Bacteriophages in the gastrointestinal tract and their implications

Łusiak-Szelachowska, Marzanna; Weber‐Dąbrowska, Beata; Jończyk‐Matysiak, Ewa; Wojciechowska, Renata; Górski, Andrzej

doi:10.1186/s13099-017-0196-7

Cited by 86 publications

(73 citation statements)

References 41 publications

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“…In contrast, serum samples were more concentrated and easier to handle than blood, and phage prevalence detected in sera was markedly higher. The Siphoviridae morphological type was the most common group, as previously reported 15,18,27 . Siphoviridae detection could have been underestimated in a percentage of samples showing icosahedral phage capsids compatible with Siphoviridae morphology but without a tail, which prevented their correct classification 18,[28][29][30] .…”

Section: Discussionsupporting

confidence: 65%

Unravelling the consequences of the bacteriophages in human samples

Blanco-Picazo

Fernández‐Orth

Brown-Jaque

et al. 2020

Sci Rep

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Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. to unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. in addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. this method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs. Bacteriophages (phages), viruses that infect bacteria 1 , are probably the most abundant entities in the world 2. The abundance of phages in the human body is beginning to be envisaged as having a critical influence on human health. The ability of phage communities to modify and regulate bacterial communities 3,4 suggests that phages are to some extent responsible for the homeostasis of the microbiota 5,6. Phages can contribute to bacterial genomic plasticity by horizontal gene transfer (transduction) 7,8 , which may benefit the metabolism 9 or affect the virulence of the bacterial host 10,11. Some phages produce transducing particles consisting of phage capsids that carry only bacterial DNA 12,13 , these transducing particles or elements similar to gene transfer agents (GTAs) 14 are thought to be mechanisms used by bacterial cells to spread their own genomic content 12. The existence of phages in human biomes presupposes their presence in human samples and their contamination of laboratory cultures initiated from these samples 15. This interference can be envisaged at two levels: 1) phages may propagate in enriched liquid culture media (used to enhance analytical sensitivity and selectively propagate the pathogen) by infecting bacteria (the pathogen targeted for isolation) and causing their lysis during the process; and 2) phages can transport bacterial DNA, including virulence genes such as toxins 16 , antibiotic resistance genes (ARG) 11,17,18 or bacterial 16S rRNA genes 18. If any of these genes are targeted by molecular methods, positive results can be a confounding factor in the interpretation of results 19. The confirmation of phage interference in microbiological diagnosis, as envisaged in prev...

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Section: Discussionsupporting

confidence: 65%

Unravelling the consequences of the bacteriophages in human samples

Blanco-Picazo

Fernández‐Orth

Brown-Jaque

et al. 2020

Sci Rep

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“…Phages present in mammalian organisms (endogenous phages, e.g. in the intestines) may exert immunomodulating action similar to probiotics 2,3 and, by their ability to translocate from the gut to other tissues, they can mediate such activities, locally contributing to maintenance of immune homeostasis. 4,5 Interestingly, phages have been shown to cause strong anti-inflammatory effects reducing levels of C-reactive protein and other indices of inflammation in patients receiving PT even though the infection has…”

Section: Phages As Regulators Of Immune and Inflammatory Responsesmentioning

confidence: 99%

Phage therapy in allergic disorders?

Górski

Jończyk‐Matysiak

Łusiak-Szelachowska

et al. 2018

Exp Biol Med (Maywood)

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Allergic disorders pose a growing challenge to medicine and our society. Therefore, novel approaches to prevention and therapy are needed. Recent progress in studies on bacterial viruses (phages) has provided new data indicating that they have significant immunomodulating activities. We show how those activities could be translated into beneficial effects in allergic disorders and present initial clinical data that support this hope.

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“…Despite being able to substantially increase the total number of viral reads in the metagenomes, sequence-independent amplification is bias prone, resulting in fewer viruses being detected and lower genome coverage due to preferential amplification of certain sequences [59-61]. However, the over-representation of bacteriophage found here could also be attributed to the fact that they make up the bulk of the virobiota in the gut, which is dominated by bacteria [62, 63]. Regardless of its known bias [58, 59], VLP metagenomics still holds merit for use in virome characterisation due to its ability to identify low abundance DNA viruses, which is especially relevant for dormant or non-active viruses.…”

Section: Discussionmentioning

confidence: 99%

Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

Chong

Shī

Grueber

et al. 2018

Preprint

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BackgroundThe Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about the viruses present in devils, and whether any of these are of potential conservation relevance for this endangered species.MethodsUsing both metagenomics based on virus-like particle (VLP) enrichment and sequence-independent amplification (VLP metagenomics), and meta-transcriptomics based on bulk RNA sequencing, we characterised and compared the faecal viromes of captive and wild Tasmanian devils.ResultsA total of 54 devil faecal samples collected from captive (n = 2) and wild (n = 4) populations were processed for virome characterisation using both approaches. We detected many novel, highly divergent viruses, including vertebrate viruses, bacteriophage and other dietary associated plant and insect viruses. In total, 18 new vertebrate viruses, including novel sapelovirus, astroviruses, bocaviruses, papillomaviruses and gammaherpesvirus were identified, as well as known mammalian pathogens including rabbit haemorrhagic disease virus 2 (RHDV2). Captive devils showed significantly lower levels of viral diversity than wild devils. Comparison of the two methodological approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics mainly identifying RNA viruses, and VLP metagenomics largely identifying DNA viruses.ConclusionThis study has greatly expanded our knowledge of eukaryotic viruses in the Tasmanian devil and provides important baseline information that will contribute to the conservation and captive management of this endangered species. In addition, our results showed that a combination of VLP metagenomics and meta-transcriptomics may be a more comprehensive approach to virome characterisation than either method alone.

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Bacteriophages in the gastrointestinal tract and their implications

Cited by 86 publications

References 41 publications

Unravelling the consequences of the bacteriophages in human samples

Unravelling the consequences of the bacteriophages in human samples

Phage therapy in allergic disorders?

Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

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