Rethinking "enterotypes".
Ontology highlight
ABSTRACT:
SUBMITTER: Knights D
PROVIDER: S-EPMC5558460 | biostudies-literature | 2014 Oct
REPOSITORIES: biostudies-literature
Publications
Rethinking "enterotypes".
Knights Dan D Ward Tonya L TL McKinlay Christopher E CE Miller Hannah H Gonzalez Antonio A McDonald Daniel D Knight Rob R
Cell host & microbe 20141001 4
Classification of the human gut microbiome into distinct types, or "enterotypes," provides an attractive framework for understanding microbial variation in health and disease. However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual. ...[more]
Similar Datasets
Project description:Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
| S-EPMC3728647 | biostudies-literature
Project description:The essence of enterotypes is stratifying the entire human gut microbiome, which modulates the association between diet and disease risk. A study was designed at the Center of Reproductive Medicine, Shengjing Hospital of China Medical University and Jinghua Hospital of Shenyang. Prevotella and Bacteroides were analyzed in 407 samples of stool, including 178 men with enterotype B (61 normal, 117 overweight/obese) and 229 men with enterotype P (74 normal, 155 overweight/obese). The ratio between Prevotella and Bacteroides abundance, P/B, was used as a simplified way to distinguish the predominant enterotype. In enterotype P group (P/B ≥ 0.01), obesity was a risk factor for a reduced rate of forward progressive sperm motility (odds ratio [OR] 3.350; 95% confidence interval [CI] 1.881-5.966; P < 0.001), and a reduced rate of total sperm motility (OR 4.298; 95% CI 2.365-7.809; P < 0.001). Obesity was also an independent risk factor (OR 3.131; 95% CI 1.749-5.607; P < 0.001) after adjusting follicle-stimulating hormone. In enterotype P, body mass index, as a diagnostic indicator of a reduced rate of forward progressive sperm motility and a decreased rate of decreased total sperm motility, had AUC values of 0.627 (P = 0.001) and 0.675 (P < 0.0001), respectively, which were significantly higher than the predicted values in all patients. However, in enterotype B group (P < 0.01), obesity was not a risk factor for asthenospermia, where no significant difference between obesity and sperm quality parameters was observed. This study is tried to introduce enterotypes as a population-based individualized classification index to investigate the correlation between BMI and asthenospermia. In our study, overweight/obese men with enterotype P were found to have poorer sperm quality. however, sperm quality was not associated with overweight/obese in men with enterotype B. Thereof, BMI is a risk factor for asthenospermia only in men with enterotype P, but not in men with enterotype B.
| S-EPMC9550853 | biostudies-literature
Project description:BackgroundThe fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.ResultsWe identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.ConclusionsWe show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.
| S-EPMC10416509 | biostudies-literature
Project description:Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are 'megafauna'? Here, we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyse associated terminology in the scientific literature. Second, we conduct a survey among ecologists and palaeontologists to assess the species traits used to identify and define megafauna. Our review indicates that definitions are highly dependent on the study ecosystem and research question, and primarily rely on ad hoc size-related criteria. Our survey suggests that body size is crucial, but not necessarily sufficient, for addressing the different applications of the term megafauna. Thus, after discussing the pros and cons of existing definitions, we propose an additional approach by defining two function-oriented megafaunal concepts: 'keystone megafauna' and 'functional megafauna', with its variant 'apex megafauna'. Assessing megafauna from a functional perspective could challenge the perception that there may not be a unifying definition of megafauna that can be applied to all eco-evolutionary narratives. In addition, using functional definitions of megafauna could be especially conducive to cross-disciplinary understanding and cooperation, improvement of conservation policy and practice, and strengthening of public perception. As megafaunal research advances, we encourage scientists to unambiguously define how they use the term 'megafauna' and to present the logic underpinning their definition.
| S-EPMC7126068 | biostudies-literature
Project description:Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called 'enterotypes', each of which is overrepresented by a distinct set of bacterial genera. Here we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.
| S-EPMC3520023 | biostudies-other
Project description:Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching's effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions-metamer mismatching and colour constancy-must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy's false premise that colour is an intrinsic attribute of an object.
| S-EPMC4565710 | biostudies-literature
Project description:Studies of morbidity compression routinely report the average number of years spent in an unhealthy state but do not report variation in age at morbidity onset. Variation was highlighted by Fries (1980) as crucial for identifying disease postponement. Using incidence of first hospitalization after age 60, as one working example, we estimate variation in morbidity onset over a 27-year period in Denmark. Annual estimates of first hospitalization and the population at risk for 1987 to 2014 were identified using population-based registers. Sex-specific life tables were constructed, and the average age, the threshold age, and the coefficient of variation in age at first hospitalization were calculated. On average, first admissions lasting two or more days shifted towards older ages between 1987 and 2014. The average age at hospitalization increased from 67.8 years (95% CI 67.7-67.9) to 69.5 years (95% CI 69.4-69.6) in men, and 69.1 (95% CI 69.1-69.2) to 70.5 years (95% CI 70.4-70.6) in women. Variation in age at first admission increased slightly as the coefficient of variation increased from 9.1 (95% CI 9.0-9.1) to 9.9% (95% CI 9.8-10.0) among men, and from 10.3% (95% CI 10.2-10.4) to 10.6% (95% CI 10.5-10.6) among women. Our results suggest populations are ageing with better health today than in the past, but experience increasing diversity in healthy ageing. Pensions, social care, and health services will have to adapt to increasingly heterogeneous ageing populations, a phenomenon that average measures of morbidity do not capture.
| S-EPMC7250949 | biostudies-literature
Project description:Resistant hypertension is common and known to be a risk factor for cardiovascular events, including stroke, myocardial infarction, heart failure, and cardiovascular mortality, as well as adverse renal events, including chronic kidney disease and end-stage kidney disease. This review will discuss the definition of resistant hypertension as well as the most recent evidence regarding its diagnosis, evaluation, and management. The issue of medication non-adherence and its association with apparent treatment-resistant hypertension will be addressed. Non-pharmacological interventions for the treatment of resistant hypertension will be reviewed. Particular emphasis will be placed on pharmacological interventions, highlighting the role of mineralocorticoid receptor antagonists and sodium-glucose cotransporter-2 inhibitors and device therapy, including renal denervation, baroreceptor activation or modulation, and central arteriovenous fistula creation.
| S-EPMC8911440 | biostudies-literature
Project description:The diversity and high genomic mutation rates of viral species hinder our understanding of viruses and their contributions to human health. Viral enterotypes as a description of the gut virome, its characteristics have not been thoroughly studied. Here we investigated the human gut virome composition using previously published sequencing data of 2,690 metagenomes from seven countries with various phenotypes. We found that the virome was dominated by double-stranded DNA viruses in our data, and young children and adults showed different stages in their fecal enterovirus composition. Beta diversity showed there were significantly less homogeneous in individuals with severe disorders of bile acid secretion, such as cirrhosis. In contrast, there were no significant differences in distances to centroids or viral components between patients with phenotypes unrelated to bile acid, such as hypertension. Enterotypes determined independently from various projects showed similar specific viruses and enrichment direction. Confounding factors, such as different sequencing platforms and library construction, did not confuse enterotyping. The gut virome composition pattern could be described by two viral enterotypes, which supported a discrete, rather than a gradient, distribution. Three main components, enterotype 1 and 2 specific viruses and the other, comprise the total viral variation in these sets. Compared with enterotype 2, enterotype 1 had a higher viral count, Shannon index, and similarity between samples. The relative abundance of enterotype-specific viruses is a crucial determinant of enterotype assignment. Samples not matching any of the defined enterotypes in the database did not necessarily correlate to sickness. Therefore, the background context must be carefully considered when using a viral enterotype as a feature for disease prediction. Our results highlight important insights into the human gut virome composition by exploring two-main viral enterotypes in population and providing an alternate covariate for early disease screening.
| S-EPMC8511818 | biostudies-literature
Project description:Advances in nanoparticle synthesis and engineering have produced nanoscale agents affording both therapeutic and diagnostic functions that are often referred to by the portmanteau 'nanotheranostics'. The field is associated with many applications in the clinic, especially in cancer management. These include patient stratification, drug-release monitoring, imaging-guided focal therapy and post-treatment response monitoring. Recent advances in nanotheranostics have expanded this notion and enabled the characterization of individual tumours, the prediction of nanoparticle-tumour interactions, and the creation of tailor-designed nanomedicines for individualized treatment. Some of these applications require breaking the dogma that a nanotheranostic must combine both therapeutic and diagnostic agents within a single, physical entity; instead, it can be a general approach in which diagnosis and therapy are interwoven to solve clinical issues and improve treatment outcomes. In this Review, we describe the evolution and state of the art of cancer nanotheranostics, with an emphasis on clinical impact and translation.
| S-EPMC5654564 | biostudies-other