A protocol for enumeration of aquatic viruses by epifluorescence microscopy using Anodisc™ 13 membranes

Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.

Adsorption Kinetics of Poly(benzyl acrylate) Chains onto Alumina Interface during the Flow-Driven Translocation through Cylindrical Nanochannels

In this work, the adsorption kinetics of the PBAN/AAO system under flushing condition has been investigated, where PBAN and AAO represent poly(benzyl acrylate) and anodic alumina oxide (AAO, average pore radius R0 ≈ 10 nm) nanochannel, respectively. Our specially designed double-pump flushing system is proved to eliminate the overshoot phenomenon and in situ monitor transmembrane pressure (ΔP) as a function of flushing time (t) and flow rate (Q), which gives the effective pore radius (R), cross-sectional coverage factor (χ = [1 - (R/R0)2]), and characteristic ratio (rc) of the increments of χ during each adsorption/desorption cycle at a given bulk solution concentration (Cbulk). Our findings include: (1) by gradient increasing Cbulk from 10 to 200 mg/L at Q = 10 mL/h, the shortest PBA40 displays a saturation adsorption behavior when Cbulk ≥ 80 mg/L and t ≥ 2000 s, which agrees well with the prediction of blob model, whereas for the longer PBAN chains, the chain length (N) and concentration-dependent adsorption tendency get stronger as N increases from 40 to 620 at t ≥ 2000 s, in particular, R/R0 ∼ N-0.20 is observed at Cbulk = 140 mg/L; (2) by focusing on the platform χ in the saturation adsorption regime (χsat), the longer PBAN displays a stronger adsorption trend with partially reversible feature at Q = 5.0 mL/h, namely, as N increases from 40 to 620, χsat increases from 0.15 to 0.83 at Cbulk = 100 mg/L, where rc changes from 0.25 ± 0.10 to 0.80 ± 0.10 as the adsorption/desorption flushing cycle increases from 1 to 8 at Cbulk = 100 mg/L; (3) by further assuming a solvent nonpenetrating and nondraining adsorption layer, χsat determined in the case of curved surface can be comparable to the physical meaning of adsorption thickness (Δad) in the case of flat-surface adsorption, and the fitting result indicates χsat ∼ Δad ∼ N0.58, falling between Δad ∼ N1/2 and Δad ∼ N1.0 predicted by the mean-field and scaling theories for real multichain adsorption, respectively. Overall, the present work not only clarifies some controversies but also provides unambiguous evidence supporting the existence of tightly adsorbed internal and loosely adsorbed external layers.

Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples

Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.

Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as "viral dark matter". However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating "rare" members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae

The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland). The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs) resulted in 204 predicted protein-coding sequences (CDSs), of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as "Bastille group") within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily.