The Experts below are selected from a list of 183411 Experts worldwide ranked by ideXlab platform
Liping Zhao - One of the best experts on this subject based on the ideXlab platform.
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Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
mBio, 2017Co-Authors: Chenhong Zhang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, R.z. Wang, Liping ZhaoAbstract:The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum Strains showed differential responses during the dietary intervention. Two Strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these Strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the Strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.IMPORTANCE The manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multiple B. pseudocatenulatum Strains isolated from the same habitat to the dietary intervention, as well as Strain-specific correlations with bioclinical parameters of the host. The comparative genomics revealed a genome-Level microdiversity of related functional genes, which may have contributed to these differences. These results highlight the necessity of understanding Strain-Level differences if precise manipulation of gut microbiota through dietary approaches is to be realized.
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Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
American Society for Microbiology, 2017Co-Authors: Chenhong Zhang, Ruirui Wang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, Liping ZhaoAbstract:The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum Strains showed differential responses during the dietary intervention. Two Strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these Strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the Strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized
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Strain Level dissection of the contribution of the gut microbiome to human metabolic disease
Genome Medicine, 2016Co-Authors: Chenhong Zhang, Liping ZhaoAbstract:The gut microbiota has been linked with metabolic diseases in humans, but demonstration of causality remains a challenge. The gut microbiota, as a complex microbial ecosystem, consists of hundreds of individual bacterial species, each of which contains many Strains with high genetic diversity. Recent advances in genomic and metabolomic technologies are facilitating Strain-Level dissection of the contribution of the gut microbiome to metabolic diseases. Interventional studies and correlation analysis between variations in the microbiome and metabolome, captured by longitudinal sampling, can lead to the identification of specific bacterial Strains that may contribute to human metabolic diseases via the production of bioactive metabolites. For example, high-quality draft genomes of prevalent gut bacterial Strains can be assembled directly from metagenomic datasets using a canopy-based algorithm. Specific metabolites associated with a disease phenotype can be identified by nuclear magnetic resonance-based metabolomics of urine and other samples. Such multi-omics approaches can be employed to identify specific gut bacterial genomes that are not only correlated with detected metabolites but also encode the genes required for producing the precursors of those metabolites in the gut. Here, we argue that if a causative role can be demonstrated in follow-up mechanistic studies—for example, using gnotobiotic models—such functional Strains have the potential to become biomarkers for diagnostics and targets for therapeutics.
Hiroto Tamura - One of the best experts on this subject based on the ideXlab platform.
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novel accurate bacterial discrimination by maldi time of flight ms based on ribosomal proteins coding in s10 spc alpha operon at Strain Level s10 germs
Journal of the American Society for Mass Spectrometry, 2013Co-Authors: Hiroto Tamura, Yudai Hotta, Hiroaki SatoAbstract:Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at Strain Level, the ribosomal subunit proteins coded in the S10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the Strains of genus Pseudomonas were successfully identified and discriminated at species and Strain Levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the Strain (pathovar) Level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.
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classification of genus pseudomonas by maldi tof ms based on ribosomal protein coding in s10 spc alpha operon at Strain Level
Journal of Proteome Research, 2010Co-Authors: Yudai Hotta, Kanae Teramoto, Hiroaki Sato, Hiromichi Yoshikawa, Akifumi Hosoda, Hiroto TamuraAbstract:We have proposed a rapid phylogenetic classification at the Strain Level by MALDI-TOF MS using ribosomal protein matching profiling. In this study, the S10−spc−alpha operon, encoding half of the ribosomal subunit proteins and highly conserved in eubacterial genomes, was selected for construction of the ribosomal protein database as biomarkers for bacterial identification by MALDI-TOF MS analysis to establish a more reliable phylogenetic classification. Our method revealed that the 14 reliable and reproducible ribosomal subunit proteins with less than m/z 15 000, except for L14, coded in the S10−spc−alpha operon were significantly useful biomarkers for bacterial classification at species and Strain Levels by MALDI-TOF MS analysis of genus Pseudomonas Strains. The obtained phylogenetic tree was consisted with that based on genetic sequence (gyrB). Since S10−spc−alpha operons of genus Pseudomonas Strains were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced Strains,...
Philipp Engel - One of the best experts on this subject based on the ideXlab platform.
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vast differences in Strain Level diversity in the gut microbiota of two closely related honey bee species
Current Biology, 2020Co-Authors: Kirsten M Ellegaard, Shota Suenami, Ryo Miyazaki, Philipp EngelAbstract:Summary Most bacterial species encompass Strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this Level and which underlying mechanisms may conStrain and maintain Strain-Level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of Strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar Levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.
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vast differences in Strain Level diversity in the gut microbiota of two closely related honey bee species
bioRxiv, 2020Co-Authors: Kirsten M Ellegaard, Shota Suenami, Ryo Miyazaki, Philipp EngelAbstract:Most bacterial species encompass Strains with vastly different gene content. Strain-Level diversity in host-associated microbial communities is therefore considered to be of functional importance. Yet, little is known about Strain-Level diversity differences in phylotypes shared among related host species, or the underlying mechanisms that may conStrain and maintain diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two closely related honey bee species, Apis mellifera and Apis cerana. While both host species are colonized by largely overlapping bacterial 16S rRNA phylotypes, our metagenomic analysis revealed that their communities are host-specific at the species- and Strain-Level with few between-host transfers being detected. Strikingly, A. mellifera displayed a much higher extent of Strain-Level diversity and functional gene content in the microbiota than A. cerana, per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Our results illustrate that the gut microbiota of two closely related animal hosts, with similar ecology and overlapping geographic distribution, can undergo dramatic changes in composition and diversity within a timespan of only 6 million years of evolution, with likely consequences for gut microbiota functioning and host-symbiont interactions. Human bee management, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota composition of these key pollinator species. Further studies are needed to evaluate both the underlying causes and functional consequences for honey bee health and bee management.
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Genomic diversity landscape of the honey bee gut microbiota
Nature Publishing Group, 2019Co-Authors: Kirsten M Ellegaard, Philipp EngelAbstract:The structure and distribution of Strain-Level diversity in host-associated bacterial communities is largely unexplored. Here, Ellegaard and Engel analyze Strain Level diversity of the honey bee gut microbiota, showing that bees from the same colony differ in Strain but not phylotype composition
Hiroaki Sato - One of the best experts on this subject based on the ideXlab platform.
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novel accurate bacterial discrimination by maldi time of flight ms based on ribosomal proteins coding in s10 spc alpha operon at Strain Level s10 germs
Journal of the American Society for Mass Spectrometry, 2013Co-Authors: Hiroto Tamura, Yudai Hotta, Hiroaki SatoAbstract:Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at Strain Level, the ribosomal subunit proteins coded in the S10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the Strains of genus Pseudomonas were successfully identified and discriminated at species and Strain Levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the Strain (pathovar) Level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.
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classification of genus pseudomonas by maldi tof ms based on ribosomal protein coding in s10 spc alpha operon at Strain Level
Journal of Proteome Research, 2010Co-Authors: Yudai Hotta, Kanae Teramoto, Hiroaki Sato, Hiromichi Yoshikawa, Akifumi Hosoda, Hiroto TamuraAbstract:We have proposed a rapid phylogenetic classification at the Strain Level by MALDI-TOF MS using ribosomal protein matching profiling. In this study, the S10−spc−alpha operon, encoding half of the ribosomal subunit proteins and highly conserved in eubacterial genomes, was selected for construction of the ribosomal protein database as biomarkers for bacterial identification by MALDI-TOF MS analysis to establish a more reliable phylogenetic classification. Our method revealed that the 14 reliable and reproducible ribosomal subunit proteins with less than m/z 15 000, except for L14, coded in the S10−spc−alpha operon were significantly useful biomarkers for bacterial classification at species and Strain Levels by MALDI-TOF MS analysis of genus Pseudomonas Strains. The obtained phylogenetic tree was consisted with that based on genetic sequence (gyrB). Since S10−spc−alpha operons of genus Pseudomonas Strains were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced Strains,...
Chenhong Zhang - One of the best experts on this subject based on the ideXlab platform.
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Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
mBio, 2017Co-Authors: Chenhong Zhang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, R.z. Wang, Liping ZhaoAbstract:The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum Strains showed differential responses during the dietary intervention. Two Strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these Strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the Strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.IMPORTANCE The manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multiple B. pseudocatenulatum Strains isolated from the same habitat to the dietary intervention, as well as Strain-specific correlations with bioclinical parameters of the host. The comparative genomics revealed a genome-Level microdiversity of related functional genes, which may have contributed to these differences. These results highlight the necessity of understanding Strain-Level differences if precise manipulation of gut microbiota through dietary approaches is to be realized.
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Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
American Society for Microbiology, 2017Co-Authors: Chenhong Zhang, Ruirui Wang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, Liping ZhaoAbstract:The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum Strains showed differential responses during the dietary intervention. Two Strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these Strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the Strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized
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Strain Level dissection of the contribution of the gut microbiome to human metabolic disease
Genome Medicine, 2016Co-Authors: Chenhong Zhang, Liping ZhaoAbstract:The gut microbiota has been linked with metabolic diseases in humans, but demonstration of causality remains a challenge. The gut microbiota, as a complex microbial ecosystem, consists of hundreds of individual bacterial species, each of which contains many Strains with high genetic diversity. Recent advances in genomic and metabolomic technologies are facilitating Strain-Level dissection of the contribution of the gut microbiome to metabolic diseases. Interventional studies and correlation analysis between variations in the microbiome and metabolome, captured by longitudinal sampling, can lead to the identification of specific bacterial Strains that may contribute to human metabolic diseases via the production of bioactive metabolites. For example, high-quality draft genomes of prevalent gut bacterial Strains can be assembled directly from metagenomic datasets using a canopy-based algorithm. Specific metabolites associated with a disease phenotype can be identified by nuclear magnetic resonance-based metabolomics of urine and other samples. Such multi-omics approaches can be employed to identify specific gut bacterial genomes that are not only correlated with detected metabolites but also encode the genes required for producing the precursors of those metabolites in the gut. Here, we argue that if a causative role can be demonstrated in follow-up mechanistic studies—for example, using gnotobiotic models—such functional Strains have the potential to become biomarkers for diagnostics and targets for therapeutics.
