scholarly journals Metagenomic Anaysis of Nasal Microbiota-Derived Extracellular Vesicle in Patients with Allergic Rhinitis.

2021 ◽  
Author(s):  
Tsai-Yeh Chiang ◽  
Yu-Ru Yang ◽  
Ming-Ying Zhuo ◽  
Feng Yang ◽  
Ying-Fei Zhang ◽  
...  
Keyword(s):  
Allergic Rhinitis ◽  
Metabolic Pathways ◽  
Beta Diversity ◽  
Immunoglobulin E ◽  
Alpha Diversity ◽  
Specific Pattern ◽  
Total Serum ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Nasal Microbiota

Abstract Nasal Microbiota is crucial for the pathogenesis of allergic rhinitis (AR). However, never study investigates the microbiota in nasal extracellular vesicles (EVs). Objective: We aim to compare the microbiome composition and diversity in EVs between AR and health controls (HCs), and reveal the potential metabolic mechanisms in AR. Eosinophil count and serum immunoglobulin E (IgE) were measured in AR patients (n=20) and HCs (n=19). Nasal EVs were identified by transmission electron microscopy and flow cytometry. 16S rRNA sequencing was used to profile microbial communities. Alpha and beta diversity were analyzed to reflect the microbial diversity. Taxonomic abundance was analyzed based on linear discriminant analysis effect size (LEfSe). Microbial metabolic pathways were characterized using PICRUSt and KEGG analyses. Eosinophils, total serum IgE, and specific IgE to Dermatophagoides were increased in AR patients. Alpha diversity in nasal EVs from AR patients were lower than that in HCs. Beta diversity showed the microbiome differences between AR and HCs. Microbial abundance was distinct between AR and HCs at different taxonomic levels. The significant higher level of genera Acetobacter, Mycoplasma, Escherichia and Halomonas in AR patients than those in HCs. Conversely, the genera Zoogloea, Streptococcus, Burkholderia as well as Pseudomonas were more abundant in the HCs group. Moreover, 35 microbial metabolic pathways were different between AR and HCs, and 25 pathways were more abundant in AR. AR patients had distinguished microbiota characteristics in nasal EVs compared with HCs. The metabolic mechanisms of microbiota regulating AR development also altered. The nasal fluid may reflect the specific pattern of microbiome EVs in patients with AR.

scholarly journals Correlation between adenotonsillar microbiome and clinical characteristics of pediatrics with snoring: a preliminary study

2020 ◽  
Author(s):  
Kyung Soo Kim ◽  
Hyun Jin Min
Keyword(s):  
Beta Diversity ◽  
Clinical Characteristics ◽  
Pediatric Patients ◽  
Immunoglobulin E ◽  
Alpha Diversity ◽  
Total Serum ◽  
Cross Sectional ◽  
Alpha And Beta Diversity ◽  
Obstructive Sleep ◽  
Subjective Discomfort

Objectives: The paired microbiome of adenoids and tonsils in pediatric patients with snoring has rarely been reported, and its correlation with clinical characteristics has not been evaluated. The aim of this study was to identify the adenotonsillar microbiome and determine its correlation with the subjective symptoms of pediatric patients with snoring and regional mucosal immune molecules.Methods: Twenty-four children who underwent tonsillectomy with adenoidectomy because of snoring were enrolled in a cross-sectional study performed between August 2017 and December 2018. The adenoid and tonsil microbiomes and their alpha- and beta-diversity were determined. Clinical characteristics, including subjective discomfort during sleep [obstructive sleep apnea (OSA)-18 questionnaire], presence of allergic rhinitis, concentrations of heat shock protein (Hsp) 27, Hsp70, and interleukin-8 (IL-8) in lavage fluids, and whole blood cell (WBC) counts were measured.Results: At the phylum level, the microbiome was not significantly different between the adenoids and tonsils. Alpha and beta indices were not significantly different between the adenoid and tonsil. Alpha-diversity of the entire adenotonsillar microbiome was associated with sex, emotional stress, and IL-8 levels in the tonsil lavage fluids. Beta-diversity of the entire adenotonsillar microbiome was associated with Hsp27 levels in the tonsil lavage fluids and WBC counts. Results of the multiple allergen simultaneous tests were not significant, but total serum immunoglobulin E levels were significantly associated with the beta-diversity of the adenotonsillar microbiome.Conclusion: These data suggest for the first time that the adenotonsillar microbiome interacts with the regional mucosal immune system. Furthermore, the association of the microbiome with subjective discomfort is a unique observation and warrants further investigation

scholarly journals Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

2021 ◽  
Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  
Keyword(s):  
Infant Formula ◽  
Beta Diversity ◽  
Milk Fat ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Term Infants ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

scholarly journals AB1232 ORAL DYSBIOSIS REFLECTS THE IMMUNOLOGICAL ALTERATION OF RA REGARDING TO ACPA AND HLA DRB1*SE: NAGASAKI ISLAND STUDY

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1907.2-1907
Author(s):  
Y. Tsuji ◽  
M. Tamai ◽  
S. Morimoto ◽  
D. Sasaki ◽  
M. Nagayoshi ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Healthy Subjects ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Unifrac Distance ◽  
Alpha And Beta Diversity ◽  
The Difference

Background:Anti-citrullinated protein antibody (ACPA) production is observed in several organs even prior to the onset of rheumatoid arthritis (RA), and oral mucosa is considered to be one of the important tissues. The presence of HLA-DRB1*SE closely associates with ACPA production. Saliva is considered to reflect the oral microbiota including periodontal disease. Alteration of oral microbiota of RA becomes to be normalized by DMARDs treatment, however, the interaction of HLA-DRB1*SE, ACPA and oral microbiota of RA patients remains to be elucidated.Objectives:The Nagasaki Island Study, which had started in 2014 collaborating with Goto City, is intended for research of the preclinical stage of RA, including ACPA/HLA genotype screening and ultrasound and magnetic resonance imaging examinations in high-risk subjects. Using the samples accumulated in this cohort, we have tried to investigate the difference of oral microbiota among RA patients and healthy subjects regarding to ACPA and HLA-DRB1*SE.Methods:Blood and salivary samples were obtained from 1422 subjects out of 4276 who have participated in the Nagasaki Island Study from 2016 to 2018. ACPA positivity was 1.7 % in total. Some of RA patients resided in Goto City participated in the Nagasaki Island Study. At this point, we selected 291 subjects, who were ACPA positive non-RA healthy subjects (n=22) and patients with RA (n=33, 11 subjects were ACPA positive and 22 ACPA negative respectively) as the case, age and gender matched ACPA negative non-RA healthy subjects (n=236) as the control. ACPA was measured by an enzyme-linked immunosorbent assay, and HLA genotyping was quantified by next-generation sequencing (Ref.1). The operational taxonomic unit (OUT) analysis using 16S rRNA gene sequencing were performed. The richness of microbial diversity within-subject (alpha diversity) was scaled via Shannon entropy. The dissimilarity between microbial community composition was calculated using Bray-Curtis distance as a scale, and differences between groups (beta diversity) were tested by permutational multivariate analysis of variance (PERMANOVA). In addition, UniFrac distance calculated in consideration of the distance on the phylogenetic tree were performed.Results:Median age 70 y.o., % Female 58.8 %. Among RA and non-RA subjects, not alpha diversity but beta diversity was statistically significance (p=0.022, small in RA). In RA subjects, both alpha and beta diversity is small (p<0.0001), especially significant in ACPA positive RA (Figure 1). Amongt RA subjects, presence of HLA-DRB1*SE did not show the difference but the tendency of being small of alpha diversity (p=0.29).Conclusion:Our study has suggested for the first time the association of oral microbiota alteration with the presence of ACPA and HLA-DRB1*SE. Oral dysbiosis may reflect the immunological status of patients with RA.References:[1]Kawaguchi S, et al. Methods Mol Biol 2018;1802: 22Disclosure of Interests:None declared

scholarly journals Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov
Keyword(s):  
Microbial Communities ◽  
Plant Communities ◽  
Plant Diversity ◽  
Beta Diversity ◽  
Mutual Influence ◽  
Plant Root ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

Impact of intrapartum antibiotics on the infant gastrointestinal microbiome: a narrative review

2021 ◽  
pp. archdischild-2021-322590
Author(s):  
Laura Diamond ◽  
Rachel Wine ◽  
Shaun K Morris
Keyword(s):  
Gestational Age ◽  
Beta Diversity ◽  
Mode Of Delivery ◽  
Alpha Diversity ◽  
First Year ◽  
Feeding Method ◽  
Alpha And Beta Diversity ◽  
Ovid Medline ◽  
First Year Of Life ◽  
The Impact

BackgroundThe composition of the infant gastrointestinal (GI) microbiome has been linked to adverse long-term health outcomes and neonatal sepsis. Several factors are known to impact the composition of the microbiome, including mode of delivery, gestational age, feeding method and exposure to antibiotics. The impact of intrapartum antibiotics (IPAs) on the infant microbiome requires further research.ObjectiveWe aimed to evaluate the impact of IPAs on the infant GI microbiome.MethodsWe searched Ovid MEDLINE and Embase Classic+Embase for articles in English reporting on the microbiome of infants exposed to IPAs from the date of inception to 3 January 2021. Primary outcomes included abundance and colonisation of Bifidobacterium and Lactobacillus, as well as alpha and beta diversity.Results30 papers were included in this review. In the first year of life, following exposure to IPAs, 30% (6/20) of infant cohorts displayed significantly reduced Bifidobacterium, 89% (17/19) did not display any significant differences in Lactobacillus colonisation, 21% (7/34) displayed significantly reduced alpha diversity and 35% (12/34) displayed alterations in beta diversity. Results were further stratified by delivery, gestational age (preterm or full term) and feeding method.ConclusionsIPAs impact the composition of the infant GI microbiome, resulting in possible reductions Bifidobacterium and alpha diversity, and possible alterations in beta diversity. Our findings may have implications for maternal and neonatal health, including interventions to prevent reductions in health-promoting bacteria (eg, probiotics) and IPA class selection.

scholarly journals Evidence supporting the microbiota–gut–brain axis in a songbird

2020 ◽  
Vol 16 (11) ◽  
pp. 20200430
Author(s):  
Morgan C. Slevin ◽  
Jennifer L. Houtz ◽  
David J. Bradshaw ◽  
Rindy C. Anderson
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Cloacal Swab ◽  
Cognitive Tasks ◽  
Captive Population ◽  
Wild Populations ◽  
Alpha And Beta Diversity ◽  
Microbiome Research ◽  
Host Development

Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 zebra finches ( Taeniopygia guttata ), we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota–gut–brain axis, building foundations for future microbiome research in wild populations and during host development.

scholarly journals Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 101 ◽  
Author(s):  
Sándor Bartha ◽  
Roberto Canullo ◽  
Stefano Chelli ◽  
Giandiego Campetella
Keyword(s):  
Beta Diversity ◽  
Management Practices ◽  
Multiple Scales ◽  
Forest Succession ◽  
Spatial Scales ◽  
Alpha Diversity ◽  
Structural Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Coppice Management

Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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