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History and First Look
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
In 1972, seven phages MAC-1, 1′, 2, 4, 4′, 5, and 7 attacking and lysing saprophytic strains of Bdellovibrio bacteriovorus were isolated from raw sewage of Lexington, Kentucky (Althauser et al. 1972). The phages were tailless, had a regular hexagonal outline, were approximately 25 nm in diameter, and for these reasons were attributed by authors to the “Bradley's group E” that was previously assigned to the RNA phages (Bradley 1967). However, further characterization of one of the discovered phages, MAC-1, led to the conclusion that the phage genome is made up by a circular single-stranded DNA (Roberts et al. 1987). Therefore, this phage appeared as a member of the Microviridae, a family of the smallest spherical somatic DNA phages typified by the phage φX174 (Sinsheimer 1959).
Other Single-Stranded DNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The Petitvirales is an order of nonenveloped T = 1 icosahedral viruses, 25–27 nm in diameter, with the covalently closed ssDNA genome, which belong, together with parvoviruses (Chapter 9) and circoviruses (Chapter 10), to the smallest DNA viruses by the virion and genome size. The order Petitvirales currently involves the sole family Microviridae with two subfamilies, Bullavirinae (former genus Microvirus) and Gokushovirinae, with 7 genera and 22 species altogether. The Bullavirinae members infect Enterobacteria, while gokushoviruses are currently known to infect only obligate intracellular parasitic bacteria. Remarkably, the name Gokushovirinae is derived from the Japanese for “very small.” The most famous representative of the Petitvirales order is the phage φX174 of the Escherichia virus phiX174 species from the Sinsheimervirus genus belonging to the Bullavirinae subfamily. The phage φX174, like the famous RNA phage MS2 of the Norzivirales order, which is described in Chapter 25, played a unique role in the general progress of molecular biology. The full-length genomic DNA of φX174, 5,375 nucleotides in length appeared as the first sequenced DNA genome (Sanger et al. 1977). The φX174 DNA was the first genome synthesized by purified enzymes and demonstrating features of the natural virus (Goulian et al. 1967). The φX174 DNA was the first genome completely assembled in vitro from synthetic oligonucleotides (Smith et al. 2003). However, φX174, as well as other members of the current order Petitvirales did not play any evident role in the development of VLP technologies because of highly sophisticated assembly of their virions. Nevertheless, the breakthroughs by successful assembly of the φX174 particles in vitro (Cherwa et al. 2011) and full decompression of the overlapping φX174 genome in yeast with independent production of viral structural proteins (Jaschke et al. 2012) are giving hope to rapid progress of the Petitvirales members as VLP models. It is worth mentioning that the bacteriophage φX174 lysis gene E was fused with the gene L of the phage MS2, formed the fused gene E-L, and applied as a critical element in the prospective technology of bacterial ghosts by putative vaccine candidates (Harkness and Lubitz 1987; Szostak et al. 1990, 1996; Mayrhofer et al. 2005; Jawale et al. 2014).
Integrated gut virome and bacteriome dynamics in COVID-19 patients
Published in Gut Microbes, 2021
Jiabao Cao, Cheng Wang, Yuqing Zhang, Guanglin Lei, Kun Xu, Na Zhao, Jingjing Lu, Fanping Meng, Linxiang Yu, Jin Yan, Changqing Bai, Shaogeng Zhang, Ning Zhang, Yuhuan Gong, Yuhai Bi, Yi Shi, Zhu Chen, Lianpan Dai, Jun Wang, Penghui Yang
To investigate viral components of the GI tract and, more importantly, potential shifts along treatment with antibiotics and antiviral medications (details in Table 1) within COVID-19 patients, we specifically analyzed the virome in our cohort using an integrated viral genome database as a reference (methods). Viral DNA and RNA were purified from preparations of enriched virus-like particles (VLPs) obtained from stool samples and characterized by metagenomic sequencing based on methods developed in our lab.25 As expected, the viromes of COVID-19 patients include DNA/RNA viruses (Herelleviridae family, Virgaviridae family), bacteriophages (Caudovirales order, CrAss-like phage, Inoviridae family, Microviridae family, Myoviridae family, Podoviridae family, and Siphoviridae family) that infect bacterial cells, and some unclassified viruses in the gut (Figure 2a). Despite the significant individual differences in viral composition, shared viruses were observed to primarily belong to the Microviridae family. SARS-CoV-2 nucletides were determined to be notably low in relative abundance compared with VLP-originated nucleotides and could not be detected in the majority of patients (reaching coverage ≥ 30% and read number ≥ 10 in only one patient).
Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome
Published in Gut Microbes, 2021
Pilar Manrique, Yifan Zhu, John van der Oost, Hilde Herrema, Max Nieuwdorp, Willem M. de Vos, Mark Young
In our study, there were not significant differences in bacteriophage community richness or diversity between treatment groups (healthy donors, MetS controls, MetS that received healthy donor FMT). Differences in total Caudovirales abundance between responders and non-responders were not detected either, and viruses from the Microviridae family were underrepresented. Additionally, the healthy donors’ invading phage profile was similar between treatment subgroups (responders vs non-responders), and no specific patterns of bacteriophage transfer based on viral family classification were identified.37 Instead, responders could be differentiated from non-responders based on the community structure, and the phage community of responders and donors had a greater overlap (Figure 3). Therefore, we hypothesized that MetS subjects with a less distorted phage community at pre-FMT are more likely to show clinical improvement. These differences likely arise from differences in disease etiology, suggesting that evidence of the impact of bacteriophages in a specific disease cannot be extrapolated to other health conditions.
Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome
Published in Gut Microbes, 2020
Tanya M. Monaghan, Tim J. Sloan, Stephen R. Stockdale, Adam M. Blanchard, Richard D. Emes, Mark Wilcox, Rima Biswas, Rupam Nashine, Sonali Manke, Jinal Gandhi, Pratishtha Jain, Shrejal Bhotmange, Shrikant Ambalkar, Ashish Satav, Lorraine A. Draper, Colin Hill, Rajpal Singh Kashyap
A total of 8,746 non-redundant viral sequences were detected in the whole community metagenomic sequencing data for 105 Indian fecal samples. These viruses group into 1,344 Viral Clusters (VCs), which are concordant with viral genera.22 Network visualization of the shared protein clusters between VCs shows the majority of Indian fecal viruses identified are connected to previously described Caudovirales (Figure 5A). Several Microviridae, Inoviridae, and archaeal viruses of the Rudiviridae and Bicaudaviridae families, were also detected. Unknown viruses were observed which did not share protein clusters with previously characterized viruses.