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  - 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  - 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 . .