scholarly journals “A different gut microbiome linked to inflammation found in cirrhotic patients with and without hepatocellular carcinoma”

2017 ◽  
Author(s):  
Federico Piñero ◽  
Martín Vazquez ◽  
Patricia Baré ◽  
Cristian Rohr ◽  
Manuel Mendizabal ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Gut Microbiome ◽  
Illumina Miseq ◽  
Differential Abundance ◽  
Receptor Signalling ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Cirrhotic Patients ◽  
Stool Samples ◽  
Inflammatory Milieu

SUMMARYBackgroundNo specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.AimTo compare the gut microbiome found in cirrhotic patients with and without HCC.MethodsFrom 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).ResultsThere were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.ConclusionsA pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.

scholarly journals Gut Microbiome Alteration after Reboxetine Administration in Type-1 Diabetic Rats

2021 ◽  
Vol 9 (9) ◽  
pp. 1948
Author(s):  
Sinem Aydin ◽  
Ceren Ozkul ◽  
Nazlı Turan Yucel ◽  
Hulya Karaca
Keyword(s):  
Gut Microbiota ◽  
Illumina Miseq ◽  
Diabetic Rats ◽  
Clinical Settings ◽  
Illumina Miseq Platform ◽  
Noradrenaline Reuptake ◽  
Miseq Platform ◽  
Stool Samples ◽  
Study Type

Antidepressants are drugs commonly used in clinical settings. However, there are very limited studies on the effects of these drugs on the gut microbiota. Herein, we evaluated the effect of reboxetine (RBX), a selective norepinephrine (noradrenaline) reuptake inhibitor (NRI), on gut microbiota in both diabetic and non-diabetic rats. This is the first report of relation between reboxetine use and the gut microbiota to our knowledge. In this study, type-1 diabetes induced by using streptozotocin (STZ) and RBX was administered to diabetic rats and healthy controls for 14 days. At the end of the treatment, stool samples were collected. Following DNA extraction, amplicon libraries for the V3-V4 region were prepared and sequenced with the Illumina Miseq platform. QIIME was used for preprocessing and analysis of the data. As a result, RBX had a significant effect on gut microbiota structure and composition in diabetic and healthy rats. For example, RBX exposure had a pronounced microbial signature in both groups, with a low Firmicutes/Bacteroidetes ratio and low Lactobacillus levels. While another abundance phylum after exposure to RBX was Proteabacteria, other notable taxa in the diabetic group included Flavobacterium, Desulfovibrionaceae, Helicobacteriaceae, Campylobacterales, and Pasteurellacae when compared to the untreated group.

scholarly journals Detection and monitoring of insect traces in bioaerosols

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10862
Author(s):  
Panyapon Pumkaeo ◽  
Junko Takahashi ◽  
Hitoshi Iwahashi
Keyword(s):  
Aerosol Particles ◽  
Illumina Miseq ◽  
Identification Accuracy ◽  
Insect Community ◽  
Cytochrome C Oxidase I ◽  
True Bugs ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Pm2.5 And Pm10 ◽  
First Time

Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.

scholarly journals Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

2020 ◽  
Vol 8 (9) ◽  
pp. 1363
Author(s):  
Julia Hankel ◽  
Amr Abd El-Wahab ◽  
Richard Grone ◽  
Birgit Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Vegetarian Diet ◽  
Rrna Gene ◽  
Feather Meal ◽  
Illumina Miseq Platform ◽  
Faecal Samples ◽  
Miseq Platform ◽  
Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

scholarly journals Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kira Moon ◽  
Suhyun Kim ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
South Korea ◽  
Illumina Miseq ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Illumina Miseq Platform ◽  
Viral Community ◽  
Viral Communities ◽  
Miseq Platform ◽  
Metagenome Sequencing ◽  
Freshwater Reservoir

Abstract A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.

scholarly journals Response of Fecal Bacterial Flora to the Exposure of Fumonisin B1 in BALB/c Mice

Toxins ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 612
Author(s):  
Fan Zhang ◽  
Zhiwei Chen ◽  
Lin Jiang ◽  
Zihan Chen ◽  
Hua Sun
Keyword(s):  
Animal Health ◽  
Bacterial Flora ◽  
Fumonisin B1 ◽  
Illumina Miseq ◽  
Fecal Microbiota ◽  
Control Group ◽  
Illumina Miseq Platform ◽  
Regulatory Limits ◽  
Miseq Platform ◽  
High Diversity

Fumonisins are a kind of mycotoxin that has harmful influence on the health of humans and animals. Although some research studies associated with fumonisins have been reported, the regulatory limits of fumonisins are imperfect, and the effects of fumonisins on fecal bacterial flora of mice have not been suggested. In this study, in order to investigate the effects of fumonisin B1 (FB1) on fecal bacterial flora, BALB/c mice were randomly divided into seven groups, which were fed intragastrically with 0 mg/kg, 0.018 mg/kg, 0.054 mg/kg, 0.162 mg/kg, 0.486 mg/kg, 1.458 mg/kg and 4.374 mg/kg of FB1 solutions, once a day for 8 weeks. Subsequently, feces were collected for analysis of microflora. The V3-V4 16S rRNA of fecal bacterial flora was sequenced using the Illumina MiSeq platform. The results revealed that fecal bacterial flora of mice treated with FB1 presented high diversity. Additionally, the composition of fecal bacterial flora of FB1 exposure groups showed marked differences from that of the control group, especially for the genus types including Alloprevotella, Prevotellaceae_NK3B31_group, Rikenellaceae_RC9_gut_group, Parabacteroides and phylum types including Cyanobacteria. In conclusion, our data indicate that FB1 alters the diversity and composition of fecal microbiota in mice. Moreover, the minimum dose of FB1 exposure also causes changes in fecal microbiota to some extent. This study is the first to focus on the dose-related effect of FB1 exposure on fecal microbiota in rodent animals and gives references to the regulatory doses of fumonisins for better protection of human and animal health.

scholarly journals Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa Using Targeted Environmental Sequencing

2021 ◽  
Vol 7 (11) ◽  
pp. 978
Author(s):  
Gilmore T. Pambuka ◽  
Tonjock Rosemary Kinge ◽  
Soumya Ghosh ◽  
Errol D. Cason ◽  
Martin M. Nyaga ◽  
...  
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Targeted Sequencing ◽  
Illumina Miseq Platform ◽  
Below Ground ◽  
Miseq Platform ◽  
Low Levels ◽  
Plant Surfaces

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

scholarly journals Illumina MiSeq reveals the influence of blueberry malvidin-3-galactoside on fecal microbial community structure and metabolizes of liver cancer mice

2018 ◽  
Author(s):  
Zhen Cheng ◽  
Yuehua Wang ◽  
Bin Li
Keyword(s):  
Liver Cancer ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Illumina Miseq ◽  
Chemotherapeutic Drugs ◽  
Computational Tools ◽  
High Incidence ◽  
Miseq Platform ◽  
Gut Microorganisms

Hepatocellular carcinoma (HCC) is a kind of cancer with high incidence and often accompanied by intestinal flora imbalance. Many studies have shown that probiotics such as anthocyanins can regulate gut microbiome and improve disease. This study was designed to evaluate the influence of blueberry malvidin-3-galactoside (M3G), a blueberry ingredient with several beneficial properties, on gut microorganisms of liver cancer (LC) mice. LC mice were fed M3G diets (LM, 40 mg/kg; HM, 80 mg/kg) or 5-fluorouracil (PC, 20 mg/kg) for three weeks. High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools adopt 16SrRNA and metagenome analyses. There was a greater abundance of Verrucomicrobiaceae (p < 0.05) and Ruminococcus (p < 0.05) in mice in the HM group than in those in the LM group. Anti-inflammatory bacteria such as Akkermansia, Sutterella increase in abundance after fed with M3G for three weeks. A significantly smaller abundance of Proinflammatory bacteria such as Dorea, Coprobacillus, Clostridium, Streptococcus, Oscillospira in HM mice(p<0.01). Both M3G and chemotherapeutic drugs can increase signal transduction, Membrane transport, and Cell Motility. In addition, the ability of cell growth and death increased in HM and PC groups but decreased in LC and LM groups. This study indicates that M3G supplementation for three weeks may not be enough to cure liver cancer. However, M3G-supplementation was associated with significant differences in the structure and metabolic function of gut microbiome compared to liver cancer controls that merit further research.

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