Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts

Nature Microbiology, Год журнала: 2022, Номер 7(2), С. 238 - 250

Опубликована: Янв. 27, 2022

Abstract Despite recent progress in our understanding of the association between gut microbiome and colorectal cancer (CRC), multi-kingdom dysbiosis CRC across cohorts is unexplored. We investigated four-kingdom microbiota alterations using metagenomic datasets 1,368 samples from 8 distinct geographical cohorts. Integrated analysis identified 20 archaeal, 27 bacterial, fungal 21 viral species for each single-kingdom diagnostic model. However, data revealed superior accuracy models constructed with markers, particular addition species. Specifically, 16 markers including 11 4 1 archaeal feature, achieved good performance diagnosing patients (area under receiver operating characteristic curve (AUROC) = 0.83) maintained 3 independent Coabundance ecological network associations bacterial species, such as Talaromyces islandicus Clostridium saccharobutylicum . Using metagenome shotgun sequencing data, predictive power microbial functional potential was explored elevated D-amino acid metabolism butanoate were observed CRC. Interestingly, model based on EggNOG genes high (AUROC 0.86). Collectively, findings uncovered CRC-associated common demonstrate applicability tools and, potentially, therapeutic targets treatment

Язык: Английский

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Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease

Science Translational Medicine, Год журнала: 2023, Номер 15(700)

Опубликована: Июнь 14, 2023

Alzheimer’s disease (AD) pathology is thought to progress from normal cognition through preclinical and ultimately symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of patients has an altered taxonomic composition compared healthy, cognitively control individuals. However, knowledge about changes in before onset limited. In this cross-sectional study accounted for clinical covariates dietary intake, we microbial function a cohort 164 individuals, 49 whom showed biomarker evidence early AD. Gut profiles individuals were distinct those without The change correlated β-amyloid (Aβ) tau pathological biomarkers but not neurodegeneration, suggesting may process. We identified specific bacterial taxa associated Inclusion these features improved accuracy, sensitivity, specificity machine learning classifiers predicting status when tested on subset (65 participants). correlates neuropathology improve our understanding etiology help identify gut-derived markers risk.

Язык: Английский

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ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization

Bioinformatics, Год журнала: 2023, Номер 39(8)

Опубликована: Авг. 1, 2023

Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences changes intestinal may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA one most popular cost-effective method to profile compositions, marker-gene sequencing cannot direct information about genes are present genomes community members. Bioinformatic tools have been developed predict function with gene data. Among them, PICRUSt2 has become prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference available test differences abundances between comparison groups. We ggpicrust2, an R package, do extensive differential abundance(DA) analyses publishable visualization highlight signals.

Язык: Английский

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Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults

Cell Reports, Год журнала: 2022, Номер 39(2), С. 110649 - 110649

Опубликована: Апрель 1, 2022

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects antibiotics on gut microbiota healthy adult volunteers, we quantify microbiome dynamics before, during, 6 months after exposure to 4 commonly used antibiotic regimens. We observe an decrease in species richness culturable bacteria antibiotics, with most microbiomes returning pre-treatment 2 months, altered taxonomy, resistome, metabolic output, as well increased resistance burden. Azithromycin delays recovery richness, resulting greater compositional distance. A subset volunteers experience a reduction diversity share similarities patients hospitalized intensive care units. These results improve our quantitative understanding impact dynamics, resilience, recovery.

Язык: Английский

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Integrated gut virome and bacteriome dynamics in COVID-19 patients

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

Опубликована: Янв. 1, 2021

SARS-CoV-2 is the cause of current global pandemic COVID-19; this virus infects multiple organs, such as lungs and gastrointestinal tract. The microbiome in these including bacteriome virome, responds to infection might also influence disease progression treatment outcome. In a cohort 13 COVID-19 patients Beijing, China, we observed that gut virome were notably different from those five healthy controls. We identified bacterial dysbiosis signature by observing reduced diversity viral shifts patients, among bacterial/viral compositions between severities, although differences are not entirely distinguishable effect antibiotics. Severe cases exhibited greater abundance opportunistic pathogens but depleted for butyrate-producing groups bacteria compared with mild moderate cases. replicated our findings mouse model, confirmed due infection, immune/infection-related genes differentially expressed epithelial cells during possibly explaining dynamics. Our results suggest components microbiome, affected infections, while their compositional signatures could reflect or even contribute severity recovery processes.

Язык: Английский

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Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men

Genome Medicine, Год журнала: 2021, Номер 13(1)

Опубликована: Июнь 17, 2021

Abstract Background A higher intake of dietary fiber is associated with a decreased risk chronic inflammatory diseases such as cardiovascular disease and bowel disease. This may function in part due to abrogation systemic inflammation induced by factors dysbiotic gut communities. Data regarding the detailed influences long-term recent differing sources on human microbiome are lacking. Methods In cohort 307 generally healthy men, we examined microbiomes, profiled shotgun metagenomic metatranscriptomic sequencing, relation plasma levels C-reactive protein (CRP), an established biomarker for inflammation. were analyzed using multivariate linear mixed models. Results We found that inflammation-associated microbial configurations corresponded CRP levels. greater was shifts composition, particularly Clostridiales, their potential carbohydrate utilization via polysaccharide degradation. true fruit (i.e., pectin). Most striking, significantly reduction individuals without substantial Prevotella copri carriage gut, whereas those P. maintained stable regardless intake. Conclusions Our findings offer evidence supporting fiber-gut microbiota interaction, well specific mechanism which gut-mediated be mitigated.

Язык: Английский

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A catalogue of 1,167 genomes from the human gut archaeome

Nature Microbiology, Год журнала: 2021, Номер 7(1), С. 48 - 61

Опубликована: Дек. 30, 2021

The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report analysis of 1,167 nonredundant genomes (608 high-quality genomes) recovered from gastrointestinal tract, sampled across 24 countries and rural urban populations. We identified previously undescribed taxa including 3 genera, 15 species 52 strains. Based on distinct genomic features, justify split Methanobrevibacter smithii clade into two separate species, with one represented by 'Candidatus intestini'. Patterns derived 28,581 protein clusters showed significant associations sociodemographic characteristics such as age groups lifestyle. additionally show that archaea are characterized specific functional adaptations to host carry a complex virome. Our work expands our current understanding archaeome provides large genome catalogue for future analyses decipher impact physiology.

Язык: Английский

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Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites

Cell Host & Microbe, Год журнала: 2023, Номер 31(3), С. 447 - 460.e6

Опубликована: Март 1, 2023

Язык: Английский

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An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Biomolecules, Год журнала: 2021, Номер 11(4), С. 530 - 530

Опубликована: Апрель 2, 2021

The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in health disease pathogenesis. Since most intestinal species are difficult to culture, next generation sequencing technologies have been widely applied study microbiome, including 16S rRNA, 18S internal transcribed spacer (ITS) sequencing, shotgun metagenomic metatranscriptomic viromic sequencing. Various software tools were developed analyze different data. In this review, we summarize commonly used computational for data analysis, extended our understanding of diseases.

Язык: Английский

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Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition

Science Translational Medicine, Год журнала: 2022, Номер 14(640)

Опубликована: Апрель 13, 2022

Disrupted development of the gut microbiota is a contributing cause childhood malnutrition.

Язык: Английский

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