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  - Swann, J. R.
AU  - Rajilić-Stojanović, Mirjana
AU  - Salonen, Anne
AU  - Sakwinska, O.
AU  - Gill, C.
AU  - Meynier, A.
AU  - Fanca-Berthon, P.
AU  - Schelkle, B.
AU  - Segata, N.
AU  - Shortt, C.
AU  - Tuohy, K.
AU  - Hasselwander, O.
PY  - 2020
UR  - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/4473
AB  - With the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota-host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.
PB  - Springer Heidelberg, Heidelberg
T2  - European Journal of Nutrition
T1  - Considerations for the design and conduct of human gut microbiota intervention studies relating to foods
EP  - 3368
IS  - 8
SP  - 3347
VL  - 59
DO  - 10.1007/s00394-020-02232-1
ER  - 

@article{
author = "Swann, J. R. and Rajilić-Stojanović, Mirjana and Salonen, Anne and Sakwinska, O. and Gill, C. and Meynier, A. and Fanca-Berthon, P. and Schelkle, B. and Segata, N. and Shortt, C. and Tuohy, K. and Hasselwander, O.",
year = "2020",
abstract = "With the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota-host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.",
publisher = "Springer Heidelberg, Heidelberg",
journal = "European Journal of Nutrition",
title = "Considerations for the design and conduct of human gut microbiota intervention studies relating to foods",
pages = "3368-3347",
number = "8",
volume = "59",
doi = "10.1007/s00394-020-02232-1"
}

Swann, J. R., Rajilić-Stojanović, M., Salonen, A., Sakwinska, O., Gill, C., Meynier, A., Fanca-Berthon, P., Schelkle, B., Segata, N., Shortt, C., Tuohy, K.,& Hasselwander, O.. (2020). Considerations for the design and conduct of human gut microbiota intervention studies relating to foods. in European Journal of Nutrition
Springer Heidelberg, Heidelberg., 59(8), 3347-3368.
https://doi.org/10.1007/s00394-020-02232-1

Swann JR, Rajilić-Stojanović M, Salonen A, Sakwinska O, Gill C, Meynier A, Fanca-Berthon P, Schelkle B, Segata N, Shortt C, Tuohy K, Hasselwander O. Considerations for the design and conduct of human gut microbiota intervention studies relating to foods. in European Journal of Nutrition. 2020;59(8):3347-3368.
doi:10.1007/s00394-020-02232-1 .

Swann, J. R., Rajilić-Stojanović, Mirjana, Salonen, Anne, Sakwinska, O., Gill, C., Meynier, A., Fanca-Berthon, P., Schelkle, B., Segata, N., Shortt, C., Tuohy, K., Hasselwander, O., "Considerations for the design and conduct of human gut microbiota intervention studies relating to foods" in European Journal of Nutrition, 59, no. 8 (2020):3347-3368,
https://doi.org/10.1007/s00394-020-02232-1 . .

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  - 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 . .