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Bioengineering (Basel, Switzerland) Aug 2022Recent studies have revealed that LuxS/AI-2 quorum sensing (QS) is the most universal cell-to-cell communication in rumen bacteria; however, it remains unknown how they...
Recent studies have revealed that LuxS/AI-2 quorum sensing (QS) is the most universal cell-to-cell communication in rumen bacteria; however, it remains unknown how they respond to nutritional stress from a diet shift. This study aimed to explore whether a diet shift could trigger rumen bacterial LuxS/AI-2 QS and its influences on rumen fermentation characteristics and bacterial community diversity and composition. A total of fifteen Hu sheep were selected to undergo a pre-shift diet (Pre, concentrate to forage ratio 75:25) for one month and then abruptly switch to a post-shift diet (Post, concentrate to forage ratio 49:51). Results showed that the serum cortisol and immunoglobulin G concentrations were higher in Post than in Pre (p < 0.05). The microbial density, AI-2 concentration, biofilm formation, and the gene expression of ftsH were higher in Post when compared with Pre (p < 0.05), whilst the gene expression of luxS tended to be lower in Post (p = 0.054). The molar concentration of valerate and fermentation efficiency decreased after the diet shift, while the acetate to propionate ratio and the molar proportion of butyrate were higher in Post compared to Pre (p < 0.05). Moreover, the diet shift increased the richness of ruminal bacteria and the relative abundances of Roseburia, Prevotellaceae UCG-001, and Lachnospira, and decreased the relative abundances of Prevotella, Megasphaera, and Dialister (p < 0.05). A difference in trends was also observed in an analysis of similarity (R = 0.1208 and p = 0.064). This study suggests that a diet shift could trigger rumen bacterial LuxS/AI-2 QS by altering microbial density, AI-2 concentration, biofilm formation, and related gene expression, as well as affect the rumen fermentation pattern and bacterial community diversity and composition. This study may provide insight into a potential strategy for relieving nutritional stress via regulating bacterial communication.
PubMed: 36004904
DOI: 10.3390/bioengineering9080379 -
Gut-microbiome-based predictive model for ST-elevation myocardial infarction in young male patients.Frontiers in Microbiology 2022ST-segment elevation myocardial infarction (STEMI) in young male patients accounts for a significant proportion of total heart attack events. Therefore, clinical...
BACKGROUND
ST-segment elevation myocardial infarction (STEMI) in young male patients accounts for a significant proportion of total heart attack events. Therefore, clinical awareness and screening for acute myocardial infarction (AMI) in asymptomatic patients at a young age is required. The gut microbiome is potentially involved in the pathogenesis of STEMI. The aim of the current study is to develop an early risk prediction model based on the gut microbiome and clinical parameters for this population.
METHODS
A total of 81 young males (age < 44 years) were enrolled in this study. Forty-one young males with STEMI were included in the case group, and the control group included 40 young non-coronary artery disease (CAD) males. To identify the differences in gut microbiome markers between these two groups, 16S rRNA-based gut microbiome sequencing was performed using the Illumina MiSeq platform. Further, a nomogram and corresponding web page were constructed. The diagnostic efficacy and practicability of the model were analyzed using K-fold cross-validation, calibration curves, and decision curve analysis (DCA).
RESULTS
Compared to the control group, a significant decrease in tendency regarding α and β diversity was observed in patients in the case group and identified as a significantly altered gut microbiome represented by and . Regarding clinical parameters, compared to the control group, the patients in the case group had a higher body mass index (BMI), systolic blood pressure (SBP), triglyceride (TG), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) and low blood urea nitrogen (BUN). Additionally, BMI and SBP were significantly (p<0.05) positively correlated with and . Further, BMI and SBP were significantly (p<0.05) negatively correlated with and . A significant negative correlation was only observed between and AST ( < 0.05). Finally, an early predictive nomogram and corresponding web page were constructed based on the gut microbiome and clinical parameters with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.877 and a C-index of 0.911. For the internal validation, the stratified -fold cross-validation ( = 3) was as follows: AUC value of 0.934. The calibration curves of the model showed good consistency between the actual and predicted probabilities. The DCA results showed that the model had a high net clinical benefit for use in the clinical setting.
CONCLUSION
In this study, we combined the gut microbiome and common clinical parameters to construct a prediction model. Our analysis shows that the constructed model is a non-invasive tool with potential clinical application in predicting STEMI in the young males.
PubMed: 36532426
DOI: 10.3389/fmicb.2022.1031878 -
Microbial Genomics Dec 2021The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual...
The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well characterized. Here, we examine two vaginal bacterial taxa grouped within the genus that have been previously associated with bacterial vaginosis (BV) and pregnancy complications. Phylogenetic analyses support the classification of these taxa as two distinct species. These two phylotypes, phylotype 1 (MP1) and phylotype 2 (MP2), differ in genomic structure and metabolic potential, suggestive of differential roles within the vaginal environment. Further, these vaginal taxa show evidence of genome reduction and changes in DNA base composition, which may be common features of host dependence and/or adaptation to the vaginal environment. In a cohort of 3870 women, we observed that MP1 has a stronger positive association with bacterial vaginosis whereas MP2 was positively associated with trichomoniasis. MP1, in contrast to MP2 and other common BV-associated organisms, was not significantly excluded in pregnancy. In a cohort of 52 pregnant women, MP1 was both present and transcriptionally active in 75.4 % of vaginal samples. Conversely, MP2 was largely absent in the pregnant cohort. This study provides insight into the evolutionary history, genomic potential and predicted functional role of two clinically relevant vaginal microbial taxa.
Topics: Bacterial Proteins; Base Composition; Case-Control Studies; Evolution, Molecular; Female; Gene Expression Regulation, Bacterial; Genome Size; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Humans; Megasphaera; Phylogeny; Pregnancy; RNA, Ribosomal, 16S; Reproductive Health; Sequence Analysis, DNA; Vagina; Vaginosis, Bacterial
PubMed: 34898422
DOI: 10.1099/mgen.0.000526 -
Schizophrenia Bulletin Sep 2023Intestinal microbiota is intrinsically linked to human health. Evidence suggests that the composition and function of the microbiome differs in those with schizophrenia... (Meta-Analysis)
Meta-Analysis
BACKGROUND AND HYPOTHESIS
Intestinal microbiota is intrinsically linked to human health. Evidence suggests that the composition and function of the microbiome differs in those with schizophrenia compared with controls. It is not clear how these alterations functionally impact people with schizophrenia. We performed a systematic review and meta-analysis to combine and evaluate data on compositional and functional alterations in microbiota in patients with psychosis or schizophrenia.
STUDY DESIGN
Original studies involving humans and animals were included. The electronic databases PsycINFO, EMBASE, Web of Science, PubMed/MEDLINE, and Cochrane were systematically searched and quantitative analysis performed.
STUDY RESULTS
Sixteen original studies met inclusion criteria (1376 participants: 748 cases and 628 controls). Ten were included in the meta-analysis. Although observed species and Chao 1 show a decrease in diversity in people with schizophrenia compared with controls (SMD = -0.14 and -0.66 respectively), that did not reach statistical significance. We did not find evidence for variations in richness or evenness of microbiota between patients and controls overall. Differences in beta diversity and consistent patterns in microbial taxa were noted across studies. We found increases in Bifidobacterium, Lactobacillus, and Megasphaera in schizophrenia groups. Variations in brain structure, metabolic pathways, and symptom severity may be associated with compositional alterations in the microbiome. The heterogeneous design of studies complicates a similar evaluation of functional readouts.
CONCLUSIONS
The microbiome may play a role in the etiology and symptomatology of schizophrenia. Understanding how the implications of alterations in microbial genes for symptomatic expression and clinical outcomes may contribute to the development of microbiome targeted interventions for psychosis.
Topics: Humans; Schizophrenia; Gastrointestinal Microbiome; Psychotic Disorders
PubMed: 37210594
DOI: 10.1093/schbul/sbad049 -
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