Cross-Domain and Viral Interactions in the Microbiome

Rowan-Nash, Aislinn D.; Korry, Benjamin J.; Mylonakis, Eleftherios; Belenky, Peter

doi:10.1128/mmbr.00044-18

Cited by 129 publications

(110 citation statements)

References 653 publications

(881 reference statements)

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“…It is thought that such a composition promotes the development of metabolic 426 syndrome, heart disease, diabetes, and a number of other chronic conditions [36][37][38][39][40][41][42][43][44][45][46]. Furthermore, 427 broad-spectrum antibiotic use and resulting microbiome dysbiosis have been associated with a 428 number of similar co-morbidities along with increased susceptibility to opportunistic infections 429 [1,[5][6][7][21][22][23]25,26]. Despite this connection, little work has been done examining how host dietary 430 composition impacts the response of the microbiota to antibiotic perturbation.…”

Section: Discussion: 422mentioning

confidence: 99%

Consumption of a Western-style diet modulates the response of the murine gut microbiome to ciprofloxacin

Cabral

Wurster

Korry

et al. 2019

Preprint

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Dietary composition and antibiotic use are known to have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption.Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome community structure and transcriptional activity. We found that mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. At the transcriptional level, we found that ciprofloxacin induced a reduction in the abundance of TCA cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this shared response, we observed extensive differences in the response of the microbiota to ciprofloxacin on each diet. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a key role in determining the extent of disruption of microbiome composition and function induced by antibiotic treatment.ImportanceWhile both diet and antibiotics are individually known to have profound impacts on gut microbiome composition, little work has been done to examine the effect of these two factors combined. A number of negative health outcomes, including diabetes and obesity, are associated with diets high in simple sugars in fats but low in host-indigestible fiber, and some of these outcomes may be mediated by the gut microbiome. Likewise, treatment with broad-spectrum antibiotics and the resulting dysbiosis is associated with many of the same detrimental side effects. Previous work has shown that nutrient availability, as influenced by host diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how the prevalence of high fat and sugar “Western”-style diets impacts the response of the microbiome to antibiotics.

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Section: Discussion: 422mentioning

confidence: 99%

Consumption of a Western-style diet modulates the response of the murine gut microbiome to ciprofloxacin

Cabral

Wurster

Korry

et al. 2019

Preprint

Self Cite

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“…Viruses, Archaea, protists, and other microbes have until recently been minority interests (see Rowan‐Nash et al. , for a comprehensive list of such studies). There are practical methodological reasons for this privileging of bacteria (i.e.…”

Section: General Microbiome Research Trendsmentioning

confidence: 99%

“…These labels usually refer to interactions between different domains of life (see Rowan‐Nash et al. ) and we will refer to them as such. This attention to eukaryotic–prokaryotic–viral interplay (or the potential of it) is at least partly due to the low abundance of eukaryotic microorganisms, with mass effects not being expected (unlike in bacterial microbiome research).…”

Section: Cross‐domain Relationships and Their Implicationsmentioning

confidence: 99%

“…Heintz-Buschart et al 2017;Koenig et al 2011;Yatsunenko et al 2012), the primary focus of both the literature and patents is indeed bacteria. Viruses, Archaea, protists, and other microbes have until recently been minority interests (see Rowan-Nash et al 2019, for a comprehensive list of such studies). There are practical methodological reasons for this privileging of bacteria (i.e.…”

Section: General Microbiome Research Trendsmentioning

confidence: 99%

“…Despite the very basic descriptive focus of most eukaryotic microbiome studies so far, some interesting findings are already emerging about so-called cross kingdom relationships (aka "interkingdom" or "transkingdom"; see Table 3). These labels usually refer to interactions between different domains of life (see Rowan-Nash et al 2019) and we will refer to them as such. This attention to eukaryotic-prokaryotic-viral interplay (or the potential of it) is at least partly due to the low abundance of eukaryotic microorganisms, with mass effects not being expected (unlike in bacterial microbiome research).…”

Section: Cross-domain Relationships and Their Implicationsmentioning

confidence: 99%

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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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Cross-Domain and Viral Interactions in the Microbiome

Cited by 129 publications

References 653 publications

Consumption of a Western-style diet modulates the response of the murine gut microbiome to ciprofloxacin

Consumption of a Western-style diet modulates the response of the murine gut microbiome to ciprofloxacin

Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

The Skin and Oral Microbiome

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