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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 -
Frontiers in Neuroscience 2022To characterize the intestinal flora of patients with epilepsy and its correlation with epilepsy.
OBJECTIVE
To characterize the intestinal flora of patients with epilepsy and its correlation with epilepsy.
METHODS
Patients with ages > 18 years were consecutively enrolled from the outpatient department, Affiliated Hospital of Guizhou Medical University from January 2018 to December 2019. A total of 71 subjects were recruited, including epilepsy patients ( = 41) as an observation group and patient family members ( = 30) as a control group. Fresh stool specimens of all the subjects were collected. The 16S ribosomal RNA sequencing was analyzed to determine changes in intestinal flora composition and its correlation with epilepsy. Subgroup analysis was then conducted. All patients with epilepsy were divided into an urban group ( = 21) and a rural group ( = 20) according to the region, and bioinformatics analyses were repeated between subgroups.
RESULTS
LEfSe analysis showed that , , , and had relatively increased abundance in the epilepsy group at the genus level. Correlation analysis suggested that sp. ( = 0.584, < 0.01), ( = 0.560, < 0.01), ( = 0.541, < 0.01), and ( = 0.506, < 0.01) were significantly positively correlated with the occurrence of epilepsy ( ≥ 0.5, < 0.05). PICRUSt function prediction analysis showed that there were significant differences in 16 pathways between the groups at level 3. Comparing the rural group with the urban group, increased at the phylum level and , , , and increased at the species level in the rural group.
CONCLUSION
There were significant differences in the composition and functional pathways of gut flora between epilepsy patients and patient family members. The may become a potential biomarker for the diagnosis of epilepsy.
PubMed: 35250450
DOI: 10.3389/fnins.2022.803538 -
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 -
Frontiers in Cellular and Infection... 2022The Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) emerged in late December 2019. Considering the important...
INTRODUCTION
The Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) emerged in late December 2019. Considering the important role of gut microbiota in maturation, regulation, and induction of the immune system and subsequent inflammatory processes, it seems that evaluating the composition of gut microbiota in COVID-19 patients compared with healthy individuals may have potential value as a diagnostic and/or prognostic biomarker for the disease. Also, therapeutic interventions affecting gut microbial flora may open new horizons in the treatment of COVID-19 patients and accelerating their recovery.
METHODS
A systematic search was conducted for relevant studies published from December 2019 to December 2021 using Pubmed/Medline, Embase, and Scopus. Articles containing the following keywords in titles or abstracts were selected: "SARS-CoV-2" or "COVID-19" or "Coronavirus Disease 19" and "gastrointestinal microbes" or "dysbiosis" or "gut microbiota" or "gut bacteria" or "gut microbes" or "gastrointestinal microbiota".
RESULTS
Out of 1,668 studies, 22 articles fulfilled the inclusion criteria and a total of 1,255 confirmed COVID-19 patients were examined. All included studies showed a significant association between COVID-19 and gut microbiota dysbiosis. The most alteration in bacterial composition of COVID-19 patients was depletion in genera , , , , , , , and and enrichment of , , , , , , and Also, some gut microbiome alterations were associated with COVID-19 severity and poor prognosis including the increment of , , , , , , , , , , and spp. and the decrement of , , , , and the Firmicutes/Bacteroidetes ratio.
CONCLUSION
Our study showed a significant change of gut microbiome composition in COVID-19 patients compared with healthy individuals. This great extent of impact has proposed the gut microbiota as a potential diagnostic, prognostic, and therapeutic strategy for COVID-19. There is much evidence about this issue, and it is expected to be increased in near future.
Topics: COVID-19; Dysbiosis; Gastrointestinal Microbiome; Humans; Prognosis; SARS-CoV-2
PubMed: 35310853
DOI: 10.3389/fcimb.2022.804644 -
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 Cellular and Infection... 2021The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a...
BACKGROUND
The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.
OBJECTIVE
Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.
METHODS
Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.
RESULTS
Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of (p-value <0.02), sp (p-value0.05), (p-value= 0.01) and (p-value0.0001) were identified in preterm samples whereas higher abundance of (p-value =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of , and sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of and indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of and in reducing the risk of PTB.
CONCLUSION
Our findings indicate that the dominance of specific species and few other facultative anaerobes are associated with birth outcomes.
Topics: Female; Fusobacteria; Humans; India; Infant, Newborn; Lactobacillus; Pregnancy; Premature Birth; RNA, Ribosomal, 16S; Vagina
PubMed: 34094994
DOI: 10.3389/fcimb.2021.622474