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 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 The Influence of Modernization and Disease on the Gastric Microbiome of Orang Asli, Myanmars and Modern Malaysians

2019 ◽  
Vol 7 (6) ◽  
pp. 174 ◽  
Author(s):  
Eng Guan Chua ◽  
Mun Fai Loke ◽  
Selva Perumal Gunaletchumy ◽  
Han Ming Gan ◽  
Kavitha Thevakumar ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Alpha Diversity ◽  
Diversity Analysis ◽  
Gastric Diseases ◽  
Developed Country ◽  
Orang Asli ◽  
Cutibacterium Acnes ◽  
Different Types ◽  
Different Populations ◽  
H Pylori

The present study explored the differences in gastric microbiome between three distinct populations of Southeast Asia. These include the isolated Orang Asli population and modern Malaysians, as well as patients from Myanmar, the least developed country in the region. All 79 subjects recruited in this study had Helicobacter pylori infection. Based on alpha diversity analysis, Orang Asli had the richest and most diverse gastric microbiome, followed by Myanmar and modern Malaysian groups. Beta diversity analysis revealed significant separation of samples between different populations. These observations are likely to be associated with the level of modernization of each population. Our data further suggested increased bacterial species richness and diversity of the gastric microbiome in individuals who were less modernized, particularly in the Orang Asli group, could suppress the growth of H. pylori. In addition, there were significant variations in the gastric microbiome between modern Malaysians with different types of gastric diseases. Notably, Cutibacterium acnes was present at significantly greater abundance level in patients with non-ulcerative dyspepsia than those with peptic-ulcer diagnosis. This suggests that C. acnes may also play a role in gastritis besides H. pylori, which merits further investigation.

scholarly journals Elderly patients of mild cognitive impairment exhibit altered profiles of the gut microbiota

2020 ◽  
Author(s):  
Qiong Pan ◽  
Ya-Qian Li ◽  
Ke Guo ◽  
Min Xue ◽  
Yu Gan ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Gut Microbiota ◽  
Bacterial Species ◽  
Natural Aging ◽  
Microbial Composition ◽  
Principal Coordinates Analysis ◽  
Transitional State ◽  
Staphylococcus Intermedius ◽  
Principal Coordinates

Abstract Background As the transitional state between normal aging and Alzheimer’s disease (AD), mild cognitive impairment (MCI) is characterized by cognitive decline greater than natural aging. While the association between AD and gut microbiota has been reported in a number of studies, there is still very limited microbial research about MCI. Methods Here we enrolled 48 participants, including 22 MCI cases and 26 normal controls. Fecal samples were collected for 16S rRNA quantitative arrays and bioinformatics analysis. Results Both Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional scaling (NMDS) demonstrated that the microbial composition of MCI individuals deviated from the cluster of healthy controls. Multiple bacterial species were significantly increased (e.g., Staphylococcus intermedius) or decreased (e.g., Bacteroides salyersiae) in the samples from MCI group. Conclusion Therefore, the composition of gut microbiota differed between control subjects and MCI cases. Our study is the first to identify a series of MCI signature species in the gut microbiota, thus providing a new direction for future development of early diagnosis and probiotics regimen.

scholarly journals The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils

2020 ◽  
Vol 8 (2) ◽  
pp. 207 ◽  
Author(s):  
Yanfen Zheng ◽  
Jing Liang ◽  
Dong-Lin Zhao ◽  
Chen Meng ◽  
Zong-Chang Xu ◽  
...  
Keyword(s):  
Root Nodule ◽  
Yellow River ◽  
Glycine Soja ◽  
Bacterial Species ◽  
Yellow River Delta ◽  
River Delta ◽  
Saline Soils ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.

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 Elderly patients of mild cognitive impairment exhibit altered profiles of the gut microbiota

2020 ◽  
Author(s):  
Qiong Pan ◽  
Ya-Qian Li ◽  
Ke Guo ◽  
Min Xue ◽  
Yu Gan ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Gut Microbiota ◽  
Bacterial Species ◽  
Natural Aging ◽  
Microbial Composition ◽  
Principal Coordinates Analysis ◽  
Transitional State ◽  
Staphylococcus Intermedius ◽  
Principal Coordinates

Abstract Background As the transitional state between normal aging and Alzheimer’s disease (AD), mild cognitive impairment (MCI) is characterized by cognitive decline greater than natural aging. While the association between AD and gut microbiota has been reported in a number of studies, there is still very limited microbial research about MCI. Methods Here we enrolled 48 participants, including 22 MCI cases and 26 normal controls. Fecal samples were collected for 16S rRNA quantitative arrays and bioinformatics analysis. Results Both Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional scaling (NMDS) demonstrated that the microbial composition of MCI individuals deviated from the cluster of healthy controls. Multiple bacterial species were significantly increased (e.g., Staphylococcus intermedius) or decreased (e.g., Bacteroides salyersiae) in the samples from MCI group. Conclusion Therefore, the composition of gut microbiota differed between control subjects and MCI cases. Our study is the first to identify a series of MCI signature species in the gut microbiota, thus providing a new direction for future development of early diagnosis and probiotics regimen.

scholarly journals Elderly Patients with Mild Cognitive Impairment Exhibit Altered Gut Microbiota Profiles

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Qiong Pan ◽  
Ya-Qian Li ◽  
Ke Guo ◽  
Min Xue ◽  
Yu Gan ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Gut Microbiota ◽  
Normal Control ◽  
Bacterial Species ◽  
Natural Aging ◽  
Microbial Composition ◽  
Principal Coordinates Analysis ◽  
Transitional State ◽  
Principal Coordinates

Background. As a transitional state between normal aging and Alzheimer’s disease (AD), mild cognitive impairment (MCI) is characterized by a worse cognitive decline than that of natural aging. The association between AD and gut microbiota has been reported in a number of studies; however, microbial research regarding MCI remains limited. Methods. This study examined 48 participants, of whom 22 were MCI cases and 26 were normal control cases. Fecal samples were collected for 16S ribosomal RNA (rRNA) quantitative arrays and bioinformatics analysis. Results. A principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) both demonstrated that the microbial composition of participants with MCI deviated from that of healthy control participants. Multiple bacterial species were significantly increased (e.g., Staphylococcus intermedius) or decreased (e.g., Bacteroides salyersiae) in samples from the MCI group. Conclusion. The composition of gut microbiota differed between normal control and MCI cases. This is the first study to identify a signature series of species in the gut microbiota of individuals with MCI. The results provide a new direction for the future development of an early diagnosis and probiotic regimen.

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 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 < 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 < 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 < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 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 < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 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 < P < 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.

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