Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have ...explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes) and Nodaviridae. These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈106 VLP/mL representing a potential contribution of 5.2%–24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈107 VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.
In this study weexplored the Atlantic Ocean from 3 to 4,296 m to enhance our understanding of RNA viruses. Data revealed that overall RNA viruses potentially accounted for 5.2‐24.4% of the virioplankton with ≈106 VLP/ml. We identified 2,481 putative viral contigs, including 88 new RNA viruses highly endemic with no apparent association with depthor geographic locations.
Abstract
Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, ...IgA has been shown to be involved in gut homeostatic regulation by ‘recognizing’ and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.
Summary
Wastewater treatment plants effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGs) into natural ecosystems. The bacterial resistome (ARG collection in a ...metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (9000 ARG hits/Gb metagenome) and diverse, while viral resistome was two orders of magnitude lower (50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment – including to polymyxin – in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (threefold increase compared with the control), which might be used as 'traps' to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5%–0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances.
Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be transmitted through various ...pathways, including air, within the context of One Health. This study used metagenomics to monitor the resistomes in urban air from two critical locations: a wastewater treatment plant and a hospital, both indoor and outdoor. The presence of cell‐like structures was confirmed through fluorescence microscopy. The metagenomic analysis revealed a wide variety of ARGs and a high diversity of antibiotic‐resistant bacteria in the airborne particles collected. The wastewater treatment plant showed higher relative abundances with 32 ARG hits per Gb and m3, followed by the main entrance of the hospital (indoor) with ≈5 ARG hits per Gb and m3. The hospital entrance exhibited the highest ARG richness, with a total of 152 different ARGs classified into nine categories of antibiotic resistance. Common commensal and pathogenic bacteria carrying ARGs, such as Moraxella, Staphylococcus and Micrococcus, were detected in the indoor airborne particles of the hospital. Interestingly, no ARGs were shared among all the samples analysed, indicating a highly variable dynamic of airborne resistomes. Furthermore, the study found no ARGs in the airborne viral fractions analysed, suggesting that airborne viruses play a negligible role in the dissemination of ARGs.
The spread of antibiotic resistance genes (ARGs) through various pathways, including air, presents a significant risk to human health. This study's air microbiology analysis revealed a high relative abundance and a wide variety of ARGs, as well as a diverse range of antibiotic‐resistant bacteria in airborne particles collected from urban hot spots. These hot spots include hospitals and wastewater treatment plants. The findings underscore the critical need for ongoing surveillance and intervention strategies to mitigate this public health threat.
The gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in ...retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.
A comprehensive characterization of the human body resistome sets of antibiotic resistance genes (ARGs) is yet to be done and paramount for addressing the antibiotic microbial resistance threat. ...Here, we study the resistome of 771 samples from five major body parts (skin, nares, vagina, gut, and oral cavity) of healthy subjects from the Human Microbiome Project (HMP) and addressed the potential dispersion of ARGs in pristine environments. A total of 28,714 ARGs belonging to 235 different ARG types were found in the HMP proteome dataset (
= 9.1 × 10
proteins analyzed). Our study reveals a distinct resistome profile (ARG type and abundance) between body sites and high interindividual variability. Nares had the highest ARG load (≈5.4 genes/genome) followed by the oral cavity, whereas the gut showed one of the highest ARG richness (shared with nares) but the lowest abundance (≈1.3 genes/genome). The fluroquinolone resistance genes were the most abundant in the human body, followed by macrolide-lincosamide-streptogramin (MLS) or tetracycline. Most ARGs belonged to common bacterial commensals and multidrug resistance trait were predominant in the nares and vagina. Many ARGs detected here were considered as low risk for human health, whereas only a few of them, such as
,
14,
17, or
, were classified as high-risk ARG. Our data also provide hope, since the spread of common ARG from the human body to pristine environments (
= 271 samples; 77 Gb of sequencing data and 2.1 × 10
proteins analyzed) thus far remains very unlikely (only one case found in an autochthonous bacterium from a pristine environment). These findings broaden our understanding of ARG in the context of the human microbiome and the One-Health Initiative of WHO uniting human host-microbes and environments as a whole.
The identification of relevant virus-host pairs that globally account for a large pool of carbon and nutrients in the ocean is paramount to build accurate ecological models. A previous work using ...single-virus genomics led to the discovery of the uncultured single-virus vSAG 37-F6, originally sorted from the Mediterranean Sea (Blanes Bay Microbial Observatory), that represents one of the most abundant dsDNA viral population in the marine surface virosphere. Here, from same sampling site, we report that a Pelagibacter single-cell contained a viral member of vSAG 37-F6 population, by means of PCR screening of sorted, genome-amplified single cells with vSAG 37-F6-specific primers and whole-genome sequencing. Furthermore, viruses from this population were also found in three other Pelagibacter single cells from the South Pacific and Atlantic oceans. These new uncultured pelagiphages were genetically different from the previously characterized pelagiphage isolates. Data showed that the uncultured vSAG 37-F6 population represents the Pelagibacter phages that inhabit the sunlit ocean better, and contains a vast unrecognized microdiversity.
Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the ...relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine
is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270-14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.
Technologies to detect the entire bacterial diversity spectra and foodborne pathogens in food represent a fundamental advantage in the control of foodborne illness. Here, we applied high-throughput ...16S rRNA sequencing of amplicons obtained by PCR and RT-PCR from extracted DNA and RNA targeting the entire bacterial community and the active bacterial fraction present in some of the most consumed and distributed ready-to-eat (RTE) salad brands in Europe. Customer demands for RTE food are increasing worldwide along with the number of associated foodborne illness and outbreaks. The total aerobic bacterial count in the analyzed samples was in the range of 2–4 × 106 CFU/g (SD ± 1.54 × 106). Culture validated methods did not detect Salmonella spp., Escherichia coli, and other fecal coliforms. 16S rRNA gene Illumina next-generation sequencing (NGS) data were congruent with these culture-based results and confirmed that these and other well-known foodborne bacterial pathogens, such as Listeria, were not detected. However, the fine-resolution of the NGS method unveiled the presence of the opportunistic pathogens Aeromonas hydrophyla and Rahnella aquatilis (relative frequency of 1.33–7.33%) that were metabolically active in addition to non-pathogenic, active members of Yersinia spp. (relative frequency of 0.0015–0.003%). The common ail and foxA marker genes of Yersinia enterocolitica were not detected by qPCR. Finally, our NGS data identified to non-pathogenic Pseudomonas spp. as the most abundant and metabolically active bacteria in the analyzed RTE salads (53–75% of bacterial abundance). Our data demonstrate the power of sequencing, in parallel, both 16S rRNA and rDNA to identify and discriminate those potentially and metabolically active bacteria and pathogens to provide a more complete view that facilitates the control of foodborne diseases, although further work should be conducted to determine the sensitivity of this method for targeting bacteria
Purpose
Intestinal dysbiosis has been linked with the pathogenesis of several degenerative diseases. Moreover, the consumption of high‐fat diets (HFD) can drove to significant changes in the gut ...microbiome. Our purpose was to investigate changes in gut microbiome and retinal degeneration associated with the ingestion of HFD in a mice model of retinitis pigmentosa (RP).
Methods
C57BL/6J mice and rd10 mice were fed either with normal chow (5.5% fat kcal) or with a HFD (61.6% fat kcal) for two weeks since P19. Retinal function was analyzed by electroretinography and optomotor test. Immunohistochemistry was employed to evaluate the structure and integrity of the retinal tissue. 16S rRNA gene sequencing was made to evaluate the gut microbiome.
Results
We found a higher retinal degeneration in rd10 mice as compared to C57BL/6J mice, both fed with normal chow. Rd10 mice exhibited significantly reduced retinal responsiveness, as well as diminished visual acuity. This loss of retina function went with a decrease in the number of photoreceptor rows, and the remaining photoreceptors showed morphologic anomalies. The photoreceptor degeneration was accompanied by an inflammatory response of the retina, characterized by the proliferation of microglial cells and reactive gliosis of Müller cells. Likewise, the gut microbiome analysis revealed differences in alpha and beta diversity at the genera, species, and amplicon sequence variants levels. HFD generated a significant dysbiosis in the gut microbiome increasing potentially pro‐inflammatory bacteria as Bilophila sp., Alistipes sp. and Mucispirillum schaedleri, and drived the exacerbation of the retinal degeneration.
Conclusions
In retinitis pigmentosa, retinal dysfunction and degeneration are related to significant changes in the gut microbiome, which can be altered by diet, conducing to a worsening of the disease.
Support
MINECOFEDER‐BFU2015‐67139‐R, FEDER‐PID2019‐106230RB‐I00, RETICS‐FEDER RD16/0008/0016, IDIFEDER/2017/064.
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