Survival, prophage induction, and invasive properties of lysogenic Salmonella Typhimurium exposed to simulated gastrointestinal conditions

Kim, Song‐Rae; Ryu, Kanghee; Biswas, Debabrata; Ahn, Juhee

doi:10.1007/s00203-014-1005-z

Cited by 22 publications

(16 citation statements)

References 33 publications

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“…To increase virion titers and search for inducing signals, A2-165 F. prausnitzii cultures were treated with different concentrations of three potent inducers of phage lytic cycle: mitomycin C, hydrogen peroxide, and bile salts (cholate/deoxycholate [1:1]) [ 13 , 42 ]. Mitomycin C in particular causes DNA damage, which is a general signal for prophage derepression.…”

Section: Resultsmentioning

confidence: 99%

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

et al. 2018

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BackgroundViral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.MethodsWe identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.ResultsWe show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.ConclusionSince IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0452-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

et al. 2018

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“…Since then many more prophages have been identified, every time a set of new Salmonella genomes is sequenced. Dormant prophages are transmitted vertically along with bacterial cell division and can be induced under stressful conditions, such as DNA damages or in animal guts (Kim et al ., ). They can also undergo spontaneous induction, which can increase the fitness of a given strain whenever in competition when entering a new niche (Bossi et al, ).…”

Section: Prophage Abundance and Integration Sites In S Enterica Genomesmentioning

confidence: 97%

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Wahl

Battesti

Ansaldi

2018

Molecular Microbiology

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Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site-specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.

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“…8C), suggesting that BBR-induced alterations in the gut microbiome observed in complex consortia may be partly due to induction of the phage lytic cycle through bile acid toxicity. Indeed, previous studies have shown that bile acids induce phage lytic cycle in intestinal pathogens [35,36].…”

Section: Discussionmentioning

confidence: 99%

Berberine alters gut microbial function through modulation of bile acids

Wolf

Devendran²,

Doden

et al. 2020

Preprint

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Background: Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the Gastrointestinal tract. The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome. Results: Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectedness in function were observed, despite similarity in gut microbial relative abundance between control and BBR treatment. BBR increased cecal bile acid concentrations and altered the taurocholic acid:tauro-β-muricholic acid ratio in the liver. Overall, analysis of correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the gastrointestinal (GI) tract increased significantly during berberine treatment and developed extensive correlation networks with expressed genes in the B4PC2 community. Conclusions: This work has important implications for interpreting the effects of berberine on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with berberine supplementation.

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Survival, prophage induction, and invasive properties of lysogenic Salmonella Typhimurium exposed to simulated gastrointestinal conditions

Cited by 22 publications

References 33 publications

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Berberine alters gut microbial function through modulation of bile acids

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