scholarly journals The Bacterial Microflora of Fish, Revised

2006 ◽  
Vol 6 ◽  
pp. 931-945 ◽  
Author(s):  
B. Austin
Keyword(s):  
Fish Tissue ◽  
Taxonomic Composition ◽  
Surrounding Water ◽  
Complex Molecules ◽  
Bacterial Populations ◽  
Modern Culture ◽  
Light Emitting ◽  
Uncultured Bacteria ◽  
Culture Independent ◽  
Kidney Liver

The results of numerous studies indicate that fish possess bacterial populations on or in their skin, gills, digestive tract, and light-emitting organs. In addition, the internal organs (kidney, liver, and spleen) of healthy fish may contain bacteria, but there is debate about whether or not muscle is actually sterile. Using traditional culture-dependent techniques, the numbers and taxonomic composition of the bacterial populations generally reflect those of the surrounding water. More modern culture-independent approaches have permitted the recognition of previously uncultured bacteria. The role of the organisms includes the ability to degrade complex molecules (therefore exercising a potential benefit in nutrition), to produce vitamins and polymers, and to be responsible for the emission of light by the light-emitting organs of deep-sea fish. Taxa, including Pseudomonas, may contribute to spoilage by the production of histamines in fish tissue.

scholarly journals The Bacterial Microflora of Fish

2002 ◽  
Vol 2 ◽  
pp. 558-572 ◽  
Author(s):  
B. Austin
Keyword(s):  
Fish Tissue ◽  
Taxonomic Composition ◽  
Internal Organs ◽  
Surrounding Water ◽  
Complex Molecules ◽  
Bacterial Populations ◽  
Light Emitting ◽  
Kidney Liver ◽  
Sea Fish

The results of numerous studies indicate that fish possess bacterial populations on or in their skin, gills, digestive tract, and light-emitting organs. In addition, the internal organs (kidney, liver, and spleen) of healthy fish may contain bacteria, but there is debate on whether or not muscle is actually sterile. The numbers and taxonomic composition of the bacterial populations often reflect those of the surrounding water. The role of the bacteria includes the ability to degrade complex molecules (therefore exercising a potential benefit in nutrition), to produce vitamins and polymers, and to be responsible for the emission of light by the light-emitting organs of deep-sea fish. Taxa, includingPseudomonas, may contribute to spoilage by the production of histamines in fish tissue.

scholarly journals Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 472
Author(s):  
Yeong-Ji Oh ◽  
Ye-Rin Park ◽  
Jungil Hong ◽  
Do-Yup Lee
Keyword(s):  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Functional Evaluation ◽  
Initial Condition ◽  
Microbial Composition ◽  
Light Emitting ◽  
Blue Led ◽  
Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

scholarly journals 176 Characterizing the mycobiome in piglets during the weaning transition

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 177-177
Author(s):  
Ann Arfken ◽  
Juli Frey ◽  
Timothy Ramsay ◽  
Katie L Summers
Keyword(s):  
Gi Tract ◽  
Fatty Acid Production ◽  
Bacterial Populations ◽  
Fiber Degradation ◽  
Host Health ◽  
Culture Independent ◽  
Fungal Organisms ◽  
Fungal Populations ◽  
High Degree ◽  
Slow Growing

Abstract The importance of the microbiota in the gastrointestinal (GI) tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time of interest to industry. In this study, we sought to assess and characterize the mycobiome and microbiome in the feces and GI tract of swine from birth through the critical weaning transition (days 1–35 post-birth). In addition, we investigated environmental factors that may alter microorganisms present in piglets. Fecal bacterial populations increased in diversity over the experimental timeline and demonstrated a transition from an Enterobacteriaceae-dominated population, to a Prevotellaceae and Ruminococcaceae-dominated population by days 24–35 post-birth. These later populations are capable of fiber degradation and short chain fatty acid production. In fecal fungal populations, richness and diversity peaked at weaning and declined post-weaning. There was also a dynamic shift in the mycobiome to a Saccharomycetaceae-dominated population that remained stable into adulthood. Fungal organisms contributing to this colonization were not found in environmental samples including water, colostrum, and feed. Despite fungal populations present in the feces of sows, these maternal fungi were not similar to the piglet mycobiome and thus did not indicate a maternally-derived effect. Furthermore, the microbiomes of the GI tract showed decreased richness and diversity in the upper GI compared to the lower GI, and a high degree of individual variation and litter effect throughout the organs. This study provides insights into the early colonization and establishment of fungi during the weaning transition. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition, including their role in fast- versus slow-growing piglets.

Diversity of ammonia-oxidising bacteria and archaea in seven different estuarine sediments from Poyang Lake

2016 ◽  
Vol 67 (12) ◽  
pp. 1897 ◽  
Author(s):  
Ping Sheng ◽  
Yizun Yu ◽  
Xiaojuan Tian ◽  
Dongsheng Wang ◽  
Zhihong Zhang ◽  
...  
Keyword(s):  
Poyang Lake ◽  
Gene Diversity ◽  
Nitrogen Concentration ◽  
Amoa Gene ◽  
Estuarine Sediments ◽  
Operational Taxonomic Units ◽  
Uncultured Bacteria ◽  
Culture Independent ◽  
Ammonia Oxidising Archaea ◽  
Ammonia Oxidising Bacteria

In the present study, we used a culture-independent method based on library construction and sequencing to analyse the genetic diversity of the ammonia monooxygenase genes (amoA) of ammonia-oxidising archaea and bacteria in seven different estuarine sediments of Poyang Lake. The total of 67 and 38 operational taxonomic units (OTUs) (similarity <95%) of archaeal (AOA) and bacterial (AOB) amoA genes were retrieved respectively. AOA had higher diversity of amoA genes than did AOB. Phylogenetic analysis showed that AOA amoA sequences were closely related to amoA sequences from Crenarchaeota, Thaumarchaeota and some other uncultured archaea. Fragments from AOB were most associated with sequences from betaproteobacteria and some other uncultured bacteria. On the basis of Kendall’s correlation coefficient, there was a significant positive correlation between AOA amoA gene diversity and temperature, and the AOB diversity was positively correlated with total nitrogen and nitrate nitrogen concentration, and negatively correlated with pH in the sediments, suggesting that AOA and AOB were probably sensitive to several environmental factors. Our work could enhance our understanding of the roles of ammonia-oxidising microorganisms in these seven estuarine sediments from Poyang Lake.

scholarly journals Isolation of Oligotrophic Denitrifiers Carrying Previously Uncharacterized Functional Gene Sequences

2010 ◽  
Vol 77 (1) ◽  
pp. 338-342 ◽  
Author(s):  
Satoshi Ishii ◽  
Naoaki Ashida ◽  
Shigeto Otsuka ◽  
Keishi Senoo
Keyword(s):  
16S Rrna ◽  
Single Cell ◽  
Nitrite Reductase ◽  
Cell Isolation ◽  
Taxonomic Composition ◽  
Functional Gene ◽  
Gene Sequences ◽  
Isolation Technique ◽  
Culture Independent ◽  
Single Cell Isolation

ABSTRACTOligotrophic denitrifying bacteria, including those belonging to the generaHerbaspirillum,Azospirillum, andBradyrhizobium, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N2O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identifiedBradyrhizobiumstrains that harbornirSsequences previously detected only in culture-independent studies.

scholarly journals Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma

2021 ◽  
Vol 1 ◽  
Author(s):  
Panagiota Tzani-Tzanopoulou ◽  
Dimitrios Skliros ◽  
Spyridon Megremis ◽  
Paraskevi Xepapadaki ◽  
Evangelos Andreakos ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Airway Epithelial Cells ◽  
Molecular Techniques ◽  
Airway Epithelial ◽  
Microbial Composition ◽  
Bacterial Populations ◽  
Tripartite Interactions ◽  
Airway Mucosa ◽  
Culture Independent ◽  
System Disorder

The airway epithelium is the primary site where inhaled and resident microbiota interacts between themselves and the host, potentially playing an important role on allergic asthma development and pathophysiology. With the advent of culture independent molecular techniques and high throughput technologies, the complex composition and diversity of bacterial communities of the airways has been well-documented and the notion of the lungs' sterility definitively rejected. Recent studies indicate that the microbial composition of the asthmatic airways across the spectrum of disease severity, differ significantly compared with healthy individuals. In parallel, a growing body of evidence suggests that bacterial viruses (bacteriophages or simply phages), regulating bacterial populations, are present in almost every niche of the human body and can also interact directly with the eukaryotic cells. The triptych of airway epithelial cells, bacterial symbionts and resident phages should be considered as a functional and interdependent unit with direct implications on the respiratory and overall homeostasis. While the role of epithelial cells in asthma pathophysiology is well-established, the tripartite interactions between epithelial cells, bacteria and phages should be scrutinized, both to better understand asthma as a system disorder and to explore potential interventions.

scholarly journals Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Jessica Chopyk ◽  
Daniel J. Nasko ◽  
Sarah Allard ◽  
Anthony Bui ◽  
Mihai Pop ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Antibiotic Resistance Genes ◽  
Pond Water ◽  
Taxonomic Composition ◽  
Storm Event ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Culture Independent ◽  
Freshwater Habitats ◽  
And Function

Abstract Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

scholarly journals Culture-independent and culture-dependent analyses of the bacterial community in the phycosphere of cyanobloom-forming Microcystis aeruginosa

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Minkyung Kim ◽  
Bora Shin ◽  
Jaebok Lee ◽  
Hye Yoon Park ◽  
Woojun Park
Keyword(s):  
Microcystis Aeruginosa ◽  
Growth Promotion ◽  
Cyanobacterial Bloom ◽  
Culturable Bacteria ◽  
Electron Microscopic ◽  
Bacterial Populations ◽  
Associated Bacteria ◽  
Scanning Electron Microscopic ◽  
Culture Independent ◽  
Growing Conditions

AbstractConfocal and scanning electron microscopic observations have previously shown the strong bacterial association of Microcystis aeruginosa cells on their surfaces. DNA-based analyses of the associated bacterial communities were carried out using two M. aeruginosa strains grown in the laboratory and eight newly collected cyanobacterial bloom samples. M. aeruginosa was the most predominant species (66–100%) within the phylum Cyanobacteria. Rhizobium, Hydrogenophaga and Brevundimonas species were commonly found, and Flavobacterium species were present in all the cyanobacterial bloom samples. In total, 396 colonies from various samples were screened, revealing that most culturable bacteria belonged to the class Alphaproteobacteria (19%) including Rhizobium, Brevundimonas, and Porphyrobacter species. The genetic variation among the M. aeruginosa strains and different habitat conditions may have led to the presence of distinct bacterial populations among the tested samples. Among all the tested seven culturable isolates, Rhizobium sp. MK23 showed the best growth-promotion effect on the axenic M. aeruginosa strains. H2O2 was observed to be produced during the growth of M. aeruginosa PCC7806 under light conditions, this strain was more resistant to H2O2 when associated with Rhizobium sp. MK23. Our data suggested that Rhizobium species along with other associated bacteria might help the growth of M. aeruginosa by decomposing H2O2 under the aerobic growing conditions.

scholarly journals Human gut microbiota and future prebiotics

2012 ◽  
Vol 33 (3) ◽  
pp. 100
Author(s):  
Michael Conlon ◽  
Anthony Bird ◽  
Claus Christohersen
Keyword(s):  
Gut Microbiota ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Bacterial Populations ◽  
Independent Analysis ◽  
Host Health ◽  
Culture Independent ◽  
The Status ◽  
Diet And Lifestyle ◽  
Contemporary Approach

Rapid advances in molecular methods that enable culture-independent analysis of the complex bacterial populations is increasing awareness and understanding of the composition and activity of the microbiota in the human gastrointestinal tract, its role in host health and response to changes in diet and lifestyle. In this article we discuss the shortcomings of the contemporary approach of targeting a few selected bacteria, notably lactobacilli and bifidobacteria, to gauge the status of the gut microbiota for promoting health of the human host.

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