Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

Nature Protocols, Год журнала: 2020, Номер 15(3), С. 799 - 821

Опубликована: Янв. 15, 2020

Язык: Английский

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Current challenges and best-practice protocols for microbiome analysis

Briefings in Bioinformatics, Год журнала: 2019, Номер 22(1), С. 178 - 193

Опубликована: Ноя. 7, 2019

Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological ecological roles environmental microorganisms. However, analysis is affected by experimental conditions (e.g. errors genomic repeats) computationally intensive cumbersome downstream quality control, assembly, binning statistical analyses). Moreover, introduction new technologies protocols led to a flood methodologies, which also have an immediate effect results analyses. The aim this work review most important workflows for 16S rRNA shotgun long-read metagenomics, as well provide best-practice design, sample processing, sequencing, binning, annotation visualization. To simplify standardize computational analysis, we set metagenomic data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).

Язык: Английский

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Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus

Gut, Год журнала: 2018, Номер 67(9), С. 1614 - 1625

Опубликована: Май 14, 2018

Objective The initial colonisation of the human microbiota and impact maternal health on neonatal at birth remain largely unknown. aim our study is to investigate possible dysbiosis associated with gestational diabetes mellitus (GDM) estimate potential risks microbial shift neonates. Design Pregnant women neonates suffering from GDM were enrolled 581 (oral, intestinal vaginal) 248 pharyngeal, meconium amniotic fluid) samples collected. To avoid vaginal bacteria contaminations, included predominantly delivered by C-section, their collected within seconds delivery. Results Numerous diverse bacterial taxa identified samples, different body sites grouped into distinct clusters. pregnant was remarkably altered in GDM, a strong correlation between certain discriminatory oral glucose tolerance test. Microbes varying same trend across observed, revealing intergenerational concordance variation GDM. Furthermore, lower evenness but more depletion KEGG orthologues higher abundance some viruses (eg, herpesvirus mastadenovirus) observed Conclusion can alter both birth, which sheds light another form inheritance highlights importance understanding formation early-life microbiome.

Язык: Английский

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Low dietary fiber intake increasesCollinsellaabundance in the gut microbiota of overweight and obese pregnant women

Gut Microbes, Год журнала: 2017, Номер 9(3), С. 189 - 201

Опубликована: Ноя. 16, 2017

The gut microbiota contributes to the regulation of glucose metabolism in pregnancy. Abundance genus Collinsella is positively correlated with circulating insulin; however, it unclear what determines abundance. This study aims validate correlation between and insulin elucidate if macronutrient intake alters abundance composition. Gut profiles were assessed by 16S rRNA sequencing 57 overweight 73 obese pregnant women from SPRING (Study PRobiotics IN Gestational diabetes) trial at 16 weeks gestation metabolic hormone levels intake. composition top bottom 10% dietary fiber was evaluated through network analysis. (rho = 0.30, p 0.0006), independent maternal BMI, but negatively -0.20, 0.025) this cohort. Low associated a favoring lactate fermentation while high promotes short-chain fatty acid-producing bacteria. may enable overgrowth alter overall pattern microbiota. suggests that choices during pregnancy can modify nutritional ecology microbiota, potential deleterious effects on inflammatory health host.ANZCTR 12611001208998, registered 23/11/2011.

Язык: Английский

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Perinatal factors affect the gut microbiota up to four years after birth

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Апрель 3, 2019

Perinatal factors impact gut microbiota development in early life, however, little is known on the effects of these microbes later life. Here we sequence DNA from faecal samples children over first four years and reveal a perpetual evolution during this period. The significant gestational age at birth delivery mode progression evident while no measurable antibiotics are found year. Microbiota profiles also characteristic dependant maturity. Full term characterised by Bacteroides (year one), Parabacteroides two) Christensenellaceae four). Preterm Lactobacillus Streptococcus Carnobacterium This study reveals that retains distinct microbial perinatal up to age.

Язык: Английский

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Probiotics drive gut microbiome triggering emotional brain signatures

Gut Microbes, Год журнала: 2018, Номер unknown, С. 1 - 11

Опубликована: Май 3, 2018

Experimental manipulation of the gut microbiome was found to modify emotional and cognitive behavior, neurotransmitter expression brain function in rodents, but corresponding human data remain scarce. The present double-blind, placebo-controlled randomised study aimed at investigating effects 4 weeks' probiotic administration on microbial composition healthy volunteers. Forty-five participants divided equally into three groups (probiotic, placebo no intervention) underwent functional MRI (emotional decision-making recognition memory tasks). In addition, stool samples were collected investigate composition. Probiotic for weeks associated with changes activation patterns response tasks, which also accompanied by subtle shifts profile. Microbiome mirrored self-reported behavioral measures performance. This is first reporting a distinct influence behavioral, neural, levels same time findings provide basis future investigations role microbiota potential therapeutic application probiotics.

Язык: Английский

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First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

mBio, Год журнала: 2017, Номер 8(6)

Опубликована: Ноя. 15, 2017

Human-associated archaea remain understudied in the field of microbiome research, although particular methanogenic were found to be regular commensals human gut, where they represent keystone species metabolic processes. Knowledge on abundance and diversity human-associated is extremely limited, little known about their function(s), overall role health, or association with parts body other than gastrointestinal tract oral cavity. Currently, methodological issues impede full assessment archaeome, as bacteria-targeting protocols are unsuitable for characterization spectrum Archaea. The goal this study was establish conservative based specifically archaea-targeting, PCR-based methods retrieve first insights into archaeomes tract, lung, nose, skin. Detection Archaea highly dependent primer selection sequence processing pipeline used. Our results enabled us a novel picture we time Methanobacterium Woesearchaeota (DPANN superphylum) associated respectively. Similar bacteria, archaeal communities group biogeographically, forming (i) thaumarchaeal skin landscape, (ii) (methano)euryarchaeal (iii) mixed skin-gastrointestinal landscape (iv) woesearchaeal lung landscape. On basis used, able detect unexpectedly high different parts.

Язык: Английский

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Intestinal Flora Modulates Blood Pressure by Regulating the Synthesis of Intestinal-Derived Corticosterone in High Salt-Induced Hypertension

Circulation Research, Год журнала: 2020, Номер 126(7), С. 839 - 853

Опубликована: Фев. 13, 2020

Rationale: High-salt diet is one of the most important risk factors for hypertension. Intestinal flora has been reported to be associated with high salt–induced hypertension (hSIH). However, detailed roles intestinal in hSIH pathogenesis have not yet fully elucidated. Objective: To reveal and mechanisms development. Methods Results: The abovementioned issues were investigated using various techniques including 16S rRNA gene sequencing, untargeted metabolomics, selective bacterial culture, fecal microbiota transplantation. We found that high-salt induced Wistar rats. healthy rats could dramatically lower blood pressure (BP) hypertensive rats, whereas had opposite effects. composition, metabolism, interrelationship considerably reshaped, increased corticosterone level reduced Bacteroides arachidonic acid levels, which tightly correlated BP. serum was also significantly hSIH. Furthermore, above abnormalities confirmed patients fragilis inhibit production intestinal-derived by through its metabolite acid. Conclusions: transferred transplantation, indicating pivotal levels B intestine, thereby promoting BP elevation. This study revealed a novel mechanism different from inflammation/immunity regulated BP, namely modulate affecting steroid hormone levels. These findings enriched understanding function effects on

Язык: Английский

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Mucin degrader Akkermansia muciniphila accelerates intestinal stem cell-mediated epithelial development

Gut Microbes, Год журнала: 2021, Номер 13(1)

Опубликована: Янв. 1, 2021

Mucin-degrading bacteria are densely populated in the intestinal epithelium; however, their interaction with stem cells (ISCs) and progeny have not been elucidated. To determine whether mucin-degrading play a role gut homeostasis, mice were treated Akkermansia muciniphila, specialized species that degrades mucin. Administration of A. muciniphila for 4 weeks accelerated proliferation Lgr5+ ISCs promoted differentiation Paneth goblet small intestine (SI). We found similar effects colon. The levels acetic propionic acids higher cecal contents muciniphila-treated than PBS-treated mice. SI organoids obtained from larger could be diminished by treatment G protein-coupled receptor (Gpr) 41/43 antagonists. Pre-treatment reduced damage caused radiation methotrexate. Further, novel isotype strain was isolated heathy human feces showed enhanced function epithelial regeneration. These findings suggest (e.g., muciniphila) may crucial promoting ISC-mediated development contribute to homeostasis maintenance.

Язык: Английский

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The Role of the Cervicovaginal Microbiome on the Genesis and as a Biomarker of Premalignant Cervical Intraepithelial Neoplasia and Invasive Cervical Cancer

International Journal of Molecular Sciences, Год журнала: 2019, Номер 21(1), С. 222 - 222

Опубликована: Дек. 28, 2019

The microbiome is able to modulate immune responses, alter the physiology of human organism, and increase risk viral infections development diseases such as cancer. In this review, we address changes in cervical microbiota potential biomarkers identify intraepithelial neoplasia (CIN) invasive cancer context papillomavirus (HPV) infection. Current approaches for clinical diagnostics manipulation with use probiotics through transplantation are also discussed.

Язык: Английский

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