scholarly journals Lacticaseibacillus casei ATCC 393 Cannot Colonize the Gastrointestinal Tract of Crucian Carp

2021 ◽  
Vol 9 (12) ◽  
pp. 2547
Author(s):  
Hongyu Zhang ◽  
Xiyan Mu ◽  
Hongwei Wang ◽  
Haibo Wang ◽  
Hui Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crucian Carp ◽  
Growth Promotion ◽  
Culture Method ◽  
Basal Diet ◽  
Experimental Period ◽  
Sequencing Analysis ◽  
Mixed Diet ◽  
Gi Tract ◽  
Elimination Kinetics

Lactic acid bacteria (LAB) are commonly applied to fish as a means of growth promotion and disease prevention. However, evidence regarding whether LAB colonize the gastrointestinal (GI) tract of fish remains sparse and controversial. Here, we investigated whether Lacticaseibacillus casei ATCC 393 (Lc) can colonize the GI tract of crucian carp. Sterile feed irradiated with 60Co was used to eliminate the influence of microbes, and 100% rearing water was renewed at 5-day intervals to reduce the fecal–oral circulation of microbes. The experiment lasted 47 days and was divided into three stages: the baseline period (21 days), the administration period (7 days: day −6 to 0) and the post-administration period (day 1 to 19). Control groups were fed a sterile basal diet during the whole experimental period, whereas treatment groups were fed with a mixed diet containing Lc (1 × 107 cfu/g) and spore of Geobacillus stearothermophilus (Gs, 1 × 107 cfu/g) during the administration period and a sterile basal diet during the baseline and post-administration periods. An improved and highly sensitive selective culture method (SCM) was employed in combination with a transit marker (a Gs spore) to monitor the elimination of Lc in the GI tract. The results showed that Lc (<2 cfu/gastrointestine) could not be detected in any of the fish sampled from the treatment group 7 days after the cessation of the mixed diet, whereas Gs could still be detected in seven out of nine fish at day 11 and could not be detected at all at day 15. Therefore, the elimination speed of Lc was faster than that of the transit marker. Furthermore, high-throughput sequencing analysis combined with SCM was used to reconfirm the elimination kinetics of Lc in the GI tract. The results show that the Lc in the crucian carp GI tract, despite being retained at low relative abundance from day 7 (0.11% ± 0.03%) to 21, was not viable. The experiments indicate that Lc ATCC 393 cannot colonize the GI tract of crucian carp, and the improved selective culture in combination with a transit marker represents a good method for studying LAB colonization of fish.

scholarly journals Arginine Alters miRNA Expression Involved in Development and Proliferation of Rat Mammary Tissue

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 535
Author(s):  
Gang Zhou ◽  
Qiaoyun Xu ◽  
Feifan Wu ◽  
Mengzhi Wang ◽  
Lianmin Chen ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Control Diet ◽  
Rna Extraction ◽  
Experimental Period ◽  
Differentially Expressed ◽  
Mammary Tissue ◽  
Control Group ◽  
Sequencing Analysis ◽  
Significant Difference

This study was designed to determine the effects of dietary arginine on development and proliferation in rat mammary tissue through changes in miRNA profiles. Twelve pregnant Wistar rats were allocated randomly to two groups. A basal diet containing arginine or the control diet containing glutamate on an equal nitrogen basis as the arginine supplemented diet were used. The experiment included a pre-experimental period of four days before parturition and an experimental period of 17 days after parturition. Mammary tissue was collected for histology, RNA extraction and high-throughput sequencing analysis. The greater mammary acinar area indicated that arginine supplementation enhanced mammary tissue development (p < 0.01). MicroRNA profiling indicated that seven miRNA (miR-206-3p, miR-133a-5p, miR-133b-3p, miR-1-3p, miR-133a-3p, miR-1b and miR-486) were differentially expressed in response to Arginine when compared with the glutamate-based control group. In silico gene ontology enrichment and KEGG pathway analysis revealed between 240 and 535 putative target genes among the miRNA. Further verification by qPCR revealed concordance with the differential expression from the sequencing results: 17 of 28 target genes were differentially expressed (15 were highly expressed in arginine and 2 in control) and 11 target genes did not have significant difference in expression. In conclusion, our study suggests that arginine may potentially regulate the development of rat mammary glands through regulating miRNAs.

scholarly journals Effect of Boulardii Yeast Wall Polysaccharides on Intestinal Microflora in Jejunum, Cecum and Colon for Early-Weaned Lambs by 16S rRNA Sequence Analysis

2021 ◽  
Vol 26 (01) ◽  
pp. 156-168
Author(s):  
Mengjian Liu
Keyword(s):  
Relative Abundance ◽  
Intestinal Microflora ◽  
High Throughput Sequencing ◽  
Basal Diet ◽  
Microbial Flora ◽  
Control Group ◽  
Sequencing Analysis ◽  
Microbial Composition ◽  
Intestinal Microbial Flora ◽  
Experimental Group

This study was conducted to investigate the effects of Boulardiiyeast wall polysaccharide (BRYP) on the intestinal micro-ecosystem of early-weaned lambs. A total of 60 early-weaned lambs (35-days-old, Kazak♂*Altay♀*Suffolk♂) were randomly assigned into two treatments: a control group with a basal diet, an experimental group with a basal diet and added 0.05% BRYP. The HiSeq high-throughput sequencing analysis of 16SrRNA was used to investigate the differences in intestinal microbial flora composition, diversity, relative abundance, principle coordination analysis, and the correlation between intestinal microbial flora composition and immune indices. After feeding for 40days, the addition of 0.5% BRYP in milk replacer significantly enhanced the species richness in the cecum and colon, but decreased the diversity of species in the colon (P <0.05); Compared with the control group, the relative abundance of Bacteroidetes in the experimental group was significantly enhanced, but the Proteobacteria was significantly decreased in all tested intestinal segments (P <0.05).In the jejunum, the relative abundance of Lactobacillus, Prevotella, and Fibrobacter of the experimental group were significantly enhanced than that of the control group, but the Ruminobacter was significantly decreased (P <0.05); In the cecum, the relative abundance of Bacteroides, Lactobacillus, Oscillospira and Bifidobacterium of the experimental group were significantly enhanced than that of the control group, but the Blautia were significantly decreased (P <0.05); In the colon, the relative abundance of Akkermansia, Bifidobacterium, Lactobacillus and Faecalibacteriumof the experimental group were significantly enhanced than that of the control group, but the Prevotella, Streptococcus, and Escherichia were significantly decreased (P <0.05). There were significant correlations between intestinal immune indices (IL-6, IL-10, TNF-α) and intestinal microbial composition in the colon (P <0.05). These results indicated that BRYP may contribute to the promotion of the proportion of helpful microbial populations and enhancing the balance of intestinal; Besides, BRYP may indirectly improve the intestinal immune function by changes of intestinal microflora composition, but suppress the inflammatory response in the bottom of intestinal mucosa of early-weaned lambs.© 2021 Friends Science Publishers

A New Approach for Predicting the Value of Gene Expression: Two-way Collaborative Filtering

2019 ◽  
Vol 14 (6) ◽  
pp. 480-490 ◽  
Author(s):  
Tuncay Bayrak ◽  
Hasan Oğul
Keyword(s):  
Gene Expression ◽  
Regression Model ◽  
Collaborative Filtering ◽  
High Throughput Sequencing ◽  
Mean Squared Error ◽  
Experimental Studies ◽  
Kernel Functions ◽  
Feature Representation ◽  
Sequencing Analysis ◽  
Computational Systems Biology

Background: Predicting the value of gene expression in a given condition is a challenging topic in computational systems biology. Only a limited number of studies in this area have provided solutions to predict the expression in a particular pattern, whether or not it can be done effectively. However, the value of expression for the measurement is usually needed for further meta-data analysis. Methods: Because the problem is considered as a regression task where a feature representation of the gene under consideration is fed into a trained model to predict a continuous variable that refers to its exact expression level, we introduced a novel feature representation scheme to support work on such a task based on two-way collaborative filtering. At this point, our main argument is that the expressions of other genes in the current condition are as important as the expression of the current gene in other conditions. For regression analysis, linear regression and a recently popularized method, called Relevance Vector Machine (RVM), are used. Pearson and Spearman correlation coefficients and Root Mean Squared Error are used for evaluation. The effects of regression model type, RVM kernel functions, and parameters have been analysed in our study in a gene expression profiling data comprising a set of prostate cancer samples. Results: According to the findings of this study, in addition to promising results from the experimental studies, integrating data from another disease type, such as colon cancer in our case, can significantly improve the prediction performance of the regression model. Conclusion: The results also showed that the performed new feature representation approach and RVM regression model are promising for many machine learning problems in microarray and high throughput sequencing analysis.

The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Hang Qian ◽  
Chunli Hou ◽  
Hao Liao ◽  
Li Wang ◽  
Shun Han ◽  
...  
Keyword(s):  
Soil Properties ◽  
Paddy Soil ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Negative Relationship ◽  
Sequencing Analysis ◽  
Nitrogen Use ◽  
Microbial Network ◽  
Α Diversity ◽  
Positive Effect

ABSTRACT To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.

scholarly journals High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 27 ◽  
Author(s):  
Marta Maciejewska ◽  
Magdalena Całusińska ◽  
Luc Cornet ◽  
Delphine Adam ◽  
Igor Pessi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Spatial Diversity ◽  
Sequencing Analysis

Macrophage-derived CXCL9 and CXCL11, T-cell skin homing and disease control in mogamulizumab-treated CTCL patients

Blood ◽  
2021 ◽  
Author(s):  
Adèle de Masson ◽  
Delphine Darbord ◽  
Gabor Dobos ◽  
Marie Boisson ◽  
Marie Roelens ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Disease Control ◽  
High Throughput Sequencing ◽  
Sequencing Analysis ◽  
Cell Clones ◽  
Skin Homing ◽  
T Cell Homing ◽  
T Cell Immune Responses

Cutaneous T-cell lymphoma (CTCL) is a malignancy of skin-homing T-cells. Long-term remissions are rare in CTCL, and the pathophysiology of long-lasting disease control is unknown. Mogamulizumab is a defucosylated anti-human CCR4 antibody that depletes CCR4-expressing CTCL tumor cells and peripheral blood memory regulatory T cells. Prolonged remissions and immune side effects have been observed in mogamulizumab-treated CTCL patients. We report that mogamulizumab induced skin rashes in 32% of 44 CTCL patients. These rashes were associated with long-term CTCL remission, even in the absence of specific CTCL treatment. CTCL patients with mogamulizumab-induced rash had significantly higher overall survival (hazard ratio, 0.16 (0.04-0.73, p=0.01)). Histopathology and immunohistochemistry of the rashes revealed granulomatous and lichenoid patterns with CD163 macrophagic and CD8 T-cell infiltrates. Depletion of skin CTCL cells was confirmed by high-throughput sequencing analysis of TCRβ genes and in blood by flow cytometry. New reactive T-cell clones were recruited in skin. Gene expression analysis showed overexpression of CXCL9 and CXCL11, two chemokines involved in CXCR3-expressing T-cell homing to skin. Single-cell RNA sequencing analysis in skin of CTCL patients confirmed that CXCL9 and CXCL11 were primarily macrophage-derived and that skin T-cells expressed CXCR3. Finally, patients with rashes had a significantly higher proportion of exhausted reactive blood T-cells expressing TIGIT and PD1 at baseline compared to patients without rash, which decreased under mogamulizumab treatment, consistent with an activation of the antitumor immunity. Together, these data suggest that mogamulizumab may induce long-term immune control in CTCL patients by activation of the macrophagic and T-cell immune responses.

PSVII-23 Experimental evaluation of the effectiveness of the Quercus cortex extract in the carp feeding system

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 339-339
Author(s):  
Mariya Miroshnikova ◽  
Elena Miroshnikova ◽  
Alexey Sizentsov ◽  
Azamat Arinzhanov ◽  
Yuliya Kilyakova
Keyword(s):  
Calcium Content ◽  
Fish Farming ◽  
Basal Diet ◽  
Experimental Period ◽  
Atomic Emission ◽  
Essential Elements ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Microbial Profile ◽  
Combined Feed

Abstract One of the most promising ways to improve the effectiveness of fish farming is the use of phytobiotics in the diet of fish. On this basis, we set the aim to evaluate the effectiveness of the Quercus cortex extract in the concentration of 1 mg/kg on biological features and the productivity of carp. The object of the research was yearling carp grown in the conditions of Orenburgskiy Osetr LLC. Two groups (n = 20) were formed by the method of analogs to conduct the research. After the adaption period (7 days), the groups came to the experimental period (35 days). The feed KRK-110–1 produced by PJSC Orenburg Combined-Feed Plant was used as the basal diet. The live fish were monitored weekly by individual weighing during the accounting period. The elemental composition was determined by the method of atomic emission and mass spectrometry (ICP-AES and ICP-MS). The microflora analysis was carried out by the method of metagenomic sequencing. The use of the Quercus cortex extract in the diet in the studied concentration increased body weight by 15.1% (P ≤ 0.05) compared to the control group. There was experimentally revealed a stimulating effect on the population growth of individual representatives of the microbiome (Luteolibacter, Lactococcus) (P ≤ 0.05) without significantly changing the overall picture of the microbial profile, which, in our view, affects the metabolic processes, in particular, by stimulating the formation of biologically available forms of essential elements and their subsequent accumulation in the tissues of the studied fish. Thus, the experimental group found: (against the background of an increase in the total mineralization (ash residue) by 17.95 % (P ≤ 0.05)) the calcium content increased by 133.9% (P ≤ 0.05), phosphorus by 83% (P ≤ 0.05), iron by 337.7% (P ≤ 0.05), respectively, in comparison with the control group.

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