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Tom Van De Wiele - One of the best experts on this subject based on the ideXlab platform.
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Comparative in vitro fermentations of cranberry and grape seed polyphenols with colonic microbiota
Food chemistry, 2015Co-Authors: Fernando Sánchez-patán, Tom Van De Wiele, Elvira Barroso, Ana Jiménez-girón, Pedro J. Martín-Álvarez, M. Victoria Moreno-arribas, M. Carmen Martínez-cuesta, Carmen Peláez, Teresa Requena, Begoña BartoloméAbstract:In this study, we have assessed the phenolic metabolism of a cranberry extract by microbiota obtained from the ascending colon and descending colon compartments of a dynamic gastrointestinal simulator (SHIME). For comparison, parallel fermentations with a grape seed extract were carried out. Extracts were used directly without previous intestinal digestion. Among the 60 phenolic compounds targeted, our results confirmed the formation of phenylacetic, phenylpropionic and benzoic acids as well as phenols such as catechol and its derivatives from the action of colonic microbiota on cranberry polyphenols. Benzoic acid (38.4μg/ml), 4-hydroxy-5-(3'-hydroxyphenyl)-valeric acid (26.2μg/ml) and phenylacetic acid (19.5μg/ml) reached the highest concentrations. Under the same conditions, microbial degradation of grape seed polyphenols took place to a lesser extent compared to cranberry polyphenols, which was consistent with the more pronounced antimicrobial effect observed for the grape seed polyphenols, particularly against Bacteroides, Prevotella and Blautia coccoides-Eubacterium rectale.
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decreased colonization of fecal clostridium coccoides Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment
FEMS Microbiology Ecology, 2012Co-Authors: Joan Vermeiren, Pieter Van Den Abbeele, Debby Laukens, Louise Kristine Vigsnaes, Martine De Vos, Nico Boon, Tom Van De WieleAbstract:The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.
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Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment
FEMS microbiology ecology, 2011Co-Authors: Joan Vermeiren, Pieter Van Den Abbeele, Debby Laukens, Louise Kristine Vigsnaes, Martine De Vos, Nico Boon, Tom Van De WieleAbstract:The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.
Maria Saarela - One of the best experts on this subject based on the ideXlab platform.
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Intra-individual diversity and similarity of salivary and faecal microbiota.
Journal of medical microbiology, 2008Co-Authors: Johanna Maukonen, Jaana Matto, Maija-liisa Suihko, Maria SaarelaAbstract:In the present study, polyphasic analysis [cultivation, combined with the fingerprinting of individual isolates, and denaturing gradient gel electrophoresis (DGGE)] was applied to study whether similar features concerning the diversity and temporal stability of selected bacterial groups could be detected intra-individually in two different niches - the oral cavity and the colon - from ten adult volunteers consuming probiotics. The predominant bacterial microbiota, Clostridium coccoides-Eubacterium rectale group and bifidobacterial populations, were generally stable in salivary and faecal samples, with the greater diversity seen in faeces. Furthermore, different species predominated at the two different sites. Lactobacillus group DGGE profiles were unstable, yet the intra-individual profiles from faecal and salivary samples collected at the same time resembled each other. The ingested probiotic product did not affect the stability of the bacterial groups studied. The culture-based analysis showed that most subjects harboured identical indigenous Lactobacillus genotypes in saliva and faeces (Lactobacillus rhamnosus, Lactobacillus gasseri, Lactobacillus paracasei and Lactobacillus plantarum group). Thus, identical indigenous lactobacilli were able to inhabit both ends of the orogastrointestinal tract, whereas the composition of the other bacterial groups studied varied between the two sites.
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Diversity and temporal stability of fecal bacterial populations in elderly subjects consuming galacto-oligosaccharide containing probiotic yoghurt
International Dairy Journal, 2008Co-Authors: Johanna Maukonen, Jaana Matto, Kajsa Kajander, Tiina Mattila-sandholm, Maria SaarelaAbstract:Abstract Denaturing gradient gel electrophoresis was applied to study the effect of 3-week consumption of probiotic yoghurt containing galacto-oligosaccharides (GOS) on intra-individual diversity and temporal stability of predominant bacterial, bifidobacterial, Lactobacillus-group, and Erec-group Eubacterium rectale–Clostridium coccoides fecal populations of elderly subjects. Diversity and temporal stability of the selected bacterial groups of elderly subjects were compared with those obtained from younger adults in our previous studies. In the present study, GOS-yoghurt consumption did not significantly affect diversity or temporal stability of the selected bacterial groups. On average, the Erec-group and the predominant bacterial and bifidobacterial populations remained almost stable, and the Lactobacillus-group was unstable in elderly subjects. No differences were found between elderly and younger adults in temporal stability of studied bacterial populations. However, the difference in diversity of predominant bacterial population and Erec-group bacteria was significantly higher in elderly subjects of this study as compared with younger adults from our previous studies.
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pcr dgge and rt pcr dgge show diversity and short term temporal stability in the clostridium coccoides Eubacterium rectale group in the human intestinal microbiota
FEMS Microbiology Ecology, 2006Co-Authors: Johanna Maukonen, Jaana Matto, Reetta Satokari, Hans Soderlund, Tiina Mattilasandholm, Maria SaarelaAbstract:As the Clostridium coccoides-Eubacterium rectale (Erec; clostridial phylogenetic cluster XIVa) group is one of the major groups of the human intestinal microbiota, DNA- and RNA-based population analysis techniques (denaturing gradient gel electrophoresis; DGGE) were developed and applied to assess the diversity and temporal stability (6 months-2 years) of this faecal clostridial microbiota in 12 healthy adults. The stability of the Erec group was compared with the stability of the predominant bacterial microbiota, which was also assessed with PCR-DGGE. In addition, the Erec group was quantified with a hybridization-based method. According to our results, the Erec group was diverse in each subject, but interindividual uniqueness was not as clear as that of the predominant bacteria. The Erec group was found to be temporally as stable as the predominant bacteria. Over 200 clones obtained from two samples proved the developed method to be specific. However, the amount of bacteria belonging to the Erec group was not related to the diversity of that same bacterial group. In conclusion, the newly developed DGGE method proved to be a valuable and specific tool for the direct assessment of the stability of the Erec group, demonstrating diversity in addition to short-term stability in most of the subjects studied.
Joan Vermeiren - One of the best experts on this subject based on the ideXlab platform.
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decreased colonization of fecal clostridium coccoides Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment
FEMS Microbiology Ecology, 2012Co-Authors: Joan Vermeiren, Pieter Van Den Abbeele, Debby Laukens, Louise Kristine Vigsnaes, Martine De Vos, Nico Boon, Tom Van De WieleAbstract:The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.
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Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment
FEMS microbiology ecology, 2011Co-Authors: Joan Vermeiren, Pieter Van Den Abbeele, Debby Laukens, Louise Kristine Vigsnaes, Martine De Vos, Nico Boon, Tom Van De WieleAbstract:The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.
George P C Salmond - One of the best experts on this subject based on the ideXlab platform.
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co evolution of quaternary organization and novel rna tertiary interactions revealed in the crystal structure of a bacterial protein rna toxin antitoxin system
Nucleic Acids Research, 2015Co-Authors: Feng Rao, Francesca L Short, Jarrod E Voss, Tim R Blower, Anastasia L Orme, Tom E Whittaker, Ben F Luisi, George P C SalmondAbstract:Genes encoding toxin–antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein–RNA complex to 2.2 A resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.
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Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein–RNA toxin–antitoxin system
Nucleic acids research, 2015Co-Authors: Feng Rao, Francesca L Short, Jarrod E Voss, Tim R Blower, Anastasia L Orme, Tom E Whittaker, Ben F Luisi, George P C SalmondAbstract:Genes encoding toxin–antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein–RNA complex to 2.2 A resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.
Jaana Matto - One of the best experts on this subject based on the ideXlab platform.
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Association between the ABO blood group and the human intestinal microbiota composition
BMC Microbiology, 2012Co-Authors: Harri Mäkivuokko, Sampo J Lahtinen, Pirjo Wacklin, Elina Tuovinen, Heli Tenkanen, Janne Nikkilä, Marika Björklund, Kari Aranko, Arthur C Ouwehand, Jaana MattoAbstract:Background The mucus layer covering the human intestinal epithelium forms a dynamic surface for host-microbial interactions. In addition to the environmental factors affecting the intestinal equilibrium, such as diet, it is well established that the microbiota composition is individually driven, but the host factors determining the composition have remained unresolved. Results In this study, we show that ABO blood group is involved in differences in relative proportion and overall profiles of intestinal microbiota. Specifically, the microbiota from the individuals harbouring the B antigen (secretor B and AB) differed from the non-B antigen groups and also showed higher diversity of the Eubacterium rectale-Clostridium coccoides (EREC) and Clostridium leptum (CLEPT) -groups in comparison with other blood groups. Conclusions Our novel finding indicates that the ABO blood group is one of the genetically determined host factors modulating the composition of the human intestinal microbiota, thus enabling new applications in the field of personalized nutrition and medicine.
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Intra-individual diversity and similarity of salivary and faecal microbiota.
Journal of medical microbiology, 2008Co-Authors: Johanna Maukonen, Jaana Matto, Maija-liisa Suihko, Maria SaarelaAbstract:In the present study, polyphasic analysis [cultivation, combined with the fingerprinting of individual isolates, and denaturing gradient gel electrophoresis (DGGE)] was applied to study whether similar features concerning the diversity and temporal stability of selected bacterial groups could be detected intra-individually in two different niches - the oral cavity and the colon - from ten adult volunteers consuming probiotics. The predominant bacterial microbiota, Clostridium coccoides-Eubacterium rectale group and bifidobacterial populations, were generally stable in salivary and faecal samples, with the greater diversity seen in faeces. Furthermore, different species predominated at the two different sites. Lactobacillus group DGGE profiles were unstable, yet the intra-individual profiles from faecal and salivary samples collected at the same time resembled each other. The ingested probiotic product did not affect the stability of the bacterial groups studied. The culture-based analysis showed that most subjects harboured identical indigenous Lactobacillus genotypes in saliva and faeces (Lactobacillus rhamnosus, Lactobacillus gasseri, Lactobacillus paracasei and Lactobacillus plantarum group). Thus, identical indigenous lactobacilli were able to inhabit both ends of the orogastrointestinal tract, whereas the composition of the other bacterial groups studied varied between the two sites.
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Diversity and temporal stability of fecal bacterial populations in elderly subjects consuming galacto-oligosaccharide containing probiotic yoghurt
International Dairy Journal, 2008Co-Authors: Johanna Maukonen, Jaana Matto, Kajsa Kajander, Tiina Mattila-sandholm, Maria SaarelaAbstract:Abstract Denaturing gradient gel electrophoresis was applied to study the effect of 3-week consumption of probiotic yoghurt containing galacto-oligosaccharides (GOS) on intra-individual diversity and temporal stability of predominant bacterial, bifidobacterial, Lactobacillus-group, and Erec-group Eubacterium rectale–Clostridium coccoides fecal populations of elderly subjects. Diversity and temporal stability of the selected bacterial groups of elderly subjects were compared with those obtained from younger adults in our previous studies. In the present study, GOS-yoghurt consumption did not significantly affect diversity or temporal stability of the selected bacterial groups. On average, the Erec-group and the predominant bacterial and bifidobacterial populations remained almost stable, and the Lactobacillus-group was unstable in elderly subjects. No differences were found between elderly and younger adults in temporal stability of studied bacterial populations. However, the difference in diversity of predominant bacterial population and Erec-group bacteria was significantly higher in elderly subjects of this study as compared with younger adults from our previous studies.
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pcr dgge and rt pcr dgge show diversity and short term temporal stability in the clostridium coccoides Eubacterium rectale group in the human intestinal microbiota
FEMS Microbiology Ecology, 2006Co-Authors: Johanna Maukonen, Jaana Matto, Reetta Satokari, Hans Soderlund, Tiina Mattilasandholm, Maria SaarelaAbstract:As the Clostridium coccoides-Eubacterium rectale (Erec; clostridial phylogenetic cluster XIVa) group is one of the major groups of the human intestinal microbiota, DNA- and RNA-based population analysis techniques (denaturing gradient gel electrophoresis; DGGE) were developed and applied to assess the diversity and temporal stability (6 months-2 years) of this faecal clostridial microbiota in 12 healthy adults. The stability of the Erec group was compared with the stability of the predominant bacterial microbiota, which was also assessed with PCR-DGGE. In addition, the Erec group was quantified with a hybridization-based method. According to our results, the Erec group was diverse in each subject, but interindividual uniqueness was not as clear as that of the predominant bacteria. The Erec group was found to be temporally as stable as the predominant bacteria. Over 200 clones obtained from two samples proved the developed method to be specific. However, the amount of bacteria belonging to the Erec group was not related to the diversity of that same bacterial group. In conclusion, the newly developed DGGE method proved to be a valuable and specific tool for the direct assessment of the stability of the Erec group, demonstrating diversity in addition to short-term stability in most of the subjects studied.