Phage synergy with the immune system

bacteriophage modelNot long after their discovery, viruses that infect bacteria – bacteriophages – were considered as therapeutic agents for treating infections. Despite many years of research on so-called phage therapy, clinical trials have produced conflicting results. They might be explained in part by the results of a new study which show that the host innate immune system is crucial for the efficacy of phage therapy.

When mice are infected intranasally with Pseudomonas aeruginosa (which causes pneumonia in patients with weak immune systems), the bacterium multiplies in the lungs and kills the animals in less than two days. When a P. aeruginosa lytic phage (i.e. that kills the bacteria) is instilled in the nose of the mice two hours after bacterial infection, all the mice survive and there are no detectable bacteria in the lungs. The phage can even be used prophylactically: it can prevent pneumonia when given up to four days before bacterial challenge.

The ability of phage to clear P. aeruginosa infection in the mouse lungs depends on the innate immune response. When bacteria infect a host, they are rapidly detected by pattern recognition receptors such as toll-like receptors. These receptors detect pathogen-specific molecular patterns and initiate a signaling cascade that leads to the production of cytokines, which may stop the infection. Phage cannot clear P. aeruginosa infection in mice lacking the myd88 gene, which is central to the activity of toll like receptors. This result shows that the innate immune response is crucial for the ability of phages to clear bacterial infections. In contrast, neither T cells, B cells, or innate lymphoid cells such as NK cells are needed for phage therapy to work.

The neutrophil is a cell of the immune system that is important in curtailing bacterial infections. Phage therapy does not work in mice depleted of neutrophils. This result suggests that humans with neutropenia, or low neutrophil counts, might not respond well to phage therapy.

A concern with phage therapy is that bacterial mutants resistant to infection might arise, leading to treatment failure. In silico modeling indicated that phage-resistant bacteria are eliminated by the innate immune response. In contrast, phage resistant bacteria dominate the population in mice lacking the myd88 gene.

These results demonstrate that in mice, successful phage therapy depends on a both the innate immune response of the host, which the authors call ‘immunophage synergy’. Whether such synergy also occurs in humans is not known, but should be studied. Even if observed in humans, immunophage synergy might not be a feature of infections in other anatomical locations, or those caused by other bacteria. Nevertheless, should immunophage synergy occur in people, then clearly only those with appropriate host immunity – which needs to be defined – should be given phage therapy.

Agar Artist Caitlin Cahak

At ASM Microbe 2017 in New Orleans, I spoke with Medical Laboratory Scientist Caitlin Cahak about her agar art.

Prions in bacteria

prion conversionBacteria do not develop transmissible spongiform encephalopathies, but they have been found to produce prions – proteins that can adopt alternative conformations with different functions.

Prion diseases, a frequent topic on this blog, are caused by misfolding of a normal cellular prion protein (illustrated; image copyright ASM Press). Prion proteins are found in other organisms, where the alternative conformation confers a new, non-pathogenic function to the protein. At least 12 different prion proteins have been found in yeast, and they confer the ability to grow more efficiently under certain conditions. Now prions have been discovered in bacteria (link to article).

A search of 60,000 bacterial genomes for proteins with prion-forming domains revealed one in the transcription termination protein Rho from Clostridium botulinum (Cb-Rho). When produced in E. coli, the protein forms amyloid – protein aggregates in the form of fibrils – that are characteristic of prions. A 68 amino acid stretch of Cb-Rho can functionally substitute for the prion-forming domain of a yeast prion-forming protein. This protein, called Sup35, can read stop codons in the prion state, and this phenotype was recapitulated in yeast by the Clostridium prion.

The Cb-Rho prion can convert between prion and non-prion conformations in E. coli. This property was demonstrated by placing a Rho-dependent terminator between a promoter and the lacZ gene, the product of which produces a blue color. In the prion state, Rho has decreased activity, leading to blue cells. In the non-prion state, normal termination leads to pale blue colonies. A mixture of blue and pale blue colonies was observed, showing that Rho exists in the prion and non-prion states.

The prion conformation was also shown to be heritable. Blue colonies always gave rise to blue colonies, while pale blue colonies formed pale blue colonies. The blue colony color lasted for over 120 generations.

The finding of a prion in bacteria indicates that this form of protein-based heredity arose before eukaryotes emerged on Earth. Similar prion-like protein domains have also been found in other phyla of bacteria, suggesting the existence of an important source of epigenetic diversity that can allow bacterial growth under diverse conditions. Exactly how bacterial prions confer new functions will be exciting to discover.

Last time we learned that eukaryotes probably didn’t invent the nucleus. Now we find that prions likely emerged first in bacteria. Did eukaryotes invent anything?

Viruses help form biofilms

Inoviridae virionBacteria frequently grow in communities called biofilms, which are aggregates of cells and polymers. An example of a biofilm is the dental plaque on your teeth. Biofilms are medically important as they can allow bacteria to persist in host tissues and on catheters, and confer increased resistance to antibiotics and dessication. Therefore understanding how biofilms form is crucial for controlling microbial infections. An advance in our understanding of biofilms formation is the observation that filamentous phages help them assemble, and contribute to their fundamental properties.

Pseudomonas aeruginosa is an important human pathogen which is a particular problem in patients with cystic fibrosis. The ability of this bacterium to form biofilms in the lung is linked to its ability to cause chronic infections. Pseudomonas aeruginosa biofilms contain large numbers of filamentous Pf bacteriophages (pictured; image credit). These viruses lyse cells and release DNA, which becomes one component of the biofilm matrix.

Mixing supernatants of P. aeruginosa cultures with hyaluronan, which is present in airways of cystic fibrosis patients, resulted in the formation of a biofilm – in the absence of bacteria. A major component of P. aeruginosa biofilms was found to be Pf bacteriophages. When purifed Pf bacteriophages were mixed with hyaluronan, biofilms formed. Similar biofilms also formed when the filamentous bacteriophage fd of E. coli was mixed with hyaluronan. Mixtures of Pf bacteriophages and various polymers (alginate, DNA, hyaluronan, polyethylene glycol) formed liquid crystals (matter in a state between a liquid and a solid crystal).

Pf phages were detected in sputum from patients with cystic fibrosis, but not in uninfected patients. Addition of Pf phage to sputum from patients infected with P. aeruginosa made the samples more birefringent, a property of liquid crystals. Compared with a strain of P. aeruginosa that does not produce Pf phage, colonies of virus-producing strains formed liquid crystals. These observations indicate that Pf phage help organize the bacteria into a biofilm matrix.

Some features of biofilms include their ability to adhere to surfaces, to protect bacteria from dessication, and to increase resistance to antibiotics. Addition of phage Pf increased biofilm adhesion and tolerance against dessication. Such addition also made the biofilm more resistant to aminoglycoside antibiotics, because these were sequestered in the biofilm. No phage-mediated increased resistance to ciprofloxacin was observed, probably because this antimicrobial does not interact with polyanions of the biofilm as do aminoglycosides.

These results show that presence of bacteriophage in a biofilm of P. aeruginosa helps organize the matrix while contributing to some of its fundamental properties. It seems likely that filamentous phages of other bacteria will play roles in biofilm formation, suggesting that targeting the phages in these matrices could be effectie strategies for treating biofilm infections.

TWiV 323: A skid loader full of viromes

On episode #323 of the science show This Week in Virology, the family TWiVidae discuss changes in the human fecal virome associated with Crohn’s disease and ulcerative colitis.

You can find TWiV #323 at

TWiM 90: Think globally, act locally

I usually don’t post TWiM episodes here, but #90 has a lot of virology. In this episode, recorded in La Jolla, CA at the annual meeting of the Southern California Branch of the American Society for Microbiology, I first speak with Laurene Mascola, Chief of Acute Communicable Diseases at the Los Angeles County Department of Public Health. Dr. Mascola talks about how Los Angeles county has prepared for an outbreak of Ebola virus. Next up is David Persing, Executive Vice President and Chief Medical and Technology Officer at Cepheid. His company has developed an amazing, modular PCR machine that is brining rapid diagnosis everywhere, including the United States Post Office. And it might even be available on your refrigerator one day.

Watch TWiM #90 below, or listen at or iTunes.


Michael Schmidt on copper at TEDx

On TWiM #55 we discussed the remarkable ability of copper to reduce hospital acquired infections. Now you can watch Michael Schmidt, TWiM co-host and a co-author on this work, discuss the findings at a recent TEDx talk in Charleston, South Carolina.

An RNA virus that infects Archaea?

Nymph Lake, Yellowstone National ParkEvery different life form on earth can probably be infected with at least one type of virus, if not many more. Most of these viruses have not yet been discovered: just over 2,000 viral species are recognized. While the majority of the known viruses infect bacteria and eukaryotes, there are only about 50 known viruses of the Archaea, and these all have DNA genomes. The first archaeal RNA viruses might have been recently discovered in a hot, acidic spring in Yellowstone National Park.

Archaea are single-cell organisms that are similar in size and shape to bacteria, but are evolutionarily and biochemically quite distinct. They inhabit a broad range of environments including those with extreme conditions such as high temperature, acidity, and salinity. Identification of archaeal RNA viruses is important because their study could provide information about the ancestors of RNA viruses that infect eukaryotes. Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses.

The acidic (pH <4) and hot (>80°C) springs in Yellowstone National Park were examined for the presence of archaeal RNA viruses because these bodies of water contain mainly Archaea. Samples were obtained from 28 different sites and extracted nucleic acids were treated with DNAase (to remove DNA genomes) and then reverse transcriptase (to copy RNA to DNA). If reverse transcription was reduced by treatment with RNAse, it was concluded that the sample contained mostly RNA. The results narrowed the sample size to three, all from Nymph Lake. New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing.

Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. The sequences are from a novel virus which does not belong to any known virus family.

These results clearly show that at least two related but distinct RNA viruses are present in Nymph Lake. However whether or not the hosts of these viruses are Archaea or Bacteria cannot be determined by these metagenomic analyses. What is needed to resolve this question is old-fashioned virology:  isolating RNA virus particles that can infect an archaeal host and produce new infectious viruses.

B Bolduc, DP Shaughnessy, YI Wolf, EV Koonin, FF Roberto and M Young J. Virol. 2012, 86(10):5562. DOI: 10.1128/JVI.07196-11.

TWiM 34: Doing the DISCO with Emiliania

On episode #34 of the science show This Week in Microbiology, Vincent, Michael, and Elio discuss changing populations of Emiliania huxleyi and their viruses in the North and Black Seas.

You can find TWiM #34 at

TWiM 33: Tuning the immune organ

On episode #33 of the science show This Week in Microbiology, Vincent, Michael, and Ivo review the requirement for segmented, filamentous bacteria for the induction of a specific type of helper T cell in the gut.

You can find TWiM #33 at