The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Science, Journal Year: 2020, Volume and Issue: 368(6494), P. 973 - 980

Published: May 28, 2020

Bacteria were first detected in human tumors more than 100 years ago, but the characterization of tumor microbiome has remained challenging because its low biomass. We undertook a comprehensive analysis microbiome, studying 1526 and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, brain tumors. found that each type distinct composition breast particularly rich diverse microbiome. The intratumor bacteria are mostly intracellular present both immune cells. also noted correlations between or predicted functions with types subtypes, patients' smoking status, response to immunotherapy.

Language: Английский

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Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation

npj Parkinson s Disease, Journal Year: 2021, Volume and Issue: 7(1)

Published: March 10, 2021

The gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked microbes to Parkinson's disease (PD) symptomatology pathophysiology. PD often preceded by gastrointestinal symptoms alterations the enteric nervous system accompany disease. Several studies have analyzed microbiome in PD, but a consensus on features PD-specific missing. Here, we conduct meta-analysis re-analyzing ten currently available 16S datasets investigate whether common patients exist across cohorts. We found significant PD-associated microbiome, which are robust study-specific technical heterogeneities, although differences structure between controls small. Enrichment genera Lactobacillus, Akkermansia, Bifidobacterium depletion bacteria belonging Lachnospiraceae family Faecalibacterium genus, both short-chain fatty acids producers, emerged most consistent alterations. This dysbiosis might result pro-inflammatory status could be recurrent affecting patients.

Language: Английский

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Mass spectrometry-based metabolomics in microbiome investigations

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(3), P. 143 - 160

Published: Sept. 22, 2021

Language: Английский

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Cropping systems in agriculture and their impact on soil health-A review

Global Ecology and Conservation, Journal Year: 2020, Volume and Issue: 23, P. e01118 - e01118

Published: June 1, 2020

Soil health is defined as the capacity of soil to function, within ecosystem boundaries, sustain crop and animal productivities, maintain or enhance environmental sustainability, improve human worldwide. In agro-ecosystems, can change due anthropogenic activities, such preferred cropping practices intensive land-use management, which further impact functions. Previous assessment in agriculture mostly relates eco-functions that are integrated with non-biological properties nutrients structures. recent years, biological microorganisms were considered an essential composition well. However, systematic reviews its potential feedback society under different still limited. this review, we discussed 1) common novel agro-systems on health, 2) evolution plant–microbe–soil complex biochemical mechanisms pressure responsible for 3) changes concept quality over decades key indicators currently used evaluating 4) issues agroecosystems affect most, particularly how various have developed time activities agroecosystem. This knowledge, along necessary policies, will help ensure healthy soil—a crucial component sustainable development.

Language: Английский

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Microbiota Composition and Metabolism Are Associated With Gut Function in Parkinson's Disease

Movement Disorders, Journal Year: 2020, Volume and Issue: 35(7), P. 1208 - 1217

Published: May 1, 2020

Abstract Background Parkinson's disease is characterized by a high burden of gastrointestinal comorbidities, especially constipation and reduced colonic transit time, gut microbiota alterations. The diverse metabolites produced the are broadly relevant to host health. How composition metabolism relate function in largely unknown. objectives current study were assesses associations between composition, stool consistency, constipation, systemic microbial better understand how intestinal microbes contribute disturbances commonly observed patients. Methods Three hundred participants (197 patients 103 controls) recruited for this cross‐sectional cohort study. Participants supplied fecal samples sequencing (n = 300) serum untargeted metabolomics 125). Data collected on motor nonmotor symptoms, medications, diet, demographics. Results Significant taxonomic differences patients, even when controlling function. was carbohydrate fermentation butyrate synthesis capacity increased proteolytic production deleterious amino acid metabolites, including p‐cresol phenylacetylglutamine. Taxonomic shifts elevated strongly associated with consistency (a proxy time) among Conclusions Compositional metabolic alterations highly function, suggesting plausible mechanistic links altered bacterial health disease. detection suggests mechanism whereby dysbiosis contributes etiology pathophysiology. © 2020 International Parkinson Movement Disorder Society

Language: Английский

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Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories

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

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Soil microbial diversity and composition: Links to soil texture and associated properties

Soil Biology and Biochemistry, Journal Year: 2020, Volume and Issue: 149, P. 107953 - 107953

Published: Aug. 8, 2020

Language: Английский

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Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

Applied Sciences, Journal Year: 2021, Volume and Issue: 11(2), P. 688 - 688

Published: Jan. 12, 2021

FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function marine species using standard microbiological references. This study, however, has attempted access application in soil environments. We hypothesized that compatible with terrestrial ecosystems. potential use assign bacteria investigated meta-analysis our newly designed experiments. Soil samples two major ecosystems, including agricultural land forest, were collected. Bacterial taxonomy analyzed Illumina sequencing gene assigned by FAPROTAX. presence all functionally OTUs (Operation Taxonomic Units) manually checked peer-reviewed articles as well microbiology books. Overall, we showed sample source not predominant factor limited FAPROTAX, but poor taxonomic identification was. proportion between aquatic non-aquatic ecosystems significantly different (p > 0.05). There strong significant correlations (σ = 0.90–0.95, p < 0.01) number genus or order level OTUs. After manual verification, found more than 97% have previously been detected potentially performed forest soils. further provided information regarding capable N-fixation, P K solubilization, which are three main important elements systems can be integrated increase Consequently, concluded used fast-functional screening grouping data its performance could enhanced through improving functional reference databases.

Language: Английский

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The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

Trends in cancer, Journal Year: 2020, Volume and Issue: 6(3), P. 192 - 204

Published: Feb. 7, 2020

The collection of microbes that live in and on the human body - microbiome can impact cancer initiation, progression, response to therapy, including immunotherapy. mechanisms by which microbiomes cancers yield new diagnostics treatments, but much remains unknown. interactions between microbes, diet, host factors, drugs, cell-cell within itself likely involve intricate feedbacks, no single component explain all behavior system. Understanding role host-associated microbial communities systems will require a multidisciplinary approach combining ecology, immunology, cell biology, computational biology approach.

Language: Английский

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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: March 10, 2021

Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions laborious, automated often fail recapitulate known processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool pathways and automatically reconstruct microbial using curated reaction database novel gap-filling algorithm. On the basis scientific literature experimental data for 14,931 bacterial phenotypes, demonstrate that outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, interactions within communities.

Language: Английский

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