TY  - JOUR
AU  - Vork, Lisa
AU  - Penders, John
AU  - Jalanka, Jonna
AU  - Bojic, Svetlana
AU  - van Kuijk, Sander M. J.
AU  - Salonen, Anne
AU  - de Vos, Willem M.
AU  - Rajilić-Stojanović, Mirjana
AU  - Weerts, Zsa Zsa R. M.
AU  - Masclee, Ad A. M.
AU  - Pozuelo, Marta
AU  - Manichanh, Chaysavanh
AU  - Jonkers, Daisy M. A. E.
PY  - 2021
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/4854
AB  - Introduction Stool consistency has been associated with fecal microbial composition. Stool consistency often varies over time, in subjects with and without gastrointestinal disorders, raising the question whether variability in the microbial composition should be considered in microbiota studies. We evaluated within-subject day-to-day variability in stool consistency and the association with the fecal microbiota in irritable bowel syndrome (IBS) and healthy subjects, over seven days. Methods Twelve IBS patients and 12 healthy subjects collected fecal samples during seven consecutive days. Stool consistency was determined by the patient-reported Bristol Stool Scale (BSS) and fecal dry weight percentage. 16S rRNA V4 gene sequencing was performed and microbial richness (alpha diversity; Chao1 index, observed number of species, effective Shannon index) and microbial community structure (beta diversity; Bray-Curtis distance, generalized UniFrac, and taxa abundance on family level) were determined. Results Linear mixed-effects models showed significant associations between stool consistency and microbial richness, but no time effect. This implies that between-subject but not within-subject variation in microbiota over time can partially be explained by variation in stool consistency. Redundancy analysis showed a significant association between stool consistency and microbial community structure, but additional linear mixed-effects models did not demonstrate a time effect on this. Conclusion This study supports an association between stool consistency and fecal microbiota, but no effect of day-to-day fluctuations in stool consistency within seven days. This consolidates the importance of considering stool consistency in gut microbiota research, though confirms the validity of single fecal sampling to represent an individual's microbiota at a given time point. NCT00775060.
T2  - Frontiers in Cellular and Infection Microbiology
T1  - Does Day-to-Day Variability in Stool Consistency Link to the Fecal Microbiota Composition?
VL  - 11
DO  - 10.3389/fcimb.2021.639667
ER  - 

@article{
author = "Vork, Lisa and Penders, John and Jalanka, Jonna and Bojic, Svetlana and van Kuijk, Sander M. J. and Salonen, Anne and de Vos, Willem M. and Rajilić-Stojanović, Mirjana and Weerts, Zsa Zsa R. M. and Masclee, Ad A. M. and Pozuelo, Marta and Manichanh, Chaysavanh and Jonkers, Daisy M. A. E.",
year = "2021",
abstract = "Introduction Stool consistency has been associated with fecal microbial composition. Stool consistency often varies over time, in subjects with and without gastrointestinal disorders, raising the question whether variability in the microbial composition should be considered in microbiota studies. We evaluated within-subject day-to-day variability in stool consistency and the association with the fecal microbiota in irritable bowel syndrome (IBS) and healthy subjects, over seven days. Methods Twelve IBS patients and 12 healthy subjects collected fecal samples during seven consecutive days. Stool consistency was determined by the patient-reported Bristol Stool Scale (BSS) and fecal dry weight percentage. 16S rRNA V4 gene sequencing was performed and microbial richness (alpha diversity; Chao1 index, observed number of species, effective Shannon index) and microbial community structure (beta diversity; Bray-Curtis distance, generalized UniFrac, and taxa abundance on family level) were determined. Results Linear mixed-effects models showed significant associations between stool consistency and microbial richness, but no time effect. This implies that between-subject but not within-subject variation in microbiota over time can partially be explained by variation in stool consistency. Redundancy analysis showed a significant association between stool consistency and microbial community structure, but additional linear mixed-effects models did not demonstrate a time effect on this. Conclusion This study supports an association between stool consistency and fecal microbiota, but no effect of day-to-day fluctuations in stool consistency within seven days. This consolidates the importance of considering stool consistency in gut microbiota research, though confirms the validity of single fecal sampling to represent an individual's microbiota at a given time point. NCT00775060.",
journal = "Frontiers in Cellular and Infection Microbiology",
title = "Does Day-to-Day Variability in Stool Consistency Link to the Fecal Microbiota Composition?",
volume = "11",
doi = "10.3389/fcimb.2021.639667"
}

Vork, L., Penders, J., Jalanka, J., Bojic, S., van Kuijk, S. M. J., Salonen, A., de Vos, W. M., Rajilić-Stojanović, M., Weerts, Z. Z. R. M., Masclee, A. A. M., Pozuelo, M., Manichanh, C.,& Jonkers, D. M. A. E.. (2021). Does Day-to-Day Variability in Stool Consistency Link to the Fecal Microbiota Composition?. in Frontiers in Cellular and Infection Microbiology, 11.
https://doi.org/10.3389/fcimb.2021.639667

Vork L, Penders J, Jalanka J, Bojic S, van Kuijk SMJ, Salonen A, de Vos WM, Rajilić-Stojanović M, Weerts ZZRM, Masclee AAM, Pozuelo M, Manichanh C, Jonkers DMAE. Does Day-to-Day Variability in Stool Consistency Link to the Fecal Microbiota Composition?. in Frontiers in Cellular and Infection Microbiology. 2021;11.
doi:10.3389/fcimb.2021.639667 .

Vork, Lisa, Penders, John, Jalanka, Jonna, Bojic, Svetlana, van Kuijk, Sander M. J., Salonen, Anne, de Vos, Willem M., Rajilić-Stojanović, Mirjana, Weerts, Zsa Zsa R. M., Masclee, Ad A. M., Pozuelo, Marta, Manichanh, Chaysavanh, Jonkers, Daisy M. A. E., "Does Day-to-Day Variability in Stool Consistency Link to the Fecal Microbiota Composition?" in Frontiers in Cellular and Infection Microbiology, 11 (2021),
https://doi.org/10.3389/fcimb.2021.639667 . .

TY  - JOUR
AU  - Cammarota, Giovanni
AU  - Ianiro, Gianluca
AU  - Tilg, Herbert
AU  - Rajilić-Stojanović, Mirjana
AU  - Kump, Patrizia
AU  - Satokari, Reetta
AU  - Sokol, Harry
AU  - Arkkila, Perttu
AU  - Pintus, Cristina
AU  - Hart, Ailsa
AU  - Segal, Jonathan
AU  - Aloi, Marina
AU  - Masucci, Luca
AU  - Molinaro, Antonio
AU  - Scaldaferri, Franco
AU  - Gasbarrini, Giovanni
AU  - Lopez-Sanroman, Antonio
AU  - Link, Alexander
AU  - De Groot, Pieter
AU  - de Vos, Willem M.
AU  - Hoegenauer, Christoph
AU  - Malfertheiner, Peter
AU  - Mattila, Eero
AU  - Milosavljević, Tomica
AU  - Nieuwdorp, Max
AU  - Sanguinetti, Maurizio
AU  - Simren, Magnus
AU  - Gasbarrini, Antonio
PY  - 2017
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/3706
AB  - Faecal microbiota transplantation (FMT) is an important therapeutic option for Clostridium difficile infection. Promising findings suggest that FMT may play a role also in the management of other disorders associated with the alteration of gut microbiota. Although the health community is assessing FMT with renewed interest and patients are becoming more aware, there are technical and logistical issues in establishing such a non-standardised treatment into the clinical practice with safety and proper governance. In view of this, an evidence-based recommendation is needed to drive the practical implementation of FMT. In this European Consensus Conference, 28 experts from 10 countries collaborated, in separate working groups and through an evidence-based process, to provide statements on the following key issues: FMT indications; donor selection; preparation of faecal material; clinical management and faecal delivery and basic requirements for implementing an FMT centre. Statements developed by each working group were evaluated and voted by all members, first through an electronic Delphi process, and then in a plenary consensus conference. The recommendations were released according to best available evidence, in order to act as guidance for physicians who plan to implement FMT, aiming at supporting the broad availability of the procedure, discussing other issues relevant to FMT and promoting future clinical research in the area of gut microbiota manipulation. This consensus report strongly recommends the implementation of FMT centres for the treatment of C. difficile infection as well as traces the guidelines of technicality, regulatory, administrative and laboratory requirements.
PB  - Bmj Publishing Group, London
T2  - GUT
T1  - European consensus conference on faecal microbiota transplantation in clinical practice
EP  - 580
IS  - 4
SP  - 569
VL  - 66
DO  - 10.1136/gutjnl-2016-313017
ER  - 

@article{
author = "Cammarota, Giovanni and Ianiro, Gianluca and Tilg, Herbert and Rajilić-Stojanović, Mirjana and Kump, Patrizia and Satokari, Reetta and Sokol, Harry and Arkkila, Perttu and Pintus, Cristina and Hart, Ailsa and Segal, Jonathan and Aloi, Marina and Masucci, Luca and Molinaro, Antonio and Scaldaferri, Franco and Gasbarrini, Giovanni and Lopez-Sanroman, Antonio and Link, Alexander and De Groot, Pieter and de Vos, Willem M. and Hoegenauer, Christoph and Malfertheiner, Peter and Mattila, Eero and Milosavljević, Tomica and Nieuwdorp, Max and Sanguinetti, Maurizio and Simren, Magnus and Gasbarrini, Antonio",
year = "2017",
abstract = "Faecal microbiota transplantation (FMT) is an important therapeutic option for Clostridium difficile infection. Promising findings suggest that FMT may play a role also in the management of other disorders associated with the alteration of gut microbiota. Although the health community is assessing FMT with renewed interest and patients are becoming more aware, there are technical and logistical issues in establishing such a non-standardised treatment into the clinical practice with safety and proper governance. In view of this, an evidence-based recommendation is needed to drive the practical implementation of FMT. In this European Consensus Conference, 28 experts from 10 countries collaborated, in separate working groups and through an evidence-based process, to provide statements on the following key issues: FMT indications; donor selection; preparation of faecal material; clinical management and faecal delivery and basic requirements for implementing an FMT centre. Statements developed by each working group were evaluated and voted by all members, first through an electronic Delphi process, and then in a plenary consensus conference. The recommendations were released according to best available evidence, in order to act as guidance for physicians who plan to implement FMT, aiming at supporting the broad availability of the procedure, discussing other issues relevant to FMT and promoting future clinical research in the area of gut microbiota manipulation. This consensus report strongly recommends the implementation of FMT centres for the treatment of C. difficile infection as well as traces the guidelines of technicality, regulatory, administrative and laboratory requirements.",
publisher = "Bmj Publishing Group, London",
journal = "GUT",
title = "European consensus conference on faecal microbiota transplantation in clinical practice",
pages = "580-569",
number = "4",
volume = "66",
doi = "10.1136/gutjnl-2016-313017"
}

Cammarota, G., Ianiro, G., Tilg, H., Rajilić-Stojanović, M., Kump, P., Satokari, R., Sokol, H., Arkkila, P., Pintus, C., Hart, A., Segal, J., Aloi, M., Masucci, L., Molinaro, A., Scaldaferri, F., Gasbarrini, G., Lopez-Sanroman, A., Link, A., De Groot, P., de Vos, W. M., Hoegenauer, C., Malfertheiner, P., Mattila, E., Milosavljević, T., Nieuwdorp, M., Sanguinetti, M., Simren, M.,& Gasbarrini, A.. (2017). European consensus conference on faecal microbiota transplantation in clinical practice. in GUT
Bmj Publishing Group, London., 66(4), 569-580.
https://doi.org/10.1136/gutjnl-2016-313017

Cammarota G, Ianiro G, Tilg H, Rajilić-Stojanović M, Kump P, Satokari R, Sokol H, Arkkila P, Pintus C, Hart A, Segal J, Aloi M, Masucci L, Molinaro A, Scaldaferri F, Gasbarrini G, Lopez-Sanroman A, Link A, De Groot P, de Vos WM, Hoegenauer C, Malfertheiner P, Mattila E, Milosavljević T, Nieuwdorp M, Sanguinetti M, Simren M, Gasbarrini A. European consensus conference on faecal microbiota transplantation in clinical practice. in GUT. 2017;66(4):569-580.
doi:10.1136/gutjnl-2016-313017 .

Cammarota, Giovanni, Ianiro, Gianluca, Tilg, Herbert, Rajilić-Stojanović, Mirjana, Kump, Patrizia, Satokari, Reetta, Sokol, Harry, Arkkila, Perttu, Pintus, Cristina, Hart, Ailsa, Segal, Jonathan, Aloi, Marina, Masucci, Luca, Molinaro, Antonio, Scaldaferri, Franco, Gasbarrini, Giovanni, Lopez-Sanroman, Antonio, Link, Alexander, De Groot, Pieter, de Vos, Willem M., Hoegenauer, Christoph, Malfertheiner, Peter, Mattila, Eero, Milosavljević, Tomica, Nieuwdorp, Max, Sanguinetti, Maurizio, Simren, Magnus, Gasbarrini, Antonio, "European consensus conference on faecal microbiota transplantation in clinical practice" in GUT, 66, no. 4 (2017):569-580,
https://doi.org/10.1136/gutjnl-2016-313017 . .

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - Jonkers, Daisy M.
AU  - Salonen, Anne
AU  - Hanevik, Kurt
AU  - Raes, Jeroen
AU  - Jalanka, Jonna
AU  - de Vos, Willem M.
AU  - Manichanh, Chaysavanh
AU  - Golić, Nataša
AU  - Enck, Paul
AU  - Philippou, Elena
AU  - Iraqi, Fuad A.
AU  - Clarke, Gerard
AU  - Spiller, Robin C.
AU  - Penders, John
PY  - 2015
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2973
AB  - Irritable bowel syndrome (IBS) is a heterogeneous functional disorder with a multifactorial etiology that involves the interplay of both host and environmental factors. Among environmental factors relevant for IBS etiology, the diet stands out given that the majority of IBS patients report their symptoms to be triggered by meals or specifi c foods. The diet provides substrates for microbial fermentation, and, as the composition of the intestinal microbiota is disturbed in IBS patients, the link between diet, microbiota composition, and microbial fermentation products might have an essential role in IBS etiology. In this review, we summarize current evidence regarding the impact of diet and the intestinal microbiota on IBS symptoms, as well as the reported interactions between diet and the microbiota composition. On the basis of the existing data, we suggest pathways (mechanisms) by which diet components, via the microbial fermentation, could trigger IBS symptoms. Finally, this review provides recommendations for future studies that would enable elucidation of the role of diet and microbiota and how these factors may be (inter) related in the pathophysiology of IBS.
PB  - Lippincott Williams & Wilkins, Philadelphia
T2  - American Journal of Gastroenterology
T1  - Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?
EP  - 287
IS  - 2
SP  - 278
VL  - 110
DO  - 10.1038/ajg.2014.427
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and Jonkers, Daisy M. and Salonen, Anne and Hanevik, Kurt and Raes, Jeroen and Jalanka, Jonna and de Vos, Willem M. and Manichanh, Chaysavanh and Golić, Nataša and Enck, Paul and Philippou, Elena and Iraqi, Fuad A. and Clarke, Gerard and Spiller, Robin C. and Penders, John",
year = "2015",
abstract = "Irritable bowel syndrome (IBS) is a heterogeneous functional disorder with a multifactorial etiology that involves the interplay of both host and environmental factors. Among environmental factors relevant for IBS etiology, the diet stands out given that the majority of IBS patients report their symptoms to be triggered by meals or specifi c foods. The diet provides substrates for microbial fermentation, and, as the composition of the intestinal microbiota is disturbed in IBS patients, the link between diet, microbiota composition, and microbial fermentation products might have an essential role in IBS etiology. In this review, we summarize current evidence regarding the impact of diet and the intestinal microbiota on IBS symptoms, as well as the reported interactions between diet and the microbiota composition. On the basis of the existing data, we suggest pathways (mechanisms) by which diet components, via the microbial fermentation, could trigger IBS symptoms. Finally, this review provides recommendations for future studies that would enable elucidation of the role of diet and microbiota and how these factors may be (inter) related in the pathophysiology of IBS.",
publisher = "Lippincott Williams & Wilkins, Philadelphia",
journal = "American Journal of Gastroenterology",
title = "Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?",
pages = "287-278",
number = "2",
volume = "110",
doi = "10.1038/ajg.2014.427"
}

Rajilić-Stojanović, M., Jonkers, D. M., Salonen, A., Hanevik, K., Raes, J., Jalanka, J., de Vos, W. M., Manichanh, C., Golić, N., Enck, P., Philippou, E., Iraqi, F. A., Clarke, G., Spiller, R. C.,& Penders, J.. (2015). Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?. in American Journal of Gastroenterology
Lippincott Williams & Wilkins, Philadelphia., 110(2), 278-287.
https://doi.org/10.1038/ajg.2014.427

Rajilić-Stojanović M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, de Vos WM, Manichanh C, Golić N, Enck P, Philippou E, Iraqi FA, Clarke G, Spiller RC, Penders J. Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?. in American Journal of Gastroenterology. 2015;110(2):278-287.
doi:10.1038/ajg.2014.427 .

Rajilić-Stojanović, Mirjana, Jonkers, Daisy M., Salonen, Anne, Hanevik, Kurt, Raes, Jeroen, Jalanka, Jonna, de Vos, Willem M., Manichanh, Chaysavanh, Golić, Nataša, Enck, Paul, Philippou, Elena, Iraqi, Fuad A., Clarke, Gerard, Spiller, Robin C., Penders, John, "Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?" in American Journal of Gastroenterology, 110, no. 2 (2015):278-287,
https://doi.org/10.1038/ajg.2014.427 . .

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - de Vos, Willem M.
PY  - 2014
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2731
AB  - The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
PB  - Oxford Univ Press, Oxford
T2  - FEMS Microbiology Reviews
T1  - The first 1000 cultured species of the human gastrointestinal microbiota
EP  - 1047
IS  - 5
SP  - 996
VL  - 38
DO  - 10.1111/1574-6976.12075
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and de Vos, Willem M.",
year = "2014",
abstract = "The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.",
publisher = "Oxford Univ Press, Oxford",
journal = "FEMS Microbiology Reviews",
title = "The first 1000 cultured species of the human gastrointestinal microbiota",
pages = "1047-996",
number = "5",
volume = "38",
doi = "10.1111/1574-6976.12075"
}

Rajilić-Stojanović, M.,& de Vos, W. M.. (2014). The first 1000 cultured species of the human gastrointestinal microbiota. in FEMS Microbiology Reviews
Oxford Univ Press, Oxford., 38(5), 996-1047.
https://doi.org/10.1111/1574-6976.12075

Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. in FEMS Microbiology Reviews. 2014;38(5):996-1047.
doi:10.1111/1574-6976.12075 .

Rajilić-Stojanović, Mirjana, de Vos, Willem M., "The first 1000 cultured species of the human gastrointestinal microbiota" in FEMS Microbiology Reviews, 38, no. 5 (2014):996-1047,
https://doi.org/10.1111/1574-6976.12075 . .

TY  - JOUR
AU  - Wacklin, Pirjo
AU  - Tuimala, Jarno
AU  - Nikkila, Janne
AU  - Tims, Sebastian
AU  - Makivuokko, Harri
AU  - Alakulppi, Noora
AU  - Laine, Pia
AU  - Rajilić-Stojanović, Mirjana
AU  - Paulin, Lars
AU  - de Vos, Willem M.
AU  - Matto, Jaana
PY  - 2014
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2814
AB  - The human intestine is colonised with highly diverse and individually defined microbiota, which likely has an impact on the host well-being. Drivers of the individual variation in the microbiota compositions are multifactorial and include environmental, host and dietary factors. We studied the impact of the host secretor status, encoded by fucosyltransferase 2 (FUT2) -gene, on the intestinal microbiota composition. Secretor status determines the expression of the ABH and Lewis histo-blood group antigens in the intestinal mucosa. The study population was comprised of 14 non-secretor (FUT2 rs601338 genotype AA) and 57 secretor (genotypes GG and AG) adult individuals of western European descent. Intestinal microbiota was analyzed by PCR-DGGE and for a subset of 12 non-secretor subjects and 12 secretor subjects additionally by the 16S rRNA gene pyrosequencing and the HITChip phylogenetic microarray analysis. All three methods showed distinct clustering of the intestinal microbiota and significant differences in abundances of several taxa representing dominant microbiota between the non-secretors and the secretors as well as between the FUT2 genotypes. In addition, the non-secretors had lower species richness than the secretors. The soft clustering of microbiota into enterotypes (ET) 1 and 3 showed that the non-secretors had a higher probability of belonging to ET1 and the secretors to ET3. Our study shows that secretor status and FUT2 polymorphism are associated with the composition of human intestinal microbiota, and appears thus to be one of the key drivers affecting the individual variation of human intestinal microbiota.
PB  - Public Library Science, San Francisco
T2  - PLoS One
T1  - Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status
IS  - 4
VL  - 9
DO  - 10.1371/journal.pone.0094863
ER  - 

@article{
author = "Wacklin, Pirjo and Tuimala, Jarno and Nikkila, Janne and Tims, Sebastian and Makivuokko, Harri and Alakulppi, Noora and Laine, Pia and Rajilić-Stojanović, Mirjana and Paulin, Lars and de Vos, Willem M. and Matto, Jaana",
year = "2014",
abstract = "The human intestine is colonised with highly diverse and individually defined microbiota, which likely has an impact on the host well-being. Drivers of the individual variation in the microbiota compositions are multifactorial and include environmental, host and dietary factors. We studied the impact of the host secretor status, encoded by fucosyltransferase 2 (FUT2) -gene, on the intestinal microbiota composition. Secretor status determines the expression of the ABH and Lewis histo-blood group antigens in the intestinal mucosa. The study population was comprised of 14 non-secretor (FUT2 rs601338 genotype AA) and 57 secretor (genotypes GG and AG) adult individuals of western European descent. Intestinal microbiota was analyzed by PCR-DGGE and for a subset of 12 non-secretor subjects and 12 secretor subjects additionally by the 16S rRNA gene pyrosequencing and the HITChip phylogenetic microarray analysis. All three methods showed distinct clustering of the intestinal microbiota and significant differences in abundances of several taxa representing dominant microbiota between the non-secretors and the secretors as well as between the FUT2 genotypes. In addition, the non-secretors had lower species richness than the secretors. The soft clustering of microbiota into enterotypes (ET) 1 and 3 showed that the non-secretors had a higher probability of belonging to ET1 and the secretors to ET3. Our study shows that secretor status and FUT2 polymorphism are associated with the composition of human intestinal microbiota, and appears thus to be one of the key drivers affecting the individual variation of human intestinal microbiota.",
publisher = "Public Library Science, San Francisco",
journal = "PLoS One",
title = "Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status",
number = "4",
volume = "9",
doi = "10.1371/journal.pone.0094863"
}

Wacklin, P., Tuimala, J., Nikkila, J., Tims, S., Makivuokko, H., Alakulppi, N., Laine, P., Rajilić-Stojanović, M., Paulin, L., de Vos, W. M.,& Matto, J.. (2014). Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status. in PLoS One
Public Library Science, San Francisco., 9(4).
https://doi.org/10.1371/journal.pone.0094863

Wacklin P, Tuimala J, Nikkila J, Tims S, Makivuokko H, Alakulppi N, Laine P, Rajilić-Stojanović M, Paulin L, de Vos WM, Matto J. Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status. in PLoS One. 2014;9(4).
doi:10.1371/journal.pone.0094863 .

Wacklin, Pirjo, Tuimala, Jarno, Nikkila, Janne, Tims, Sebastian, Makivuokko, Harri, Alakulppi, Noora, Laine, Pia, Rajilić-Stojanović, Mirjana, Paulin, Lars, de Vos, Willem M., Matto, Jaana, "Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status" in PLoS One, 9, no. 4 (2014),
https://doi.org/10.1371/journal.pone.0094863 . .

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  - Shanahan, Fergus
AU  - Guarner, Francisco
AU  - de Vos, Willem M.
PY  - 2013
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2551
AB  - Background: Presence of intestinal microbes is a prerequisite for the development of ulcerative colitis (UC), although deviation of the normal intestinal microbiota composition, dysbiosis, is presumably implicated in the etiology of UC. Methods: The fecal microbiota of 30 UC samples obtained from 15 patients who were sampled twice and from 15 healthy control subjects originating from 2 geographic locations was analyzed using highly reproducible phylogenetic microarray that has the capacity for detection and quantification of more than 1000 intestinal bacteria in a wide dynamic range. Results: The fecal microbiota composition is not significantly influenced by geographic location, age, or gender, but it differs significantly between the patients with UC and the control subjects (P = 0.0004). UC-associated microbiota is stable during remission and similar among all patients with UC. Significant reduction of bacterial diversity of members of the Clostridium cluster IV and significant reduction in the abundance of bacteria involved in butyrate and propionate metabolism, including Ruminococcus bromii et rel. Eubacterium rectale et rel., Roseburia sp., and Akkermansia sp. are markers of dysbiosis in UC. Increased abundance of (opportunistic) pathogens including Fusobacterium sp., Peptostreptococcus sp., Helicobacter sp., and Campylobacter sp. as well as Clostridium difficile were found to be associated with UC. Conclusions: Dysbiosis in UC is stable in time and shared between patients from different geographic locations. The microbial alterations offer a mechanistic insight into the pathogenesis of the disease. (Inflamm Bowel Dis 2013;19:481-488)
PB  - Lippincott Williams & Wilkins, Philadelphia
T2  - Inflammatory Bowel Diseases
T1  - Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission
EP  - 488
IS  - 3
SP  - 481
VL  - 19
DO  - 10.1097/MIB.0b013e31827fec6d
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and Shanahan, Fergus and Guarner, Francisco and de Vos, Willem M.",
year = "2013",
abstract = "Background: Presence of intestinal microbes is a prerequisite for the development of ulcerative colitis (UC), although deviation of the normal intestinal microbiota composition, dysbiosis, is presumably implicated in the etiology of UC. Methods: The fecal microbiota of 30 UC samples obtained from 15 patients who were sampled twice and from 15 healthy control subjects originating from 2 geographic locations was analyzed using highly reproducible phylogenetic microarray that has the capacity for detection and quantification of more than 1000 intestinal bacteria in a wide dynamic range. Results: The fecal microbiota composition is not significantly influenced by geographic location, age, or gender, but it differs significantly between the patients with UC and the control subjects (P = 0.0004). UC-associated microbiota is stable during remission and similar among all patients with UC. Significant reduction of bacterial diversity of members of the Clostridium cluster IV and significant reduction in the abundance of bacteria involved in butyrate and propionate metabolism, including Ruminococcus bromii et rel. Eubacterium rectale et rel., Roseburia sp., and Akkermansia sp. are markers of dysbiosis in UC. Increased abundance of (opportunistic) pathogens including Fusobacterium sp., Peptostreptococcus sp., Helicobacter sp., and Campylobacter sp. as well as Clostridium difficile were found to be associated with UC. Conclusions: Dysbiosis in UC is stable in time and shared between patients from different geographic locations. The microbial alterations offer a mechanistic insight into the pathogenesis of the disease. (Inflamm Bowel Dis 2013;19:481-488)",
publisher = "Lippincott Williams & Wilkins, Philadelphia",
journal = "Inflammatory Bowel Diseases",
title = "Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission",
pages = "488-481",
number = "3",
volume = "19",
doi = "10.1097/MIB.0b013e31827fec6d"
}

Rajilić-Stojanović, M., Shanahan, F., Guarner, F.,& de Vos, W. M.. (2013). Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission. in Inflammatory Bowel Diseases
Lippincott Williams & Wilkins, Philadelphia., 19(3), 481-488.
https://doi.org/10.1097/MIB.0b013e31827fec6d

Rajilić-Stojanović M, Shanahan F, Guarner F, de Vos WM. Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission. in Inflammatory Bowel Diseases. 2013;19(3):481-488.
doi:10.1097/MIB.0b013e31827fec6d .

Rajilić-Stojanović, Mirjana, Shanahan, Fergus, Guarner, Francisco, de Vos, Willem M., "Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission" in Inflammatory Bowel Diseases, 19, no. 3 (2013):481-488,
https://doi.org/10.1097/MIB.0b013e31827fec6d . .

TY  - JOUR
AU  - Nylund, Lotta
AU  - Satokari, Reetta
AU  - Nikkila, Janne
AU  - Rajilić-Stojanović, Mirjana
AU  - Kalliomaki, Marko
AU  - Isolauri, Erika
AU  - Salminen, Seppo
AU  - de Vos, Willem M.
PY  - 2013
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/2493
AB  - Background: Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo. Results: Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition. Conclusion: A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.
PB  - Biomed Central Ltd, London
T2  - BMC Microbiology
T1  - Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease
VL  - 13
DO  - 10.1186/1471-2180-13-12
ER  - 

@article{
author = "Nylund, Lotta and Satokari, Reetta and Nikkila, Janne and Rajilić-Stojanović, Mirjana and Kalliomaki, Marko and Isolauri, Erika and Salminen, Seppo and de Vos, Willem M.",
year = "2013",
abstract = "Background: Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo. Results: Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition. Conclusion: A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.",
publisher = "Biomed Central Ltd, London",
journal = "BMC Microbiology",
title = "Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease",
volume = "13",
doi = "10.1186/1471-2180-13-12"
}

Nylund, L., Satokari, R., Nikkila, J., Rajilić-Stojanović, M., Kalliomaki, M., Isolauri, E., Salminen, S.,& de Vos, W. M.. (2013). Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease. in BMC Microbiology
Biomed Central Ltd, London., 13.
https://doi.org/10.1186/1471-2180-13-12

Nylund L, Satokari R, Nikkila J, Rajilić-Stojanović M, Kalliomaki M, Isolauri E, Salminen S, de Vos WM. Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease. in BMC Microbiology. 2013;13.
doi:10.1186/1471-2180-13-12 .

Nylund, Lotta, Satokari, Reetta, Nikkila, Janne, Rajilić-Stojanović, Mirjana, Kalliomaki, Marko, Isolauri, Erika, Salminen, Seppo, de Vos, Willem M., "Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease" in BMC Microbiology, 13 (2013),
https://doi.org/10.1186/1471-2180-13-12 . .

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  - Salonen, Anne
AU  - Nikkila, Janne
AU  - Jalanka-Tuovinen, Jonna
AU  - Immonen, Outi
AU  - Rajilić-Stojanović, Mirjana
AU  - Kekkonen, Riina A.
AU  - Palva, Airi
AU  - de Vos, Willem M.
PY  - 2010
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1694
AB  - Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations  gt 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.
PB  - Elsevier Science Bv, Amsterdam
T2  - Journal of Microbiological Methods
T1  - Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis
EP  - 134
IS  - 2
SP  - 127
VL  - 81
DO  - 10.1016/j.mimet.2010.02.007
ER  - 

@article{
author = "Salonen, Anne and Nikkila, Janne and Jalanka-Tuovinen, Jonna and Immonen, Outi and Rajilić-Stojanović, Mirjana and Kekkonen, Riina A. and Palva, Airi and de Vos, Willem M.",
year = "2010",
abstract = "Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations  gt 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "Journal of Microbiological Methods",
title = "Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis",
pages = "134-127",
number = "2",
volume = "81",
doi = "10.1016/j.mimet.2010.02.007"
}

Salonen, A., Nikkila, J., Jalanka-Tuovinen, J., Immonen, O., Rajilić-Stojanović, M., Kekkonen, R. A., Palva, A.,& de Vos, W. M.. (2010). Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. in Journal of Microbiological Methods
Elsevier Science Bv, Amsterdam., 81(2), 127-134.
https://doi.org/10.1016/j.mimet.2010.02.007

Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilić-Stojanović M, Kekkonen RA, Palva A, de Vos WM. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. in Journal of Microbiological Methods. 2010;81(2):127-134.
doi:10.1016/j.mimet.2010.02.007 .

Salonen, Anne, Nikkila, Janne, Jalanka-Tuovinen, Jonna, Immonen, Outi, Rajilić-Stojanović, Mirjana, Kekkonen, Riina A., Palva, Airi, de Vos, Willem M., "Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis" in Journal of Microbiological Methods, 81, no. 2 (2010):127-134,
https://doi.org/10.1016/j.mimet.2010.02.007 . .

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  - 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 . .

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  - CHAP
AU  - Rajilić-Stojanović, Mirjana
AU  - de Vos, Willem M.
AU  - Zoetendal, Erwin
PY  - 2008
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/6384
PB  - ASM Press
T2  - Accessing uncultivated microorganisms: from the environment to organisms and genomes and back
T1  - The Human Intestinal Microbiota and Its Impact on Human Health
EP  - 32
SP  - 11
UR  - https://hdl.handle.net/21.15107/rcub_technorep_6384
ER  - 

@inbook{
author = "Rajilić-Stojanović, Mirjana and de Vos, Willem M. and Zoetendal, Erwin",
year = "2008",
publisher = "ASM Press",
journal = "Accessing uncultivated microorganisms: from the environment to organisms and genomes and back",
booktitle = "The Human Intestinal Microbiota and Its Impact on Human Health",
pages = "32-11",
url = "https://hdl.handle.net/21.15107/rcub_technorep_6384"
}

Rajilić-Stojanović, M., de Vos, W. M.,& Zoetendal, E.. (2008). The Human Intestinal Microbiota and Its Impact on Human Health. in Accessing uncultivated microorganisms: from the environment to organisms and genomes and back
ASM Press., 11-32.
https://hdl.handle.net/21.15107/rcub_technorep_6384

Rajilić-Stojanović M, de Vos WM, Zoetendal E. The Human Intestinal Microbiota and Its Impact on Human Health. in Accessing uncultivated microorganisms: from the environment to organisms and genomes and back. 2008;:11-32.
https://hdl.handle.net/21.15107/rcub_technorep_6384 .

Rajilić-Stojanović, Mirjana, de Vos, Willem M., Zoetendal, Erwin, "The Human Intestinal Microbiota and Its Impact on Human Health" in Accessing uncultivated microorganisms: from the environment to organisms and genomes and back (2008):11-32,
https://hdl.handle.net/21.15107/rcub_technorep_6384 .

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 . .

TY  - JOUR
AU  - Zoetendal, Erwin G.
AU  - Rajilić-Stojanović, Mirjana
AU  - de Vos, Willem M.
PY  - 2008
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1226
AB  - The human gastrointestinal (GI) tract microbiota plays a pivotal role in our health. For more than a decade a major input for describing the diversity of the GI tract microbiota has been derived from the application of small subunit ribosomal RNA (SSU rRNA)-based technologies. These not only provided a phylogenetic framework of the GI tract microbiota, the majority of which has not yet been cultured, but also advanced insights into the impact of host and environmental factors on the microbiota community structure and dynamics. In addition, it emerged that GI tract microbial communities are host and GI tract location-specific. This complicates establishing relevant links between the host's health and the presence or abundance of specific microbial populations and argues for the implementation of novel high-throughput technologies in studying the diversity and functionality of the GI tract microbiota. Here, we focus on the recent developments and applications of phylogenetic microarrays based on SSU rRNA sequences and metagenomics approaches exploiting rapid sequencing technologies in unravelling the secrets of our GI tract microbiota.
PB  - Bmj Publishing Group, London
T2  - GUT
T1  - High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota
EP  - 1615
IS  - 11
SP  - 1605
VL  - 57
DO  - 10.1136/gut.2007.133603
ER  - 

@article{
author = "Zoetendal, Erwin G. and Rajilić-Stojanović, Mirjana and de Vos, Willem M.",
year = "2008",
abstract = "The human gastrointestinal (GI) tract microbiota plays a pivotal role in our health. For more than a decade a major input for describing the diversity of the GI tract microbiota has been derived from the application of small subunit ribosomal RNA (SSU rRNA)-based technologies. These not only provided a phylogenetic framework of the GI tract microbiota, the majority of which has not yet been cultured, but also advanced insights into the impact of host and environmental factors on the microbiota community structure and dynamics. In addition, it emerged that GI tract microbial communities are host and GI tract location-specific. This complicates establishing relevant links between the host's health and the presence or abundance of specific microbial populations and argues for the implementation of novel high-throughput technologies in studying the diversity and functionality of the GI tract microbiota. Here, we focus on the recent developments and applications of phylogenetic microarrays based on SSU rRNA sequences and metagenomics approaches exploiting rapid sequencing technologies in unravelling the secrets of our GI tract microbiota.",
publisher = "Bmj Publishing Group, London",
journal = "GUT",
title = "High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota",
pages = "1615-1605",
number = "11",
volume = "57",
doi = "10.1136/gut.2007.133603"
}

Zoetendal, E. G., Rajilić-Stojanović, M.,& de Vos, W. M.. (2008). High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. in GUT
Bmj Publishing Group, London., 57(11), 1605-1615.
https://doi.org/10.1136/gut.2007.133603

Zoetendal EG, Rajilić-Stojanović M, de Vos WM. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. in GUT. 2008;57(11):1605-1615.
doi:10.1136/gut.2007.133603 .

Zoetendal, Erwin G., Rajilić-Stojanović, Mirjana, de Vos, Willem M., "High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota" in GUT, 57, no. 11 (2008):1605-1615,
https://doi.org/10.1136/gut.2007.133603 . .

TY  - JOUR
AU  - Rajilić-Stojanović, Mirjana
AU  - de Vos, Willem M.
PY  - 2007
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1188
AB  - Our gastro-intestinal tract is populated by reportedly the densest microbial ecosystem that is essential for the digestion of foods and affects health. The basic understanding of the human microbiota is rapidly expanding by the implementation of molecular approaches that obviate the need for microbial cultivation as well as by a variety of functional, comparative and metagenomics developments. This report aims to provide an overview of the most relevant molecular techniques to describe the microbiota in our gastrointestinal tract within a historic perspective and with specific attention for its association with health and disease.
PB  - Teknoscienze Publ, Milano
T2  - Agro Food Industry Hi-Tech
T1  - Diversity of the human gastrointestinal microbiota
EP  - 19
IS  - 2
SP  - 15
VL  - 18
UR  - https://hdl.handle.net/21.15107/rcub_technorep_1188
ER  - 

@article{
author = "Rajilić-Stojanović, Mirjana and de Vos, Willem M.",
year = "2007",
abstract = "Our gastro-intestinal tract is populated by reportedly the densest microbial ecosystem that is essential for the digestion of foods and affects health. The basic understanding of the human microbiota is rapidly expanding by the implementation of molecular approaches that obviate the need for microbial cultivation as well as by a variety of functional, comparative and metagenomics developments. This report aims to provide an overview of the most relevant molecular techniques to describe the microbiota in our gastrointestinal tract within a historic perspective and with specific attention for its association with health and disease.",
publisher = "Teknoscienze Publ, Milano",
journal = "Agro Food Industry Hi-Tech",
title = "Diversity of the human gastrointestinal microbiota",
pages = "19-15",
number = "2",
volume = "18",
url = "https://hdl.handle.net/21.15107/rcub_technorep_1188"
}

Rajilić-Stojanović, M.,& de Vos, W. M.. (2007). Diversity of the human gastrointestinal microbiota. in Agro Food Industry Hi-Tech
Teknoscienze Publ, Milano., 18(2), 15-19.
https://hdl.handle.net/21.15107/rcub_technorep_1188

Rajilić-Stojanović M, de Vos WM. Diversity of the human gastrointestinal microbiota. in Agro Food Industry Hi-Tech. 2007;18(2):15-19.
https://hdl.handle.net/21.15107/rcub_technorep_1188 .

Rajilić-Stojanović, Mirjana, de Vos, Willem M., "Diversity of the human gastrointestinal microbiota" in Agro Food Industry Hi-Tech, 18, no. 2 (2007):15-19,
https://hdl.handle.net/21.15107/rcub_technorep_1188 .

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 . .

TY  - JOUR
AU  - Lay, C
AU  - Rigottier-Gois, L
AU  - Holmstrom, K
AU  - Rajilić-Stojanović, Mirjana
AU  - Vaughan, EE
AU  - de Vos, Willem M.
AU  - Collins, MD
AU  - Thiel, R
AU  - Namsolleck, P
AU  - Blaut, M
AU  - Dore, J
PY  - 2005
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/845
AB  - The composition of the colonic microbiota of 91 northern Europeans was characterized by fluorescent in situ hybridization using 18 phylogenetic probes. On average 75% of the bacteria were identified, and large interindividual variations were observed. Clostridium coccoides and Clostridium leptum were the dominant groups (28.0% and 25.2%), followed by the Bacteroides (8.5%). According to principal component analysis, no significant grouping with respect to geographic origin, age, or gender was observed.
PB  - Amer Soc Microbiology, Washington
T2  - Applied and Environmental Microbiology
T1  - Colonic microbiota signatures across five northern European countries
EP  - 4155
IS  - 7
SP  - 4153
VL  - 71
DO  - 10.1128/AEM.71.7.4153-4155.2005
ER  - 

@article{
author = "Lay, C and Rigottier-Gois, L and Holmstrom, K and Rajilić-Stojanović, Mirjana and Vaughan, EE and de Vos, Willem M. and Collins, MD and Thiel, R and Namsolleck, P and Blaut, M and Dore, J",
year = "2005",
abstract = "The composition of the colonic microbiota of 91 northern Europeans was characterized by fluorescent in situ hybridization using 18 phylogenetic probes. On average 75% of the bacteria were identified, and large interindividual variations were observed. Clostridium coccoides and Clostridium leptum were the dominant groups (28.0% and 25.2%), followed by the Bacteroides (8.5%). According to principal component analysis, no significant grouping with respect to geographic origin, age, or gender was observed.",
publisher = "Amer Soc Microbiology, Washington",
journal = "Applied and Environmental Microbiology",
title = "Colonic microbiota signatures across five northern European countries",
pages = "4155-4153",
number = "7",
volume = "71",
doi = "10.1128/AEM.71.7.4153-4155.2005"
}

Lay, C., Rigottier-Gois, L., Holmstrom, K., Rajilić-Stojanović, M., Vaughan, E., de Vos, W. M., Collins, M., Thiel, R., Namsolleck, P., Blaut, M.,& Dore, J.. (2005). Colonic microbiota signatures across five northern European countries. in Applied and Environmental Microbiology
Amer Soc Microbiology, Washington., 71(7), 4153-4155.
https://doi.org/10.1128/AEM.71.7.4153-4155.2005

Lay C, Rigottier-Gois L, Holmstrom K, Rajilić-Stojanović M, Vaughan E, de Vos WM, Collins M, Thiel R, Namsolleck P, Blaut M, Dore J. Colonic microbiota signatures across five northern European countries. in Applied and Environmental Microbiology. 2005;71(7):4153-4155.
doi:10.1128/AEM.71.7.4153-4155.2005 .

Lay, C, Rigottier-Gois, L, Holmstrom, K, Rajilić-Stojanović, Mirjana, Vaughan, EE, de Vos, Willem M., Collins, MD, Thiel, R, Namsolleck, P, Blaut, M, Dore, J, "Colonic microbiota signatures across five northern European countries" in Applied and Environmental Microbiology, 71, no. 7 (2005):4153-4155,
https://doi.org/10.1128/AEM.71.7.4153-4155.2005 . .