Mutualistic interplay between bacteriophages and bacteria in the human gut

Despite recent advances in therapeutic strategies and drug treatments (e.g., statins) for coronary artery disease (CAD), CAD-related mortality and morbidity remain high. Active bidirectional interactions between the gut microbiota and the heart implicate that probiotic application could be a novel therapeutic strategy for CAD. ABSTRACT Accumulating evidence suggests that gut dysbiosis may play a role in cardiovascular problems like coronary artery disease (CAD). Thus, target steering the gut microbiota/metabolome via probiotic administration could be a promising way to protect against CAD. A 6-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the added benefits and mechanism of the probiotic strain, Bifidobacterium lactis Probio-M8, in alleviating CAD when given together with a conventional regimen. Sixty patients with CAD were randomly divided into a probiotic group (n = 36; received Probio-M8, atorvastatin, and metoprolol) and placebo group (n = 24; placebo, atorvastatin, and metoprolol). Conventional treatment significantly improved the Seattle Angina Questionnaire (SAQ) scores of the placebo group after the intervention. However, the probiotic group achieved even better SAQ scores at day 180 compared with the placebo group (P < 0.0001). Moreover, Probio-M8 treatment was more conducive to alleviating depression and anxiety in patients (P < 0.0001 versus the placebo group, day 180), with significantly lower serum levels of interleukin-6 and low-density lipoprotein cholesterol (P < 0.005 and P < 0.001, respectively). In-depth metagenomic analysis showed that, at day 180, significantly more species-level genome bins (SGBs) of Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, and Butyricicoccus porcorum were detected in the probiotic group compared with the placebo group, while the abundances of SGBs representing Flavonifractor plautii and Parabacteroides johnsonii decreased significantly among the Probio-M8 receivers (P < 0.05). Furthermore, significantly more microbial bioactive metabolites (e.g., methylxanthine and malonate) but less trimethylamine-N-oxide and proatherogenic amino acids were detected in the probiotic group than placebo group during/after intervention (P < 0.05). Collectively, we showed that coadministering Probio-M8 synergized with a conventional regimen to improve the clinical efficacy in CAD management. The mechanism of the added benefits was likely achieved via probiotic-driven modulation of the host’s gut microbiota and metabolome, consequently improving the microbial metabolic potential and serum metabolite profile. This study highlighted the significance of regulating the gut-heart/-brain axes in CAD treatment. IMPORTANCE Despite recent advances in therapeutic strategies and drug treatments (e.g., statins) for coronary artery disease (CAD), CAD-related mortality and morbidity remain high. Active bidirectional interactions between the gut microbiota and the heart implicate that probiotic application could be a novel therapeutic strategy for CAD. This study hypothesized that coadministration of atorvastatin and probiotics could synergistically protect against CAD. Our results demonstrated that coadministering Probio-M8 with a conventional regimen offered added benefits to patients with CAD compared with conventional treatment alone. Our findings have provided a wide and integrative view of the pathogenesis and novel management options for CAD and CAD-related diseases.

Bifidobacterium lactis Probio-M8 Adjuvant Treatment Confers Added Benefits to Patients with Coronary Artery Disease via Target Modulation of the Gut-Heart/-Brain Axes

http://www.cell.com/article/S2589004222006897/pdf

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome

Rheumatoid arthritis (RA) is influenced by oral and gut bacteria; however, much less is known about the relationship between oral or gut viromes and RA. Here, we performed whole-oral- and whole-gut-virome analyses based on shotgun sequencing of 497 samples. A comparative analysis of the oral and gut viromes in healthy controls and untreated and treated RA patients was performed, and system interaction networks among viruses, bacteria, and RA-associated clinical indices were constructed to address the potential relationship between the virome and RA by principal-coordinate analysis, distance-based redundancy analysis, permutational multivariate analysis, Spearman correlation coefficient analysis, and random-forest model analysis. The results showed that the viromes could be profiled in dental plaque, saliva, and fecal samples, among which saliva had the highest within-sample diversity. Importantly, significantly different diversities and compositions of the oral (i.e., dental plaque and saliva) viromes were observed not only between RA patients and healthy controls but also between untreated and treated RA patients, yet there were relatively minor differences in the gut viromes. Furthermore, to understand how these viruses affected the bacteriome, a virus-bacterium interaction network was constructed from dental plaque, saliva, and fecal samples of RA patients. Additionally, some RA-associated oral taxa, including Lactococcus phage (vOTU70), Bacteroides vulgatus, Lactococcus lactis, Escherichia coli, and Neisseria elongata, were correlated with the RA-related clinical indices. Whole-virome analysis illustrated the potential role of the oral and gut viromes in affecting our body either directly or via bacteria, which characterized neglected and new candidates contributing to the development of RA. IMPORTANCE Our results demonstrated community variation among dental plaque, saliva, and fecal viromes. In oral and gut samples from untreated and treated RA patients, the perturbance of viral composition and the correlation network of microbes and RA-associated clinical indices might be involved in the pathogenicity of RA. The findings in this study expand the knowledge of the potential role of oral and gut viral communities in the development of RA and may contribute to research on correlations between viruses and other diseases. 

Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients

The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. ABSTRACT The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), Prevotella sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and Blautia A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), Dialister sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of Faecalibacterium and Prevotella were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), and Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned Siphoviridae (95 vOTUs), Myoviridae (70 vOTUs), and Microviridae (5 vOTUs), while 30 Siphoviridae vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. IMPORTANCE The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.

Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis

Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remains unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, for example ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing twenty-four healthy adults and six children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals' gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were not only inherited from that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (P < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis.

Background: Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated. Methods and Results: Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individual gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa. Conclusions: This study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome. Keywords: virus-like particle, gut virome, viral community, RNA virus, metagenomic sequencing, bacterial microbiome, nationality

https://www.biorxiv.org/content/biorxiv/early/2020/07/29/2020.07.28.226019.full.pdf

Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

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Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis.

Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis