LDA Effect Size Analysis Research Articles

Exploration of the Changes in Facial Microbiota of Maskne Patients and Healthy Controls Before and After Wearing Masks Using 16S rRNA Analysis.

Whether in the field of medical care, or in people's daily life and health protection, the importance of masks has been paid more and more attention. Acne, the most common complication after wearing masks, which is also called maskne, has been successfully introduced into the common language as a common topic of dermatologist consultations. This study aims to study the changes of microflora in maskne patients and healthy controls before and after wearing masks. In the summer of 2023, we collected a total of 50 samples from 15 maskne patients and 10 healthy controls before and after wearing surgical masks for a long time. 16S ribosomal DNA sequencing and identification technology with V3-V4 variable region were adopted to explore the microbiome changes caused by mask wearing, analyze the changes in microbial diversity, and make interaction network. LDA effect size analysis was used to identify which bacteria showed significant changes in their relative abundance from phylum to genus. After wearing a mask, the microbiome of the maskne patients changed significantly more than that of the healthy controls, with both α diversity and β diversity lower than those of maskne patients before wearing masks and those of healthy controls after wearing masks. Co-occurrence network analysis showed that compared with other groups, the network of maskne patients after wearing masks for a long time had the lowest connectivity and complexity, but the highest clustering property, while the opposite was true for healthy controls. Many microbes that are potentially beneficial to the skin decreased significantly after wearing a mask. There was almost no difference in healthy controls before and after wearing a mask.

Spatial distribution of airborne bacterial communities in caged poultry houses

ABSTRACT Microbial aerosols in intensive broiler houses whose species and concentrations are closely related to human health are ubiquitous. Based on 16S rRNA gene sequencing, the aim of this study was to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. Significant spatial variations in airborne bacterial concentrations were observed inside the poultry farmhouse. The results indicated that bacteria in the air samples could be grouped into a total of 1,674 OTUs. Alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (p < 0.01). The Sankey diagram illustrated species dynamic changes in Proteobacteria, Firmicutes, and Actinobacteria among the different locations. From the aspect of LEfSe (LDA Effect Size) analysis, we discovered that the abundance of Planctomycetes was significantly higher in the entry than in the rear and middle. This study shows the spatial distribution of the entire bacterial community in intensive broiler houses, which offers a new perspective for studying airborne total bacteria in those environments. Implications: The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. The results observed that bacterial aerosol concentrations in the examined broilers house varied greatly at different positions, and a significantly higher exposure to bacterial aerosol was observed at the middle than at the other positions (p < 0.05). The alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (P<0.01). Sankey diagram illustrated species dynamic changes of Proteobacteria, Firmicutes and Actinobacteria among the different locations. The microbial communities in genus level in the samples of entry and rear were closer, while the species diversity of middle and rear samples in chicken house was highly similar (P>0.05). Altogether, results revealed that the effects of spatial factors on the diversity and abundance of bacteria in the air of closed-cage broiler houses, which poses a potential threat to the health of animals and workers in those environments.

A study on the correlation between intrauterine microbiota and uterine pyogenesis in dogs

Pyometra is a common and high-incidence reproductive system disease in female dogs, and its development involves both hormonal and bacterial factors. Characterization of the endometrial microbiome in healthy dogs and diseased dogs with pyometra remains unclear at present, however. In this study, dogs with pyometra were identified based on the clinical examinations, hematology examinations, vaginal smears and uterine histopathology. The endometrial samples of healthy dogs (n = 30) and diseased dogs (n = 41) were then collected and sequenced by 16S rRNA high-throughput sequencing technology. Dogs with pyometra suffered from inflammation, and their endometrial microbial diversity (ACE and Chao 1 indices) was significantly lower than that of healthy dogs (P < 0.05). The endometrial samples of both groups were enriched in four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria), with a greater abundance of Firmicutes in diseased dogs (P < 0.05). At the genus level, the most prevalent microbes in diseased dogs belonged to Pseudomonas, Escherichia-Shigella, Mycoplasma, Enterococcus, Haemophilus, Vibrio and Ralstonia, with lower levels of Mycoplasma, Enterococcus and Haemophilus in the healthy control. Principal co-ordinates analysis and non-metric multi-dimensional scaling showed that the endometrial microbiome of diseased dogs clustered separately from that of the healthy controls (P < 0.05). In the LDA effect size analysis, 18 members of the endometrial microbiome were screened. Of these, the bacterial species Pseudomonas_aeruginosa and microbes within the genera Mycoplasma, Enterococcus and Haemophilus were found to be enriched in the uteruses of diseased dogs. Furthermore, the Random Forests model further confirmed that Mycoplasma and Haemophilus could be considered as biomarkers of diseased endometrium. In conclusion, this study provided a theoretical basis for the development of probiotic preparation in the future.

The Effects of Secondary Growth of Spartina alterniflora after Treatment on Sediment Microorganisms in the Yellow River Delta.

As a typical invasive species, Spartina alterniflora is widely recognized as one of the primary threats to biodiversity in various habitats, including wetlands. Although the invasion by S. alterniflora has been managed in multiple ways, it may reappear after treatment. How S. alterniflora affects the soil microbial community in coastal wetlands during its regeneration process has not yet been clarified. Here, rhizosphere soil samples (RSPs) and bulk soil samples (SSPs) were collected in the S. alterniflora community and a high-throughput sequencing method was conducted to analyze the composition and diversity of soil microorganisms. Meanwhile, we also obtain the soil physicochemical properties. In the present study, there was no significant difference in the alpha diversity of both bacterial and fungal communities in the SSP and RSP groups. The PCoA (principal coordinate analysis) also showed that the microbial community structure did not differ significantly between the SSP and RSP groups. The results showed that except for pH, the total sulfur (TS) content, total nitrogen (TN) content, and electrical conductivity (EC) did not differ significantly (p > 0.05) between the SSP and RSP groups. The composition of the bacterial and fungal community in the rhizosphere of S. alterniflora was similar to that found in the surrounding soils. The top two dominant bacterial phyla were Proteobacteria and Desulfobacterota in the present study. Venn diagram results also support this view; most OTUs belong to the common OTUs of the two groups, and the proportion of unique OTUs is relatively small. The LEfSe (LDA effect size) analysis showed that Campylobacterota (at the phylum level) and Sulfurimonas (at the genus level) significantly increased in the RSP group, implying that the increased Sulfurimonas might play an essential role in the invasion by S. alterniflora during the under-water period. Overall, these results suggest that the bacterial and fungal communities were not significantly affected by the S. alterniflora invasion due to the short invasion time.

Response of soil bacterial community structure and function under two salt-tolerant plants in a coastal saline soil area of eastern Hebei province of China

The plants Feicai (Sedum aizoon L.) and dandelion(Taraxacum mongolicum Hand.-Mazz.) have good salt tolerance, and can improve soil quality and the micro-ecological environment. Coastal saline-soil plots planted with S. aizoon and T. mongolicum and bare plots were used to explore their effects on the microbial community structure of coastal saline soil. The diversity and function of soil bacterial communities were analyzed using Illumina MiSeq high-throughput sequencing technology. The results showed that the α-diversity of soil bacterial communities were higher in planted than in bare plots, in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The soil bacterial communities also changed after planting S. aizoon and T. mongolicum. The LDA effect size analysis showed that there were 37 indicator species among the three plot types. Correlation analysis of environmental factors showed that EC, AP, and OM were the main factors influencing bacterial community composition in this coastal saline soil. The PICRUSt functional prediction showed that the numbers of metabolic functions of bacterial communities were in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The results provide a theoretical basis and plant species for developing salt-tolerant bacterial resources and phytoremediation of coastal saline soil.

Effects of Spartina alterniflora Invasion on Soil Microbial Community Structure and Ecological Functions.

It has been reported that the invasion of Spartina alterniflora changed the soil microbial community in the mangrove ecosystem in China, especially the bacterial community, although the response of soil fungal communities and soil microbial ecological functions to the invasion of Spartina alterniflora remains unclear. In this study, we selected three different communities (i.e., Spartina alterniflora community (SC), Spartina alterniflora–mangrove mixed community (TC), and mangrove community (MC)) in the Zhangjiangkou Mangrove Nature Reserve in China. High-throughput sequencing technology was used to analyze the impact of Spartina alterniflora invasion on mangrove soil microbial communities. Our results indicate that the invasion of Spartina alterniflora does not cause significant changes in microbial diversity, but it can alter the community structure of soil bacteria. The results of the LEfSe (LDA Effect Size) analysis show that the relative abundance of some bacterial taxa is not significantly different between the MC and SC communities, but different changes have occurred during the invasion process (i.e., TC community). Different from the results of the bacterial community, the invasion of Spartina alterniflora only cause a significant increase in few fungal taxa during the invasion process, and these taxa are at some lower levels (such as family, genus, and species) and classified into the phylum Ascomycota. Although the invasion of Spartina alterniflora changes the taxa with certain ecological functions, it may not change the potential ecological functions of soil microorganisms (i.e., the potential metabolic pathways of bacteria, nutritional patterns, and fungal associations). In general, the invasion of Spartina alterniflora changes the community structure of soil microorganisms, but it may not affect the potential ecological functions of soil microorganisms.

Effects of changes on gut microbiota in children with acute Kawasaki disease.

BackgroundKawasaki disease (KD) is an acute febrile illness of early childhood. The exact etiology of the disease remains unknown. At present, research on KD is mostly limited to susceptibility genes, infections, and immunity. However, research on the correlation between gut microbiota and KD is rare.MethodsChildren with a diagnosis of acute KD and children undergoing physical examination during the same period were included. At the time of admission, the subjects’ peripheral venous blood and feces were collected. Faecal samples were analyzed for bacterial taxonomic content via high-throughput sequencing. The abundance, diversity, composition, and characteristic differences of the gut microbiota in KD and healthy children were compared by alpha diversity, beta diversity, linear discriminant analysis and LDA effect size analysis. Blood samples were used for routine blood examination, biochemical analysis, and immunoglobulin quantitative detection.ResultsCompared with the control group, the community richness and structure of gut microbiota in the KD group was significantly reduced (Chao1 richness estimator, mean 215.85 in KD vs. mean 725.76 in control, p < 0.01; Shannon diversity index, mean 3.32 in KD vs. mean 5.69 in control, p < 0.05). LEfSe analysis identified two strains of bacteria significantly associated with KD: Bacteroidetes and Dorea. Bacteroidetes were enriched in healthy children (mean 0.16 in KD vs. mean 0.34 in control, p < 0.05). Dorea was also enriched in healthy children but rarely existed in children with KD (mean 0.002 in KD vs. mean 0.016 in control, p < 0.05). Compared with the control, IgA and IgG in the KD group decreased (IgA, median 0.68 g/L in KD vs. median 1.06 g/L in control, p < 0.001; IgG, median 6.67 g/L in KD vs. median 9.71 g/L in control, p < 0.001), and IgE and IgM levels were not significantly changed.ConclusionsDysbiosis of gut microbiota occurs in children with acute KD and may be related to the etiology or pathogenesis of KD. It is worth noting that for the first time, we found that Dorea, a hydrogen-producing bacterium, was significantly reduced in children with acute KD. Overall, our results provide a theoretical basis for the prevention or diagnosis of KD based on intestinal microecology.

Identifying human-induced influence on microbial community: A comparative study in the effluent-receiving areas in Hangzhou Bay

Microbial community structure is affected by both natural processes and human activities. In coastal area, anthropegenetic activity can usually lead to the discharge of the effluent from wastewater treatment plant (WWTP) to sea, and thus the water quality chronically turns worse and marine ecosystem becomes unhealthy. Microorganisms play key roles in pollutants degradation and ecological restoration; however, there are few studies about how the WWTP effluent disposal influences coastal microbial communities. In this study, sediment samples were collected from two WWTP effluent-receiving areas (abbreviated as JX and SY) in Hangzhou Bay. First, based on the high-throughput sequencing of 16S rRNA gene, microbial community structure was analyzed. Secondly, several statistical analyses were conducted to reveal the microbial community characteristics in response to the effluent disposal. Using PCoA, the significant difference of in microbial community structure was determined between JX and SY; using RDA, water COD and temperature, and sediment available phosphate and ammonia nitrogen were identified as the key environmental factors for the community difference; using LDA effect size analysis, the most distinctive microbes were found and their correlations with environmental factors were investigated; and according to detrended beta-nearest-taxon-index, the sediment microbial communities were found to follow “niche theory”. An interesting and important finding was that in SY that received more and toxic COD, many distinctive microbes were related to the groups that were capable of degrading toxic organic pollutants. This study provides a clear illustration of eco-environmental deterioration under the long-term human pressure from the view of microbial ecology.

Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing.

BackgroundThe objective of this study was to characterize the oral microflora profile of primary Sjögren’s syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the “core microbiome” in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique.MethodsTwenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform.ResultsBoth two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively.DiscussionThese findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in pSS patients. This study also provides basic data regarding microbiology in pSS.

Microflora changes in upper digestive tract and bile in acute liver failure mice

Objective: To study the changes of upper digestive tract and bile flora associated with acute liver failure in mice. Methods: Mice were randomly divided into 2 groups: control group and acute liver failure group (group M). Acute liver failure in group M was induced by intraperitoneal injection of D-galactosamine (D-GaIN). The information of relative abundance and diversity were observed by high-throughput sequencing of V3 + V4 region in 16 S rDNA from bacteria of oral cavity, stomach, duodenal and bile.Bacterial translocation and changes associated with acute liver injury were identified by LEfSe (LDA effect size) analysis. Results: At the phylum level, compared with control group, the relative abundance of TM7 in oral cavity and stomach increased in group M. At the family level, compared with control group, group M resulted in a significant decrease in Pasteurellaceae in the stomach (P<0.05) and a increase in Lactobacillaceae in the bile (P<0.05). Conclusion: The diversity of bacteria and relative abundance of each bacterium in upper digestive tract and the bile are significantly changed during the process of acute liver injure in mice.

Changes in the composition of intestinal microbiota in mice with acute liver failure induced by D-galactosamine

Objective: To investigate the changes in the composition of intestinal microbiota in mice with acute liver failure and identify characteristic bacteria, and to provide a basis for the diagnosis and treatment of acute liver failure with intestinal microbiota disorders. Methods: A total of 30 specific pathogen-free male BALB/c mice were used in this study, including 25 mice in the model group and 5 mice in the control group. An acute liver failure model was induced by D-galactosamine. Microbial DNA was extracted from intestinal contents in different segments of the lower digestive tract (ileum and colon) and feces and then were amplified using PCR. The regions of 16S V3-V4 were subjected to high-throughput sequencing, followed by bioinformatics analyses, including OTU hierarchical clustering, species annotation, alpha-diversity analysis, and LEfSe (LDA Effect Size) analysis. Comparison of continuous data was made using t-test, while comparison of categorical data was made using χ2 test. Results: A total of 10 mice survived in the two groups, with 80% mortality rate in the model group. The alpha-diversity analysis revealed increased bacterial diversity and abundance in the ileum, increased bacterial diversity and reduced bacterial abundance in the colon, and reduced bacterial diversity and insignificantly changed bacterial abundance in feces in the model group compared with the control group. Based on the optimized classification level, significantly reduced abundance of Clostridiaceae (44.95% ± 19.28% vs 7.51% ± 16.57%, P = 0.011) in the ileum, whereas significantly increased abundance of Rikenellaceae (1.08% ± 1.01% vs 4.18% ± 2.39%, P = 0.028), S24-7 (4.75% ± 4.87% vs 22.77% ± 13.05%, P = 0.020), and F16 (0.24% ± 0.28% vs 2.18% ± 1.61%, P = 0.029) in the colon were found in model group compared with the control group. The LEfSe analysis demonstrated that there were significant differences in Staphylococcaceae and S24-7 between the two groups, and S24-7 could be defined as the characteristic bacteria. Conclusion: Intestinal microbiota disorders, especially the excessive growth of microbes in the ileum, are observed in mice with acute liver failure. Moreover, acute liver failure may be closely associated with the excessive growth of S24-7.