The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Yiming Zeng - One of the best experts on this subject based on the ideXlab platform.
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disruption of sleep architecture in prevotella Enterotype of patients with obstructive sleep apnea hypopnea syndrome
Brain and behavior, 2019Co-Authors: Jimim Fan, Jiaohong Yang, Limei Huang, Furong Yan, Huaping Zhang, Yiming ZengAbstract:Introduction Intermittent hypoxia and sleep fragmentation are critical pathophysiological processes involved in obstructive sleep apnea-hypopnea syndrome (OSAHS). Those manifestations independently affect similar brain regions and contribute to OSAHS-related comorbidities that are known to be related to the host gut alteration microbiota. We hypothesized that gut microbiota disruption may cross talk the brain function via the microbiota-gut-brain axis. Thus, we aim to survey Enterotypes and polysomnographic data of patients with OSAHS. Methods Subjects were diagnosed by polysomnography, from whom fecal samples were obtained and analyzed for the microbiome composition by variable regions 3-4 of 16S rRNA pyrosequencing and bioinformatic analyses. We examined the fasting levels of interleukin-6 and tumor necrosis factor-alpha of all subjects. Results Three Enterotypes Bacteroides, Ruminococcus, and Prevotella were identified in patients with OSAHS. Arousal-related parameters or sleep stages are significantly disrupted in apnea-hypopnea index (AHI) ≥15 patients with Prevotella Enterotype; further analysis this Enterotype subjects, obstructive, central, and mixed apnea indices, and mean heart rate are also significantly elevated in AHI ≥15 patients. However, blood cytokines levels of all subjects were not significantly different. Conclusions This study indicates the possibility of pathophysiological interplay between Enterotypes and sleeps structure disruption in sleep apnea through a microbiota-gut-brain axis and offers some new insight toward the pathogenesis of OSAHS.
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association of prevotella Enterotype with polysomnographic data in obstructive sleep apnea hypopnea syndrome patients
bioRxiv, 2018Co-Authors: Jimim Fan, Jiaohong Yang, Limei Huang, Huaping Zhang, Yiming ZengAbstract:Abstract Intermittent hypoxia and sleep fragmentation are critical pathophysiological processes involved in obstructive sleep apnea/hypopnea syndrome (OSAHS). These manifestation independently affect similar brain regions and contribute to OSAHS-related comorbidities that are known to be related to the host gut alteration microbiota. We hypothesized that microbiota disruption influences the pathophysiological processes of OSAHS through a microbiota–gut–brain axis. Thus, we aim to survey Enterotypes and polysomnographic data of OSAHS patients. Subjects were diagnosed by polysomnography, from whom fecal samples were obtained and analyzed for the microbiome composition by variable regions 3–4 of 16S rRNA pyrosequencing and bioinformatic analyses. We examined blood cytokines level of all subjects. Three Enterotypes Bacteroides (n=73), Ruminococcus (n=14), and Prevotella (n=26) were identified. Central apnea indices, mixed apnea indices, N1 sleep stage, mean apnea–hypopnea duration, and arousal indices were increased in apnea–hypopnea indices (AHI) ≥15 patients with the Prevotella Enterotype. However, for AHI Importance Intermittent hypoxia (IH) and sleep fragmentation (SF) are hallmarks of are the predominant mechanism underlying obstructive sleep apnea/hypopnea syndrome (OSAHS). Moreover, IH and SF of pathophysiological roles in the gut microbiota dysbiosis in OSAHS have been demonstrated. We hypothesized that gut microbiota disruption may cross-talk the brain function via microbiota–gut–brain axis. Indeed, we observed central apnea indices and other parameters of disturbances during sleep were significantly elevated in AHI≥15 patients with the Prevotella Enterotype. This Enterotype prone to endotoxin production, driving systemic inflammation, ultimately contributes to OSAHS-linked comorbidities. Vice versa, increasing the arousal index leads to systemic inflammatory changes and accompanies metabolic dysfunction. We highlight that the possibility that the microbiota–gut–brain axis operates a bidirectional effect on the development of OSAHS pathology.
Suguru Nishijima - One of the best experts on this subject based on the ideXlab platform.
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revealing the microbial assemblage structure in the human gut microbiome using latent dirichlet allocation
Microbiome, 2020Co-Authors: Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki HamadaAbstract:The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the Enterotype and assemblage is not well-understood. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between Enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized Enterotypes. Conversely, the fourth assemblage corresponded to no Enterotypes and emerged in all Enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an Enterotype-independent assemblage.
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revealing microbial assemblage structure in the human gut microbiome using latent dirichlet allocation
bioRxiv, 2019Co-Authors: Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki HamadaAbstract:Abstract Recent research has revealed that there are various microbial species in the human gut microbiome. To clarify the structure of the human gut microbiome, many data mining methods have been applied to microbial composition data. Cluster analysis, one of the key data mining methods that have been used in human gut microbiome research, can classify the human gut microbiome into three clusters, called Enterotypes. The human gut microbiome has been suggested to be composed of the microbial assemblages or groups of co-occurring microbes, and one human gut microbiome can contain several microbial assemblages. However, cluster analysis can cluster samples into groups without capturing minor assemblages. In addition, a reliable method of assemblage detection has not been established, and little is known about the distributions of microbial assemblages at a population-level scale. Accordingly, the purpose of this study was to clarify the microbial assemblages in the human gut microbiome. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method, which was first proposed for the classification of documents in natural language processing. We applied LDA to a large-scale human gut metagenome dataset and found that a four-assemblage LDA model can represent relationships between Enterotypes and assemblages with high interpretability. This model indicates that each individual tends to have several assemblages, and each of three assemblages corresponded to each Enterotype. However, the C-assemblage can exist in all Enterotypes. Interestingly, the dominant genera of the C-assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Finally, we revealed that genera mainly appearing in the same assemblage were correlated to each other. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA, a powerful method for detection of microbial assemblages. This approach has the potential to reveal the structure of the human gut microbiome.
Shion Hosoda - One of the best experts on this subject based on the ideXlab platform.
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revealing the microbial assemblage structure in the human gut microbiome using latent dirichlet allocation
Microbiome, 2020Co-Authors: Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki HamadaAbstract:The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the Enterotype and assemblage is not well-understood. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between Enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized Enterotypes. Conversely, the fourth assemblage corresponded to no Enterotypes and emerged in all Enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an Enterotype-independent assemblage.
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revealing microbial assemblage structure in the human gut microbiome using latent dirichlet allocation
bioRxiv, 2019Co-Authors: Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki HamadaAbstract:Abstract Recent research has revealed that there are various microbial species in the human gut microbiome. To clarify the structure of the human gut microbiome, many data mining methods have been applied to microbial composition data. Cluster analysis, one of the key data mining methods that have been used in human gut microbiome research, can classify the human gut microbiome into three clusters, called Enterotypes. The human gut microbiome has been suggested to be composed of the microbial assemblages or groups of co-occurring microbes, and one human gut microbiome can contain several microbial assemblages. However, cluster analysis can cluster samples into groups without capturing minor assemblages. In addition, a reliable method of assemblage detection has not been established, and little is known about the distributions of microbial assemblages at a population-level scale. Accordingly, the purpose of this study was to clarify the microbial assemblages in the human gut microbiome. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method, which was first proposed for the classification of documents in natural language processing. We applied LDA to a large-scale human gut metagenome dataset and found that a four-assemblage LDA model can represent relationships between Enterotypes and assemblages with high interpretability. This model indicates that each individual tends to have several assemblages, and each of three assemblages corresponded to each Enterotype. However, the C-assemblage can exist in all Enterotypes. Interestingly, the dominant genera of the C-assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Finally, we revealed that genera mainly appearing in the same assemblage were correlated to each other. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA, a powerful method for detection of microbial assemblages. This approach has the potential to reveal the structure of the human gut microbiome.
Jimim Fan - One of the best experts on this subject based on the ideXlab platform.
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disruption of sleep architecture in prevotella Enterotype of patients with obstructive sleep apnea hypopnea syndrome
Brain and behavior, 2019Co-Authors: Jimim Fan, Jiaohong Yang, Limei Huang, Furong Yan, Huaping Zhang, Yiming ZengAbstract:Introduction Intermittent hypoxia and sleep fragmentation are critical pathophysiological processes involved in obstructive sleep apnea-hypopnea syndrome (OSAHS). Those manifestations independently affect similar brain regions and contribute to OSAHS-related comorbidities that are known to be related to the host gut alteration microbiota. We hypothesized that gut microbiota disruption may cross talk the brain function via the microbiota-gut-brain axis. Thus, we aim to survey Enterotypes and polysomnographic data of patients with OSAHS. Methods Subjects were diagnosed by polysomnography, from whom fecal samples were obtained and analyzed for the microbiome composition by variable regions 3-4 of 16S rRNA pyrosequencing and bioinformatic analyses. We examined the fasting levels of interleukin-6 and tumor necrosis factor-alpha of all subjects. Results Three Enterotypes Bacteroides, Ruminococcus, and Prevotella were identified in patients with OSAHS. Arousal-related parameters or sleep stages are significantly disrupted in apnea-hypopnea index (AHI) ≥15 patients with Prevotella Enterotype; further analysis this Enterotype subjects, obstructive, central, and mixed apnea indices, and mean heart rate are also significantly elevated in AHI ≥15 patients. However, blood cytokines levels of all subjects were not significantly different. Conclusions This study indicates the possibility of pathophysiological interplay between Enterotypes and sleeps structure disruption in sleep apnea through a microbiota-gut-brain axis and offers some new insight toward the pathogenesis of OSAHS.
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association of prevotella Enterotype with polysomnographic data in obstructive sleep apnea hypopnea syndrome patients
bioRxiv, 2018Co-Authors: Jimim Fan, Jiaohong Yang, Limei Huang, Huaping Zhang, Yiming ZengAbstract:Abstract Intermittent hypoxia and sleep fragmentation are critical pathophysiological processes involved in obstructive sleep apnea/hypopnea syndrome (OSAHS). These manifestation independently affect similar brain regions and contribute to OSAHS-related comorbidities that are known to be related to the host gut alteration microbiota. We hypothesized that microbiota disruption influences the pathophysiological processes of OSAHS through a microbiota–gut–brain axis. Thus, we aim to survey Enterotypes and polysomnographic data of OSAHS patients. Subjects were diagnosed by polysomnography, from whom fecal samples were obtained and analyzed for the microbiome composition by variable regions 3–4 of 16S rRNA pyrosequencing and bioinformatic analyses. We examined blood cytokines level of all subjects. Three Enterotypes Bacteroides (n=73), Ruminococcus (n=14), and Prevotella (n=26) were identified. Central apnea indices, mixed apnea indices, N1 sleep stage, mean apnea–hypopnea duration, and arousal indices were increased in apnea–hypopnea indices (AHI) ≥15 patients with the Prevotella Enterotype. However, for AHI Importance Intermittent hypoxia (IH) and sleep fragmentation (SF) are hallmarks of are the predominant mechanism underlying obstructive sleep apnea/hypopnea syndrome (OSAHS). Moreover, IH and SF of pathophysiological roles in the gut microbiota dysbiosis in OSAHS have been demonstrated. We hypothesized that gut microbiota disruption may cross-talk the brain function via microbiota–gut–brain axis. Indeed, we observed central apnea indices and other parameters of disturbances during sleep were significantly elevated in AHI≥15 patients with the Prevotella Enterotype. This Enterotype prone to endotoxin production, driving systemic inflammation, ultimately contributes to OSAHS-linked comorbidities. Vice versa, increasing the arousal index leads to systemic inflammatory changes and accompanies metabolic dysfunction. We highlight that the possibility that the microbiota–gut–brain axis operates a bidirectional effect on the development of OSAHS pathology.
Otto X Cordero - One of the best experts on this subject based on the ideXlab platform.
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strain level diversity drives alternative community types in millimetre scale granular biofilms
bioRxiv, 2018Co-Authors: Gabriel E Leventhal, Carles Boix, Tim N Enke, Otto X CorderoAbstract:Microbial communities are often highly diverse in their composition, both at the level of coarse-grained taxa such as genera as well as at the level of strains within species. This variability can be driven by both extrinsic factors like temperature, pH, etc., as well as by intrinsic ones, such as demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community structure remain poorly understood, in part because of the difficulty of identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimeter scale biofilm granules represent true community replicates whose differences in composition are expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation, however, did not translate into any clear partitioning into discrete community types, i.e. the equivalent of Enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the most abundant organism: strains of Candidatus Accumulibacter that coexisted in the metacommunity---i.e. the reactor---excluded each other within community replicates. Single-granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall species composition of the community, indicating high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most likely observed at the level of recently differentiated genotypes but not higher orders of genetic resolution.
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strain level diversity drives alternative community types in millimetre scale granular biofilms
Nature microbiology, 2018Co-Authors: Gabriel E Leventhal, Carles Boix, Tim N Enke, Otto X Cordero, Urs Kuechler, Elzbieta Sliwerska, Christof HolligerAbstract:Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such as temperature and or by intrinsic ones, for example demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community composition remain poorly understood, in part because of the difficulty in identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimetre-scale biofilm granules represent true community replicates. Differences in composition are then expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation did not translate into any clear partitioning into discrete community types, that is, distinct compositional states, such as Enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the dominant organism: genotypes of Candidatus Accumulibacter that coexisted in the metacommunity (the reactor) excluded each other within community replicates (granules). Individual granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall composition of the community, indicating a high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most probably observed at the level of recently differentiated genotypes but not at higher orders of genetic resolution. Using millimetre-scale replicate granules from an enhanced biological phosphorus removal reactor, the authors observe strain-level variability providing insights into the intrinsic drivers of microbial assembly at relevant spatial scales.