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2021 ◽  
Author(s):  
xuxin zhang ◽  
Chongxuan Han

Objective: In the past, the zokor, which lived in northern China, caused great harm to agriculture and forestry production due to its large and sophisticated diet. Since the rat lives underground for most of its life, researchers know little about its dietary habits. Further understanding of its diet in the field is of important meaning for developing green and sustainable control strategies for the rat.Methods:Longde County in Liupan Mountain area of Ningxia Hui Autonomous Region was selected as the interest area to capture zokor and investigate the species of habitat plants.We selected chloroplast trnL gene and eukaryotic internal transcription spacer 1 (ITS 1) primers to amplify DNA from the gastric contents of zokor,and then sequenced on Illumina Miseq PE300 platform.Results:The gastric contents of Eospalax smithii (n=16) and E.cansus(n=9) were analyzed by operational taxonomic units (OTU) clustering and amplicon sequence variants(ASVs).The OTU clustering method obtained 2,995 OTUs, and the ASV method obtained 4,657 ASVs. The ASV method was better than the OTU clustering method, and the ASV method was adopted in the subsequent analysis. The food list of 32 families, 80 genera and 154 species was obtained by ASV method after the error was removed. The food composition of zokor was evaluated by relative abundance(%RA) method and frequency of occurrence(%ROO) method. At the Family level, it was found that zokor mainly fed on Asteraceae, Poaceae, Rosaceae, Pinaceae, Brassicaceae, Apiaceae, etc. At the Genus level, they are mainlyEchinops, Littledalea,Artemisia,P icea, Cirsium, Elymus and so on. The diet alpha diversity of E.cansus was slightly higher than that of E.smithii (P > 0.05). The correlation coefficient between Sobs index of alpha diversity and body weight of zokor was -0.382 (P = 0.059). The diet beta diversity proved that most zokors (22/25) clustered together, with low heterogeneity. They fed positively on Calamagrostis, Cirsium, Echinops, M edicago, Sanguisorba and T araxacum. We found that zokor mainly fed on the roots of perennial herbs(PH), which were rich in water, carbohydrate, fat and protein, which provided an important energy source for its survival. Conclusion: High-throughput sequencing(HTS) based DNA metabarcoding technology has well revealed the diet of zokor, which are generalist.


Author(s):  
Mengxue Yang ◽  
Fei Li ◽  
Rui Zhang ◽  
Yueyue Wu ◽  
Qian Yang ◽  
...  

<b><i>Background:</i></b> Intestinal flora is associated with Graves’ disease (GD). This study explored the association of serum 25(OH)D with the diversity of the intestinal flora and serum IL-17 in GD patients. <b><i>Methods:</i></b> Patients newly diagnosed with GD at 2 centers between 2018 and 2021 were consecutively included. According to their 25(OH)D levels, they were divided into the deficiency group, the insufficiency group, and the sufficiency group. Some patients with vitamin D deficiency or insufficiency were randomly selected and were matched with healthy volunteers (normal control [NC]) in terms of sex, age, and case number. The diversity and differential species of the intestinal flora and serum IL-17 levels were compared. <b><i>Results:</i></b> Serum 25(OH)D negatively correlated with serum IL-17, the platelet/lymphocyte ratio, and TSH receptor antibody. The diversity of the intestinal flora decreased in the GD group, with noticeable differences in the composition of the intestinal flora when compared with the NC group. At the phylum level, the GD group exhibited a significantly lower abundance of Firmicutes but a higher abundance of Actinobacteria. At the genus level, the GD group exhibited higher relative abundances of Bifidobacterium, Collinsella, and Pediococcus but lower abundances of Roseburia and Dialister. <b><i>Conclusions:</i></b> The changes in the vitamin D level and the composition of the intestinal flora may partially contribute to the development of GD.


2021 ◽  
Author(s):  
Macarena P. Quintana-Hayashi ◽  
Mattias Erhardsson ◽  
Maxime Mahu ◽  
Vignesh Venkatakrishnan ◽  
Freddy Haesebrouck ◽  
...  

Brachyspira hyodysenteriae is commonly associated with swine dysentery (SD), a disease that has an economic impact in the swine industry. B. hyodysenteriae infection results in changes to the colonic mucus niche with a massive mucus induction, which substantially increases the amount of B. hyodysenteriae binding sites in the mucus. We have previously determined that a B. hyodysenteriae strain binds to colon mucins in a manner that differs between pigs and mucin types. Here, we investigated if adhesion to mucins is a trait observed across a broad set of B. hyodysenteriae strains and isolates and furthermore at a genus level ( B. innocens, B. pilosicoli, B. murdochii, B. hampsonii and B. intermedia strains). Our results show that binding to mucins appears to be specific to B. hyodysenteriae , and within this species, the binding ability to mucins varies between strains/isolates, increases to mucins from pigs with SD, and is associated to sialic acid epitopes on mucins. Infection with B. hyodysenteriae strain 8dII results in mucin glycosylation changes in the colon including a shift in sialic acid containing structures. Thus, we demonstrate through hierarchical cluster analysis and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) models of the relative abundances of sialic acid-containing glycans, that sialic acid containing structures in the mucin O -glycome are good predictors of B. hyodysenteriae strain 8dII infection in pigs. The results emphasize the role of sialic acids in governing B. hyodysenteriae interactions with its host, which may open perspectives for therapeutic strategies.


2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaoxia Liu ◽  
Ke Zhao ◽  
Nana Jing ◽  
Qingjun Kong ◽  
Xingbin Yang

This study aimed to investigate the regulatory effect of epigallocatechin gallate (EGCG) on the composition of the gut microbiome, the transcriptomic profiling of ileum, and their interplay in high fat diet (HFD) induced obese mice. Intragastric administration of EGCG to C57BL/6J mice for 14 consecutive weeks remarkably decreased HFD induced excessive fat deposition (p &lt; 0.001), and the increment of serum TG, TC, HDL-C (p &lt; 0.05), as well as improved glucose tolerance (p &lt; 0.001). EGCG shifted the gut microbiota mainly by elevating the relative abundance of Parasutterrlla, Bacteroides, and Akkermansia (p &lt; 0.01), decreasing that of norank_f_Erysipelotrichaceae, unclassified_f_Ruminococcaceae, Anaerotruncus, Roseburia, norank_Lachnospiraceae, and Lachnospiraceae_UCG_006 (p &lt; 0.01) at the genus level. In addition, EGCG affected the transcriptomic profiling of ileum, and the differentially expressed (DE) genes after HFD or/and EGCG treatment were mostly enriched in the immune reaction of ileum, such as the GO term of “immune effector process” and “phagocytosis, recognition.” Furthermore, the KEGG category of “immune diseases,” “immune system,” and “infection diseases: bacterial” were commonly enriched by the DE genes of the two treatments. Among those DE genes, 16 immunoglobulins heavy chain variable region encoded genes (Ighvs) and other immunity-related genes, such as complement component 2 (C2), interferon-induced transmembrane protein 1 (Iftm1), polymeric immunoglobulin receptor (pigR), and alanyl aminopeptidase (Anpep), were highly correlated with the shifted microbes in the gut (p &lt; 0.05, absolute r &gt; 0.5). Overall, the results suggested that EGCG ameliorated the HFD induced metabolic disorder mainly by regulating gut microbiome profiling and the immunoglobulin production of ileum, while the genes expressed in the ileum, especially Ighvs, C2, Iftm1, pigR, and Anpep, might play important roles in coordinating the immunity of mice regarding the gut microbes and the host interactions.


Cancers ◽  
2021 ◽  
Vol 13 (18) ◽  
pp. 4687
Author(s):  
Jae-Yong Park ◽  
Chil-Sung Kang ◽  
Ho-Chan Seo ◽  
Jin-Chul Shin ◽  
Sung-Min Kym ◽  
...  

Early detection is crucial for improving the prognosis of gastric cancer, but there are no non-invasive markers for the early diagnosis of gastric cancer in real clinical settings. Recently, bacteria-derived extracellular vesicles (EVs) emerged as new biomarker resources. We aimed to evaluate the microbial composition in gastric cancer using bacteria-derived EVs and to build a diagnostic prediction model for gastric cancer with the metagenome data. Stool, urine, and serum samples were prospectively collected from 453 subjects (gastric cancer, 181; control, 272). EV portions were extracted from the samples for metagenome analysis. Differences in microbial diversity and composition were analyzed with 16S rRNA gene profiling, using the next-generation sequencing method. Biomarkers were selected using logistic regression models based on relative abundances at the genus level. The microbial composition of healthy groups and gastric cancer patient groups was significantly different in all sample types. The compositional differences of various bacteria, based on relative abundances, were identified at the genus level. Among the diagnostic prediction models for gastric cancer, the urine-based model showed the highest performance when compared to that of stool or serum. We suggest that bacteria-derived EVs in urine can be used as novel metagenomic markers for the non-invasive diagnosis of gastric cancer by integrating the liquid biopsy method and metagenome analysis.


Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 837
Author(s):  
Muhammad Majid ◽  
Huang Yuan

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.


2021 ◽  
Vol 12 ◽  
Author(s):  
Wen Song ◽  
Dapeng Xu ◽  
Xiao Chen ◽  
Alan Warren ◽  
Mann Kyoon Shin ◽  
...  

Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids.


2021 ◽  
Author(s):  
Jin-Tai Yu ◽  
Jing Ning ◽  
Shu-Yi Huang ◽  
Shi-Dong Chen ◽  
Yu-Xiang Yang ◽  
...  

Abstract Background Recent studies had explored that the gut microbiota was associated with neurodegenerative diseases (including Alzheimer’s disease (AD), Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS)) through the gut-brain axis, among which metabolic pathways played an important role. However, the underlying causality remained unclear. Our study aimed to evaluate potential causal relationships between gut microbiota, metabolites and neurodegenerative diseases through Mendelian randomization (MR) approach. Methods We selected genetic variants associated with gut microbiota traits (N = 18340) and gut microbiota-derived metabolites (N = 7824) from genome-wide association studies (GWASs). Summary statistics of neurodegenerative diseases were obtained from IGAP (AD: 17008 cases; 37154 controls), IPDGC (PD: 37 688 cases; 141779 controls) and IALSC (ALS: 20806 cases; 59804 controls) respectively. Results A total of 19 gut microbiota traits were found to be causally associated with risk of neurodegenerative diseases, including 1 phylum, 2 classes, 2 orders, 2 families and 12 genera. We found genetically predicted greater abundance of Ruminococcus, at genus level (OR:1.245, 95%CI:1.103,1.405; P = 0.0004) was significantly related to higher risk of ALS. We also found suggestive association between 12 gut microbiome-dependent metabolites and neurodegenerative diseases. For serotonin pathway, our results revealed serotonin as protective factor of PD, and kynurenine as risk factor of ALS. Besides, reduction of glutamine was found causally associated with occurrence of AD. Conclusions Our study firstly applied a two-sample MR approach to detect causal relationships among gut microbiota, gut metabolites and the risk of AD, PD and ALS, and we revealed several causal relationships. These findings may provide new targets for treatment of these neurodegenerative diseases, and may offer valuable insights for further researches on the underlying mechanisms.


2021 ◽  
Author(s):  
Yutong Lin ◽  
Yuan Lai ◽  
Songbo Tang ◽  
Zhangfen Qin ◽  
Jianfeng Liu ◽  
...  

Abstract Purpose Leaf stoichiometry of carbon (C), nitrogen (N) and phosphorus (P) is indicative of plant nutrient limitation, community composition, ecosystem function. Understanding leaf stoichiometry patterns of C, N, P of eurytopic species at genus-level across large-scale geographic regions and identifying their driven factors are of great importance to assess and to predict species’ distribution range shifts affected by climate change. Methods Here, we determined the patterns of leaf C, N, P stoichiometry of five deciduous oaks species (Quercus) across China covering ~ 20 latitude (~ 21–41˚ N) and longitude (~ 99–119˚ E) degrees, and detected their relationships with climatic, edaphic variables. Results We found that the concentrations ([ ]) of leaf C, N and the ratios ( / ) of N: P, C: P significantly increased, while leaf [P] and C/N decreased with the increasing latitude. However, leaf stoichiometry had no significant trends along the longitudinal gradient with an exception of leaf [C] which decreased with increasing longitude. The climatic variables, i.e. mean annual temperature precipitation (MAP), the max temperature of the warmest month (Tmax), temperature seasonality (TS), aridity index (AI) were the determinants on the geographic patterns of leaf C, N, P stoichiometry. The studied deciduous Quercus species growing in warm and wet environments tended to increase leaf [C], [N], C/P, and N/P, but to decrease leaf [P] and C/N, which maybe their nutritional strategies to improve adaptability. Conclusion The adaptative mechanisms of leaf stoichiometry should be further studied to assess the fate of deciduous Quercus species affected by climate change.


Diagnostics ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1683
Author(s):  
Yousun Chung ◽  
Minje Han ◽  
Jae-Seok Kim

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has been widely used for microbial identification, because of its speed and accuracy, since its introduction to clinical microbiology laboratories. In this study, we evaluated the performance of ASTA MicroIDSys, a newly developed MALDI–TOF, and compared it with the widely used Bruker Biotyper. Microbial identification with the Bruker Biotyper system was performed by using a direct smear method and the Bruker Biotyper database (reference library version 6.0.0.0). The isolates were also tested in parallel, using the ASTA MicroIDSys system with a direct smear method and the MicroIDSys database, CoreDB v1.26. A total of 914 clinical isolates were recovered from the clinical specimens. Identical results with confidence scores (≥2.0, for the Bruker Biotyper) and acceptable scores (≥140 for the ASTA MicroIDSys) were obtained for 840 (91.9%) isolates. The minor errors were defined as misidentification at the species level, and the rate was 1.1% (9/792) for Bruker Biotyper and 1.6% (13/792) for ASTA MicroIDSys. Major errors were defined as misidentification at the genus level, and the rate was 0.3% (2/792) for both Bruker Biotyper and ASTA MicroIDSys. ASTA MicroIDSys showed reliable performance for microbial identification, which was comparable to that of the Bruker Biotyper. Therefore, ASTA MicroIDSys can be applied for the identification of microorganisms in clinical microbiology laboratories.


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