scholarly journals Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 603
Author(s):  
Miguel Blanco-Fuertes ◽  
Florencia Correa-Fiz ◽  
Lorenzo Fraile ◽  
Marina Sibila ◽  
Virginia Aragon
Keyword(s):  
Pathological Finding ◽  
Systemic Infection ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Mycoplasma Hyorhinis ◽  
Predisposing Factor ◽  
Glässer’S Disease ◽  
Glasser's Disease ◽  
Nasal Microbiota

Fibrinous polyserositis in swine farming is a common pathological finding in nursery animals. The differential diagnosis of this finding should include Glaesserella parasuis (aetiological agent of Glässer’s disease) and Mycoplasma hyorhinis, among others. These microorganisms are early colonizers of the upper respiratory tract of piglets. The composition of the nasal microbiota at weaning was shown to constitute a predisposing factor for the development of Glässer’s disease. Here, we unravel the role of the nasal microbiota in the subsequent systemic infection by M. hyorhinis, and the similarities and differences with Glässer’s disease. Nasal samples from farms with recurrent problems with polyserositis associated with M. hyorhinis (MH) or Glässer’s disease (GD) were included in this study, together with healthy control farms (HC). Nasal swabs were taken from piglets in MH farms at weaning, before the onset of the clinical outbreaks, and were submitted to 16S rRNA gene amplicon sequencing (V3–V4 region). These sequences were analyzed together with sequences from similar samples previously obtained in GD and HC farms. Animals from farms with disease (MH and GD) had a nasal microbiota with lower diversity than those from the HC farms. However, the composition of the nasal microbiota of the piglets from these disease farms was different, suggesting that divergent microbiota imbalances may predispose the animals to the two systemic infections. We also found variants of the pathogens that were associated with the farms with the corresponding disease, highlighting the importance of studying the microbiome at strain-level resolution.

scholarly journals A cross-sectional study of the nasal and fecal microbiota of sows from different health status within six commercial swine farms

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12120
Author(s):  
Andreia G. Arruda ◽  
Loic Deblais ◽  
Vanessa L. Hale ◽  
Christopher Madden ◽  
Monique Pairis-Garcia ◽  
...  
Keyword(s):  
Health Status ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Upper Respiratory Tract ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Swine Farms ◽  
Nasal Microbiota

Background Cull sows are a unique population on swine farms, often representing poor producing or compromised animals, and even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome of the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in fecal and upper respiratory tract microbiota composition for groups of sows of different health status (healthy, cull, and compromised/ clinical sows) and from different farms (1 to 6). Methods Six swine farms were visited once. Thirty individual fecal samples and nasal swabs were obtained at each farm and pooled by five across health status and farm. Samples underwent 16S rRNA gene amplicon sequencing and nasal and fecal microbiota were analyzed using QIIME2 v.2021.4. Results Overall, the diversity of the nasal microbiota was lower than the fecal microbiota (p < 0.01). No significant differences were found in fecal or nasal alpha diversity by sow’s health status or by farm. There were significant differences in nasal microbial composition by farm and health status (PERMANOVA, p < 0.05), and in fecal microbiota by farm (PERMANOVA, p < 0.05), but not by health status. Lastly, at the L7 level, there was one differentially abundant taxa across farms for each nasal and fecal pooled samples. Discussion This study provided baseline information for nasal and fecal microbiota of sows under field conditions, and results suggest that farm of origin can affect microbial diversity and composition. Furthermore, sow’s health status may have an impact on the nasal microbiota composition.

scholarly journals The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network

2021 ◽  
Vol 2 ◽  
Author(s):  
Malik Aydin ◽  
Cornelius Weisser ◽  
Olivier Rué ◽  
Mahendra Mariadassou ◽  
Sandra Maaß ◽  
...  
Keyword(s):  
Bacterial Abundance ◽  
Amplicon Sequencing ◽  
Nasopharyngeal Swab ◽  
Rrna Gene ◽  
Cell Integrity ◽  
Α Diversity ◽  
Children With Asthma ◽  
16 S Rrna ◽  
Nasal Microbiota ◽  
Insight Into

Although the nose, as a gateway for organism–environment interactions, may have a key role in asthmatic exacerbation, the rhinobiome of exacerbated children with asthma was widely neglected to date. The aim of this study is to understand the microbiome, the microbial immunology, and the proteome of exacerbated children and adolescents with wheeze and asthma. Considering that a certain proportion of wheezers may show a progression to asthma, the comparison of both groups provides important information regarding clinical and phenotype stratification. Thus, deep nasopharyngeal swab specimens, nasal epithelial spheroid (NAEsp) cultures, and blood samples of acute exacerbated wheezers (WH), asthmatics (AB), and healthy controls (HC) were used for culture (n = 146), 16 S-rRNA gene amplicon sequencing (n = 64), and proteomic and cytokine analyses. Interestingly, Proteobacteria were over-represented in WH, whereas Firmicutes and Bacteroidetes were associated with AB. In contrast, Actinobacteria commonly colonized HCs. Moreover, Staphylococcaceae, Enterobacteriaceae, Burkholderiaceae, Xanthobacteraceae, and Sphingomonadaceae were significantly more abundant in AB compared to WH and HC. The α-diversity analyses demonstrated an increase of bacterial abundance levels in atopic AB and a decrease in WH samples. Microbiome profiles of atopic WH differed significantly from atopic AB, whereby atopic samples of WH were more homogeneous than those of non-atopic subjects. The NAEsp bacterial exposure experiments provided a disrupted epithelial cell integrity, a cytokine release, and cohort-specific proteomic differences especially for Moraxella catarrhalis cultures. This comprehensive dataset contributes to a deeper insight into the poorly understood plasticity of the nasal microbiota, and, in particular, may enforce our understanding in the pathogenesis of asthma exacerbation in childhood.

scholarly journals Development and application of an antibody detection ELISA for Haemophilus parasuis based on a monomeric autotransporter passenger domain

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Yunbao Liu ◽  
Yujiao Du ◽  
Yuping Song ◽  
Yang Tian ◽  
Yi Qi ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Large Scale ◽  
Disease Diagnosis ◽  
Antibody Detection ◽  
Haemophilus Parasuis ◽  
Upper Respiratory Tract ◽  
Serum Samples ◽  
Passenger Domain ◽  
Glässer’S Disease ◽  
Glasser's Disease

Abstract Background Haemophilus parasuis is a commensal pathogen in the swine upper respiratory tract and causes Glässer’s disease. Surveillance, screening for infection, and vaccination response of H. parasuis is hindered by the lack of a rapid antibody detection method. Results In the present study, a monomeric autotransporter was identified as a novel antigen for developing an indirect ELISA. The autotransporter passenger domain (Apd) was expressed, purified, and demonstrated to be specific in ELISA and western blotting. Mouse antiserum of recombinant Apd (rApd) recognized native Apd in the 15 serotype reference strains and five non-typeable isolate stains, but showed no reaction with seven other bacterial pathogens. The rApd ELISA was optimized and validated using 67 serum samples with known background, including 27 positive sera from experimentally infected and vaccinated pigs along with 40 negative sera that had been screened with H. parasuis whole cell ELISA from clinically healthy herds. The rApd ELISA provided positive and negative percent agreements of 96.4 and 94.9%, respectively, and an AUC value of 0.961, indicating that the assay produced accurate results. Conclusion Apd was a universal antigen component among 15 serotype and non-typeable strains of H. parasuis and was also specific to this pathogen. The rApd ELISA could detect antibodies elicited by H. parasuis infection and vaccination, thereby exhibiting the potential to be applied for Glässer’s disease diagnosis, H. parasuis vaccination evaluation, and large-scale serological surveillance.

scholarly journals Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection

2020 ◽  
Author(s):  
Sai N. Nimmagadda ◽  
Firas S. Midani ◽  
Heather Durand ◽  
Aspen T. Reese ◽  
Caitlin C. Murdoch ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Healthy Human ◽  
Human Volunteers ◽  
Before And After ◽  
Rrna Gene Sequencing ◽  
Nasal Microbiota

ABSTRACTBackgroundHow human-associated microbial communities resist and respond to perturbations remains incompletely understood. Viral challenge provides one opportunity to test how human microbiota respond to disturbance.MethodsUsing an experimental human rhinovirus infection challenge model, we explored how viral infection may alter microbiota of the upper respiratory tract (URT). Healthy human volunteers were inoculated with HRV serotype 39. Samples were collected by lavage before and after inoculation from healthy (sham inoculated, n=7) and infected (n=15) individuals and subjected to 16S rRNA gene sequencing through amplification of the V4 hypervariable region.ResultsNo evidence for differences in community alpha-diversity between cohorts was observed. The composition of microbiota of sham-treated and infected subjects did not appear distinguishable and no taxa were significantly associated with infection status. We did not observe support for a correlation between microbial dynamics and counts of specific monocytes. Subject identity was found to be the strongest determinant of community structure in our dataset.ConclusionsOverall, our findings do not suggest a consistent nasopharyngeal microbiota response to rhinovirus challenge. We support the conclusion that this microbial community is individualized. Broadly, our findings contribute to our understanding of how and when immune responses to viruses affect bacterial communities in the URT.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children

2021 ◽  
Author(s):  
Andrea Coleman ◽  
Seweryn Bialasiewicz ◽  
Robyn L Marsh ◽  
Eva Grahn Håkansson ◽  
Kyra Cottrell ◽  
...  
Keyword(s):  
Healthy Children ◽  
Upper Respiratory Tract ◽  
Indigenous Australian ◽  
Ionization Time ◽  
Australian Aboriginal ◽  
Flight Mass Spectrometry ◽  
Upper Respiratory ◽  
Corynebacterium Pseudodiphtheriticum ◽  
Nasal Microbiota ◽  
Respiratory Microbiota

Abstract Background We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. Methods In total, 103 Indigenous Australian children aged 2–7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children’s ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. Results Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P &lt; .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P &lt; .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. Conclusions Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.

scholarly journals Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

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