scholarly journals Characterization and Analysis of the Skin Microbiota in Rosacea: Impact of Systemic Antibiotics

2020 ◽  
Vol 9 (1) ◽  
pp. 185 ◽  
Author(s):  
Yu Ri Woo ◽  
Se Hoon Lee ◽  
Sang Hyun Cho ◽  
Jeong Deuk Lee ◽  
Hei Sung Kim
Keyword(s):  
Relative Abundance ◽  
Alpha Diversity ◽  
Age Group ◽  
Skin Microbiota ◽  
Principal Coordinates Analysis ◽  
Doxycycline Treatment ◽  
Principal Coordinates ◽  
Cutibacterium Acnes ◽  
Before And After ◽  
Systemic Antibiotics

Systemic antibiotics are extensively used to control the papules and pustules of rosacea. Hence, it is crucial to understand their impact on the rosacea skin microbiota which is thought to be perturbed. The purpose of this study was to compare the makeup and diversity of the skin microbiota in rosacea before and after taking oral antibiotics. We also compared the skin microbiota at baseline according to age and rosacea severity. A longitudinal cohort study was performed on 12 rosacea patients with papules/pustules and no recent use of oral and topical antimicrobials/retinoids. Patients were prescribed oral doxycycline, 100 mg, twice daily for six weeks. Skin areas on the cheek and nose were sampled for 16S ribosomal RNA gene sequencing at baseline, and after six weeks of doxycycline treatment. Eleven females and one male aged 20–79 (median 51) with a median Investigator’s Global Assessment score of 3 (moderate) were enrolled. At baseline, Staphylococcus epidermidis was the most dominant species followed by Cutibacterium acnes (formerly Propionibacterium acnes). In the 60 Over-age group, the prevalence of Cutibacterium acnes was lower than that of the 60 & Under-age group. Rosacea severity increased with age and was associated with a decrease in the relative abundance of Cutibacterium acnes and an increase of Snodgrassella alvi. Across all subjects, antibiotic treatment reduced clinical rosacea grades and was associated with an increase in the relative abundance of Weissella confusa (P = 0.008, 95% CI 0.13% to 0.61%). Bacterial diversity (alpha diversity) was not significantly altered by antibiotics treatment. Principal coordinates analysis showed mild clustering of samples by patient (ANOSIM, Analysis of Similarity, R = 0.119, P = 0.16) and scant clustering with treatment (ANOSIM, R = 0.002; P = 0.5). In conclusion, we believe that rosacea has a unique age-dependent characteristic (i.e., severity). Although we were not able to pinpoint a causative microbiota, our study provides a glimpse into the skin microbiota in rosacea and its modulation by systemic antibiotics.

scholarly journals Characterization and Analysis of the Skin Microbiota in Acne: Impact of Systemic Antibiotics

2020 ◽  
Vol 9 (1) ◽  
pp. 168 ◽  
Author(s):  
Seo-Yeon Park ◽  
Hei Sung Kim ◽  
Se Hoon Lee ◽  
Sungjoo Kim
Keyword(s):  
Bacterial Species ◽  
Alpha Diversity ◽  
Skin Microbiota ◽  
Principal Coordinates Analysis ◽  
Severe Acne ◽  
Doxycycline Treatment ◽  
Principal Coordinates ◽  
Cutibacterium Acnes ◽  
Before And After ◽  
Systemic Antibiotics

Systemic antibiotics are extensively used to control moderate to severe acne. Hence, it is crucial to understand their impact on the skin microbiota, which is supposedly perturbed. The purpose of this study was to compare the makeup and diversity of the skin microbiota in acne patients before and after taking oral antibiotics. A longitudinal cohort study was performed on 20 participants with moderate to severe facial acne with no recent use of oral and topical antibiotics/retinoids. Patients were prescribed oral doxycycline, 100 mg, twice daily for six weeks. Skin areas on the cheek were sampled for 16S ribosomal RNA gene sequencing at baseline, and after six weeks of doxycycline treatment. Ten males and 10 females aged 11 to 44 years with a median Investigator’s Global Assessment score of 3 (moderate) were enrolled. At baseline, Cutibacterium acnes (formerly Propionibacterium acnes) was the most dominant species followed by Staphylococcus epidermidis. Acne severity showed a positive correlation with the abundance of Cutibacterium acnes. Across all subjects, antibiotic treatment reduced clinical acne grades and was associated with a 1.96-fold reduction in the relative abundance of Cutibacterium acnes (p = 0.01, 95% CI −22% to −3%). Marked changes were also identified in other bacterial species, such as Cutibacterium granulosum (formerly Propionibacterium granulosum), which increased by 4.46-fold (p = 0.02, 95% CI 0.004% to 0.9%) in the treated samples. In general, antibiotics administration was associated with an increase in bacterial diversity (alpha diversity). Principal coordinates analysis showed mild clustering of samples by patient (analysis of similarity, R = 0.135, p = 0.04) whereas there was scant clustering with treatment (ANOSIM, R = 0.005; p = 0.29). In conclusion, we found individuals with acne to have a unique microbial signature. Acne treatment with systemic antibiotics was associated with changes in the composition and diversity of skin microbiota, especially Cutibacterium acnes, which correlates with acne severity. Our study provides insight into the skin microbiota in acne and how it is modulated by systemic antibiotics.

scholarly journals The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation

2020 ◽  
Author(s):  
Andrew Nelson ◽  
Christopher J Stewart ◽  
Nicholas A Kennedy ◽  
John K Lodge ◽  
Mark Tremelling ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Relative Abundance ◽  
Mucosal Inflammation ◽  
Rrna Gene ◽  
Wild Type ◽  
Candida Spp ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
The Impact

Abstract Background and Aims Historical and emerging data implicate fungi in Crohn’s disease [CD] pathogenesis. However, a causal link between mycobiota, dysregulated immunity, and any impact of NOD2 variants remains elusive. This study aims to evaluate associations between NOD2 variants and faecal mycobiota in CD patients and non-CD subjects. Methods Faecal samples were obtained from 34 CD patients [18 NOD2 mutant, 16 NOD2 wild-type] identified from the UK IBD Genetics Consortium. To avoid confounding influence of mucosal inflammation, CD patients were in clinical remission and had a faecal calprotectin <250 μg/g; 47 non-CD subjects were included as comparator groups, including 22 matched household [four NOD2 mutant] and 25 non-household subjects with known NOD2 genotype [14 NOD2 mutant] identified by the NIHR BioResource Cambridge. Faecal mycobiota composition was determined using internal transcribed spacer 1 [ITS1] sequencing and was compared with 16S rRNA gene sequences and volatile organic compounds. Results CD was associated with higher numbers of fungal observed taxonomic units [OTUs] [p = 0.033]. Principal coordinates analysis using Jaccard index [p = 0.018] and weighted Bray-Curtis dissimilarities [p = 0.01] showed Candida spp. clustered closer to CD patients whereas Cryptococcus spp. clustered closer to non-CD. In CD, we found higher relative abundance of Ascomycota [p = 0.001] and lower relative abundance Basidiomycota [p = 0.019] phyla. An inverse relationship was found between bacterial and fungal Shannon diversity in NOD2 wild-type which was independent of CD [r = -0.349; p = 0.029]. Conclusions This study confirms compositional changes in the gut mycobiota in CD and provides evidence that fungi may play a role in CD pathogenesis. No NOD2 genotype-specific differences were observed in the faecal mycobiota.

scholarly journals Variations in the Compositions of Soil Bacterial and Fungal Communities Due to Microhabitat Effects Induced by Simulated Nitrogen Deposition of a Bamboo Forest in Wetland

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1098 ◽  
Author(s):  
Weicheng Li ◽  
Haiyan Sheng ◽  
Desy Ekawati ◽  
Yueping Jiang ◽  
Huimin Yang
Keyword(s):  
Nitrogen Deposition ◽  
Soil Ph ◽  
Solid Phase ◽  
Wetland Management ◽  
Alpha Diversity ◽  
Principal Coordinates Analysis ◽  
Linear Discriminant ◽  
Fungal Abundance ◽  
Principal Coordinates ◽  
Bacteria And Fungi

Although numerous studies have been published on nitrogen (N) deposition, little is known about its impact on microbial communities in wetland forests. Here, we used simulated nitrogen deposition (SND) to analyze the importance of differences in soil microhabitats in promoting the diversity of soil bacteria and fungi. We compared various levels of SND (control (CK), low N (N30), medium N (N60), and high N (N90)) and found that these were associated with changes in soil microhabitats. Additionally, SND affected soil pH, clay and sand content of the soil, and specific surface area (SSA). Bacteria and fungi responded differently to increased SND levels. The alpha diversity of bacteria decreased with an increased SND level, while fungal abundance, diversity, and community evenness reached their maximum values at the N60 threshold. Principal coordinates analysis (PCoA), nonparametric multivariate analysis of variance (PERMANOVA), and linear discriminant analysis (LDA) coupled with effect size measurements (LefSe) also confirmed that the bacterial composition was different at N90 compared to other levels of SND while that of fungi was different at N60. A higher discriminant level (LDA score ≥4) may be a valuable index of selecting indicator microbial clades sensitive to SND for wetland management. Further, an increased pH was associated with a greater abundance of bacteria and fungi. In addition, the volume contents of clay and SSA were negatively correlated with bacteria but fungi are associated with soil specific gravity (SSG). Overall, in a neutral soil pH environment, pH fluctuation is the main influencing factor in terms of bacterial and fungal abundance and diversity. The diversity of fungi is more dependent on the type and relative content of solid phase components in soil than that of bacteria, implying the presence of species-specific niches for bacteria and fungi. These results demonstrate that changes in SND can induce short-term microbial and microhabitat changes.

scholarly journals Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau

Toxins ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 894
Author(s):  
Dini Hu ◽  
John P. Giesy ◽  
Min Guo ◽  
Wai Kin Ung ◽  
Yijun Kong ◽  
...  
Keyword(s):  
16S Rrna ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Viral Metagenomics ◽  
Principal Coordinates Analysis ◽  
Algae Blooms ◽  
Principal Coordinates ◽  
Viral Communities ◽  
Insight Into ◽  
Generation Sequencing

Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.

scholarly journals Effects of Dietary Tributyrin on Growth Performance, Biochemical Indices, and Intestinal Microbiota of Yellow-Feathered Broilers

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3425
Author(s):  
Li Gong ◽  
Gengsheng Xiao ◽  
Liwei Zheng ◽  
Xia Yan ◽  
Qien Qi ◽  
...  
Keyword(s):  
Growth Performance ◽  
Intestinal Microbiota ◽  
Relative Abundance ◽  
Size Analysis ◽  
Control Group ◽  
Feed Conversion ◽  
Principal Coordinates Analysis ◽  
Linear Discriminant ◽  
Principal Coordinates ◽  
Biochemical Indices

This study aimed to evaluate the effects of tributyrin on growth performance, biochemical indices and intestinal microbiota of yellow-feathered broilers. 360 one-day-old chicks were randomly allocated to three treatments with six replicates of 20 chicks each, including a normal control group (NC), an antibiotic group (PC), and a tributyrin (250 mg/kg) group (TB) for 63 days. The results showed that compared with the control, the feed conversion ratio (FCR) in the TB group decreased during the d22 to d42 (p < 0.05) and overall, the final weight and FCR of broilers tended to increase and decrease, respectively. Moreover, the TB group showed the highest creatine concentrations at the entire period (p < 0.05). TB treatment increased the Bacteroidetes relative abundance and decreased Firmicutes. Principal coordinates analysis yielded clear clustering of the three groups. Linear discriminant analysis effect size analysis found seven differentially abundant taxa in the TB group, including several members of Bacteroidedetes. The relative abundance of Eisenbergiella, Phascolarctobacterium, Megasphaera and Intestinimonas increased in tributyrin-treated broilers. Spearman correlation analysis identified a correlation between Eisenbergiella abundance and overall feed efficiency. These results demonstrated that tributyrin could improve the growth performance by modulating blood biochemical indices and the cecal microflora composition of broilers.

scholarly journals Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai–Tibetan Plateau

2020 ◽  
Vol 11 ◽  
Author(s):  
Jian Ma ◽  
Yixiao Zhu ◽  
Zhisheng Wang ◽  
Xiong Yu ◽  
Rui Hu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Retardation ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Principal Coordinates Analysis ◽  
Bacterial Composition ◽  
Opposite Trend ◽  
Principal Coordinates ◽  
Bacterial Structure ◽  
Relative Abundances

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P &lt; 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P &lt; 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P &lt; 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P &lt; 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P &lt; 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P &lt; 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 &lt; P &lt; 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

scholarly journals Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ricardo Sousa ◽  
Joana Vasconcelos ◽  
Iván Vera-Escalona ◽  
João Delgado ◽  
Mafalda Freitas ◽  
...  
Keyword(s):  
Large Scale ◽  
Alpha Diversity ◽  
Marine Species ◽  
Principal Coordinates Analysis ◽  
Study Region ◽  
The North ◽  
Mainland Portugal ◽  
Model Study ◽  
Principal Coordinates ◽  
Ne Atlantic Ocean

AbstractStudies on microbial communities are pivotal to understand the role and the evolutionary paths of the host and their associated microorganisms in the ecosystems. Meta-genomics techniques have proven to be one of the most effective tools in the identification of endosymbiotic communities of host species. The microbiome of the highly exploited topshell Phorcus sauciatus was characterized in the Northeastern Atlantic (Portugal, Madeira, Selvagens, Canaries and Azores). Alpha diversity analysis based on observed OTUs showed significant differences among regions. The Principal Coordinates Analysis of beta-diversity based on presence/absence showed three well differentiated groups, one from Azores, a second from Madeira and the third one for mainland Portugal, Selvagens and the Canaries. The microbiome results may be mainly explained by large-scale oceanographic processes of the study region, i.e., the North Atlantic Subtropical Gyre, and specifically by the Canary Current. Our results suggest the feasibility of microbiome as a model study to unravel biogeographic and evolutionary processes in marine species with high dispersive potential.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals The Acute Effects of a Swimming Session on the Shoulder Rotators Strength and Balance of Age Group Swimmers

2021 ◽  
Vol 18 (15) ◽  
pp. 8109
Author(s):  
Nuno Batalha ◽  
Jose A. Parraca ◽  
Daniel A. Marinho ◽  
Ana Conceição ◽  
Hugo Louro ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Training Session ◽  
Age Group ◽  
Acute Effects ◽  
Muscle Strengthening ◽  
Repeated Measures Design ◽  
Before And After ◽  
Shoulder Strength ◽  
Isometric Torque ◽  
Gender Specific

The purpose of this study was to analyze the acute effects of a standardized water training session on the shoulder rotators strength and balance in age group swimmers, in order to understand whether a muscle-strengthening workout immediately after the water training is appropriate. A repeated measures design was implemented with two measurements performed before and after a standardized swim session. 127 participants were assembled in male (n = 72; age: 16.28 ± 1.55 years, height: 174.15 ± 7.89 cm, weight: 63.97 ± 6.51 kg) and female (n = 55; age: 15.29 ± 1.28 years, height: 163.03 ± 7.19 cm, weight: 52.72 ± 5.48 kg) cohorts. The isometric torque of the shoulder internal (IR) and external (ER) rotators, as well as the ER/IR ratios, were assessed using a hand-held dynamometer. Paired sample t-tests and effect sizes (Cohen’s d) were used (p ≤ 0.05). No significant differences were found on the shoulder rotators strength or balance in males after training. Females exhibited unchanged strength values after practice, but there was a considerable decrease in the shoulder rotators balance of the non-dominant limb (p < 0.01 d = 0.366). This indicates that a single practice seems not to affect the shoulders strength and balance of adolescent swimmers, but this can be a gender specific phenomenon. While muscle-strengthening workout after the water session may be appropriate for males, it can be questionable regarding females. Swimming coaches should regularly assess shoulder strength levels in order to individually identify swimmers who may or may not be able to practice muscle strengthening after the water training.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2139
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Yunjuan Peng ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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