Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories DOI Creative Commons
Shan Sun, Roshonda B. Jones, Anthony A. Fodor

et al.

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: April 2, 2020

Despite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict functional profiles microbial communities based on their taxonomic composition. In this study, we evaluated performance three commonly used prediction tools (PICRUSt, PICRUSt2, and Tax4Fun) by comparing significance differential abundance predicted gene those from across different environments.We selected 7 datasets human, non-human animal, environmental (soil) samples that publicly available sequences. As would expect previous literature, strong Spearman correlations were observed between compositions relative measured However, these preserved even when genes permuted samples. This suggests simple correlation coefficient is a highly unreliable measure for tools. an alternative, PICRUSt, Tax4Fun sequenced inference models associated metadata within each dataset. With approach, found reasonable human datasets, performing better related "housekeeping" functions. degraded sharply outside inference.We conclude utility default database likely limited development specific warranted. Video abstract.

Language: Английский

Sex differences in immune responses DOI Open Access
Sabra L. Klein, Katie L. Flanagan

Nature reviews. Immunology, Journal Year: 2016, Volume and Issue: 16(10), P. 626 - 638

Published: Aug. 22, 2016

Language: Английский

Citations

4832
Gut microbiota are related to Parkinson's disease and clinical phenotype DOI
Filip Scheperjans, Velma T. E. Aho, Pedro A. B. Pereira

et al.

Movement Disorders, Journal Year: 2014, Volume and Issue: 30(3), P. 350 - 358

Published: Dec. 5, 2014

In the course of Parkinson's disease (PD), enteric nervous system (ENS) and parasympathetic nerves are amongst structures earliest most frequently affected by alpha-synuclein pathology. Accordingly, gastrointestinal dysfunction, in particular constipation, is an important non-motor symptom PD often precedes onset motor symptoms years. Recent research has shown that intestinal microbiota interact with autonomic central via diverse pathways including ENS vagal nerve. The gut microbiome not been previously investigated. We compared fecal microbiomes 72 patients control subjects pyrosequencing V1-V3 regions bacterial 16S ribosomal RNA gene. Associations between clinical parameters were analyzed using generalized linear models, taking into account potential confounders. On average, abundance Prevotellaceae feces was reduced 77.6% as controls. Relative 6.5% or less had 86.1% sensitivity 38.9% specificity for PD. A logistic regression classifier based on four families severity constipation identified 66.7% 90.3% specificity. relative Enterobacteriaceae positively associated postural instability gait difficulty. These findings suggest altered related to phenotype. Further studies warranted elucidate temporal causal relationships suitability a biomarker.

Language: Английский

Citations

1729
Sex differences and hormonal effects on gut microbiota composition in mice DOI Open Access
Elin Org, Margarete Mehrabian, Brian W. Parks

et al.

Gut Microbes, Journal Year: 2016, Volume and Issue: 7(4), P. 313 - 322

Published: June 29, 2016

We previously reported quantitation of gut microbiota in a panel 89 different inbred strains mice, and we now examine the question sex differences composition. When total population 689 mice was examined together, several taxa exhibited significant abundance between sexes but larger number were observed at single strain level, suggesting that can be obscured by host genetics environmental factors. also subset on chow high fat diets sex-by-diet interactions. further investigated using gonadectomized hormone treated from 3 strains. Principal coordinate analysis with unweighted UniFrac distances revealed very clear effects gonadectomy replacement composition all Moreover, bile acid analyses showed gender-specific as well gonodectomy, providing one possible mechanism mediating

Language: Английский

Citations

646
Progress in fish gastrointestinal microbiota research DOI Creative Commons

An R. Wang,

Chao Ran, Einar Ringø

et al.

Reviews in Aquaculture, Journal Year: 2017, Volume and Issue: 10(3), P. 626 - 640

Published: Feb. 2, 2017

Abstract The gastrointestinal (GI) microbiota of vertebrates plays critical roles in nutrition, development, immunity and resistance against invasive pathogens. In the past decade, research GI mammals has drastically increased our knowledge on their relationship with health disease. However, understanding fish intestinal is limited. This review provides an overview gut microbiota, including microbial composition, formation, factors that affect microbes characteristics compared human mice. Further, updated gnotobiotic zebrafish elaborated insights gained functions are discussed. Understanding will guide development probiotics, prebiotics hopefully probiotic effectors as novel additives to improve fish.

Language: Английский

Citations

572
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights DOI Creative Commons
Edoardo Pasolli, Duy Tin Truong, Faizan Malik

et al.

PLoS Computational Biology, Journal Year: 2016, Volume and Issue: 12(7), P. e1004977 - e1004977

Published: July 11, 2016

Shotgun metagenomic analysis of the human associated microbiome provides a rich set microbial features for prediction and biomarker discovery in context diseases health conditions. However, use such high-resolution presents new challenges, validated computational tools learning tasks are lacking. Moreover, classification rules have scarcely been independent studies, posing questions about generality generalization disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based quantitative assessment strength potential microbiome-phenotype associations. We develop framework using profiles, including species-level relative abundances presence strain-specific markers. A comprehensive meta-analysis, with particular emphasis on cohorts, was performed collection 2424 publicly available samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were general improved by feature selection markers instead taxonomic abundance. cross-study analysis, transferred between studies some cases less accurate than tested within-study cross-validation. Interestingly, addition healthy (control) other training sets disease capabilities. Some species (most notably Streptococcus anginosus) seem characterize dysbiotic states rather connections specific disease. Our results modelling "healthy" can be considered first step toward defining dysbiosis. The software framework, metadata thousands at http://segatalab.cibio.unitn.it/tools/metaml.

Language: Английский

Citations

561
A new view of the fish gut microbiome: Advances from next-generation sequencing DOI
Mahdi Ghanbari, Wolfgang Kneifel, Konrad J. Domig

et al.

Aquaculture, Journal Year: 2015, Volume and Issue: 448, P. 464 - 475

Published: June 26, 2015

Language: Английский

Citations

554
Gut microbiota, obesity and diabetes DOI Open Access
Elaine Patterson, Paul M. Ryan, John F. Cryan

et al.

Postgraduate Medical Journal, Journal Year: 2016, Volume and Issue: 92(1087), P. 286 - 300

Published: Feb. 24, 2016

Abstract The central role of the intestinal microbiota in progression and, equally, prevention metabolic dysfunction is becoming abundantly apparent. symbiotic relationship between and host ensures appropriate development system humans. However, disturbances composition turn, functionality can disrupt gut barrier function, a trip switch for endotoxemia. This low-grade chronic inflammation, brought about by influx inflammatory bacterial fragments into circulation through malfunctioning barrier, has considerable knock-on effects adiposity insulin resistance. Conversely, recent evidence suggests that there are certain species may interact with metabolism metabolite-mediated stimulation enteric hormones other systems outside gastrointestinal tract, such as endocannabinoid system. When abundance these keystone begins to decline, we see collapse symbiosis, reflected deterioration health. review will investigate intricate axis metabolism, while also addressing promising novel field probiotics therapies.

Language: Английский

Citations

493
Sex Hormones Determine Immune Response DOI Creative Commons
Veena Taneja

Frontiers in Immunology, Journal Year: 2018, Volume and Issue: 9

Published: Aug. 27, 2018

OPINION article Front. Immunol., 27 August 2018Sec. Cytokines and Soluble Mediators in Immunity Volume 9 - 2018 | https://doi.org/10.3389/fimmu.2018.01931

Language: Английский

Citations

493
Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock DOI Open Access
Xue Liang, Frederic D. Bushman, Garret A. FitzGerald

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(33), P. 10479 - 10484

Published: Aug. 3, 2015

Significance Recent studies of the murine microbiome have revealed circadian behavior and linked it to host feeding time, but mechanism responsible for rhythmicity has not been fully clarified. Here we report that both system gender influence total load taxonomic abundances in fecal microbiota, regulation by clock is dominant. Disruption deletion Bmal1 altered microbial composition a gender-dependent fashion. Our analyses suggest need consider factors design studies, highlight importance analyzing absolute abundance understanding microbiota.

Language: Английский

Citations

492
Sex Differences in Gut Microbiota DOI Creative Commons
Yong Sung Kim, Tatsuya Unno, Byung‐Yong Kim

et al.

The World Journal of Men s Health, Journal Year: 2019, Volume and Issue: 38(1), P. 48 - 48

Published: March 27, 2019

Humans carry numerous symbiotic microorganisms in their body, most of which are present the gut. Although recent technological advances have produced extensive research data on gut microbiota, there various confounding factors (e.g., diet, race, medications) to consider. Sex is one important variables affecting but association has not yet been sufficiently investigated. results inconsistent, several animal and human studies shown sex differences microbiota. Herein, we review these discuss sex-dependent as well possible mechanisms involved.

Language: Английский

Citations

466