scholarly journals Red Cusk-Eel (Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens

2022 ◽  
Vol 10 (1) ◽  
pp. 105
Author(s):  
Jaime Romero ◽  
Osmán Díaz ◽  
Claudio D. Miranda ◽  
Rodrigo Rojas
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Acid Synthesis ◽  
Intestinal Content ◽  
Meat Production ◽  
Rrna Gene ◽  
Potential Contribution ◽  
Ion Torrent ◽  
The 16S Rrna Gene ◽  
Genypterus Chilensis

Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.

scholarly journals Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Laura Glendinning ◽  
Kellie A. Watson ◽  
Mick Watson
Keyword(s):  
Microbial Community ◽  
Intestinal Microbiota ◽  
Intestinal Tract ◽  
Microbial Community Composition ◽  
Intestinal Content ◽  
Rrna Gene ◽  
Large Role ◽  
The 16S Rrna Gene ◽  
Caecal Microbiota ◽  
Over Time

Abstract Background The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare. Results In this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identified significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterised the development of the microbiota at each intestinal site over time. Conclusions Our study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

scholarly journals Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

2019 ◽  
Author(s):  
Laura Glendinning ◽  
Kellie A Watson ◽  
Mick Watson
Keyword(s):  
Microbial Community ◽  
Intestinal Microbiota ◽  
Intestinal Tract ◽  
Microbial Community Composition ◽  
Intestinal Content ◽  
Rrna Gene ◽  
Large Role ◽  
The 16S Rrna Gene ◽  
Caecal Microbiota ◽  
Over Time

AbstractBackgroundThe chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare.ResultsIn this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identify significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterise the development of the microbiota at each intestinal site over time.ConclusionsOur study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

scholarly journals Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia

2020 ◽  
Vol 8 (12) ◽  
pp. 1967
Author(s):  
Tamara N. Nazina ◽  
Salimat K. Bidzhieva ◽  
Denis S. Grouzdev ◽  
Diyana S. Sokolova ◽  
Tatyana P. Tourova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Petroleum Reservoir ◽  
Ph Range ◽  
The 16S Rrna Gene

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.

scholarly journals Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments

2020 ◽  
Vol 12 (9) ◽  
pp. 3624 ◽  
Author(s):  
Tatyana Tourova ◽  
Diyana Sokolova ◽  
Tamara Nazina ◽  
Denis Grouzdev ◽  
Eugeni Kurshev ◽  
...  
Keyword(s):  
Amino Acids ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Petrochemical Plant ◽  
Industrial Water ◽  
Aqueous Environments ◽  
The 16S Rrna Gene ◽  
Xenobiotic Degradation

The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater. Both communities have a high potential ability to carry out the carbohydrates and amino acids metabolism, but the potential for xenobiotic degradation, including styrene degradation, was relatively higher in the biofilms in industrial water. Bacteria of the genera Erythrobacter, Maribacter, and Mycobacterium were potential styrene-degraders in seawater, and Pseudomonas and Arenimonas in industrial water. Our results suggest that marine and industrial waters contain microbial populations potentially capable of degrading PS, and these populations may be used for the isolation of efficient PS degraders.

scholarly journals Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41484 ◽  
Author(s):  
Marcio C. Costa ◽  
Luis G. Arroyo ◽  
Emma Allen-Vercoe ◽  
Henry R. Stämpfli ◽  
Peter T. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
The 16S Rrna Gene

16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

2018 ◽  
Vol 81 (5) ◽  
pp. 848-859
Author(s):  
MIYO NAKANO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Animal Feed ◽  
Rrna Gene ◽  
Universal Primer ◽  
Food Matrices ◽  
Taxonomic Groups ◽  
The 16S Rrna Gene

ABSTRACT High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.

scholarly journals Analysis of Microbial Diversity and Dynamics During Bacon Storage Inoculated With Potential Spoilage Bacteria by High-Throughput Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Xinfu Li ◽  
Qiang Xiong ◽  
Hui Zhou ◽  
Baocai Xu ◽  
Yun Sun
Keyword(s):  
High Throughput ◽  
Storage Time ◽  
High Throughput Sequencing ◽  
Bacterial Load ◽  
Meat Products ◽  
Rrna Gene ◽  
C Dynamics ◽  
Spoilage Bacteria ◽  
Leuconostoc Gelidum ◽  
The 16S Rrna Gene

Staphylococcus xylosus, Leuconostoc mesenteroides, Carnobacterium maltaromaticum, Leuconostoc gelidum, and Serratia liquefaciens were investigated for their roles in in the spoilage of sterilized smoked bacon. These five strains, individually and in combination, were applied as starters on sliced bacon at 4–5 log10 CFU/g using a hand-operated spraying bottle and stored for 45 days at 0–4°C. Dynamics, diversity, and succession of microbial community during storage of samples were studied by high-throughput sequencing (HTS) of the V3–V4 region of the 16S rRNA gene. A total of 367 bacterial genera belonging to 21 phyla were identified. Bacterial counts in all the inoculated specimens increased significantly within the first 15 days while the microbiota developed into more similar communities with increasing storage time. At the end of the storage time, the highest abundance of Serratia (96.46%) was found in samples inoculated with S. liquefaciens. Similarly, for samples inoculated with C. maltaromaticum and L. mesenteroides, a sharp increase in Carnobacterium and Leuconostoc abundance was observed as they reached a maximum relative abundance of 97.95 and 81.6%, respectively. Hence, these species were not only the predominant ones but could also have been the more competitive ones, potentially inhibiting the growth of other microorganisms. By analyzing the bacterial load of meat products using the SSO model, the relationships between the microbial communities involved in spoilage can be understood to assist further research.

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