be beneficial. Aim To investigate the effects of multispecies probiotic supplementation (Lactobacillus rhamnosus GG, L. rhamnosus Lc705, Propionibacterium freudenreichii ssp. shermanii JS and Bifidobacterium animalis ssp. lactis Bb 12) on abdominal symptoms, quality of life, intestinal microbiota and inflammatory markers in irritable bowel syndrome. Methods Eighty-six irritable bowel syndrome patients (Rome 11 criteria) participated in this randomized, placebo-controlled 5-month intervention. Patients were randomized to receive daily either multispecies probiotic supplementation or placebo. Irritable bowel syndrome symptoms, quality of life, microarray-based intestinal microbiota stability (n = 20), serum cytokines and sensitive C-reactive protein were monitored. Results The composite irritable bowel syndrome score had at 5 months decreased 14 points (95% CI: -19 to -9) from baseline with the multispecies probiotic vs. three points (95% CI: -8 to 1) with placebo (P = 0.0083). Especially, distension and abdominal pain were affected. A stabilization of the microbiota was observed, as the microbiota similarity index increased with the probiotic supplementation (1.9 +/- 3.1), while it decreased with placebo (-2.9 +/- 1.7). No differences were seen in C-reactive protein. Conclusions This multispecies probiotic seems to be an effective and safe option to alleviate symptoms of irritable bowel syndrome, and to stabilize the intestinal microbiota.",
publisher = "Wiley, Hoboken",
journal = "Alimentary Pharmacology & Therapeutics",
title = "Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota",
pages = "57-48",
number = "1",
volume = "27",
doi = "10.1111/j.1365-2036.2007.03542.x"
}

Kajander, K., Myllyluoma, E., Rajilić-Stojanović, M., Kyronpalo, S., Rasmussen, M., Jarvenpaa, S., Zoetendal, E. G., de Vos, W. M., Vapaatalo, H.,& Korpela, R.. (2008). Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. in Alimentary Pharmacology & Therapeutics
Wiley, Hoboken., 27(1), 48-57.
https://doi.org/10.1111/j.1365-2036.2007.03542.x

Kajander K, Myllyluoma E, Rajilić-Stojanović M, Kyronpalo S, Rasmussen M, Jarvenpaa S, Zoetendal EG, de Vos WM, Vapaatalo H, Korpela R. Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. in Alimentary Pharmacology & Therapeutics. 2008;27(1):48-57.
doi:10.1111/j.1365-2036.2007.03542.x .

Kajander, Kajsa, Myllyluoma, E., Rajilić-Stojanović, Mirjana, Kyronpalo, S., Rasmussen, M., Jarvenpaa, S., Zoetendal, Erwin G., de Vos, Willem M., Vapaatalo, H., Korpela, R., "Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota" in Alimentary Pharmacology & Therapeutics, 27, no. 1 (2008):48-57,
https://doi.org/10.1111/j.1365-2036.2007.03542.x . .