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.

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 The growth response of rice (Oryza sativa L. var. FARO 44) in vitro after inoculation with bacterial isolates from a typical ferruginous ultisol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Musa Saheed Ibrahim ◽  
Beckley Ikhajiagbe
Keyword(s):  
16S Rrna ◽  
Bacillus Cereus ◽  
Proteus Mirabilis ◽  
Growth Response ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rice Seedlings ◽  
Rrna Gene Sequencing

Abstract Background Rice forms a significant portion of food consumed in most household worldwide. Rice production has been hampered by soil factors such as ferruginousity which has limited phosphorus availability; an important mineral component for the growth and yield of rice. The presence of phosphate-solubilizing bacteria (PSB) in soils has been reported to enhance phosphate availability. In view of this, the present study employed three bacteria species (BCAC2, EMBF2 and BCAF1) that were previously isolated and proved P solubilization capacities as inocula to investigate the growth response of rice germinants in an in vitro setup. The bacteria isolates were first identified using 16S rRNA gene sequencing and then applied as inoculum. The inolula were prepared in three concentrations (10, 7.5 and 5.0 ml) following McFarland standard. Viable rice (var. FARO 44) seeds were sown in petri dishes and then inoculated with the three inocula at the different concentrations. The setup was studied for 28 days. Results 16S rRNA gene sequencing identified the isolates as: isolate BCAC2= Bacillus cereus strain GGBSU-1, isolate BCAF1= Proteus mirabilis strain TL14-1 and isolate EMBF2= Klebsiella variicola strain AUH-KAM-9. Significant improvement in rice germination, morphology, physiology and biomass parameters in the bacteria-inoculated setups was observed compared to the control. Germination percentage after 4 days was 100 % in the inoculated rice germinants compared to 65% in the control (NiS). Similarly, inoculation with the test isolates enhanced water-use efficiency by over 40%. The rice seedlings inoculated with Bacillus cereus strain GGBSU-1 (BiS) showed no signs of chlorosis and necrosis throughout the study period as against those inoculated with Proteus mirabilis strain TL14-1 (PiS) and Klebsiella variicola strain AUH-KAM-9 (KiS). Significant increase in chlorophyll-a, chlorophyll-b and alpha amylase was observed in the rice seedlings inoculated with BiS as against the NiS. Conclusion Inoculating rice seeds with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 in an in vitro media significantly improved growth parameters of the test plant. Bacillus cereus strain GGBSU-1 showed higher efficiency due to a more improved growth properties observed.

Phenotypic properties and genotyping analysis of Bacillus cereus group isolates from dairy and potato products

LWT ◽  
2021 ◽  
Vol 140 ◽  
pp. 110853
Author(s):  
Yiying Huang ◽  
Steve H. Flint ◽  
Shubo Yu ◽  
Yu Ding ◽  
Jon S. Palmer
Keyword(s):  
Bacillus Cereus ◽  
Bacillus Cereus Group ◽  
Phenotypic Properties ◽  
Potato Products

Development of Rapid Real-Time PCR and Most-Probable-Number Real-Time PCR Assays To Quantify Enterotoxigenic Strains of the Species in the Bacillus cereus Group

2007 ◽  
Vol 70 (12) ◽  
pp. 2774-2781 ◽  
Author(s):  
I-CHEN YANG ◽  
DANIEL YANG-CHIH SHIH ◽  
JAN-YI WANG ◽  
TZU-MING PAN
Keyword(s):  
Bacillus Cereus ◽  
Real Time ◽  
Real Time Pcr ◽  
Food Samples ◽  
Most Probable Number ◽  
Pcr Assay ◽  
Bacillus Cereus Group ◽  
Probable Number ◽  
Cooked Rice ◽  
Group Detection

Members of the Bacillus cereus group may produce diarrheal enterotoxins and could be potential hazards if they enter the food chain. Therefore, a method capable of detecting all the species in the B. cereus group rather than B. cereus alone is important. We selected nhe as the target and developed a real-time PCR assay to quantify enterotoxigenic strains of the B. cereus group. The real-time PCR assay was evaluated with 60 B. cereus group strains and 28 others. The assay was also used to construct calibration curves for different food matrices and feces. The assay has an excellent quantification capacity, as proved by its linearity (R2 > 0.993), wide dynamic quantification range (102 to 107 CFU/g for cooked rice and chicken, 103 to 107 CFU/ml for milk, and 104 to 107 CFU/g for feces), and adequate relative accuracy (85.5 to 101.1%). For the low-level contaminations, a most-probable-number real-time PCR assay was developed that could detect as low as 100 CFU/ml. Both assays were tested with real food samples and shown to be considerably appropriate for B. cereus group detection and quantification.

scholarly journals Functional Genomic Identification of Cadmium Resistance Genes from a High GC Clone Library by Coupling the Sanger and PacBio Sequencing Strategies

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 7
Author(s):  
Jinghao Chen ◽  
Chao Xing ◽  
Xin Zheng ◽  
Xiaofang Li
Keyword(s):  
High Throughput ◽  
Resistance Genes ◽  
Sanger Sequencing ◽  
Genomic Library ◽  
Full Length ◽  
Host Cells ◽  
Full Genome Sequence ◽  
Functional Screening ◽  
Functional Genomic ◽  
Pacbio Sequencing

Functional (meta) genomics allows the high-throughput identification of functional genes in a premise-free way. However, it is still difficult to perform Sanger sequencing for high GC DNA templates, which hinders the functional genomic exploration of a high GC genomic library. Here, we developed a procedure to resolve this problem by coupling the Sanger and PacBio sequencing strategies. Identification of cadmium (Cd) resistance genes from a small-insert high GC genomic library was performed to test the procedure. The library was generated from a high GC (75.35%) bacterial genome. Nineteen clones that conferred Cd resistance to Escherichia coli subject to Sanger sequencing directly. The positive clones were in parallel subject to in vivo amplification in host cells, from which recombinant plasmids were extracted and linearized by selected restriction endonucleases. PacBio sequencing was performed to obtain the full-length sequences. As the identities, partial sequences from Sanger sequencing were aligned to the full-length sequences from PacBio sequencing, which led to the identification of seven unique full-length sequences. The unique sequences were further aligned to the full genome sequence of the source strain. Functional screening showed that the identified positive clones were all able to improve Cd resistance of the host cells. The functional genomic procedure developed here couples the Sanger and PacBio sequencing methods and overcomes the difficulties in PCR approaches for high GC DNA. The procedure can be a promising option for the high-throughput sequencing of functional genomic libraries, and realize a cost-effective and time-efficient identification of the positive clones, particularly for high GC genetic materials.

Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 458-463 ◽  
Author(s):  
Sonia R. Vartoukian ◽  
Julia Downes ◽  
Richard M. Palmer ◽  
William G. Wade
Keyword(s):  
New Genus ◽  
Novel Species ◽  
Fusobacterium Nucleatum ◽  
Oral Bacteria ◽  
Rrna Gene ◽  
Good Growth ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Peptone Yeast Extract Glucose

SGP1T, a strain belonging to a lineage of the phylum Synergistetes with no previously cultivated representatives was subjected to a comprehensive range of phenotypic and genotypic tests. For good growth the strain was dependent on co-culture with, or extracts from, selected other oral bacteria. Cells of strain SGP1T were asaccharolytic and major amounts of acetic acid and moderate amounts of propionic acid were produced as end products of metabolism in peptone-yeast extract-glucose broth supplemented with a filtered cell sonicate of Fusobacterium nucleatum subsp. nucleatum ATCC 25586T (25 %, v/v). Hydrogen sulphide was produced and gelatin was weakly hydrolysed. The major cellular fatty acids were C14 : 0, C18 : 0 and C16 : 0. The DNA G+C content of strain SGP1T was 63 mol%. Phylogenetic analysis of the full-length 16S rRNA gene showed that strain SGP1T represented a novel group within the phylum Synergistetes . A novel species in a new genus, Fretibacterium fastidiosum gen. nov., sp. nov., is proposed. The type strain of Fretibacterium fastidiosum is SGP1T ( = DSM 25557T = JCM 16858T).

scholarly journals Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount

2004 ◽  
Vol 54 (5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Koji Mori ◽  
Takeshi Kakegawa ◽  
Yowsuke Higashi ◽  
Ko-ichi Nakamura ◽  
Akihiko Maruyama ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Growth Conditions ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Good Growth ◽  
Chain Link ◽  
Circular Structure ◽  
Hybridization Test ◽  
A Chain ◽  
Cellular Fatty Acid Profile

A novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BT was isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BT used oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Oceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BT differed from O. profundus in terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate and O. profundus. For the reasons given above, the name Oceanithermus desulfurans sp. nov. is proposed for strain St55BT (=NBRC 100063T=DSM 15757T).

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