The role of the microbiota in infectious diseases

Libertucci, Josie; Young, Vincent B.

doi:10.1038/s41564-018-0278-4

Cited by 285 publications

(213 citation statements)

References 156 publications

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Section: Comparing Bacterial and Eukaryotic Gut Microbiome Research Smentioning

confidence: 99%

“…It is often suggested that bacterial probiotics such as lactobacilli or bifidobacteria can revert the microbiota to a healthier state for the human host (e.g. Libertucci and Young 2019;Rauch and Lynch 2012;Walsh et al 2014). Many contested claims are made about probiotics, and despite some consistent findings in mouse studies, human probiotic meta-analyses and systematic reviews are at best "ambiguous" about probiotic benefits for most illnesses (see Marchesi et al 2016;Suez et al 2019).…”

Section: Eukaryotic Microbiota Treatments: Probiotics and Fmtsmentioning

confidence: 99%

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Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Hooks

O’Malley

2019

J Eukaryotic Microbiology

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Most discussions of human microbiome research have focused on bacterial investigations and findings. Our target is to understand how human eukaryotic microbiome research is developing, its potential distinctiveness, and how problems can be addressed. We start with an overview of the entire eukaryotic microbiome literature (578 papers), show tendencies in the human‐based microbiome literature, and then compare the eukaryotic field to more developed human bacterial microbiome research. We are particularly concerned with problems of interpretation that are already apparent in human bacterial microbiome research (e.g. disease causality, probiotic interventions, evolutionary claims). We show where each field converges and diverges, and what this might mean for progress in human eukaryotic microbiome research. Our analysis then makes constructive suggestions for the future of the field.

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Section: Comparing Bacterial and Eukaryotic Gut Microbiome Research Smentioning

confidence: 99%

Section: Eukaryotic Microbiota Treatments: Probiotics and Fmtsmentioning

confidence: 99%

Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Hooks

O’Malley

2019

J Eukaryotic Microbiology

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“…The fungi, bacteria, and viruses that comprise an organism's microbiome can interact 58 with parasites in ways that have consequences for host susceptibility, disease severity, and 59 transmission (Berg & Koskella, 2018). Yet, while investigations of the association between the 60 microbiome and a single parasite species are becoming increasingly common (Aivelo & 61 Norberg, 2018;Libertucci & Young, 2019), how such associations vary among parasite species 62 is still poorly understood. Here, we evaluated potential mechanisms through which parasites alter 63 the fungal microbiome using a trait-based analysis of multiple co-occurring fungal parasites in a 64 grass host.…”

Section: Introduction 57mentioning

confidence: 99%

Parasites as niche modifiers for the microbiome: A field test with multiple parasites

O’Keeffe

Halliday

Jones

et al. 2020

Preprint

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Parasites can affect and be affected by the host’s microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, there are two aspects of the relationship between parasite infection and the host microbiome that remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasite species. To overcome these limitations, we assayed the within-leaf fungal community in a grass population to investigate how diversity and composition of the fungal microbiome are associated with natural infection by fungal parasites with different feeding strategies. We hypothesized that parasites that more strongly modify niches available within a host will thereby alter the microbial taxa that can colonize the community and be associated with greater changes in microbiome diversity and composition. A parasite that creates necrotic tissue to extract resources (necrotrophs) may act as a particularly strong niche modifier whereas one that does not (biotrophs) may not. Barcoded amplicon sequencing of the fungal ITS region revealed that the microbiome of leaf segments that were symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments that were symptomatic of other parasite feeding strategies. This supports the hypothesis that within-host niches link infection by parasites to the host’s microbiome. Together, these results highlight the importance of parasite traits in determining parasite impacts on the host’s microbiome.

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“…The microorganisms that inhabit a host-associated environment can have a substantial impact on host health (The Human Microbiome Project Consortium 2012, Libertucci & Young 2018, Lloyd-Price et al 2019. Each microbial taxon present in an environment has a bacterial concentration, reflecting the absolute abundance of the taxon per unit volume and therefore the bacterial load on the host.…”

Section: Introductionmentioning

confidence: 99%

A multi-view model for relative and absolute microbial abundances

Williamson

Willis

2019

Preprint

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The absolute abundance of bacterial taxa in human host-associated environments play a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species is comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a sensitivity study where we jackknife the taxa with observed absolute abundances, and a study of women with bacterial vaginosis.

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The role of the microbiota in infectious diseases

Cited by 285 publications

References 156 publications

Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Parasites as niche modifiers for the microbiome: A field test with multiple parasites

A multi-view model for relative and absolute microbial abundances

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