scholarly journals Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia

2021 ◽  
Vol 12 ◽  
Author(s):  
Yousri Abdelhafiz ◽  
Jorge M. O. Fernandes ◽  
Erika Stefani ◽  
Davide Albanese ◽  
Claudio Donati ◽  
...  
Keyword(s):  
Nile Tilapia ◽  
Buccal Cavity ◽  
Amplicon Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Opportunistic Pathogens ◽  
Female Fish ◽  
Microbial Composition ◽  
Opportunistic Bacteria ◽  
Power Play

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

scholarly journals Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

2021 ◽  
Vol 9 (8) ◽  
pp. 1657
Author(s):  
Anders Esberg ◽  
Linda Johansson ◽  
Ingegerd Johansson ◽  
Solbritt Rantapää Dahlqvist
Keyword(s):  
Rheumatoid Arthritis ◽  
Early Onset ◽  
Amplicon Sequencing ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Disease Manifestation ◽  
Periodontal Status ◽  
Quality Register

Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

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 The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

2018 ◽  
Vol 7 (1) ◽  
pp. 4 ◽  
Author(s):  
Kelly Ugarelli ◽  
Peeter Laas ◽  
Ulrich Stingl
Keyword(s):  
Carbon Sink ◽  
Amplicon Sequencing ◽  
Thalassia Testudinum ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Carbon Cycles ◽  
Syringodium Filiforme ◽  
Turtle Grass ◽  
Shoreline Protection ◽  
The 16S Rrna Gene

Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassia testudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.

scholarly journals Taxonomic Analysis of Oral Microbiome during Orthodontic Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Alessandra Campobasso ◽  
Eleonora Lo Muzio ◽  
Giovanni Battista ◽  
Domenico Ciavarella ◽  
Vito Crincoli ◽  
...  
Keyword(s):  
Orthodontic Treatment ◽  
Data Extraction ◽  
Human Study ◽  
Oral Microbiome ◽  
Orthodontic Appliances ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Fixed Appliance ◽  
Gene Search ◽  
Evidence Quality

Background. Orthodontic appliances induce significant changes in the oral microbiome, but this shift in microbial composition has not been well established by the available evidence yet. Objectives. To perform a systematic review of existing literature in order to assess the taxonomic microbial changes in orthodontic patients during Fixed Appliance Treatment (FAT) and Clear Aligner Treatment (CAT), using next-generation sequencing (NGS) technique of the bacterial 16S rRNA gene. Search Methods and Selection Criteria. The search for articles was carried out in PubMed, including articles published in English until May 2021. They included every human study report potentially relevant to the review. Data Collection and Analysis. After duplicate study selection and data extraction procedures according to the PICOS scheme, the methodological quality of the included papers was assessed by the Swedish Council on Technology Assessment in Health Care Criteria for Grading Assessed Studies (SBU) method. Results. The initial search identified 393 articles, 74 of which were selected by title and abstract. After full-text reading, six articles were selected according to inclusion criteria. The evidence quality for all the studies was moderate. Conclusions. Orthodontic treatment seems to transiently affect the composition of subgingival microbiome, although not salivary, maintaining a stable microbial diversity. Different results were found in the shift of microbiome between plaque and saliva, depending on the type of orthodontic treatment. This review should be interpreted with some caution because of the number, quality, and heterogeneity of the included studies.

scholarly journals Bacterial Diversity of Water and Sediment Samples from Gull Point State Park (West Okoboji, Iowa) Determined Using 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (33) ◽  
Author(s):  
John A. Kyndt
Keyword(s):  
16S Rrna ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Great Lakes Region ◽  
Primary State ◽  
Microbial Composition ◽  
The West ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Water And Sediment Samples

Gull Point State Park is located on a peninsula on the west shore of West Okoboji Lake (Iowa, USA). It is the primary state park in the Iowa Great Lakes region. Sediment and water samples from three locations at the Gull Point pond were analyzed for their microbial composition.

scholarly journals Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System

2021 ◽  
Vol 12 ◽  
Author(s):  
Yousri Abdelhafiz ◽  
Jorge M. O. Fernandes ◽  
Simone Larger ◽  
Davide Albanese ◽  
Claudio Donati ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Nile Tilapia ◽  
16S Rrna Gene Sequencing ◽  
Study Groups ◽  
Breeding Strategy ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Core Microbiome ◽  
Recirculating Aquaculture ◽  
Opportunistic Bacteria

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

scholarly journals Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2245
Author(s):  
Yiping Zhu ◽  
Wuyan Jiang ◽  
Reed Holyoak ◽  
Bo Liu ◽  
Jing Li
Keyword(s):  
Dental Treatment ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Dental Procedures ◽  
Significant Difference ◽  
Dental Diseases ◽  
Rrna Gene Sequencing ◽  
The Impact

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis

2020 ◽  
pp. 238008442094877
Author(s):  
P. Balan ◽  
B.W. Brandt ◽  
Y.S. Chong ◽  
W. Crielaard ◽  
M.L. Wong ◽  
...  
Keyword(s):  
Oral Health ◽  
Pregnant Women ◽  
Oral Microbiome ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Health Maintenance ◽  
Prenatal Health ◽  
Healthy Women ◽  
Healthy Pregnancy

Introduction: Previous studies have largely explored the microbial composition and pathogenesis of pregnancy gingivitis. However, the patterns of microbial colonization during pregnancy in the absence of pregnancy gingivitis have rarely been studied. Characterization of the oral microbiome in pregnant women with healthy gingiva is an important initial step in understanding the role of the microbiome in progression to pregnancy gingivitis. Objectives: In this study, we compared the oral microbiome of pregnant women without gingivitis (healthy pregnancy) with pregnant women having gingivitis and nonpregnant healthy women to understand how pregnancy modifies the oral microbiome and induces progression to pregnancy gingivitis. Methods: Subgingival plaque samples were collected from Chinese pregnant women with gingivitis ( n = 10), healthy pregnant women ( n = 10), and nonpregnant healthy women ( n = 10). The Illumina MiSeq platform was used to perform 16S rRNA gene sequencing targeting the V4 region. Results: The alpha and beta diversity was significantly different between pregnant and nonpregnant women, but minimal differences were observed between pregnant women with and without gingivitis. Interestingly, the oral bacterial community showed higher abundance of pathogenic taxa during healthy pregnancy as compared with nonpregnant women despite similar gingival and plaque index scores. However, when compared with overt pregnancy gingivitis, pathogenic taxa were less abundant during healthy pregnancy. PICRUSt analysis (phylogenetic investigation of communities by reconstruction of unobserved states) also suggested no difference in the functional capabilities of the microbiome during pregnancy, irrespective of gingival disease status. However, metabolic pathways related to amino acid metabolism were significantly increased in healthy pregnant women as compared with nonpregnant women. Conclusion: The presence of pathogenic taxa in healthy pregnancy and pregnancy gingivitis suggests that bacteria may be necessary for initiating disease development but progression to gingivitis may be influenced by the host environmental factors. More efforts are required to plan interventions aimed at sustaining health before the appearance of overt gingivitis. Knowledge Transfer Statement: The results of this study draw attention to the importance of oral health maintenance during pregnancy, as women without any prenatal oral conditions are predisposed to the risk of developing pregnancy gingivitis. Hence, it is important to incorporate comprehensive assessment of oral health in the prenatal health care schedules. Pregnant woman should be screened for oral risks, counseled on proper oral hygiene and expected oral changes, and referred for dental treatment, when necessary.

scholarly journals Comparative evaluation of cheese whey microbial composition from four Italian cheese factories by viable counts and 16S rRNA gene amplicon sequencing

2020 ◽  
Vol 104 ◽  
pp. 104656 ◽  
Author(s):  
Vinícius da Silva Duarte ◽  
Milena Carlot ◽  
Shadi Pakroo ◽  
Armin Tarrah ◽  
Angiolella Lombardi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Comparative Evaluation ◽  
Cheese Whey ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbial Composition

scholarly journals High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens

Foods ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 608
Author(s):  
Mikhail Y. Syromyatnikov ◽  
Anastasia V. Kokina ◽  
Sergey A. Solodskikh ◽  
Anna V. Panevina ◽  
Evgeny S. Popov ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
High Throughput ◽  
Sanger Sequencing ◽  
Klebsiella Pneumonia ◽  
Rrna Gene ◽  
Good Growth ◽  
Opportunistic Pathogens ◽  
Bacillus Cereus Group ◽  
Opportunistic Bacteria ◽  
Enterococcus Spp

Microbial contamination of dairy products with a high fat content (e.g., butter) has been studied insufficiently. No studies using modern molecular methods to investigate microbial communities in butter have been conducted so far. In this work, we used high-throughput sequencing and Sanger sequencing of individual bacterial colonies to analyze microbial content of commercially available butter brands. A total of 21 samples of commercially available butter brands were analyzed. We identified a total of 94 amplicon sequence variants corresponding to different microbial taxa. The most abundant lactic acid bacteria in butter were Lactobacillus kefiri, Lactobacillus parakefiri, Lactococcus taiwanensis and Lactococcus raffinolactis. A large amount of Streptococcus spp. bacteria (87.9% of all identified bacteria) was found in one of the butter samples. Opportunistic pathogens such as Bacillus cereus group, Pseudomonas aeruginosa, Cronobacter spp., Escherichia coli, Listeria innocua, Citrobacter spp., Enterococcus spp., Klebsiella pneumonia were detected. The analyzed butter samples were most strongly contaminated with bacteria from the Bacillus cereus group, and to a lesser extent - with Cronobacter spp. and Enterococcus spp. The plating and Sanger sequencing of individual colonies revealed the presence of Enterobacter cloacae and Staphylococcus epidermidis. The Sanger sequencing also showed the presence of Cronobacter sakazakii in butter which can be dangerous for children under the age of 1 year. We demonstrated that butter is a good growth medium for opportunistic pathogenic bacteria. Our data indicate that despite the fact that butter is a dairy product with a long shelf life, it should be subjected to quality control for the presence of opportunistic bacteria.

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