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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Culturing the human microbiota and culturomics

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(9), С. 540 - 550

Опубликована: Июнь 24, 2018

Язык: Английский

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Role of the microbiome in human development

Gut, Год журнала: 2019, Номер 68(6), С. 1108 - 1114

Опубликована: Янв. 22, 2019

The host-microbiome supraorganism appears to have coevolved and the unperturbed microbial component of dyad renders host health sustainable. This coevolution has likely shaped evolving phenotypes in all life forms on this predominantly planet. microbiota seems exert effects next generation from gestation, via maternal immune responses. ecosystems develop, restricted their epithelial niches by system, concomitantly with chronological development, providing early modulation physiological development functions for nutrition, immunity resistance pathogens at ages. Here, we review role microbiome human including evolutionary considerations, maternal/fetal relationships, contributions nutrition growth. We also discuss what constitutes a healthy microbiota, how antimicrobial modern practices are impacting associations between perturbations, responses diseases rocketing urban societies potential future restoration.

Язык: Английский

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MicroRNAs and complex diseases: from experimental results to computational models

Briefings in Bioinformatics, Год журнала: 2017, Номер 20(2), С. 515 - 539

Опубликована: Сен. 15, 2017

Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one the most important components cell, miRNAs play growing role various essential biological processes. For recent few decades, amounts experimental methods computational models have been designed implemented to identify novel miRNA-disease associations. In this review, functions miRNAs, miRNA-target interactions, associations some publicly available miRNA-related databases discussed detail. Specially, considering fact that an increasing number experimentally confirmed, we selected five human diseases crucial disease-related provided corresponding introductions. Identifying has become goal biomedical research, which will accelerate understanding disease pathogenesis molecular level tools design for diagnosis, treatment prevention. Computational means association identification, could select promising pairs validation significantly reduce time cost experiments. Here, reviewed 20 state-of-the-art predicting from different perspectives. Finally, summarized four factors difficulties potential framework constructing powerful predict including feasible research schemas, future directions further development models.

Язык: Английский

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Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

Frontiers in Plant Science, Год журнала: 2021, Номер 12

Опубликована: Март 2, 2021

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, mediating organismal interactions. Similarly, plant microbiomes participate in of the above-mentioned processes directly or indirectly by regulating metabolism. Studies have shown that plants can influence their microbiome secreting various and, turn, may also impact metabolome host plant. However, not much is known about communications between interacting partners phenotypic changes. In this article, we review patterns potential underlying mechanisms interactions PSMs microbiomes. We describe recent developments analytical approaches methods field. The applications these new increased our understanding relationships Though current studies primarily focused on model organisms, results obtained so far should help future agriculturally important facilitate development manipulate PSMs–microbiome with predictive outcomes for sustainable crop productions.

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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Targeting zonulin and intestinal epithelial barrier function to prevent onset of arthritis

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Апрель 24, 2020

Gut microbial dysbiosis is associated with the development of autoimmune disease, but mechanisms by which affects transition from asymptomatic autoimmunity to inflammatory disease are incompletely characterized. Here, we identify intestinal barrier integrity as an important checkpoint in translating inflammation. Zonulin family peptide (zonulin), a potent regulator for tight junctions, highly expressed mice and humans can be used predict arthritis. Increased serum zonulin levels accompanied leaky barrier, Restoration pre-phase arthritis using butyrate or cannabinoid type 1 receptor agonist inhibits Moreover, treatment antagonist larazotide acetate, specifically increases integrity, effectively reduces onset. These data preventive approach onset targeting impaired function.

Язык: Английский

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Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity

Immunity, Год журнала: 2022, Номер 55(2), С. 324 - 340.e8

Опубликована: Фев. 1, 2022

The aryl hydrocarbon receptor (AhR) is a sensor of products tryptophan metabolism and potent modulator immunity. Here, we examined the impact AhR in tumor-associated macrophage (TAM) function pancreatic ductal adenocarcinoma (PDAC). TAMs exhibited high activity Ahr-deficient macrophages developed an inflammatory phenotype. Deletion Ahr myeloid cells or pharmacologic inhibition reduced PDAC growth, improved efficacy immune checkpoint blockade, increased intra-tumoral frequencies IFNγ+CD8+ T cells. Macrophage was not required for this effect. Rather, dependent on Lactobacillus metabolization dietary to indoles. Removal TAM promoted accumulation TNFα+IFNγ+CD8+ cells; provision indoles blocked In patients with PDAC, AHR expression associated rapid disease progression mortality, as well immune-suppressive phenotype, suggesting conservation regulatory axis human disease.

Язык: Английский

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The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Июнь 4, 2019

The human microbiome includes trillions of bacteria, many which play a vital role in host physiology. Numerous studies have now detected bacterial DNA first-pass meconium and amniotic fluid samples, suggesting that the may commence utero. However, these data remained contentious due to underlying contamination issues. Here, we used previously described method for reducing workflows determine if there is fetal beyond level background contamination. We recruited 50 women undergoing non-emergency cesarean section deliveries with no evidence intra-uterine infection collected samples. Full-length 16S rRNA gene sequencing was performed using PacBio SMRT cell technology, allow high resolution profiling gut microbiomes. Levels inflammatory cytokines were measured fluid, levels immunomodulatory short chain fatty acids (SCFAs) quantified meconium. All samples most (36/43) contained DNA. dominated by reads mapped Pelomonas puraquae. Aside from this species, remarkably heterogeneous between patients. more diverse mainly typical skin commensals, including Propionibacterium acnes Staphylococcus spp. acetate propionate, at ratios similar those reported infants. P. puraquae inversely correlated propionate levels. Amniotic cytokine associated microbiome. Our results demonstrate SCFAs are present utero, potential influence developing immune system.

Язык: Английский

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Mass spectrometry-based metabolomics in microbiome investigations

Nature Reviews Microbiology, Год журнала: 2021, Номер 20(3), С. 143 - 160

Опубликована: Сен. 22, 2021

Язык: Английский

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