Auto-immunoproteomics analysis of COVID-19 ICU patients revealed increased levels of autoantibodies related to the male reproductive system

Background: Coronavirus disease (COVID-19) manifests many clinical symptoms, including an exacerbated immune response and cytokine storm. Autoantibodies in COVID-19 may have severe prodromal effects that are poorly understood. The interaction between these autoantibodies and self-antigens can result in systemic inflammation and organ dysfunction. However, the role of autoantibodies in COVID-19 complications has yet to be fully understood. Methods: The current investigation screened two independent cohorts of 97 COVID-19 patients [discovery (Disc) cohort from Qatar (case = 49 vs. control = 48) and replication (Rep) cohort from New York (case = 48 vs. control = 28)] utilizing high-throughput KoRectly Expressed (KREX) Immunome protein-array technology. Total IgG autoantibody responses were evaluated against 1,318 correctly folded and full-length human proteins. Samples were randomly applied on the precoated microarray slides for 2 h. Cy3-labeled secondary antibodies were used to detect IgG autoantibody response. Slides were scanned at a fixed gain setting using the Agilent fluorescence microarray scanner, generating a 16-bit TIFF file. Group comparisons were performed using a linear model and Fisher's exact test. Differentially expressed proteins were used for KEGG and WIKIpathway annotation to determine pathways in which the proteins of interest were significantly over-represented. Results and conclusion: Autoantibody responses to 57 proteins were significantly altered in the COVID-19 Disc cohort compared to healthy controls (p ≤ 0.05). The Rep cohort had altered autoantibody responses against 26 proteins compared to non-COVID-19 ICU patients who served as controls. Both cohorts showed substantial similarities (r 2 = 0.73) and exhibited higher autoantibody responses to numerous transcription factors, immunomodulatory proteins, and human disease markers. Analysis of the combined cohorts revealed elevated autoantibody responses against SPANXN4, STK25, ATF4, PRKD2, and CHMP3 proteins in COVID-19 patients. The sequences for SPANXN4 and STK25 were cross-validated using sequence alignment tools. ELISA and Western blot further verified the autoantigen-autoantibody response of SPANXN4. SPANXN4 is essential for spermiogenesis and male fertility, which may predict a potential role for this protein in COVID-19-associated male reproductive tract complications, and warrants further research.

Microbiome profiling of rotavirus infected children suffering from acute gastroenteritis

Background

Rotavirus (RV) is a leading cause of pediatric diarrhea and mortality worldwide. The virus causes acute gastroenteritis characterized by moderate to severe vomiting, diarrhea, dehydration, and fever. Microbial dysbiosis caused by RV infection may significantly influence disease prognosis and the development of other chronic diseases. The gut microbiome plays a vital role in enteric immune response for rotavirus vaccine (RVV) that requires further elucidations. The current study evaluates the gut microbiome of RV positive children and compares gastroenteritis manifestation in children admitted to the Pediatric Emergency Centre, Hamad Medical Cooperation, Doha, Qatar. Stool samples were collected from thirty-nine RV positive and eight healthy control children. 16S rRNA sequence was performed using the Illumina MiSeq platform.

Results

The data demonstrated a significant increase in microbiome diversity denoted by higher relative abundances of phylum Proteobacteria (p = 0.031), Fusobacteria (p = 0.044) and genus Streptococcus (p ≤ 0.001) in the infected group relative to the control. Similarly, district clustering pattern (PERMANOVA p = 0.01) and higher species richness (Shannon entropy p = 0.018) were observed in the children who received two RVV doses compared with the non-vaccinated or single-dose groups. These microbiome changes were represented by over-abundance of phylum Bacteroidetes (p = 0.003) and Verrucomicrobia (p ≤ 0.001), and lower expression of family Enterobacteriaceae in two RVV doses group. However, microbiome composition was not associated with diarrhea, vomiting, and other parameters of gastroenteritis.

Conclusions

The observations assert significant microbial signatures of RVV, which is dose-dependent, and suggest manipulating these microbes as a novel approach for improving RVV efficacy. Further studies are warranted to investigate the immune status of these patients and mechanistic investigation to enhance RVV seroconversion.

Dysbiosis of the Salivary Microbiome is Associated with Hypertension and Correlated with Metabolic Syndrome Biomarkers

BACKGROUND

Hypertension (HT) is an idiopathic disease with severe complications and a high incidence of global mortality. Although the disease shares characteristic features with diabetes and obesity, the complex interplay of endogenous and environmental factors is not well characterized. The oral microbiome has recently been studied to better understand the role of commensal microorganisms in metabolic disorders, including HT, although its role in disease etiology is unclear.

METHODS

To bridge this gap, we compared the oral microbiome and clinical chemistry of adult subjects enrolled at Qatar Biobank. Clinical chemistry was performed using Roche Cobas-6000 analyzer. Saliva samples were subjected to 16S rRNA sequencing using Illumina MiSeq platform. Cross-gender comparisons were made between control (males/females) (C-M and C-F) and HT (HT-M and HT-F) groups.

RESULTS

The HT groups had higher (p ≤ 0.05) BMI, plasma glucose, insulin, C-peptide, and alkaline phosphatase (ALP) concentrations. Triglycerides, cholesterol, LDL-cholesterol, and sodium ions were similar among the groups. The microbiome was predominantly occupied by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Firmicutes were higher (p ≤ 0.05) in the HT groups, whereas Proteobacteria was only higher in the C-F group. Prevotella and Veillonella were significantly higher in the HT groups and exhibited a positive correlation with blood pressure and hyperglycemia. In contrast to other studies, the mathematical summation of priori-select microbes reveals that nitrate-reducing microbes were higher in the HT groups compared with the controls.

CONCLUSION

In conclusion, these observations suggest a strong association of HT with microbial dysbiosis, where microbial species other than nitrate-reducing microbes contribute to blood pressure regulation. The findings affirm plausible microbial signatures of hypertension and suggest manipulating these microbes as a novel treatment modality. Future experiments are warranted for the mechanistic investigation of hypertension metagenomics and microbial activity.

Assessment of Serum Cytokines and Oxidative Stress Markers in Elite Athletes Reveals Unique Profiles Associated With Different Sport Disciplines

Objectives

Circulating cytokines and oxidative stress markers vary in response to different exercise regimens. This study aims to compare the immune-inflammatory and oxidative stress profiles of elite athletes from different sport disciplines as potential biomarkers of muscle damage, and cardiovascular demand.

Methods

Serum samples from 88 consented elite male athletes from different sports disciplines (aquatics, n = 11, athletics, n = 22, cycling, n = 19, football, n = 28 and weightlifting, n = 8) collected at the anti-doping lab in Italy were screened for 38 cytokines and oxidative stress markers. Comparisons were made between different level of power, cardiovascular demand (CD) and endurance, as well as among the sport types.

Results

The anti-inflammatory interleukin (IL)-10 was higher (p = 0.04) in moderate power compared with the high power group. Conversely, superoxide dismutase (SOD; p = 0.001) and malondialdehyde (MDA; p = 0.007) levels were greater in the higher power groups compared with the lower power counterpart. Among athletes who belong to different CD ranks, IL-1β and monocyte chemoattractant protein-1(MCP1) levels were higher (p = 0.03) in the low CD-rank group compared with high CD counterpart, whereas, SOD levels were higher (p = 0.001) in high and moderate CD-rank groups compared to low counterpart. For endurance groups, IL-10 and macrophage inflammatory protein (MIP)-1beta were increased (p = 0.03) in low/moderate endurance compared with the high endurance group. Finally, MIP1-beta, SOD and catalase varied significantly among the sports groups.

Conclusion

Specific markers of inflammation and oxidative stress are associated with different sports disciplines and could be utilized as potential biomarkers of athletes' health, performance, and recovery from injury.

Profiling the Oral Microbiome and Plasma Biochemistry of Obese Hyperglycemic Subjects in Qatar

The present study is designed to compare demographic characteristics, plasma biochemistry, and the oral microbiome in obese (N = 37) and lean control (N = 36) subjects enrolled at Qatar Biobank, Qatar. Plasma hormones, enzymes, and lipid profiles were analyzed at Hamad Medical Cooperation Diagnostic Laboratory. Saliva microbiome characterization was carried out by 16S rRNA amplicon sequencing using Illumina MiSeq platform. Obese subjects had higher testosterone and sex hormone-binding globulin (SHBG) concentrations compared to the control group. A negative association between BMI and testosterone (p < 0.001, r = −0.64) and SHBG (p < 0.001, r = −0.34) was observed. Irrespective of the study groups, the oral microbiome was predominantly occupied by Streptococcus, Prevotella, and Veillonella species. A generalized linear model revealed that the Firmicutes/Bacteroidetes ratio (2.25 ± 1.83 vs. 1.76 ± 0.58; corrected p-value = 0.04) was higher, and phylum Fusobacteria concentration (4.5 ± 3.0 vs. 6.2 ± 4.3; corrected p-value = 0.05) was low in the obese group compared with the control group. However, no differences in microbiome diversity were observed between the two groups as evaluated by alpha (Kruskal–Wallis p ≥ 0.78) and beta (PERMANOVA p = 0.37) diversity indexes. Certain bacterial phyla (Acidobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Firmicutes/Bacteroidetes) were positively associated (p = 0.05, r ≤ +0.5) with estradiol, fast food consumption, creatinine, breastfed during infancy, triglycerides, and thyroid-stimulating hormone concentrations. In conclusion, no differences in oral microbiome diversity were observed between the studied groups. However, the Firmicutes/Bacteroidetes ratio, a recognized obesogenic microbiome trait, was higher in the obese subjects. Further studies are warranted to confirm these findings in a larger cohort.

Impact of Physical Exercise on Gut Microbiome, Inflammation, and the Pathobiology of Metabolic Disorders

BACKGROUND

The gastrointestinal tract (GIT) harbors a complex and diverse microbial composition that outnumbers our own body cells and their gene contents. These microbes play a significant role in host metabolism and energy homeostasis. Emerging evidence suggests that the GIT microbiome significantly contributes to host health and that impairments in the microbiome may cause the development of metabolic diseases. The microbiome architecture is shaped by several genetic and environmental factors, including nutrition and physical activity. Physical exercise has preventive or therapeutic effects in respiratory, cardiovascular, neuroendocrine, and muscular diseases. Yet, we still have little information of the beneficial effects of physical exercise on GIT health and microbial composition. Furthermore, we are not aware whether exercise-derived benefits on microbiome diversity can beneficially influence other tissues and body organs.

OBJECTIVES

The aim of this article is to review the available literature on exercise-induced microbiome changes and to explain how these changes may induce inflammatory, immune, and oxidative responses that may contribute to the improvement of metabolic disorders.

METHODS

A systemic and comprehensive search of the relevant literature using MEDLINE and Google Scholar databases was conducted during fall 2018 and spring 2019. The search identified sixty-two research and review articles that discussed exercise-induced microbiome changes.

RESULTS

The review of the relevant literature suggests that exercise-induced microbial changes affect the host's immune pathways and improve energy homeostasis. Microbes release certain neuroendocrine and immune-modulatory factors that may lower inflammatory and oxidative stress and relieve patients suffering from metabolic disorders.

CONCLUSIONS

Exercise-induced changes in microbial diversity are able to improve tissue metabolism, cardiorespiratory fitness, and insulin resistance.

Shiitake Culinary-Medicinal Mushroom, Lentinus edodes (Agaricomycetes), Supplementation Alters Gut Microbiome and Corrects Dyslipidemia in Rats

Recent interest in diet-induced modulation of the gut microbiome has led to research on the impact that dietary fibers can have on host health. Lentinus edodes mushroom-derived fibers may act as an appropriate substrate for gut microbe digestion and metabolism. The metabolites that gut microbes excrete can modulate host energy balance, gut absorption, appetite, and lipid metabolism. In the present study, we explored the dynamics of the gut microbiome of hypercholesterolemic rats supplemented with L. edodes. Wistar rats were offered a chow maintenance diet (CMD; CON group) or the same CMD ration with cholesterol (1.5% w/w) and cholic acid (0.5% w/w) added to induce hypercholesterolemia (day 1 to day 24). Hypercholesterolemic rats were subsequently offered either the same cholesterol-cholic acid diet (HC-CON group) or were supplemented with L. edodes (5% w/w; LE group) for 42 days (day 25 to day 66). At the end of the experiment, serum triglycerides, total cholesterol, high-density lipoprotein (HDL) cholesterol, and low-density lipoprotein (LDL) cholesterol concentrations were determined. Colon digesta were subjected to DNA extraction and subsequent 16S rRNA gene sequencing. Raw sequences were quality filtered and statistically analyzed using QIIME and LEfSe tools. Triglyceride concentrations were lower (P = 0.002) in the LE group than in the CON and HC-CON groups. Total cholesterol and LDL cholesterol concentrations were slightly decreased, whereas HDL cholesterol concentrations were increased by L. edodes supplementation compared with the HC-CON group. The gut microbiome of the LE group had higher species richness characterized by increased abundance of Clostridium and Bacteroides spp. Linear discriminant analysis identified bacterial clades that were statistically different among treatment groups. In conclusion, manipulation of gut microbiota through the administration of L. edodes could manage dyslipidemia.

Genetic characterization of canine parvovirus from dogs in Pakistan

Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64.71%) were found positive both in hemagglutination and PCR assays. Phylogenetic and evolutionary analysis demonstrated higher genetic heterogeneity in studied strains and constituted seven clusters within the CPV-2a group, however, they shared high level of identity with Chinese strains. Further studies are necessary to elucidate genetic analysis and epidemiology of CPV variants across a wide geographical area of the country.

Role of the Gastrointestinal Tract Microbiome in the Pathophysiology of Diabetes Mellitus

The incidence of diabetes mellitus is rapidly increasing throughout the world. Although the exact cause of the disease is not fully clear, perhaps, genetics, ethnic origin, obesity, age, and lifestyle are considered as few of many contributory factors for the disease pathogenesis. In recent years, the disease progression is particularly linked with functional and taxonomic alterations in the gastrointestinal tract microbiome. A change in microbial diversity, referred as microbial dysbiosis, alters the gut fermentation profile and intestinal wall integrity and causes metabolic endotoxemia, low-grade inflammation, autoimmunity, and other affiliated metabolic disorders. This article aims to summarize the role of the gut microbiome in the pathogenesis of diabetes. Additionally, we summarize gut microbial dysbiosis in preclinical and clinical diabetes cases reported in literature in the recent years.

Molecular analysis of the caecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic

The gastrointestinal tract commensal microbiome is important for host nutrition, health and immunity. Little information is available regarding the role of these commensals at other mucosal surfaces in poultry. Tracheal mucosal surfaces offer sites for first-line health and immunity promotion in broilers, especially under stress-related conditions. The present study is aimed at elucidating the effects of feed supplementations with mannanoligosaccharides (MOS) prebiotic and a probiotic mixture (PM) on the caecal and tracheal microbiome of broilers kept under chronic heat stress (HS; 35 ± 2°C). Day-old chickens were randomly divided into five treatment groups: thermoneutral control (TN-CONT), HS-CONT, HS-MOS, HS-PM and HS synbiotic (fed MOS and PM). Caecal digesta and tracheal swabs were collected at day 42 and subjected to DNA extraction, followed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. The PCR-DGGE dendrograms revealed significant (49.5% similarity coefficients) differences between caecal and tracheal microbiome. Tracheal microbiome pyrosequencing revealed 9 phyla, 17 classes, 34 orders, 68 families and 125 genera, while 11 phyla, 19 classes, 34 orders, 85 families and 165 genera were identified in caeca. An unweighted UniFrac distance metric revealed a distinct clustering pattern (analysis of similarities, P = 0.007) between caecal and tracheal microbiome. Lactobacillus was the most abundant genus in trachea and caeca and was more abundant in caeca and trachea of HS groups compared with the TN-CONT group. Distinct bacterial clades occupied the caecal and tracheal microbiomes, although some bacterial groups overlapped, demonstrating a core microbiome dominated by Lactobacillus. No positive effects of supplementations were observed on abundance of probiotic bacteria.

The fecal microbiome in cats with diarrhea

Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI) diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21) and cats with acute (n = 19) or chronic diarrhea (n = 29) and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA) effect size (LEfSe) revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration), while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001) altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or therapeutic targets.

Effect of dietary supplementation of prebiotics and probiotics on intestinal microarchitecture in broilers reared under cyclic heat stress

This study was designed to evaluate the effect of dietary supplementation of prebiotics, mannanoligosaccharides (MOS) and/or probiotics (LBP) on intraepithelial lymphocytes (IEL) count, goblet cells (GC) count and differentiation and intestinal micro-architecture in broilers reared under cyclic heat stress. Day-old broilers (n = 250) were randomly divided into five groups. Fifty birds were reared within the thermoneutral zone (TNZ). Remaining birds were subjected to cyclic heat stress from day 21 to 42 (35° C, 75% RH, 8 h/d). The birds were fed corn-soy-based basal diet or the same diet supplemented with 0.5% MOS (HS-MOS), or 0.1% LBP (HS-LBP), or their combination (HS-SYN). The birds were slaughtered on day 42. Tissue samples were collected from mid-duodenum, jejunum and ileum, and stained with haematoxylin and eosin or combined Alcian blue and PAS technique. All differences were considered significant at p < 0.05. The IEL count increased in all intestinal segments of the HS group compared with the TNZ group and decreased in all supplemented groups compared with the HS group. Compared with the TNZ, heat stress reduced villus height, crypt depth and surface area in duodenum and ileum, and increased crypt depth in ileum. Villus width decreased in duodenum and jejunum compared with the TNZ group. Supplementation of LBP, MOS and SYN reversed all these changes in duodenum, while only increased villus height and surface area in ileum. In jejunum, the villus height and surface area increased with HS-LBP, and crypt depth increased with HS-MOS. The number of GC containing acid mucins (duodenum and ileum) and mixed mucins (ileum) were increased in the HS compared with the TNZ. Supplementation of MOS, LBP and SYN maintained the enhanced activity of goblet cells. In conclusion, dietary supplementation of MOS and/or LBP may be helpful in alleviating some of the detrimental effects of heat stress on microstructure of the broiler gut.