scholarly journals Hepatic stellate cell activation and senescence induced by intrahepatic microbiota disturbances drive progression of liver cirrhosis toward hepatocellular carcinoma

2022 ◽  
Vol 10 (1) ◽  
pp. e003069
Author(s):  
Boyuan Liu ◽  
Zewei Zhou ◽  
Yu Jin ◽  
Jinying Lu ◽  
Dongju Feng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Activation ◽  
Molecular Mechanisms ◽  
Stellate Cell ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Composition ◽  
Inflammatory Factors ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Rrna Gene Sequencing

BackgroundThe significance of the relationship between the microbiota and diseases is increasingly being recognized. However, the characterization of tumor microbiome and their precise molecular mechanisms through which microbiota promotes hepatocellular carcinoma (HCC) development are still unclear.MethodsThe intrahepatic microbiota was investigated from tumor, normal adjacent tissues in 46 patients with HCC and normal hepatic tissues in 33 patients with hemangioma by 16S rRNA gene sequencing. Taxonomic composition differences in patients were evaluated using Linear discriminant analysis Effect Size (LefSe) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict microbial functional pathways. Associations between the most relevant taxa and clinical characteristics of HCC patients were analyzed by Spearman rank correlations. The effects of microbe on hepatic stellate cells (HSCs) activation and HCC progression were examined.ResultsWe observed intrahepatic microbiota disturbances by reduced microbial diversity in HCC. The tumor microbiota of the HCC patients with cirrhosis showed higher abundance of Stenotrophomonas maltophilia (S. maltophilia). S. maltophilia provoked senescence-associated secretory phenotype (SASP) in HSCs by activating TLR-4-mediated NF-κB signaling pathway, which in turn induced NLRP3 inflammasome complex formation and secreted various inflammatory factors in the liver, thus facilitating HCC progression in mice. Moreover, signs of SASP were also observed in the HSCs in the area of HCC with higher S. maltophilia enrichment arising in patients with cirrhosis.ConclusionsOur analysis of the hepatic microbiota revealed for the first time that patients with HCC exhibited a dysbiotic microbial community with higher S. maltophilia abundance, which induced the expression SASP factors of HSCs and cirrhosis in the liver, concurring in the process of hepatocarcinogenesis.

scholarly journals Dynamic changes in intestinal microbiota in young forest musk deer during weaning

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8923
Author(s):  
Yimeng Li ◽  
Minghui Shi ◽  
Tianxiang Zhang ◽  
Xin Hu ◽  
Baofeng Zhang ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Musk Deer ◽  
Dynamic Changes ◽  
Linear Discriminant ◽  
Bacterial Phyla ◽  
Young Forest ◽  
Rrna Gene Sequencing

Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer.

scholarly journals Restoration of soil microbiome in various soil horizons after crown and surface wildfires.

2020 ◽  
Author(s):  
Grigory V. Gladkov ◽  
Ekaterina Chebykina ◽  
Elizaveta Evdokimova ◽  
Ekaterina Ivanova ◽  
Anastasiia Kimeklis ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Taxonomic Composition ◽  
Soil Microbiome ◽  
Soil Restoration ◽  
Rrna Gene ◽  
Crown Fire ◽  
Soil Horizons ◽  
Rrna Gene Sequencing ◽  
And Shifts ◽  
The City

Fires have a strong effect on soil microbiome, and the mechanisms of soil restoration after fires are currently not well understood.Thisstudy describes the characteristics of microbial communities in the Psamment Entisol soils of pine forests in the city of Togliatti after forest crown and surface fires.Geochemistry, soil respiration and microbial community structure via 16S rRNA gene sequencing were studied in different soil horizons. Both crown and surface fires resulted in the variations of microbial diversity and shifts in taxonomic composition. There is a tendency to an increase in the proportion of representatives from phylaActinobacteria and Gemmatimonadetes for soil samples recovering after fires. An increase in the proportion of bacteria (Micrococcaceae, Blastocatellaceae) associated with the degradation of substances formed after combustionalsohas been shown. The research has shown that the crown fire has a smaller effect on the soil microbiome than thesurfacefire,the largest changes in the microbiome structure were found in the intermediate horizon.At the same time, differences in the structure of the soil microbiome between horizons are intensified after exposure to the soil of asurfacefire.

scholarly journals Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium

2019 ◽  
Author(s):  
Andre Mu ◽  
Glen P. Carter ◽  
Lucy Li ◽  
Nicole S. Isles ◽  
Alison F. Vrbanac ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Enterococcus Faecium ◽  
Molecular Mechanisms ◽  
Microbial Community Composition ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Functional Roles ◽  
Specific Pathogen ◽  
Vancomycin Resistant ◽  
Rrna Gene Sequencing

AbstractVancomycin resistant Enterococcus faecium (VREfm) is an emerging antibiotic resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenerricutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone, and to subsequent VREfm challenge. Using neural networking approaches to find co-occurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition towards a pre-antibiotic naïve microbiome. This study shows the impacts of antibiotics on the gut ecosystem, and the progression of the microbiome in response to colonisation with VREfm. Our results offer insights towards identifying potential non-antibiotic alternatives to eliminate VREfm through metabolic re-engineering to preferentially select for Bacteroides.ImportanceThis study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.

scholarly journals PSIX-12 Inclusion of dried distillers grains with solubles in Lespedeza or alfalfa-based diets for meat goats is associated with a unique ruminal microbiome

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 421-421
Author(s):  
Andres A Pech-Cervantes ◽  
Ibukun M Ogunade ◽  
Donielle Pannell ◽  
Brou Kouakou
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sericea Lespedeza ◽  
Linear Discriminant ◽  
Distillers Grains With Solubles ◽  
Randomized Design ◽  
Meat Goats ◽  
Rrna Gene Sequencing

Abstract This study evaluated the effect of replacement of corn and soybean meal with distillers dried grains with solubles (DDGS) in lespedeza or alfalfa-based diets on the ruminal microbiome of growing meat goats. A total of 36 meat goats with average body weight (BW) of 24 ± 1.8 kg were blocked by BW and randomly assigned to four isonitrogenous (18.0) and isocaloric (3.2 Mcal/ kg DM) diets in a completely randomized design for 60 days. The treatment diets were: (1) alfalfa-based diet (ALC; containing 40.5% alfalfa, 26% corn and 13% SBM), (2) alfalfa and DDGS (ALD; replacement of corn and SBM with DDGS), (3) Sericea lespedeza (SL)-based diet (SLC; containing 47.25% SL, 20% corn, 13% SBM), (4) SL and DDGS (SLD; replacement of corn and SBM with DDGS). At the end of the experiment, the goats were slaughtered and rumen contents were immediately sampled for 16S rRNA gene sequencing. Linear discriminant analysis (LDA) effect size (LEfSe) were used to detect differentially abundant taxa among treatments. The relative abundance of 11 taxa, including Ruminococcaceae UCG 002, Succinivibrionaceae UCG 002 and Prevotellaceae YAB2003 were reduced (LDA > 2; P < 0.05) while 62 taxa, including Ruminococcaceae UCG 013, Ruminococcaceae UCG 001, and Saccharofermentans were enriched (LDA > 2; P < 0.05) in ALD compared to ALC. Relative abundance of 35 taxa, including Ruminococcus YE281, Succinivibrio, and Lachnospiraceae ND3007 were reduced while 42 taxa, including Prevotellaceae UCG 003 and Ruminococcus were enriched (LDA > 2; P < 0.05) in SLD, compared to SLC. A total of 68, 35, 61, and 91 taxa were respectively detected ALC, SLC, SLD, and ALD, but not in other treatments. These results showed that inclusion of DDGS in lespedeza or alfalfa-based diet causes a shift in ruminal microbial community and is associated with a unique ruminal microbial community

scholarly journals Matrine-chitosan hydrogels for treating subclinical bovine mastitis by intramammary infusion—effect on milk microbiome and metabolites

2020 ◽  
Author(s):  
Fuxin Wu ◽  
Hua Zhang ◽  
Hui Niu ◽  
Benhai Xiong ◽  
Jinjin Tong ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Bovine Mastitis ◽  
Principal Component ◽  
16S Rrna Gene Sequencing ◽  
Subclinical Mastitis ◽  
Rrna Gene ◽  
Anticancer Properties ◽  
Milk Samples ◽  
Rrna Gene Sequencing ◽  
Chitosan Hydrogels

Abstract BackgroundThe metabolic processes of cows undergo significant changes during subclinical mastitis, but their molecular mechanisms have not been clearly elucidated. This study investigated the changes in milk metabolites after intramammary infusion of matrine, a plant alkaloid with anticancer properties, in the form of a chitosan hydrogel into bovine mammary glands with subclinical mastitis. Infusions were continued for seven days, and milk samples were collected on day 1 and day 7 for analysis of the microbiome by 16S rRNA gene sequencing and metabolites by liquid chromatography-mass spectrometry.ResultsMatrine-chitosan hydrogels (MCHs) significantly decreased the somatic cell count on day 7 and the Simpson index indicated that microbial diversity was significantly lower on day 7 than on day 1. On day 7, the numbers of Aerococcus, Corynebacterium_1 and Staphylococcus were significantly lower, while the abundance of Firmicutes was very significantly decreased. The numbers of Probacteria increased, however. In milk samples, we identified 74 differentially expressed metabolites and the MCH infusion group had the most significantly upregulated metabolites including sphingolipids, glycerophospholipids, flavonoids and fatty acyls. Principal component analysis and the orthogonal partial least squares discriminant test confirmed good separation of the milk metabolites. The identification of active milk metabolic pathways after MCH treatment supported the known antimicrobial and anti-inflammatory properties of matrine that are associated with glycerophospholipid metabolism and the sphingolipid metabolic signaling pathways.ConciusionsThese insights into the mechanisms and the corresponding biological responses to matrine demonstrate its potential immunoregulatory activity and emphasize the need for continued investigation.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

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