P–385 The relationship between systemic oestradiol and vaginal microbiota composition in miscarriage and normal pregnancy

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
H Fourie ◽  
M Al-Memar ◽  
A Smith ◽  
S Ng ◽  
Y Lee ◽  
...  

Abstract Study question Is there an association between serum oestradiol, vaginal microbial composition and pregnancy outcome in the early first trimester? Summary answer In women with a vaginal microbiome deplete of Lactobacillus species at the time of Pregnancy of Uncertain Viability (IPUV), higher serum oestradiol associates with livebirth. What is known already During pregnancy, oestradiol mediates vaginal mucosal properties and increases glycogen deposition in epithelial cells which is thought to support colonisation of Lactobacillus species. Low levels of Lactobacillus associates with adverse outcomes such as miscarriage and preterm birth. The direct relationship between systemic oestradiol and the vaginal microbiome has never been studied in pregnancy. However studies have shown a positive correlation between serum oestrone, vaginal glycogen and Lactobacillus abundance in menopausal women. Study design, size, duration This was a prospective cohort study where one-hundred women were recruited in early pregnancy at the time of IPUV and donated paired blood and vaginal samples. 40 women had an eventual miscarriage, 58 had a livebirth and two pregnancies were terminated. All 100 women donated one paired serum and vaginal sample at this time point, and 22 women with Lactobacillus depletion at the time of IPUV donated further longitudinal vaginal samples. Participants/materials, setting, methods Participants were recruited from an Early Pregnancy Unit and underwent transvaginal ultrasound assessment of their pregnancy. Serum samples were analysed with an immunoassay on a ROCHE COBAS E411 analyser for Oestradiol (pg/ml) and Progesterone (ng/ml). Bacterial DNA was extracted from paired vaginal swabs and sequenced using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Main results and the role of chance Lactobacillus dominance of the vagina was associated with higher serum levels of E2 and progesterone compared to depletion (E2=398pg/ml vs 302pg/ml(p = 0.02), P4=23.1ng/ml vs 17ng/ml(p = 0.02)). E2 and P4 were positively correlated (r = 0.6, p < 0.05). At species level, L. crispatus dominance associated with significantly higher levels of E2 compared to high-diversity communities (468pg/ml vs 302pg/ml(p = 0.03) but no such relationship was observed for P4. Both E2 and P4 levels were lower in women who eventually miscarried. However there was no significant difference in the vaginal bacterial composition at genera or species level at this early gestational age (P = 0.08) regardless of per vaginal bleeding. However in women with Lactobacillus depleted microbiota, livebirth was associated with significantly higher E2 levels compared to women suffering miscarriage (212pg/ml in miscarriage vs 395pg/ml in livebirth, p = 0.003) (OR = 22.4 P = 0.004). In 22 women who had Lactobacillus depletion at the time of IPUV (7 with an eventual outcome of miscarriage, and 15 with an eventual outcome of livebirth), longitudinal vaginal bacterial DNA sequencing was performed. In 7/15 women with livebirth, and higher E2 levels, the microbial composition changed to become more Lactobacillus dominant during pregnancy, whereas in those with miscarriage, only 1/7 changed to become Lactobacillus dominant. Limitations, reasons for caution In this study, serum oestradiol levels were compared to the local vaginal bacterial environment. The ideal would be to study local vaginal oestradiol, glycogen and the bacterial composition. Wider implications of the findings: In contrast to previous studies in menopause where low oestrogen levels associate with the vaginal microbial composition, this study uses the high oestradiol environment of early pregnancy to study the mechanistic relationship between oestradiol and vaginal Lactobacillus abundance. Trial registration number NA

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.


Author(s):  
Shiju Xiao ◽  
Guangzhong Zhang ◽  
Chunyan Jiang ◽  
Xin Liu ◽  
Xiaoxu Wang ◽  
...  

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.


2019 ◽  
Vol 12 ◽  
pp. 194008291987607 ◽  
Author(s):  
Muhammad Tahir Jatoi ◽  
Guoyu Lan ◽  
Zhixiang Wu ◽  
Rui Sun ◽  
Chuan Yang ◽  
...  

This study aimed to compare monoculture and mixed rubber plantations in terms of their soil bacterial and fungal composition. An Illumina MiSeq sequencing analysis was performed to investigate the composition and diversity of the soil bacterial and fungal communities among three different rubber ( Hevea brasiliensis) plantations: monoculture, Mixed 1 ( Hevea brasiliensis and Mytilaria laosensis), and Mixed 2 ( Hevea brasiliensis and Michelia macclurei) in Hainan. The results showed that the bacterial composition of the three rubber plantations was basically similar. However, there was a significant difference in fungal communities among the three rubber plantations at both the phylum and operational taxonomic unit level. The species richness, Chao, and Shannon diversity of bacterial communities of monoculture rubber plantations were higher than the Mixed 1 and Mixed 2 rubber plantations, whereas all diversity indexes of fungal communities were relatively equal for the monoculture and mixed rubber plantations. Soil nutrition (such as total nitrogen and total potassium) and soil pH are the main drivers of the bacterial composition ( p <  .001). However, soil pH and water content are the main drivers of the fungal composition ( p <  .001), and to some extent, soil pH can increase soil bacteria diversity. We suggest that alkaline fertilizers should be applied in mixed rubber plantations to improve the soil pH and, consequently, to increase the total diversity of the rubber plantation.


Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 358
Author(s):  
Pamela Aravena ◽  
Rodrigo Pulgar ◽  
Javiera Ortiz-Severín ◽  
Felipe Maza ◽  
Alexis Gaete ◽  
...  

Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.


2010 ◽  
Vol 1 (2) ◽  
pp. 197-207 ◽  
Author(s):  
W. Fernando ◽  
J. Hill ◽  
G. Zello ◽  
R. Tyler ◽  
W. Dahl ◽  
...  

The effects of diets supplemented with either chickpea or its main oligosaccharide raffinose on the composition of the faecal microbial community were examined in 12 healthy adults (18-65 years) in a randomised crossover intervention study. Subjects consumed their usual diet supplemented with soups and desserts that were unfortified, or fortified with either 200 g/d of canned chickpeas or 5 g/d of raffinose for 3 week periods. Changes in faecal bacterial populations of subjects were examined using 16S rRNA-based terminal restriction fragment length polymorphisms (T-RFLP) and clone libraries generated from the diet pools. Classification of the clone libraries and T-RFLP analysis revealed that Faecalibacterium prausnitzii, reported to be an efficient butyrate producer and a highly metabolically active bacterium in the human intestinal microbiota, was more abundant in the raffinose diet and the chickpea diet compared to the control diet. However, no significant difference was observed in the faecal total short chain fatty acid concentration or in the levels of the components (butyrate, acetate and propionate) with the chickpea diet or the raffinose diet compared to the control diet. Bifidobacterium species were detected by T-RFLP in all three diet groups and quantitative real-time PCR (qPCR) analysis showed a marginal increase in 16S rRNA gene copies of Bifidobacterium with the raffinose diet compared to control (P>0.05). The number of individuals showing TRFs for the Clostridium histolyticum - Clostridum lituseburense groups, which include pathogenic bacteria species and putrefactive bacteria, were lower in the chickpea diet compared to the other two treatments. Diet appeared to affect colonisation by a high ammonia-producing bacterial isolate which was detected in 83%, 92% and 42% of individuals in the control, raffinose and chickpea groups, respectively. Our results indicate that chickpea and raffinose have the potential to modulate the intestinal microbial composition to promote intestinal health in humans.


2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
T Goolam Mahomed ◽  
RPH Peters ◽  
GHJ Pretorius ◽  
A Goolam Mahomed ◽  
V Ueckermann ◽  
...  

Abstract Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.


2021 ◽  
Vol 12 ◽  
Author(s):  
Miriam J. Oost ◽  
Francisca C. Velkers ◽  
Aletta D. Kraneveld ◽  
Koen Venema

The digestive system of the chicken plays an important role in metabolism, immunity, and chicken health and production performance. The chicken ceca harbor a diverse microbial community and play a crucial role in the microbial fermentation and production of energy-rich short-chain fatty acids (SCFA). For humans, dogs, and piglets in vitro digestive system models have been developed and are used to study the microbiota composition and metabolism after intervention studies. For chickens, most research on the cecal microbiota has been performed in in vivo experiments or in static in vitro models that may not accurately resemble the in vivo situations. This paper introduces an optimized digestive system model that simulates the conditions in the ceca of the chicken, i.e., the Chicken ALIMEntary tRact mOdel-2 (CALIMERO-2). The system is based on the well-validated TNO in vitro model of the colon-2 (TIM-2) and is the first dynamic in vitro digestion model for chickens species. To validate this model, the pH, temperature, and different types of microbial feeding were compared and analyzed, to best mimic the conditions in the chicken ceca. The bacterial composition, as well as the metabolite production at 72 h, showed no significant difference between the different microbial feedings. Moreover, we compared the CALIMERO-2 digestive samples to the original inoculum and found some significant shifts in bacterial composition after the fermentation started. Over time the bacterial diversity increased and became more similar to the original inoculum. We can conclude that CALIMERO-2 is reproducible and can be used as a digestive system model for the chicken ceca, in which the microbial composition and activity can be maintained and shows similar results to the in vivo cecum. CALIMERO-2 can be used to study effects on composition and activity of the chicken cecum microbiota in response to in-feed interventions.


Author(s):  
Caspar Bundgaard-Nielsen ◽  
Nadia Ammitzbøll ◽  
Yusuf Abdi Isse ◽  
Abdisalam Muqtar ◽  
Ann-Maria Jensen ◽  
...  

AbstractBackgroundNew sensitive techniques have revealed a large population of bacteria in the human urinary tract, challenging the perception of the urine of healthy humans being sterile. While the role of this urinary microbiota is unknown, dysbiosis has been linked to disorders like urgency urinary incontinence and interstitial cystitis. When comparing studies it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether storage condition or time of collection, had any impact on the urinary microbial composition.ResultsFor comparison of different storage conditions, urine was collected from five healthy adult female donors, and analyzed by 16S rRNA gene sequencing. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in nineteen healthy donors, including four women, five men, five girls, and five boys. With the exception of two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of the urinary microbiota was found to be highly resilient to changes introduced by storage temperature and duration. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys.Together our study supports flexibility in study design, when conducting urinary microbiota studies.Author summaryThe discovery of bacteria native to the urinary tract in healthy people, a location previously believed to be sterile, has prompted research into the clinical potential of these bacteria. However, methodological weaknesses can significantly influence such studies, and thus development of robust techniques for investigating these bacteria are needed. In the present study, we investigated whether differences in storage following collection, could affect the bacterial composition of urine samples. Next, we investigated if this composition exhibited daily or day-to-day variations.Firstly, we found, that the bacterial composition of urine could be maintained by storage at −80 °C, −20 °C, or refrigerated at 4 °C. Secondly, the bacterial composition of urine remained stable over time. Overall, the results of this study provide information important to study design in future investigations into the clinical implications of urinary bacteria.


2019 ◽  
Author(s):  
Ana Elena Pérez-Cobas ◽  
Christophe Ginevra ◽  
Christophe Rusniok ◽  
Sophie Jarraud ◽  
Carmen Buchrieser

ABSTRACTBackgroundLung microbiome analyses have shown that the healthy lung is not sterile but it is colonized like other body sites by bacteria, fungi and viruses. However, little is known about the microbial composition of the lung microbiome during infectious diseases such as pneumonia and how it evolves during antibiotic therapy. To better understand the impact of the composition of the pulmonary microbiome on severity and outcome of pneumonia we analysed the composition and evolution of the human lung microbiome during pneumonia caused by the bacterium Legionella pneumophila.ResultsWe collected 10 bronchoalveolar lavage (BAL) samples from three patients during long-term hospitalisation due to severe pneumonia and performed a longitudinal in-depth study of the composition of their lung microbiome by high-throughput Illumina sequencing of the 16S rRNA gene (bacteria and archaea), ITS region (fungi) and 18S rRNA gene (eukaryotes). We found that the composition of the bacterial lung microbiome during pneumonia is hugely disturbed containing a very high percentage of the pathogen, a very low bacterial diversity, and an increased presence of opportunistic microorganisms such as species belonging to Staphylococcaceae and Streptococcaceae. The microbiome of antibiotic treated patients cured from pneumonia represented a different perturbation state with a higher abundance of resistant bacteria (mainly Firmicutes) and a significantly different bacterial composition as that found in healthy individuals. In contrast, the mycobiome remains more stable during pneumonia and antimicrobial therapy. Interestingly we identified possible cooperation within and between both communities. Furthermore, archaea (Methanobrevibacter) and protozoa (Acanthamoeba and Trichomonas) were detected.ConclusionsBacterial pneumonia leads to a collapse of the healthy microbiome and a strongly disturbed bacterial composition of the pulmonary microbiome that is dominated by the pathogen. Antibiotic treatment allows some bacteria to regrow or recolonize the lungs but the restoration of a healthy lung microbiome composition is only regained a certain time after the antibiotic treatment. Archaea and protozoa should also be considered, as they might be important but yet overseen members of the lung microbiome. Interactions between the micro- and the mycobiome might play a role in the restoration of the microbiome and the clinical evolution of the disease.


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