scholarly journals Gut Microbiota: A New Strategy to Study the Mechanism of Electroacupuncture and Moxibustion in Treating Ulcerative Colitis

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Daneng Wei ◽  
Lushuang Xie ◽  
Zhiqi Zhuang ◽  
Na Zhao ◽  
Biao Huang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Treg Cells ◽  
Detailed Mechanism ◽  
New Strategy ◽  
Flora Diversity ◽  
The Relationship

Previous studies have confirmed that acupuncture and moxibustion is an effective way for treating ulcerative colitis (UC). However, the exact mechanism is unclear yet. In this study, DSS-induced UC mice were treated by electroacupuncture and moxibustion, and the genome of intestinal flora was subsequently detected by high-throughput sequencing in order to explore the detailed mechanism in terms of intestinal flora. The results indicated that the alpha diversity indices and beta diversity of intestinal flora were improved by electroacupuncture and moxibustion treatments, especially by the moxibustion treatment. These treatments inhibited Streptococcus, Odoribacter, and Allobaculum whereas it facilitated Lactobacillus on genus level. Further correlation analysis showed that the alpha diversity indices were positively correlated with the percentage of Treg cells in CD4+ cells but negatively correlated with the percentage of Th17 in CD4+ cells. These data indicated that both electroacupuncture and moxibustion can promote the intestinal flora diversity, providing a new view to understand the relationship between host and microbiome when using some external therapies.

scholarly journals Effect of Periampullary Diverticulum on Biliary Flora and the Formation of Common Bile Duct Stone

2020 ◽  
Author(s):  
Senlin Hou ◽  
Hao Wang ◽  
Lichao Zhang ◽  
Tingting Yu ◽  
Zhanying Qiao
Keyword(s):  
Bile Duct ◽  
Common Bile Duct ◽  
High Throughput Sequencing ◽  
Bile Duct Stone ◽  
Stone Formation ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
Intestinal Fluid ◽  
Bacterial Gene ◽  
Periampullary Diverticulum

Abstract Background: Bile duct stone is closely related to periampullary diverticulum, but it is not clear whether the formation of it was affected by the diverticulum through the biliary flora. To explore the diversity and correlation of biliary and intestinal flora in the patients with choledocholithiasis and the effects of periampullary diverticulum on the flora and bile duct stone. Methods: Bile and intestinal fluid were collected from patients with primary common bile duct stones, and then divided into diverticulum group and none- diverticulum group according to the presence or absence of paravertebral diverticula, DNA of these samples was extracted and a bacterial gene library was constructed, and related bioinformatics analysis was performed after high-throughput sequencing to obtain the bacterial components and community structure of the sample. Result: A total of 3001,613 valid sequences were obtained, with an average of 136436.95±3696.842 sequences, which were classified into 6021 ASV/OUT. Alpha diversity analysis showed that the species richness and diversity in the diverticulum group were lower than those in the nondiverticulum group. According to the species annotation results, the advantage bacterium group of the bile is Proteobacteria (BG 80.41%, Bg 70.95%), and advantage bacterium group of the intestinal fluid is Firmicutes and Proteobacteria (BG 89.39%, Bg 74.11%). A large proportion of Enterobacter was found in bile. Escherichia coli, Klebsiella, Streptococcus and other bacteria closely related to stone formation have been found. The proportion of E. coli in the diverticulum group was increased and due to the existence of the diverticulum Enterobacteria in the bile were increased and more complex. The bacteria that produce Betaglucuronidase are found to be increased in bile. Due to the influence of the periampullary diverticulum, the intestinal flora will be changed and then the biliary flora will also change. Conclusion: The existence of periampullary diverticulum will affect the biliary tract flora and lead to the increase of bacteria related to stone formation, which will affect the formation of choledocholithiasis and make it easier for choledocholithiasis to form.

scholarly journals Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Qing Tong ◽  
Li-Yong Cui ◽  
Jia Bie ◽  
Xiao-Yun Han ◽  
Zong-Fu Hu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Positive Association ◽  
Diversity Indices ◽  
Control Group ◽  
Functional Composition ◽  
Significant Positive Association ◽  
Collateral Effect

Abstract Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota.

scholarly journals Diet Induces the Difference of Gut Fungal Communities between Anser erythropus Wintering at Shengjin and Caizi Lakes, China

2021 ◽  
Author(s):  
Gang Liu ◽  
Zhizhong Gong ◽  
Jiahui Feng ◽  
Na Xu
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Fungal Communities ◽  
Pathogenic Species ◽  
Potential Pathogen ◽  
Host Nutrition ◽  
The Difference ◽  
Serious Disease ◽  
Anser Erythropus

Abstract The gut microbiota play major roles in host nutrition and metabolism, and even potential to cause serious disease for animals and human, however, the knowledge of waterbirds’ gut fungal communities are quite limited at present. In this paper, the gut fungal communities and infer the potential pathogens isolated from the feces of Anser erythropus wintering at Shengjin Lake (SJ) and Caizi Lake (CZ) were investigated based on ITS gene region by using high-throughput sequencing. 1,302,562 valid tags corresponding to 2,102 OTUs were retained from 20 fecal samples, including 10 samples per lake. The OTUs from SJ geese represented seven phyla and 27 classes, seven phyla and 28 classes were identified from CZ samples. Ascomycota, Basidiomycota, Zygomycota and Rozellomycota were the dominant gut fungal phyla in this study, accounted for 61.60%, 35.60%, 1.84%, and 0.30% of the OTUs, respectively. The alpha diversity indices showed significantly different between the geese from SJ and CZ. The Anser erythropus mainly ate Poaceae spp. at SJ, while Carex spp. component was identified at CZ, suggesting that the variations in fungal community between the two lake geese might be induced by different diets. We also observed a fungal pattern with a higher number of significant correlations to bacterial genus, and Ceratobasidium, Tomentella, Paurocotylis, Tuber, Podospora and Mortierella were core fungal genus in the two lake geese. Nine potential pathogenic species were identified in the guts across all samples of Anser erythropus at SJ and CZ, it also showed the relative abundance of potential pathogen was significantly higher from SJ samples than that from CZ samples. These findings expanded our knowledge on the gut fungi for waterbirds, indicating the fungi are highly sensitive to diet at two lakes and should pay more attention to the potential pathogenic species of Anser erythropus.

scholarly journals Characterization of fungal microbial diversity in healthy and diarrheal Tibetan piglets

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qinghui Kong ◽  
Suozhu Liu ◽  
Aoyun Li ◽  
Yaping Wang ◽  
Lihong Zhang ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Dynamic Balance ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Republic Of China ◽  
Tibet Autonomous Region ◽  
The Tibet Autonomous Region

Abstract Background Diarrhea is an important ailment limiting the production of the Tibetan pig industry. Dynamic balance of the intestinal microbiota is important for the physiology of the animal. The objective of this work was to study fungal diversity in the feces of early weaning Tibetan piglets in different health conditions. Results In the present study, we performed high-throughput sequencing to characterize the fungal microbial diversity in healthy, diarrheal and treated Tibetan piglets at the Tibet Autonomous Region of the People’s Republic of China. The four alpha diversity indices (Chao1, ACE, Shannon and Simpson) revealed no significant differences in the richness across the different groups (P > 0.05). In all samples, the predominant fungal phyla were Ascomycota, Basidiomycota and Rozellomycota. Moreover, the healthy piglets showed a higher abundance of Ascomycota than the treated ones with a decreased level of Basidiomycota. One phylum (Rozellomycota) showed higher abundance in the diarrheal piglets than in the treated. At genus level, compared with that to the healthy group, the proportion of Derxomyces and Lecanicillium decreased, whereas that of Cortinarius and Kazachstania increased in the diarrheal group. The relative abundances of Derxomyces, Phyllozyma and Hydnum were higher in treated piglets than in the diarrheal ones. Conclusions A decreased relative abundance of beneficial fungi (e.g. Derxomyces and Lecanicillium) may cause diarrhea in the early-weaned Tibetan piglets. Addition of probiotics into the feed may prevent diarrhea at this stage. This study presented the fungal diversity in healthy, diarrheal and treated early-weaned Tibetan piglets.

scholarly journals Microbial Community Structure Drives Predatory Myxobacteria Distribution Under Different Compost Manures

2021 ◽  
Author(s):  
Wei Dai ◽  
Ning Wang ◽  
Wenhui Wang ◽  
Xianfeng Ye ◽  
Zhongli Cui ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Distribution Patterns ◽  
Diversity Indices ◽  
Community Diversity ◽  
Microbial World ◽  
Significant Difference ◽  
Compost Manure

Abstract Myxobacteria are unique predatory microorganisms with a distinct social lifestyle. The associated taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, under organic conditions, myxobacteria abundance increases in the soil, which could be related to the presence of abundant myxobacteria in the applied compost manure. In the present study, high-throughput sequencing technologies were used to investigate the distribution patterns and drivers of predatory myxobacteria community distribution patterns in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (P < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing myxobacteria distribution patterns under different compost manure treatments. In addition, pH, total nitrogen, and organic carbon influenced myxobacteria distribution in compost manure. The predator–prey relationship between prey bacteria and myxobacteria and the interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure could explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ distribution patterns of predatory myxobacteria and the key bacteria influencing their distribution are would advance our understanding of the ecological distribution patterns and functions of predatory microorganisms in the microbial world.

Potential of Lactobacillus plantarum ZDY2013 and Bifidobacterium bifidum WBIN03 in relieving colitis by gut microbiota, immune, and anti-oxidative stress

2018 ◽  
Vol 64 (5) ◽  
pp. 327-337 ◽  
Author(s):  
Yuanyuan Wang ◽  
Yilin Guo ◽  
Hui Chen ◽  
Hua Wei ◽  
Cuixiang Wan
Keyword(s):  
Oxidative Stress ◽  
Gut Microbiota ◽  
Lactobacillus Plantarum ◽  
High Throughput Sequencing ◽  
Cell Model ◽  
Intestinal Flora ◽  
Bifidobacterium Bifidum ◽  
Transcriptional Level ◽  
Bioinformatics Analyses ◽  
New Strategy

Ulcerative colitis (UC) is an inflammatory bowel disease that is difficult to cure, with rising incidence in recent decades. Probiotics have become a new strategy for UC treatment. In this study, we chose 2 new multisource probiotics, Lactobacillus plantarum ZDY2013 from acid beans and Bifidobacterium bifidum WBIN03 from infant feces, and a mixture of both, to investigate the anti-inflammatory and antioxidant effect on H2O2-induced oxidative damage in a HT-29 cell model and dextran sodium sulfate (DSS)-induced UC in mice. Compared with the model group, the general relative indices results showed L. plantarum ZDY2013 and B. bifidum WBIN03 have a significant effect on DSS-induced UC in mice, by downregulating the pro-inflammatory cytokines (e.g., TNF-α) and upregulating antioxidant factors (e.g., SOD1, SOD2, GPX2) at the transcriptional level. By means of high-throughput sequencing (16S V3–V4) and systematical bioinformatics analyses, we found that colitis may be associated with the changes in intestinal flora, especially Firmicutes and Bacteroides. Administration of L. plantarum ZDY2013 increased the abundance of Lactobacillus animalis, whereas B. bifidum WBIN03 increased the abundance of Lachnospiraceae bacterium COE1. Our results revealed that a supplement of L. plantarum ZDY2013 and B. bifidum WBIN03 remit UC through modification of gut microbiota to regulate oxidative stress and inflammatory mediators.

scholarly journals Study on the effect of Koumiss on the intestinal flora of mice infected with Toxoplasma gondii

2021 ◽  
Author(s):  
Xinlei Yan ◽  
Wenying Han ◽  
Xindong Jin ◽  
Yufei Sun ◽  
Jialu Gao ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Food Borne ◽  
Almost All ◽  
Brain Cysts ◽  
Effective Drugs ◽  
The Relationship ◽  
The Brain

Abstract Toxoplasma gondii is a worldwide food-borne parasite that can infect almost all warm-blooded animals, including humans. To date, there are no effective drugs to prevent or eradicate T. gondii infection. Recent studies have shown that probiotics could influence the relationship between the microbiota and parasites in the host. Koumiss has been used to treat many diseases based on its probiotic diversity. Therefore, we explored the effect of koumiss on T. gondii infection via its effect on the host intestinal flora. BALB/c mice were infected with T. gondii and treated with PBS, koumiss and mares’ milk. Brain cysts were counted, and long-term changes in the microbiota and the effect of koumiss on gut flora were investigated with high-throughput sequencing technology. The results suggested that koumiss treatment significantly decreased the cyst counts in the brain (P < 0.05). Moreover, T. gondii infection changed the microbiota composition, and koumiss treatment increased the relative abundance of Lachnospiraceae and Akkermansia muciniphila, which were associated with preventing T. gondii infection. Moreover, koumiss could inhibit or ameliorate T. gondii infection by increasing the abundance of certain bacteria that control unique metabolic pathways. The study not only established a close interaction among the host, intracellular pathogens and intestinal flora but also provided a novel focus for drug development to prevent and eradicate T. gondii infection.

scholarly journals Cetobacterium Is a Major Component of the Microbiome of Giant Amazonian Fish (Arapaima gigas) in Ecuador

Animals ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 189 ◽  
Author(s):  
Carolina Ramírez ◽  
Jaime Coronado ◽  
Arturo Silva ◽  
Jaime Romero
Keyword(s):  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Large Fish ◽  
Differential Distribution ◽  
Intestinal Bacterial Community ◽  
Arapaima Gigas ◽  
Fast Growth Rate

Arapaima gigas is a large air-breathing fish found in Amazonian rivers, a characteristic that gives this species an advantage in oxygen-deprived waters. It shows high potential for aquaculture in the Amazon region due to its fast growth rate that approaches 10–15 kg/year. The aim of this study was to explore the composition of the intestinal bacterial community of Arapaima gigas reared in Ecuador using 16S rRNA gene high-throughput sequencing. The analysis revealed significant differences in alpha diversity indices (p < 0.05) and differential distribution of minor components of the intestinal microbiome between small and large fish. However, components with greater relative abundance, such as Cetobacterium, are found in similar proportions.

scholarly journals Analysis of the relationship between caecal flora difference and production performance of two rabbit species by high-throughput sequencing

2021 ◽  
Author(s):  
Zhiqiang Guo ◽  
Bin Wang ◽  
Jingzhi Lu ◽  
Congyan Li ◽  
Liangde Kuang ◽  
...  
Keyword(s):  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Average Daily Gain ◽  
Intestinal Flora ◽  
Nutritional Composition ◽  
Production Performance ◽  
Light Cycle ◽  
The Difference ◽  
The Relationship

The purpose of this experiment is to study the relationship between the difference in production performance between Sichuan White (SC) rabbits and New Zealand (NZL) rabbits and the diversity of caecal flora. Twelve pregnant SC rabbits and 12 NZL female rabbits were selected for this experiment. After delivery, the young rabbits were divided into two groups according to breeds, each group had 30 replicates, and each replicate had one rabbit. During the experiments, these rabbits were kept in the same room, and the temperature in the room was controlled at 12–25 °C, with a 16-hour light cycle every 24 hours. The nutritional composition of the feed and other environmental conditions were consistent. On the 59<sup>th</sup> day of the experiment, the caecum contents of the two groups of young rabbits were collected. The results showed that the survival rate of the SC rabbit group was higher than that of the NZL rabbit group, and the diarrhoea rate and average daily gain were lower than those of the NZL rabbit group (P &lt; 0.05). The results of high-throughput sequencing of the 16S gene showed that compared with the NZL rabbit group, the relative abundance of Bacteroides increased, and the abundance of harmful flora Verrucomicrobia and Proteobacteria decreased (P &lt; 0.05). Functional analysis of the microflora showed that the relative abundance of carbohydrate metabolism genes in the SC rabbit group was higher than in the NZL rabbit group. In conclusion, compared with the NZL rabbits, the SC rabbits have a more optimized intestinal flora structure and lower abundance of harmful bacteria. Moreover, the intestinal health level of SC rabbits is improved, and the tolerance to roughage of SC rabbits is increased.

scholarly journals Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1767
Author(s):  
Federica Cattonaro ◽  
Alessandro Spadotto ◽  
Slobodanka Radovic ◽  
Fabio Marroni
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Species Abundance ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Biological Matrices ◽  
Single Experiment ◽  
Shotgun Metagenomics ◽  
Full Dataset ◽  
Conserved Genes

Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine  if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are alpha diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct—even partially—the metagenome.

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