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Signal Transduction and Targeted Therapy May 2021COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity....
COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients, 29 influenza B patients, and 28 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium, Rothia, and Streptococcus. Based on the relative abundance of the oropharyngeal microbiome, we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889, in which Veillonella was identified as the most prominent biomarker for COVID-19 group. Several members of the genus Veillonella, especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients, were also overrepresented in the BALF of COVID-19 patients, indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients. We also found the increased ratios of Klebsiella sp., Acinetobacter sp., and Serratia sp. were correlated with both disease severity and elevated systemic inflammation markers (neutrophil-lymphocyte ratio, NLR), suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response. Moreover, the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism. In addition, all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group, and were significantly enriched in critical cases. In conclusion, we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.
Topics: Adult; Bacteria; COVID-19; Female; Humans; Male; Metagenomics; Microbiota; Middle Aged; Oropharynx; SARS-CoV-2
PubMed: 33986253
DOI: 10.1038/s41392-021-00614-3 -
Genes Feb 2022Polycystic ovary syndrome (PCOS) is a very common endocrine condition in women in India. Gut microbiome alterations were shown to be involved in PCOS, yet it is...
Polycystic ovary syndrome (PCOS) is a very common endocrine condition in women in India. Gut microbiome alterations were shown to be involved in PCOS, yet it is remarkably understudied in Indian women who have a higher incidence of PCOS as compared to other ethnic populations. During the regional PCOS screening program among young women, we recruited 19 drug naive women with PCOS and 20 control women at the Sher-i-Kashmir Institute of Medical Sciences, Kashmir, North India. We profiled the gut microbiome in faecal samples by 16S rRNA sequencing and included 40/58 operational taxonomic units (OTUs) detected in at least 1/3 of the subjects with relative abundance (RA) ≥ 0.1%. We compared the RAs at a family/genus level in PCOS/non-PCOS groups and their correlation with 33 metabolic and hormonal factors, and corrected for multiple testing, while taking the variation in day of menstrual cycle at sample collection, age and BMI into account. Five genera were significantly enriched in PCOS cases: , , and previously reported for PCOS , and confirmed by different statistical models. At the family level, the relative abundance of was enriched, whereas was decreased among cases. We observed increased relative abundance of and with higher fasting blood glucose levels, and and with larger hip, waist circumference, weight, and with lower prolactin levels. We also detected a novel association between and follicle-stimulating hormone levels and between and alkaline phosphatase, independently of the BMI of the participants. Our report supports that there is a relationship between gut microbiome composition and PCOS with links to specific reproductive health metabolic and hormonal predictors in Indian women.
Topics: Bacteroidetes; Bifidobacterium; Feces; Female; Gastrointestinal Microbiome; Humans; Polycystic Ovary Syndrome; RNA, Ribosomal, 16S
PubMed: 35205422
DOI: 10.3390/genes13020379 -
Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions.Microorganisms Sep 2022High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and... (Review)
Review
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla , , , , , and . Among the African population, the typical members of the microbiota are and . The gut microbiome of Asians is very diverse and rich in members of the genera , , , , , , , and . Among Buddhists and Muslims, the enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn's disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.
PubMed: 36144468
DOI: 10.3390/microorganisms10091866 -
Microbiology Spectrum Jun 2023Recent evidence emphasized the role of the microbiota in the etiopathogenesis of rheumatoid arthritis (RA). Indeed, it has been demonstrated that urinary tract...
Recent evidence emphasized the role of the microbiota in the etiopathogenesis of rheumatoid arthritis (RA). Indeed, it has been demonstrated that urinary tract infections are implicated in RA pathogenesis. However, a definitive association between the urinary tract microbiota and RA remains to be investigated. Urine samples from 39 patients affected by RA, including treatment-naive patients, and 37 age- and sex-matched healthy individuals were collected. In RA patients, the urinary microbiota showed an increase in microbial richness and a decrease in microbial dissimilarity, especially in treatment-naive patients. A total of 48 altered genera with different absolute quantities were detected in patients with RA. The 37 enriched genera included Proteus, , and , while the 11 deficient genera included , , , and . Notably, the more abundant genera in RA patients were correlated with the disease activity score of 28 joints-erythrocyte sedimentation rates (DAS28-ESR) and an increase in plasma B cells. Furthermore, the altered urinary metabolites, such as proline, citric acid, and oxalic acid, were positively associated with RA patients, and they were closely correlated with urinary microbiota. These findings suggested a strong association between the altered urinary microbiota and metabolites with disease severity and dysregulated immune responses in RA patients. We revealed that the profile of the urinary tract microbiota in RA featured with increased microbial richness and shifted taxa, associated with immunological and metabolic changes of the disease, underlining the interplay between urinary microbiota and host autoimmunity.
Topics: Humans; Arthritis, Rheumatoid; Microbiota; Gastrointestinal Microbiome; Patient Acuity; Immunity
PubMed: 37227288
DOI: 10.1128/spectrum.03662-22 -
Scientific Reports Nov 2020Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary...
Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary microbiome composition and body weight is unclear. Herein we investigate this relation by analyzing saliva samples from 35 adult patients with obesity undergoing bariatric surgery. Our aim was to describe salivary microbiome changes during body weight loss on an individual-specific level, and to elucidate the effect of bariatric surgery on the salivary microbiome which has not been studied before. Analysis of samples collected before and 1 day after surgery, as well as 3 and 12 months after surgery, showed that the salivary microbiome changed in all study participants, but these changes were heterogeneous. In the majority of participants proportions of Gemella species, Granulicatella elegans, Porphyromonas pasteri, Prevotella nanceiensis and Streptococcus oralis decreased, while Veillonella species, Megasphaera micronuciformis and Prevotella saliva increased. Nevertheless, we found participants deviating from this general trend which suggests that a variety of individual-specific factors influence the salivary microbiome composition more effectively than the body weight dynamics alone. The observed microbiome alternations could be related to dietary changes. Therefore, further studies should focus on association with altered taste preferences and potential oral health consequences.
Topics: Adult; Bacteria; Bariatric Surgery; Female; Humans; Male; Metagenome; Microbiota; Middle Aged; Obesity; RNA, Ribosomal, 16S; Saliva
PubMed: 33208788
DOI: 10.1038/s41598-020-76991-6 -
Animal Microbiome Oct 2021The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify...
BACKGROUND
The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs.
RESULTS
To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h; proportion of phenotypic variance explained by the host genetics) and microbiability (m; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m (0.275) compared to h (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively.
CONCLUSIONS
Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs.
PubMed: 34689834
DOI: 10.1186/s42523-021-00138-9 -
Frontiers in Microbiology 2019has a positive effect on the host intestinal microbiota. In piglets, dietary supplementation with affects general health and plays an important role in nutrient...
has a positive effect on the host intestinal microbiota. In piglets, dietary supplementation with affects general health and plays an important role in nutrient digestion and fermentation. However, this association requires further investigation. Here, we studied newborn piglets from 12 litters. The nursed piglets were given a creep feed beginning on day 10 and weaned at day 30. Piglets were fed either a control basic diet or a diet including supplementation with ZLR003 at 6.0 × 10 CFU/g feed. At day 30 and 60, feces samples were taken and used for sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. At day 60, feces samples and serum samples were also taken and used to measure the short chain fatty acids (SCFAs) and to detect long chain fatty acids (LCFAs) and free amino acids (FAAs), respectively. The results revealed that ZLR003 could improve piglet fecal microbiota composition, especially at the end of weaned period. The concentrations of lactic acid and butyric acid in feces were higher, and acetic acid concentration was lower in the ZLR003 group compared with the control group ( < 0.05). The serum polyunsaturated fatty acids C18:2n6c, C18:3n3, C20:4n6, and C22:6n3 were significantly higher ( < 0.05), as were the serum FAAs Gly, Ala, Val, Iso, Asn, Asp, Glu, Met, Phe, and Leu ( < 0.05), in the group compared with the control group. A correlation analysis revealed that the genera _UCG-010 and _UCG-014 had a negative correlation with the SCFAs content in feces, the genus _9 had a higher positive correlation with C18:2n6c, and the genera and had a more positive significant effect on the serum FAAs content in weaned piglets in the ZLR003 group compared with the control group. In conclusion, ZLR003 influenced the fecal microbiota composition of piglets, and its effects were related to the metabolism of SCFAs, LCFAs, and FAAs. Our findings will help facilitate the application of strains in pig production.
PubMed: 31040835
DOI: 10.3389/fmicb.2019.00785 -
Foods (Basel, Switzerland) Nov 2022The appropriate domestic cooking methods can retain and protect the biological properties of foods well. Thus, the objective of this study was to unravel the effect of...
The appropriate domestic cooking methods can retain and protect the biological properties of foods well. Thus, the objective of this study was to unravel the effect of different cooking methods on the microbiota modulatory properties of yam and their non-starch polysaccharides by an in vitro simulated digestion and fermentation model. The results showed that different cooking processes led to different changes in polysaccharide content. The polysaccharide content of yam increased by 21.3~108.2% or decreased by 12.0% compared with that of raw yam. Additionally, the soluble polysaccharides contents in all cooked yam samples significantly increased by 16.85~119.97% after in vitro digestion. The regulation of whole-yam digesta on gut microbiota was partly related with yam polysaccharides. Both yam and yam polysaccharide fermentation appeared to promote beneficial bacteria, such as , spp. and and suppressed bacterial pathogens such as and . Household cooking significantly influenced the prebiotic performances of yam and yam polysaccharides by changing the heat-sensitive microbial substrates and their physiology properties. According to our results, normal-pressure steaming and normal-pressure boiling processes can retain the microbiota modulatory effects of Chinese yam.
PubMed: 36496601
DOI: 10.3390/foods11233794 -
Frontiers in Microbiology 2021Acute myocardial infarction (AMI) continues as the main cause of morbidity and mortality worldwide. Interestingly, emerging evidence highlights the role of gut...
Acute myocardial infarction (AMI) continues as the main cause of morbidity and mortality worldwide. Interestingly, emerging evidence highlights the role of gut microbiota in regulating the pathogenesis of coronary heart disease, but few studies have systematically assessed the alterations and influence of gut microbiota in AMI patients. As one approach to address this deficiency, in this study the composition of fecal microflora was determined from Chinese AMI patients and links between gut microflora and clinical features and functional pathways of AMI were assessed. Fecal samples from 30 AMI patients and 30 healthy controls were collected to identify the gut microbiota composition and the alterations using bacterial 16S rRNA gene sequencing. We found that gut microflora in AMI patients contained a lower abundance of the phylum and a slightly higher abundance of the phylum compared to the healthy controls. Chao1 ( = 0.0472) and PD-whole-tree ( = 0.0426) indices were significantly lower in the AMI versus control group. The AMI group was characterized by higher levels of the genera , , , and , and lower levels of , , , , and as compared to that in the healthy controls ( < 0.05). The common metabolites of these genera are mostly short-chain fatty acids, which reveals that the gut flora is most likely to affect the occurrence and development of AMI through the short-chain fatty acid pathway. In addition, our results provide the first evidence revealing remarkable differences in fecal microflora among subgroups of AMI patients, including the STEMI vs. NSTEMI, IRA-LAD vs. IRA-Non-LAD and Multiple (≥2 coronary stenosis) vs. Single coronary stenosis groups. Several gut microflora were also correlated with clinically significant characteristics of AMI patients, including LVEDD, LVEF, serum TnI and NT-proBNP, Syntax score, counts of leukocytes, neutrophils and monocytes, and fasting serum glucose levels. Taken together, the data generated enables the prediction of several functional pathways as based on the fecal microfloral composition of AMI patients. Such information may enhance our comprehension of AMI pathogenesis.
PubMed: 34295318
DOI: 10.3389/fmicb.2021.680101 -
Metabolites Jun 2021Halitosis is mainly caused by the action of oral microbes. The purpose of this study was to investigate the differences in salivary microbes and metabolites between...
Halitosis is mainly caused by the action of oral microbes. The purpose of this study was to investigate the differences in salivary microbes and metabolites between subjects with and without halitosis. Of the 52 participants, 22 were classified into the halitosis group by the volatile sulfur compound analysis on breath samples. The 16S rRNA gene amplicon sequencing and metabolomics approaches were used to investigate the difference in microbes and metabolites in saliva of the control and halitosis groups. The profiles of microbiota and metabolites were relatively different between the halitosis and control groups. The relative abundances of , , and were significantly higher in the halitosis group. In contrast, the relative abundances of , , and were considerably higher in the control group. The levels of 5-aminovaleric acid and n-acetylornithine were significantly higher in the halitosis group. The correlation between identified metabolites and microbiota reveals that and might be related to the cadaverine and putrescine pathways that cause halitosis. This study could provide insight into the mechanisms of halitosis.
PubMed: 34200451
DOI: 10.3390/metabo11060362