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Order Caudovirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
As described in the ninth official ICTV report by Lavigne et al. (2012), the Caudovirales order originally consisted of the three huge families of the tailed bacteriophages infecting bacteria and archaea, which were classified by the structure of their tails: Myoviridae with the long contractile tails, Siphoviridae with the long noncontractile tails, and Podoviridae with the short noncontractile tails. Figure 1.1 demonstrates typical images (we will call them portraits) of the representatives of these three great classical families.
Nutritional and Health Benefits of Marine Mollusks
Published in Se-Kwon Kim, Marine Biochemistry, 2023
The number of viruses in oceans is enormous (about 107 particles/milliliter) and the number of marine viral infections is estimated at 1023 infections/second (Suttle 2007). Some metabolites isolated from eight gastropods (Rapana venosa, Valenciennes, 1846; Haliotis rubra, Leach, 1814; Haliotis laevigata, Donovan, 1808; Haliotis rufescens, Swainson, 1822; Buccinulum corneum, Linnaeus, 1758; Buccinum undatum, Linnaeus, 1758; Tegula gallina, Forbes, 1850; and Littorina littorea, Linnaeus, 1758) and nine bivalves (Ruditapes philippinarum, Adams & Reeve, 1850; Mercenaria mercenaria, Linnaeus, 1758; Mytilus galloprovincialis, Lamarck, 1819; Mya arenaria, Linnaeus, 1758; Cerastoderma edule, Linnaeus, 1758; Crenomytilus grayanus, Dunker, 1853; Crassostrea gigas, Thunberg, 1793; Crassostrea virginica, Gmelin, 1791; and Ostrea edulis, Linnaeus, 1758) were described as powerful against many human viruses (Khan and Liu 2019). For examples, hemocyanin (from Rapana venosa, Valenciennes, 1846) was perceived active against respiratory syncytial virus, herpes simplex virus (HSV)-1 and -2 and Epstein–Barr virus (EBV; Genova-Kalou et al. 2008; Dolashka-Angelova et al. 2009; Dolashka et al. 2010); kelletinin A (from Buccinulum corneum, Linnaeus, 1758) against human T-cell leukemia virus type 1 (Orlando et al. 1996), mytilin (from Mytilus galloprovincialis, Lamarck, 1819) against white spot syndrome virus (Dupuy et al. 2004), defensin (also from Mytilus galloprovincialis) against human immunodeficiency virus type 1 (HIV-1; Roch et al. 2004), while lectin (from Crenomytilus grayanus, Dunker, 1853) against HIV (Luk’yanov et al. 2007). Moreover, some representatives of the families Podoviridae (T3 coliphage; Bachère et al. 1990), Adenoviridae (human adenovirus type 5; Carriel-Gomes et al. 2007), Herpesviridae (HSV type 1) and Birnaviridae (infectious pancreatic necrosis virus; Olicard et al. 2005) turned out vulnerable to active ingredients present in oyster hemolymph. These active elements apparently neutralize invading viruses either by directly inactivating them and preventing their binding to or access into target cells or by inhibiting their replication and transcription (Dang et al. 2015). Thereby, several mollusks constitute widely available and economically viable sources of antiviral compounds.
Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor
Published in Gut Microbes, 2021
Jilei Zhang, Yongguo Zhang, Yinglin Xia, Jun Sun
We observed that a total of 12 viral species were differential in the conditional VDR knockout mice compared to the control VDRLoxP mice, of which 6 had q-values <0.001, 2 had q-values <0.01 and 4 had q-values <0.05 (Figure 3a). The log-ratio of fold change with significant differences (q < 0.05) is shown with colored histograms (Figure 3). There were two enriched viral species in the comparison of VDRΔIEC/VDRLoxP, Vibrio phage JSF5 (q < 0.001) and bovine viral diarrhea virus 1 (q < 0.05), and one enriched viral species in the comparison of VDRΔPC/VDRLoxP, Vibrio phage JSF5 (q < 0.01). Vibrio phage JSF5 was more abundant in both VDRΔIEC and VDRΔPC mice, whereas enriched BVDV1 was only found in VDRΔIEC compared with the other groups (Figure 3a). For the comparison of VDRΔLyz and VDRLoxP, nine virus species were found to be significantly altered (5 with a q value <0.001, 1 with q < 0.01, and 3 with a q value <0.05). Of these species, three were enriched (Vibrio phage JSF5, bovine viral diarrhea virus 1 and Vibrio phage JSF6), while six were depleted (Lactobacillus prophage phiadh, Cherry green ring mottle virus, Lactobacillus phage KC5a, avian avulavirus 1, Mycobacterium virus Phayonce, and one unidentified species in the Podoviridae family) (Figure 3a).
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
PCoA based on Bray-Curtis distance showed significant differences in bacterial communities among disease severities (Figure 4a, P = .001, PERMANOVA), as did the viral communities (Figure 4b, P = .001, PERMANOVA). Next, we performed a species – and genus-level differential enrichment analysis of bacterial and viral communities within COVID-19 cases of varying disease severity. At the species level, a total of 19 bacterial taxa were observed to be enriched in various disease severities. Eighteen out of 19 showed significant enrichment in severe cases of COVID-19, including Corynebacterium durum, Rothia mucilaginosa, Enterococcus faecium, and Campylobacter gracilis, while only Eubacterium rectale showed significant enrichment in mild cases of COVID-19 (Table 2, FDR < 0.05, Wilcoxon test). At the genus level, such genera as Corynebacterium, Enterococcus, Rothia, Megasphaera, and Campylobacter were significantly enriched in severe cases, while Eubacterium was depleted in severe cases (Table S4). Additionally, 17 viruses, including 14 Microviridae phages, one Inoviridae phage, one Podoviridae phage and one unclassified virus, were enriched in severe cases, while no viral communities were determined to be enriched in mild cases (Table S5, FDR < 0.05, Wilcoxon test).
Gut non-bacterial microbiota contributing to alcohol-associated liver disease
Published in Gut Microbes, 2021
Wenkang Gao, Yixin Zhu, Jin Ye, Huikuan Chu
Fortunately, the Gut Virome Database (GVD)110 and the Gut Phage Database111 have been established and are continuously updating, which will advance research of gut virome considerably. According to the GVD,110 97.7% of viral populations are phages, 2.1% are eukaryotic viruses, and 0.1% are archaeal viruses. About 1015 bacteriophages settle in a healthy human intestine, which is 10 times the number of symbiotic bacteria.112 The main phages come from the order Caudovirales including Siphoviridae, Myoviridae, and Podoviridae.113,114 Some phages are highly specific to certain bacterial strains, while others have broader ranges of host cells.115 After infection of host by phages, highly virulent phages often cause cell lysis (lytic cycle) while mild phages either lyse the host cell or keep the host cell alive and reproduce normally (lysogenic cycle).116,117