ABSTRACT
In order to explore the endophytic fungi of Fagopyrum Mill and Avena sativa, Illumina Miseq high-throughput sequencing was used to analyze the community structure and diversity of endophytic fungi in leaves and roots of buckwheat and oat at the mature stage. The results of community structure showed that there were 205 operational taxonomic units (OTUs) in buckwheat roots and 181 OTUs in buckwheat leaves based on 97% sequence similarity level. There were 152 OTUs and 127 OTUs in the root and the leaf of oat, respectively. At the phylum level, Ascomycota and Basidiomycota were the dominant endophytic fungi in buckwheat roots and leaves, while Ascomycota was the dominant endophytic fungus in oat roots and leaves. Alpha diversity analysis showed that the Ace index, Chao index and Shannon index of buckwheat roots were higher than that of buckwheat leaves, and the three indices of oat roots were also higher than that of oat leaves, indicating that the richness and diversity of endophytic fungi community in roots were higher than that in leaves. Biomarkers were found by significant difference analysis in buckwheat and oat. The endophytic functional groups of buckwheat and oat were mainly distributed in Pathotroph and Saprotroph. The results of this study laid a foundation for fully exploiting the dominant endophytic fungal resources of buckwheat and oat and further developing microbial fertilizers.
Subject(s)
Ascomycota , Basidiomycota , Avena , Fagopyrum , High-Throughput Nucleotide SequencingABSTRACT
Objective:To study the structure and diversity of intestinal flora in IgA nephropathy (IgAN) patients, and to explore the correlation of intestinal microorganisms with clinical indicators and renal pathology.Methods:Fifteen IgAN patients in the First Affiliated Hospital of Baotou Medical College from May 2020 to September 2020 were retrospectively enrolled as IgAN group, and 8 healthy families and 7 health checkups were enrolled as healthy control group. Illumina high-throughput sequencing technology was performed for DNA sequencing in the 16S rDNA-V4 region of all bacteria in the feces sample. QIIME 2 was used to process and analyze original sequence, compared with Greengenes (V138) database. The DADA2 software was called to denoise the data, which was equivalent to a 100% similarity cluster (OTU was a 97% similarity cluster). PCoA was used to analyze the structure and diversity of intestinal flora. Spearman correlation or Pearson correlation analysis was used to analyze the correlation of differential flora with renal pathology and clinical indicators.Results:(1) The intestinal microbial β diversity in IgAN patients was significantly different from that in healthy controls ( P=0.010). (2) Compared with the healthy control group, the numbers of intestinal flora species in IgAN group were significantly increased in 1 phylum, 3 families and 22 genus. At the levels from phylum to family, the species numbers of Firmicutes and Ruminococcaceae in IgAN patients reduced than those in healthy controls and the species numbers of Chloroflexi, Gaiellaceae, Staphylococcaceae and Family-XⅢ in IgAN patients increased than those in healthy controls (all P<0.05). At the genus level, compared with the healthy controls, the species number of Subdoligranulum in IgAN patients was significantly reduced ( P=0.020), and the species number of Ruminococcus- gnavus- group was significantly increased ( P=0.004). (3) At the phylum level of the species number, Firmicutes in IgAN patients was positively correlated to albumin (ALB) ( r=0.637, P=0.037) and IgG ( r=0.452, P=0.046), Gemmatimonadetes was negatively correlated to serum creatinine ( r=-0.453, P=0.045), Verrucomicrobia was negatively correlated to IgM ( r=-0.450, P=0.046), and Patescibacteria was positively correlated to IgA ( r=0.469, P=0.037). At the genus level of the species number, Ruminococcus- gnavus- group ( r=-0.614, P=0.004) and Megamonas ( r=-0.451, P=0.042) were negatively correlated to ALB; Subdoligranulum was positively correlated to ALB ( r=0.563, P=0.009); Dialister was negatively correlated to C3 ( r=-0.427, P=0.041) and was positively correlated to IgA ( r=0.434, P=0.035); Veillonella was positively correlated to estimated glomerular filtration rate ( r=0.452, P=0.043). The species numbers of Eisenbergiella ( r=-0.850, P=0.007), Holdemania ( r=-0.845, P=0.008), Flavonifractor ( r=-0.845, P=0.008), and Ruminiclostridium- 9 ( r=-0.845, P=0.008) were negatively correlated to glomerulosclerosis or adhesion (S) of Oxford classification; the species number of Fusicatenibacter was negatively correlated to mesangial hypercellularity ( r=-0.845, P=0.008); the number of Coprococcus- 2 was positively correlated to S ( r=0.738, P=0.037) and tubular atrophy or interstitial fibrosis ( r=0.756, P=0.030). (4) Random forest model was built with Ruminococcus- gnavus- group and Subdoligranulum, after fitting the area under the receiver operating characteristic curve was 0.927. Conclusions:The intestinal flora of IgAN patients is different from that in healthy subjects. Changes of intestinal flora in IgAN patients are related to clinical indicators and renal pathology. In particular, Ruminococcus- gnavus- group and Subdoligranulum may play an important role in IgAN.
ABSTRACT
Illumina Hiseq 2500 high-throughput sequencing platform was used to study the bacteria richness and diversity, the soil enzyme activities, nutrients in unplanted soil, root-rot and healthy rhizophere soil of Coptis chinensis for deeply discussing the mechanism of the root-rot of C. chinensis. The high-throughput sequencing result showed that the artificial cultivation effected the bacteria community richness and diversity. The bacteria community richness in healthy and diseased rhizosphere soil showed significant lower than that of in unplanted soil (P<0.05) and declined bacteria diversity. The bacteria community richness in root-rot rhizosphere soil increased significantly than that of health and unplanted soil and the diversity was lower significant than that of unplanted soil (P<0.05). The results of soil nutrients and enzyme activities detected that the pH value, available phosphorus and urease activity decreased and the sucrase activity increased significantly (P<0.05). The content of organic carbon and alkaline hydrolysis nitrogen the catalase and urease activity in root rot soil samples was significantly lower than that of healthy soil samples (P<0.05). However, the contents of available phosphorus and available potassium were significantly in root-rot sample higher than that of healthy soil samples (P<0.05). Comprehensive analysis showed that the artificial cultivation declined the bacteria community richness and diversity. The bacteria community richness decreased significantly and the decreased diversity may be the cause of the root-rot. Meanwhile, the decrease of carbon and the catalase activity may be another cause of the root-rot in C. chinensis produced in Shizhu city, Chongqing province.
ABSTRACT
Objective:To acquire potential HBsAb sequences,we have analyzed the BCR CDR3 repertoire of the peripheral blood with HBsAb titer higher than 10 000 mU/ml,which could provide a data basis for follow-up study.Methods:Genomic DNA of pe-ripheral blood mononuclear cells was extracted from samples with HBsAb titer higher than 10 000 mU/ml.We have adopted Illumina Solexa high-throughput sequencing technology of the Adaptive Biotechnologies ImmunoSEQ platform to acquire sequence data.IMGT/High V-QUEST was used to preliminary analyze our sequence data,including usage of IGHV,IGHJ and IGHD gene subgroups,IGHV-J matching,distribution of CDR3 amino acid (AA) length and usage of total CDR3 AA.And these sequences were compared with the HBsAb sequences from NCBI database.Results:Experimental samples have highly selected gene subgroups IGHV3,IGHV4,IGHJ4, IGHJ6,IGHD3,IGHD6,and IGHV3-J4 pairing,IGHV3-J6 pairing.The AA length distributions of CDR3 region were normal distribution with the length of 14/15 AA as the midline.In the regard to amino acid usage in CDR3 region, each sample prior used Alanine, Tyrosine,Glycine,Alanine,Aspartic acid and Serine.The amino acid usages of 107,108,109,113,114 positions were diversified but 105,106,115,116,117 positions taking conservative amino acids usages.We have found 48 unique sequences that have same IGHV, IGHJ and CDR3 AA length with the HBsAb sequences from NCBI database.Conclusion:There were almost the same characteristics of BCR CDR3 repertoire of the peripheral blood with HBsAb titer higher than 10 000 mU/ml.The 48 unique sequences provided a solid data basis for the follow-up study.