Diarrheal disease and gut microbiome.

Diarrheal disease remains a great public health problem in many countries. Enteric infections caused by several viral, bacterial and parasitic species not only affect the host, but also alter the gut microbiome. The host physiology dictates the intestinal milieu and decides the composition and richness of gut microbiota, which forms a homeostatic ecosystem with numerous functions and provide protection against invading pathogens. During diarrheal infection, patients are affected by gut microbial dysbiosis, which benefits the pathogenic and pro-inflammatory bacteria by enhancing their colonization and proliferation. Gut microbes are associated with several pathophysiological mechanisms, including distorted motility, intestinal barrier dysfunction, malabsorption, immunity disorder, systemic inflammation and changes in the gut-organ axis. Several abiotic factors and childhood malnutrition have negative influences on the gut microbiota, including antibiotics that lead to antibiotic-associated diarrhea and persistent infection. DNA sequencing and bioinformatic analyses enhanced our perception of the gut microbiota, network of metabolic interdependence and their role in health and disease. However, the precise functions of microbiota in gut homeostasis are not well defined. In this chapter, we recapitulate the impact of gut microbiota on diarrheal pathogens, their importance in the immune system and how reshaping the gut microbiota can help during the recovery phase. Additionally, we discuss about impediments and influences beyond diarrhea, particularly on the nutritional status of children.

Two dimensions of chemical variation of the human microbiome across body sites and in COVID-19 patients (preprint)

A better understanding of dysbiosis is a major goal of human microbiome studies, but more knowledge about chemical effects on microbial communities is needed. Oxidation-reduction and hydration-dehydration reactions are chemical processes that are important for physiological functions and, it is hypothesized here, may also influence the elemental composition of microbial proteins. Chemical metrics of biomolecules relevant to these processes are carbon oxidation state (ZC) and stoichiometric hydration state (nH2O). I calculated these metrics for protein sequences derived from microbial genomes (multiplied by 16S rRNA-based taxonomic abundances to obtain community reference proteomes), shotgun metagenomes, and metaproteomes. Metaproteomes of gut communities are reduced (i.e., have lower ZC) compared to oral communities. In contrast, community reference proteomes have lower nH2O in gut compared to nasal, skin, and oral communities, and metagenomes for gut and oral communities exhibit the same trend. The chemical differences for metaproteomes may be explained by physiological adjustment of protein expression levels to anaerobic, reducing conditions in the gut, whereas metagenomes and reference proteomes may reflect evolutionary adaptation to dehydrating conditions brought on by intestinal absorption of water. Community reference proteomes, metagenome-assembled genomes (MAGs), and metaproteomes compiled from various studies yield a common trend of more reduced proteins in gut communities of COVID-19 patients compared to controls. These chemical differences imply more reducing conditions in the guts of COVID-19 patients, a finding that contrasts with oxidative conditions that have been previously associated with dysbiosis in inflammatory bowel disease and HIV infection. These results reveal how the human microbiome is shaped by multiple chemical factors over a range of timescales and suggest a new strategy for using multi-omics data to infer changes in gut redox conditions in COVID-19 patients.

Potential role of the microbiome in liver injury during COVID-19: Further research is needed.

Although different studies have associated coronavirus disease 2019 (COVID-19) with the occurrence of liver injury, the hepatic injury route during the COVID-19 course is not yet fully understood. In order to better understand the mechanisms of the disease, the human gut microbiota has been the subject of extensive discussion in the context of COVID-19 pathophysiology. However, many questions remain, including the risks of liver injury due to COVID-19 specific populations. Further research in this field could allow the discovery of new personalized treatment strategies aimed at improving the microbiota composition, thereby reducing COVID-19 severity and its complications in different populations. In this article, we discussed basic mechanisms of severe acute respiratory syndrome coronavirus 2 infection and recent evidence on the relationship between COVID-19, the gut microbiome and liver injury as well as proposed recommendations for further research.

Viral infectious diseases severity: co-presence of transcriptionally active microbes (TAMs) can play an integral role for disease severity.

Humans have been challenged by infectious diseases for all of their recorded history, and are continually being affected even today. Next-generation sequencing (NGS) has enabled identification of, i) culture independent microbes, ii) emerging disease-causing pathogens, and iii) understanding of the genome architecture. This, in turn, has highlighted that pathogen/s are not a monolith, and thereby allowing for the differentiation of the wide-ranging disease symptoms, albeit infected by a primary pathogen. The conventional 'one disease - one pathogen' paradigm has been positively revisited by considering limited yet important evidence of the co-presence of multiple transcriptionally active microbes (TAMs), potential pathogens, in various infectious diseases, including the COVID-19 pandemic. The ubiquitous microbiota presence inside humans gives reason to hypothesize that the microbiome, especially TAMs, contributes to disease etiology. Herein, we discuss current evidence and inferences on the co-infecting microbes particularly in the diseases caused by the RNA viruses - Influenza, Dengue, and the SARS-CoV-2. We have highlighted that the specific alterations in the microbial taxonomic abundances (dysbiosis) is functionally connected to the exposure of primary infecting pathogen/s. The microbial presence is intertwined with the differential host immune response modulating differential disease trajectories. The microbiota-host interactions have been shown to modulate the host immune responses to Influenza and SARS-CoV-2 infection, wherein the active commensal microbes are involved in the generation of virus-specific CD4 and CD8 T-cells following the influenza virus infection. Furthermore, COVID-19 dysbiosis causes an increase in inflammatory cytokines such as IL-6, TNF-α, and IL-1ß, which might be one of the important predisposing factors for severe infection. Through this article, we aim to provide a comprehensive view of functional microbiomes that can have a significant regulatory impact on predicting disease severity (mild, moderate and severe), as well as clinical outcome (survival and mortality). This can offer fresh perspectives on the novel microbial biomarkers for stratifying patients for severe disease symptoms, disease prevention and augmenting treatment regimens.

Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients.

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

Composition of nasopharyngeal microbiota in individuals with SARS-COV-2 infection across three COVID-19 waves in India (preprint)

Background: SARS-COV-2 is an enveloped RNA virus that is responsible for the global pandemic COVID-19. The virus is reported to cause dysbiosis of the Human Nasopharyngeal microbiota, consequently regulating the host immunity and infection pathophysiology. The compositional change in microbial diversity due to the virus has been reported by independent authors in smaller cohorts and different geographical regions, with a few correlating with fungal and bacterial co-infections. Here, we study for the first time, the nasopharyngeal microbial diversity in the COVID-19 patients, across the three waves in India and explore its correlation with the causative virus variant (and/or the severity of symptoms, if any). Methods: We profiled the nasopharyngeal microbiota of 589 Indian subjects, across the three waves (First; n=181, Second; n=217, Third; n=191), which were further categorized as COVID-19 positives and COVID-19 negatives. These respective groups were further divided into subgroups based on the symptoms as Asymptomatic and Symptomatic. The nasopharyngeal swabs were collected from subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India. Using high throughput 16S rRNA gene amplicon-based sequencing, we sequenced and profiled the nasopharyngeal DNA microbiome prior to subjecting them to diversity, composition and network analyses. Results: Patients infected with SARS-COV-2 showed a reduced microbial alpha diversity compared to the COVID-19 negatives, in a wave-dependent manner, as implicated by measuring the alpha diversity indices. Furthermore, the compositional change in the community was found to be significantly associated with the viral load as well as the severity of the symptoms observed in the patients. Preliminary taxonomic analysis indicated that, overall, Firmicutes, Proteobacteria, and Actinobacteriota were amongst the dominating Phyla, while Staphylococcaceae and Corynebacteriaceae were the most abundant Families. Also, the microbiota signatures of the first and third wave were more similar to each other at the phylum level compared to the second wave. However, the abundance of microbes varied greatly between the major groups i.e COVID-19 positives and the negatives at the family level, in the respective waves. A similar observation was made where both the commensals and pathobionts differed in abundance between the patient subgroups. Interestingly, the change in microbial network architecture from first to second wave was driven by opportunistic pathogens such as Paenibacillus, Peptostreptococcus, and Solobacterium while Leptotrichia and Actinomyces were noted to be taxonomic groups driving the changes during the third wave when compared to the second wave. Conclusion: In the Indian cohort examined, SARS-COV-2 infection perturbs the nasopharyngeal microbiome, resulting in lower & varied diversity in the niche, irrespective of the virus variant (& thus, the COVID wave) and the disease severity. Whether these changes assist in COVID-19 disease onset & progression, would be interesting to explore in the future.

Rapamycin and inulin for third-dose vaccine response stimulation (RIVASTIM): Inulin - study protocol for a pilot, multicentre, randomised, double-blinded, controlled trial of dietary inulin to improve SARS-CoV-2 vaccine response in kidney transplant recipients.

INTRODUCTION: Kidney transplant recipients (KTRs) are at an increased risk of hospitalisation and death from COVID-19. Vaccination against SARS-CoV-2 is our primary risk mitigation strategy, yet vaccine effectiveness in KTRs is suboptimal. Strategies to enhance vaccine efficacy are therefore required. Current evidence supports the role of the gut microbiota in shaping the immune response to vaccination. Gut dysbiosis is common in KTRs and is a potential contributor to impaired COVID-19 vaccine responses. We hypothesise that dietary fibre supplementation will attenuate gut dysbiosis and promote vaccine responsiveness in KTRs. METHODS AND ANALYSIS: Rapamycin and inulin for third-dose vaccine response stimulation-inulin is a multicentre, randomised, prospective, double-blinded, placebo-controlled pilot trial examining the effect of dietary inulin supplementation prior to a third dose of COVID-19 vaccine in KTRs who have failed to develop protective immunity following a 2-dose COVID-19 vaccine schedule. Participants will be randomised 1:1 to inulin (active) or maltodextrin (placebo control), administered as 20 g/day of powdered supplement dissolved in water, for 4 weeks prior to and following vaccination. The primary outcome is the proportion of participants in each trial arm that achieve in vitro neutralisation of live SARS-CoV-2 virus at 4 weeks following a third dose of COVID-19 vaccine. Secondary outcomes include the safety and tolerability of dietary inulin, the diversity and differential abundance of gut microbiota, and vaccine-specific immune cell populations and responses. ETHICS AND DISSEMINATION: Ethics approval was obtained from the Central Adelaide Local Health Network (CALHN) Human Research Ethics Committee (HREC) (approval number: 2021/HRE00354) and the Sydney Local Health District (SHLD) HREC (approval numbers: X21-0411 and 2021/STE04280). Results of this trial will be published following peer-review and presented at scientific meetings and congresses. TRIAL REGISTRATION NUMBER: ACTRN12621001465842.

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases.

BACKGROUND: Dozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the specific COVID-19 associated bacteria is missing. In this study, we performed a meta-analysis to explore whether robust and reproducible alterations in the gut microbiota of COVID-19 patients exist across different populations. METHODS: A systematic review was conducted for studies published prior to May 2022 in electronic databases. After review, we included 16 studies that comparing the gut microbiota in COVID-19 patients to those of controls. The 16S rRNA sequence data of these studies were then re-analyzed using a standardized workflow and synthesized by meta-analysis. RESULTS: We found that gut bacterial diversity of COVID-19 patients in both the acute and recovery phases was consistently lower than non-COVID-19 individuals. Microbial differential abundance analysis showed depletion of anti-inflammatory butyrate-producing bacteria and enrichment of taxa with pro-inflammatory properties in COVID-19 patients during the acute phase compared to non-COVID-19 individuals. Analysis of microbial communities showed that the gut microbiota of COVID-19 recovered patients were still in unhealthy ecostates. CONCLUSIONS: Our results provided a comprehensive synthesis to better understand gut microbial perturbations associated with COVID-19 and identified underlying biomarkers for microbiome-based diagnostics and therapeutics.

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19 (preprint)

The clinical course of the 2019 coronavirus disease (COVID-19) is variable and to a substantial degree still unpredictable, especially in persons who have neither been vaccinated nor recovered from previous infection. We hypothesized that disease progression and inflammatory responses were associated with alterations in the microbiome and metabolome. To test this, we integrated metagenome, metabolome, cytokine, and transcriptome profiles of longitudinally collected samples from hospitalized COVID-19 patients at the beginning of the pandemic (before vaccines or variants of concern) and non-infected controls, and leveraged detailed clinical information and post-hoc confounder analysis to identify robust within- and cross-omics associations. Severe COVID-19 was directly associated with a depletion of potentially beneficial intestinal microbes mainly belonging to Clostridiales, whereas oropharyngeal microbiota disturbance appeared to be mainly driven by antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine, and reduced levels of various other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Decreased abundance of Clostridiales potentially mediated the observed reduction in 5-hydroxytryptophan levels. Moreover, altered plasma levels of various tryptophan metabolites and lower abundances of Clostridiales explained significant increases in the production of IL-6, IFN{gamma} and/or TNF. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.

Evaluation of the gut microbiota patterns in patients with COVID-19: a protocol for a pilot study (preprint)

Background SARS-CoV-2 caused an outbreak in late December 2019. It has been suggested that the gut microbiota dysbiosis influences severity, mortality, and quality of life of patients with COVID-19. So, identifying the gut microbiota pattern could be helpful to determine prognosis of the disease, and maybe determine some potential treatment approaches. Our aim will be to compare gut microbiota patterns between patients with severe or non-severe COVID-19, and healthy controls.Methods We will include 40 samples: 20 samples from COVID-19 patients, including 10 severe patients and 10 non-severe patients, and 20 samples from healthy controls. Total bacterial DNA will be extracted from samples and 16S rRNA gene will be amplified through two PCR stages. Fecal samples will be analyzed using a targeted metabolomics technique, and a total of 198 compounds will be measured. The differences in each RNA or DNA expression between patients with severe COVID-19, patients with non-severe COVID-19, and controls will be compared. Also, we will assess the relationships between each DNA or RNA as well as the risk of COVID-19 severity, sort of clinical manifestations, and comorbiditiesDiscussion The results of our study could be the backbone for further trials which might lead to development of prognostic factors and treatment options.

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia.

Although microbial populations in the gut microbiome are associated with COVID-19 severity, a causal impact on patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is associated with translocation of bacteria into the blood during COVID-19, causing life-threatening secondary infections. We first demonstrate SARS-CoV-2 infection induces gut microbiome dysbiosis in mice, which correlated with alterations to Paneth cells and goblet cells, and markers of barrier permeability. Samples collected from 96 COVID-19 patients at two different clinical sites also revealed substantial gut microbiome dysbiosis, including blooms of opportunistic pathogenic bacterial genera known to include antimicrobial-resistant species. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data indicates that bacteria may translocate from the gut into the systemic circulation of COVID-19 patients. These results are consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19.

Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2.

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS2) affected the geriatric population. Among research models, Golden Syrian hamsters (GSH) are one of the most representative to study SARS2 pathogenesis and host responses. However, animal studies that recapitulate the effects of SARS2 in the human geriatric population are lacking. To address this gap, we inoculated 14 months old GSH with a prototypic ancestral strain of SARS2 and studied the effects on virus pathogenesis, virus shedding, and respiratory and gastrointestinal microbiome changes. SARS2 infection led to high vRNA loads in the nasal turbinates (NT), lungs, and trachea as well as higher pulmonary lesions scores later in infection. Dysbiosis throughout SARS2 disease progression was observed in the pulmonary microbial dynamics with the enrichment of opportunistic pathogens (Haemophilus, Fusobacterium, Streptococcus, Campylobacter, and Johnsonella) and microbes associated with inflammation (Prevotella). Changes in the gut microbial community also reflected an increase in multiple genera previously associated with intestinal inflammation and disease (Helicobacter, Mucispirillum, Streptococcus, unclassified Erysipelotrichaceae, and Spirochaetaceae). Influenza A virus (FLUAV) pre-exposure resulted in slightly more pronounced pathology in the NT and lungs early on (3 dpc), and more notable changes in lungs compared to the gut microbiome dynamics. Similarities among aged GSH and the microbiome in critically ill COVID-19 patients, particularly in the lower respiratory tract, suggest that GSHs are a representative model to investigate microbial changes during SARS2 infection. The relationship between the residential microbiome and other confounding factors, such as SARS2 infection, in a widely used animal model, contributes to a better understanding of the complexities associated with the host responses during viral infections.

Alterations in human intestinal microbiota in the course of SARS-CoV-2 virus infection.

There is an interaction between the bacteria and the host at the genetic, metabolic and immunological levels. The intestine is the largest immune organ in the human's body, and the microbes present in it influence the immune response. An imbalance in the type and the number of bacteria can affect human health. The study attempts to review the current reports on intestinal dysbiosis in the course of SARS-CoV-2 infection and the impact of the composition of the intestinal microbiome on the course and severity of COVID-19 disease.

The Role of the Gut-Lung Axis in COVID-19 Infections and Its Modulation to Improve Clinical Outcomes.

The main entry point of SARS-CoV-2 is the respiratory tract and as such immune defence in this site determines if the virus will spill-over to the systemic circulation and circulate and infect other major organs. The first line of mucosal immune defence is composed of mucins, an epithelial barrier, and immune cells in the nasal cavity. The lung immune defence is carried out by numerous alveoli. The lung microbiota is a key factor in determining the efficacy of lung mucosal immunity protection. The intestinal microbiota has been demonstrated to affect the severity of COVID-19. Gut dysbiosis is involved in hyperinflammation and multiple organ failure through communications with multiple organs. The gut lung axis could be the earliest axis affected in COVID-19. Through the gut-lung axis, gut dysbiosis can affect the pathogenesis of the lung in COVID-19. In this review, we summarise the effects that gut dysbiosis can progress on the lung, and the lung microbiota. The possible mechanisms and approaches for modulation are discussed.

Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients.

BACKGROUND: At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. METHODS: To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). RESULTS: In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. CONCLUSIONS: In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.

Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lung infection. Post-hoc studies of previous SARS outbreaks postulate secondary bacterial infections with microbial dysbiosis. Oral microbial dysbiosis, particularly the altered proportion of Firmicutes and Proteobacteria, observed in other respiratory virus infection, like influenza, has shown to be associated with increased morbidity and mortality. Oropharynx and lung share similar kinds of bacterial species. We hypothesized that alteration in the Human Oropharyngeal Microbiome in SARS-CoV-2 patients can be a clinical indicator of bacterial infection related complications. We made a longitudinal comparison of oropharyngeal microbiome of 20 SARS-CoV-2 patients over a period of 30 days; at three time points, with a 15 days interval; contrasting them with a matched group of 10 healthy controls. Present observation indicates that posterior segment of the oropharyngeal microbiome is a key reservoir for bacteria causing pneumonia and chronic lung infection on SARS-CoV-2 infection. Oropharyngeal microbiome is indeed altered and its α-diversity decreases, indicating reduced stability, in all SARS-CoV-2 positive individuals right at Day-1; i.e. within ~24 h of post clinical diagnosis. The dysbiosis persists long-term (30 days) irrespective of viral clearance and/or administration of antibiotics. There is a severe depletion of commensal bacteria phyla like Firmicutes among the patients and that depletion is compensated by higher proportion of bacteria associated with sepsis and severe lung infection from phyla Proteobacteria. We also found elevated proportions of certain genus that have previously been shown to be causal for lung pneumonia in studies of model organisms and human autopsies' including Stenotrophomonas, Acenetobactor, Enterobactor, Klebsiella and Chryseobacterium that were to be elevated among the cases. We also show that responses to the antibiotics (Azithromycin and Doxycycline) are not uniform for all individuals.

Long-term implications of COVID-19 on bone health: pathophysiology and therapeutics.

BACKGROUND: SARS-CoV-2 is a highly infectious respiratory virus associated with coronavirus disease (COVID-19). Discoveries in the field revealed that inflammatory conditions exert a negative impact on bone metabolism; however, only limited studies reported the consequences of SARS-CoV-2 infection on skeletal homeostasis. Inflammatory immune cells (T helper-Th17 cells and macrophages) and their signature cytokines such as interleukin (IL)-6, IL-17, and tumor necrosis factor-alpha (TNF-α) are the major contributors to the cytokine storm observed in COVID-19 disease. Our group along with others has proven that an enhanced population of both inflammatory innate (Dendritic cells-DCs, macrophages, etc.) and adaptive (Th1, Th17, etc.) immune cells, along with their signature cytokines (IL-17, TNF-α, IFN-γ, IL-6, etc.), are associated with various inflammatory bone loss conditions. Moreover, several pieces of evidence suggest that SARS-CoV-2 infects various organs of the body via angiotensin-converting enzyme 2 (ACE2) receptors including bone cells (osteoblasts-OBs and osteoclasts-OCs). This evidence thus clearly highlights both the direct and indirect impact of SARS-CoV-2 on the physiological bone remodeling process. Moreover, data from the previous SARS-CoV outbreak in 2002-2004 revealed the long-term negative impact (decreased bone mineral density-BMDs) of these infections on bone health. METHODOLOGY: We used the keywords "immunopathogenesis of SARS-CoV-2," "SARS-CoV-2 and bone cells," "factors influencing bone health and COVID-19," "GUT microbiota," and "COVID-19 and Bone health" to integrate the topics for making this review article by searching the following electronic databases: PubMed, Google Scholar, and Scopus. CONCLUSION: Current evidence and reports indicate the direct relation between SARS-CoV-2 infection and bone health and thus warrant future research in this field. It would be imperative to assess the post-COVID-19 fracture risk of SARS-CoV-2-infected individuals by simultaneously monitoring them for bone metabolism/biochemical markers. Importantly, several emerging research suggest that dysbiosis of the gut microbiota-GM (established role in inflammatory bone loss conditions) is further involved in the severity of COVID-19 disease. In the present review, we thus also highlight the importance of dietary interventions including probiotics (modulating dysbiotic GM) as an adjunct therapeutic alternative in the treatment and management of long-term consequences of COVID-19 on bone health.

Disease-associated dysbiosis and potential therapeutic role of Akkermansia muciniphila, a mucus degrading bacteria of gut microbiome.

The unique functionality of Akkermansia muciniphila in gut microbiota indicates it to be an indispensable microbe for human welfare. The importance of A. muciniphila lies in its potential to convert mucin into beneficial by-products, regulate intestinal homeostasis and maintain gut barrier integrity. It is also known to competitively inhibit other mucin-degrading bacteria and improve metabolic functions and immunity responses in the host. It finds a pivotal perspective in various diseases and their treatment. It has future as a promising probiotic, disease biomarker and therapeutic agent for chronic diseases. Disease-associated dysbiosis of A. muciniphila in the gut microbiome makes it a potential candidate as a biomarker for some diseases and can provide future theranostics by suggesting ways of diagnosis for the patients and best treatment method based on the screening results. Manipulation of A. muciniphila in gut microbiome may help in developing a novel personalized therapeutic action and can be a suitable next generation medicine. However, the actual pathway governing A. muciniphila interaction with hosts remains to be investigated. Also, due to the limited availability of products containing A. muciniphila, it is not exploited to its full potential. The present review aims at highlighting the potential of A. muciniphila in mucin degradation, contribution towards the gut health and host immunity and management of metabolic diseases such as obesity and type 2 diabetes, and respiratory diseases such as cystic fibrosis and COVID-19.

Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling (preprint)

Patients with liver injury such as cirrhosis are at increased risk of intractable viral infections and are hyporesponsive to vaccination. Here, we report that liver injury leads to inhibition of systemic T cell immunity (LIST), which abrogated anti-viral immunity and caused persistent infection in preclinical liver injury models. Enhanced gut microbial-translocation but not dysbiosis induced tonic type-I-interferon (IFN) signaling in hepatic myeloid cells, which was responsible for their excessive production of IL-10 after viral infection. Antibiotic treatment reducing intestinal microbial burden or inhibition of IFN- and IL-10-signaling all restored anti-viral immunity without immune pathology. Importantly, inhibition of IL-10 restored virus-specific immune responses to vaccination in cirrhotic patients. Thus, LIST results from sequential events involving intestinal microbial translocation, hepatic myeloid cell-derived IFN-/IL-10 expression, and finally inhibitory IL-10 receptor-signaling in T cells, of which IL-10Ra-signaling may serve as target to reconstitute anti-viral T cell immunity in cirrhotic patients.