Genomics, Год журнала: 2021, Номер 113(6), С. 3635 - 3643
Опубликована: Авг. 24, 2021
Язык: Английский
mSphere, Год журнала: 2021, Номер 6(1)
Опубликована: Фев. 24, 2021
In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, inadequate pipeline settings. Concerning the last, quality thresholds as well bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such truncation) are responsible for a number of observed differences between studies.
Язык: Английский
Процитировано
286
Journal of Clinical Investigation, Год журнала: 2022, Номер 132(7)
Опубликована: Март 31, 2022
Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for discovery and characterization unculturable microbes with prediction their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic RNA sequencing. The choice which methodology to pursue a given purpose is often unclear clinicians researchers. In this Review, we describe fundamentals NGS, focus on We also discuss pros cons each as well important concepts in data variability, study design, clinical metadata collection. further present examples how studies have disease pathophysiology across diverse contexts, including development diagnostics therapeutics. Finally, share insights might be integrated into advance research care coming years.
Язык: Английский
Процитировано
264
Nature Communications, Год журнала: 2021, Номер 12(1)
Опубликована: Май 28, 2021
Abstract Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics demonstrate carbohydrate secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal bacterial iron metabolism functionality is correlated with enrichment. Using time-series RNA-Seq data, homeostasis impacted by stress, loss of a plant phytosiderophore transporter impacts microbial community composition, leading significant increases lineage, Actinobacteria. Finally, show exogenous application disrupts drought-induced enrichment Actinobacteria, as well their improvement host phenotype during stress. Collectively, our findings implicate microbiome’s response may inform efforts improve tolerance increase food security.
Язык: Английский
Процитировано
171
Nature Communications, Год журнала: 2021, Номер 12(1)
Опубликована: Май 24, 2021
Abstract Associations between gut microbiota and colorectal cancer (CRC) have been widely investigated. However, the replicable markers for early-stage adenoma diagnosis across multiple populations remain elusive. Here, we perform an integrated analysis on 1056 public fecal samples, to identify adenoma-associated microbial early detection of CRC. After adjusting potential confounders, Random Forest classifiers are constructed with 11 discriminate from control (area under ROC curve (AUC) = 0.80), 26 CRC (AUC 0.89), respectively. Moreover, validate in two independent cohorts achieving AUCs 0.78 0.84, Functional reveals that altered microbiome is characterized increased ADP- l -glycero-beta- d -manno-heptose biosynthesis elevated menaquinone-10 These findings validated a newly-collected cohort 43 samples using quantitative real-time PCR. This work proves validity adenoma-specific multi-populations, which would contribute treatment
Язык: Английский
Процитировано
169
Journal of Dental Research, Год журнала: 2020, Номер 100(1), С. 21 - 28
Опубликована: Авг. 12, 2020
Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, esthetic functions. Like natural teeth, orally exposed part offers pristine nonshedding surface for salivary pellicle-mediated microbial adhesion biofilm formation. In early colonization stages, these bacterial communities closely resemble those healthy periodontal sites, with lower diversity. Because peri-implant tissues more susceptible endogenous oral infections, understanding ecological triggers that underpin pathogenesis peri-implantitis is central developing improved prevention, diagnosis, therapeutic strategies. The advent next-generation sequencing (NGS) technologies, notably applied 16S ribosomal RNA gene amplicons, has enabled comprehensive taxonomic characterization health disease, revealing differentially abundant microbiota between 2 states, or periodontitis. With that, niche highlighted as distinct ecosystem shapes its individual resident community. Shifts from disease include an increase diversity gradual depletion commensals, along enrichment classical emerging pathogens. Metatranscriptomic profiling revealed similarities virulence characteristics periodontitis, nonetheless some distinctive pathways interbacterial networks. Deeper functional assessment physiology well-characterized will elucidate further etiopathogenic mechanisms drivers disease.
Язык: Английский
Процитировано
159
Circulation Research, Год журнала: 2021, Номер 128(7), С. 934 - 950
Опубликована: Апрель 1, 2021
The pathogenesis of hypertension is known to involve a diverse range contributing factors including genetic, environmental, hormonal, hemodynamic and inflammatory forces, name few. There mounting evidence suggest that the gut microbiome plays an important role in development hypertension. gastrointestinal tract, which houses largest compartment immune cells body, represents intersection environment host. Accordingly, lifestyle shape are modulated by microbiome, modifying risk for hypertensive disease. One well-studied example consumption dietary fibers, leads production short-chain fatty acids can contribute expansion anti-inflammatory cells, consequently protecting against progression Dietary interventions such as fasting have also been shown impact via microbiome. Studying disease presents variety unique challenges use traditional model systems. Integrating considerations into preclinical research crucial, novel strategies account reciprocal host-microbiome interactions, wildling mouse model, may provide new opportunities translation. intricacies matter ongoing research, there several technical should be accounted moving forward. In this review we insights interaction summarize its importance regulation blood pressure. Additionally, recommendations future from field at large readily integrated context
Язык: Английский
Процитировано
125
Advanced Composites and Hybrid Materials, Год журнала: 2024, Номер 7(1)
Опубликована: Фев. 1, 2024
Язык: Английский
Процитировано
40
Frontiers in Microbiology, Год журнала: 2021, Номер 12
Опубликована: Июль 15, 2021
The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most what we currently know about microbiome, especially in early stages development, was described using culture-independent sequencing methods that allow us to identify taxonomic composition genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there not been a direct comparison utility stool samples from very young children, which have different features than those adults. We compared effects profiling infant with 16S rRNA vs. techniques 338 fecal samples; younger 15, 15–30, older 30 months age. demonstrate observed changes alpha-diversity beta-diversity age occur similar extents both methods. also show identified larger number genera find several are missed underrepresented by each method. present link between alpha diversity depth for children ages. These findings provide guide selecting an appropriate three studied groups.
Язык: Английский
Процитировано
97
Chinese Medical Journal, Год журнала: 2020, Номер 133(15), С. 1844 - 1855
Опубликована: Июнь 26, 2020
Abstract The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary the concepts and technologies used in microbiome research. First, we define primary such as microbiota, microbiome, metagenome. Then, discuss study design schemes, methods sample size calculation, for improving reliability We emphasize importance negative positive controls section. Next, statistical analysis research, focusing on problems multiple comparisons ways compare β-diversity between groups. Finally, step-by-step pipelines analysis. In summary, meticulous key step obtaining meaningful results, appropriate are important accurate interpretation data. researchers insights into newly developed methods.
Язык: Английский
Процитировано
90
Ophthalmology and Therapy, Год журнала: 2020, Номер 9(3), С. 499 - 513
Опубликована: Июль 2, 2020
A healthy gut microbiota is essential in maintaining the human body a homeostatic state by its functions digestion and immune tolerance. Under states of aberrant microbial composition or function (dysbiosis), induces systemic inflammation that can lead to onset many diseases. In this review, we describe some evidence, largely from rodent studies, supports possible role dysbiotic exacerbation ocular diseases, primarily diabetic retinopathy, age-related macular degeneration, choroidal neovascularization, uveitis. Furthermore, examine several potential therapeutic measures show promise restoring eubiotic state, preventing aforementioned disease pathologies.
Язык: Английский
Процитировано
88