Kekkonen, Riina A.

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  • Kekkonen, Riina A. (2)
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Author's Bibliography

Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome

Rajilić-Stojanović, Mirjana; Biagi, Elena; Heilig, Hans G. H. J.; Kajander, Kajsa; Kekkonen, Riina A.; Tims, Sebastian; de Vos, Willem M.

(W B Saunders Co-Elsevier Inc, Philadelphia, 2011)

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 . .
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Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Salonen, Anne; Nikkila, Janne; Jalanka-Tuovinen, Jonna; Immonen, Outi; Rajilić-Stojanović, Mirjana; Kekkonen, Riina A.; Palva, Airi; de Vos, Willem M.

(Elsevier Science Bv, Amsterdam, 2010)

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 . .
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