Nanopore and Illumina sequencing reveal different viral populations from human gut samples

The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.

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.

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.

Complete Genome Sequence of a Bacteroides fragilis Bacteriophage, vB_BfrS_NCTC

Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames.

Genome Characterization of a Novel Wastewater Bacteroides fragilis Bacteriophage (vB_BfrS_23) and its Host GB124

Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs.

IL-6 secretion in osteoarthritis patients is mediated by chondrocyte-synovial fibroblast cross-talk and is enhanced by obesity

Increasing evidence suggests that inflammation plays a central role in driving joint pathology in certain patients with osteoarthritis (OA). Since many patients with OA are obese and increased adiposity is associated with chronic inflammation, we investigated whether obese patients with hip OA exhibited differential pro-inflammatory cytokine signalling and peripheral and local lymphocyte populations, compared to normal weight hip OA patients. No differences in either peripheral blood or local lymphocyte populations were found between obese and normal-weight hip OA patients. However, synovial fibroblasts from obese OA patients were found to secrete greater amounts of the pro-inflammatory cytokine IL-6, compared to those from normal-weight patients (p < 0.05), which reflected the greater levels of IL-6 detected in the synovial fluid of the obese OA patients. Investigation into the inflammatory mechanism demonstrated that IL-6 secretion from synovial fibroblasts was induced by chondrocyte-derived IL-6. Furthermore, this IL-6 inflammatory response, mediated by chondrocyte-synovial fibroblast cross-talk, was enhanced by the obesity-related adipokine leptin. This study suggests that obesity enhances the cross-talk between chondrocytes and synovial fibroblasts via raised levels of the pro-inflammatory adipokine leptin, leading to greater production of IL-6 in OA patients.

A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients

Pseudomonas aeruginosa (Pa), normally a soil commensal, is an important opportunistic pathogen in Cystic Fibrosis (CF) and non-Cystic Fibrosis Bronchiectasis (nCFBR). Persistent infection correlates with accelerated decline in lung function and early mortality. The horizontal transfer of DNA by temperate bacteriophages can add gene function and selective advantages to their bacterial host within the constrained environment of the lower lung. In this study, we chemically induce temperate bacteriophages from clonal cultures of Pa and identify their mixed viral communities employing metagenomic approaches. We compared 92 temperate phage metagenomes stratified from these clinical backgrounds (47 CF and 45 nCFBR Pa isolates) using MG-RAST and GeneWise2. KEGG analysis shows the complexity of temperate phage accessory gene carriage increases with duration and severity of the disease. Furthermore, we identify the presence of Ig-like motifs within phage structural genes linked to bacterial adhesion and carbohydrate binding including Big_2, He_Pig, and Fn3. This study provides the first clinical support to the proposed bacteriophage adherence to mucus (BAM) model and the evolution of phages interacting at these mucosal surfaces over time.

Prevalence of hearing impairment in siblings of deaf children

OBJECTIVE

To assess the prevalence of hearing impairment in siblings of children with profound to total hearing impairment.

METHOD

Two hundred and twenty siblings of children at a deaf school in Karachi completed the screening program. This consisted of a questionnaire and pure tone audiometry.

RESULTS

One out of three (73 siblings) had a threshold of 25 dB or greater in their better ear. In a population, already aware of hearing loss, we note that only fifteen siblings had a previous audiogram. Although a positive family history is associated with hearing impairment in the siblings, no increase due to consanguineous marriages was noted.

CONCLUSION

This assessment has underlined the need to increase public awareness of hearing impairment. It has also exposed the lack of it in families exposed to the condition.

Concentrations of Cu, Cd, Ni, and Pb in the blood and tissues of cancerous persons in a Pakistani population

The Cu, Cd, Ni, and Pb contents of blood and tissue samples of some cancer patients in a Pakistani population were measured by atomic absorption spectroscopy. The results were compared with those found in the blood samples of healthy controls selected from persons with known previous health record. The trace element contents were found to be different in various cancer types, age groups, and between male and females. The results of this investigation showed that the average Cd and Ni concentrations were higher in the blood of cancer patients as compared to controls. Copper levels in the blood of male cancer patients were higher than the controls and the opposite was the case for females. The concentration levels of Pb in the blood were almost the same in all groups. In cancerous tissues the concentrations of Cu were found to be lower as compared to the unaffected part of the same organ of the same patient. The relationship of Cd and Ni to carcinogenesis is well established now and their abnormal levels could indicate an exposure to them. Changes in copper levels could be due to the altered metabolic requirements of the subjects under biological stress i.e. presence of cancer.

Synthesis of three hetero disaccharides, 4-O-beta-glucopyranosyl-6-deoxy-D-glucose, 4-O-beta-D-glucopyranosyl-D-mannosamine, and 4-O-beta-D-glucopyranosyl-D-mannose, and confirmation of their structures by C-13 NMR and MS

The three disaccharides, 4-O-beta-D-glucopyranosyl-6-deoxy-D-glucose (Glc-6-deoxy-Glc), 4-O-beta-D-glucopyranosyl-D-mannosamine (Glc-ManN), 4-O-beta-D-glucopyranosyl-D-mannose (Glc-Man), were synthesized from equimolar amounts of 6-deoxy-glucose and alpha-D-glucose-1-phosphate (G-1-P), D-mannosamine and alpha-D-glucose-1-phosphate (G-1-P), and D-mannose and alpha-D-glucose-1-phosphate (G-1-P), respectively, using cellobiose phosphorylase from Cellvibrio gilvus. The yields were 60%, 10% and 50% based on the initial amounts of 6-deoxy-D-glucose, D-mannosamine and D-mannose, respectively. The structures of disaccharides were confirmed by NMR and mass spectroscopy analysis.

Fluctuations in Fe, Cu, Zn, Br, As, Se, and Rb concentrations in C57L/J mice bearing BW7756 murine hepatoma using radioisotope-induced X-ray fluorescence

The effects of selenite or selenate supplementation on the concentration and distribution of Fe, Cu, Zn, As, Br, and Rb are investigated using the radioisotope-induced X-ray fluorescence, RIXRF. These effects are studied in the animals bearing BW7756 murine hepatoma and healthy animals for both of the oxidation states. Selenite and selenate induce different effects on the distribution of selenium, zinc, copper, bromine, and rubidium. The differences may be attributed to the differences in the inter element interaction after absorption into the bloodstream as well as to the mode of their intestinal absorption. Simultaneous supplementation of copper with selenite or selenate at the described levels has a profound influence on the concentration levels of other elements in the normal as well as in the diseased mice. The administration of selenium (0.67 micrograms/g body wt sodium selenite or sodium selenate, daily) and selenium and copper (0.67 and 1.35 micrograms/g body wt, respectively) has no effect on the incidence rate of hepatoma development.

[75Se]selenite and [75Se]selenate fluctuations during the development of murine hepatoma

The distribution of selenate and selenite selenium in C57L/J mice during the progression of BW7756 murine hepatoma was investigated using intra-ocular injection with the oxyanions labeled with 75Se radioisotope. Comparison is made with the normal distribution of selenium studied by the RIXRF method. The trace elemental profiles, TEP, for the two oxidation states are compared in healthy and disease states. It has been found that the presence of tumor significantly changes the level of tracer in various uninvolved organs. These changes are prominent in the early growth phase of the tumor. The two oxidation states show differences in the TEP for kidney, spleen, stomach and testes.

Time-dependent distribution of selenate and selenite selenium in male C57L/J mice

The distribution and retention of selenate and selenite in C57L/J mice was investigated using 75Se radioisotope. The comparison is made with the normal distribution of the element determined by using radioisotope-induced x-ray fluorescence, RIXRF methods. The distribution of the two oxidation states measured as activity of 75Se was almost identical but differed from the normal trace elemental profile, TEP. The excretion rates of the two selenium species in the initial phase are different with more selenate being excreted than selenite in the first 2 days. It was found that the wholebody excretion rates followed a pure first-order pattern this was not true for the individual organs of the animals.