Characterisation of the bacterial flora of modified atmosphere packaged farmed Atlantic cod (Gadus morhua) by PCR-DGGE of conserved 16S rRNA gene regions

Isolates 302, 334, 356, 377 and 379, detected in modified-atmosphere-packaged broiler meat, together with strains LMG 12317T and LMG 13617, detected in dog tonsils, were analysed in a polyphasic taxonomy study, including numerical analysis of ribopatterns and whole-cell protein patterns, 16S rRNA gene sequence analysis, DNA–DNA hybridization and determination of some phenotypic properties. The results indicated that these isolates represent a novel species in the genus Enterococcus. The isolates showed classical phenotypic reactions for the genus Enterococcus with the exception of not possessing the Lancefield group D antigen. Isolates 334, LMG 12317T and LMG 13617 showed the highest 16S rRNA gene sequence similarity (98·3–99·0 %) to the Enterococcus pallens type strain. In the distance matrix tree based on 16S rRNA gene sequences, the three isolates were located in the Enterococcus avium group with E. pallens as their closest phylogenetic neighbour. Numerical analyses of whole-cell protein patterns and HindIII/EcoRI ribotypes placed all seven isolates together in a single cluster separated from the E. avium group reference strains. The DNA–DNA hybridization level between strains 334 and LMG 12317T was 93·5 %, confirming that they represent the same species. Low hybridization levels (12–30 %) were, by contrast, obtained with the E. pallens and Enterococcus raffinosus type strains. The name Enterococcus hermanniensis sp. nov. is proposed, with strain LMG 12317T (=CCUG 48100T) as the type strain.

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The bacterial flora of vacuum-packed cold-smoked salmon stored at 7°C, identified by direct 16S rRNA gene analysis and pure culture technique

Journal of Applied Microbiology ◽

10.1111/j.1365-2672.2006.03216.x ◽

2006 ◽

Vol 103 (1) ◽

pp. 109-119 ◽

Cited By ~ 39

Author(s):

T.C. Olofsson ◽

S. Ahrné ◽

G. Molin

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Pure Culture ◽

Bacterial Flora ◽

Culture Technique ◽

Gene Analysis ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Smoked Salmon

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Characterization of The Microbiome In Bile From Normal Human Gallbladders

10.21203/rs.3.rs-820802/v1 ◽

2021 ◽

Author(s):

Shin Watanabe ◽

Tadashi Shinoda ◽

Masaaki Minagawa ◽

Mari Toya ◽

Daisuke Motooka ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Profile Analysis ◽

Bacterial Flora ◽

Normal Liver ◽

Ribosomal Gene ◽

Gallbladder Bile ◽

Rrna Gene ◽

Sequencing Analysis ◽

Gene Profile

Abstract Background: Scientists previously believed that bacteria could not grow in bile, which is rich in bacteriostatic compounds such as bile acids. Therefore, the biliary tract was considered to be a sterile environment. However, high-throughput (i.e., amplicon) sequencing analysis methods have recently been used to discover the bacterial flora in gallbladder bile in brain-dead patients with normal gallbladders. In a bacterial flora analysis targeting the 16S ribosomal gene, a specific flora was present in the bile of normal gallbladders. However, these results were not obtained from truly healthy individuals. Therefore, the aim of this study was to analyze the microbial flora of bile collected from pathologically normal gallbladders that were surgically removed from patients with hepatobiliary pancreatic diseases who had normal liver function.Results: All 12 bile samples obtained from the gallbladders had negative culture results, although a bacterial flora was detected in all samples via 16S ribosome gene analysis. The composition of the bacterial flora was very simple, and the Firmicutes, Proteobacteria, and Actinobacteria phyla were identified in all samples. Based on 16S rRNA gene profile analysis, the composition ratio accounted for more than 80% of the total number of reads. The Anaerobacillus, Delftia, Bacillus, Ralstonia, Ochrobactrum, Acidovorax, and Curvibacter genera were detected in all 12 samples. Based on 16S rRNA gene profile analysis, at the genus level, Anaerobacillus and Delftia accounted for 58.62%–87.63% of the identified bacteria in each sample. Conclusions: In this study, the bacterial flora in the gallbladder bile was not diverse. Contrary to previous reports, few bacteria belonging to the Bacteroidetes phylum were detected. The functional significance of the gallbladder bacterial flora requires further investigation.

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Francisella philomiragia subsp. noatunensis subsp. nov., isolated from farmed Atlantic cod (Gadus morhua L.)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64765-0 ◽

2007 ◽

Vol 57 (9) ◽

pp. 1960-1965 ◽

Cited By ~ 78

Author(s):

J. Mikalsen ◽

A. B. Olsen ◽

T. Tengs ◽

D. J. Colquhoun

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Atlantic Cod ◽

Sequence Similarity ◽

Molecular Genetic ◽

Housekeeping Gene ◽

Rrna Gene ◽

Strictly Aerobic ◽

Gene Sequences

Seven bacterial isolates from farmed Atlantic cod displaying chronic granulomatous disease were characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-negative, facultatively intracellular, non-motile, strictly aerobic coccobacilli which produced H2S from cysteine-supplemented media and are therefore phenotypically consistent with members of the genus Francisella. Comparison of 16S rRNA gene sequences and six partial housekeeping gene sequences (groEL, shdA, rpoB, rpoA, pgm and atpA) confirmed the organism as a member of the genus Francisella, with Francisella philomiragia as its closest relative (99.3 % 16S rRNA gene sequence similarity, 92.2–99.0 % housekeeping gene sequence similarity). Despite the close relationship with F. philomiragia, isolates from Atlantic cod could be readily distinguished phenotypically and genetically from F. philomiragia ATCC 25015T. DNA–DNA hybridization studies revealed a mean reassociation value of 68 %. Thus, on the basis of phenotypic and molecular genetic evidence, we propose that the strains isolated from Atlantic cod should be recognized as Francisella philomiragia subsp. noatunensis subsp. nov. with the type strain 2005/50/F292-6CT (=NCIMB 14265T=LMG 23800T). Francisella philomiragia ATCC 25015T (=DSM 735T) is reclassified as Francisella philomiragia subsp. philomiragia subsp. nov.

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Comprehensive Analysis of Bacterial Flora in Postoperative Maxillary Cyst Fluid by 16S rRNA Gene and Culture Methods

ISRN Dentistry ◽

10.5402/2012/840483 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Naoto Sano ◽

Yoshio Yamashita ◽

Kazumasa Fukuda ◽

Hatsumi Taniguchi ◽

Masaaki Goto ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Species ◽

Bacterial Flora ◽

Gene Analysis ◽

Rrna Gene ◽

Culture Methods ◽

16S Rrna Gene Analysis ◽

Staphylococcus Capitis ◽

Maxillary Cyst

Intracystic fluid was aseptically collected from 11 patients with postoperative maxillary cyst (POMC), and DNA was extracted from the POMC fluid. Bacterial species were identified by sequencing after cloning of approximately 580 bp of the 16S rRNA gene. Identification of pathogenic bacteria was also performed by culture methods. The phylogenetic identity was determined by sequencing 517–596 bp in each of the 1139 16S rRNA gene clones. A total of 1114 clones were classified while the remaining 25 clones were unclassified. A total of 103 bacterial species belonging to 42 genera were identified in POMC fluid samples by 16S rRNA gene analysis. Species of Prevotella (91%), Neisseria (73%), Fusobacterium (73%), Porphyromonas (73%), and Propionibacterium (73%) were found to be highly prevalent in all patients. Streptococcus mitis (64%), Fusobacterium nucleatum (55%), Propionibacterium acnes (55%), Staphylococcus capitis (55%), and Streptococcus salivarius (55%) were detected in more than 6 of the 11 patients. The results obtained by the culture method were different from those obtained by 16S rRNA gene analysis, but both approaches may be necessary for the identification of pathogens, especially of bacteria that are difficult to detect by culture methods, and the development of rational treatments for patients with POMC.

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Effect of commercially purified deoxynivalenol and zearalenone mycotoxins on microbial diversity of pig cecum contents

Animal Bioscience ◽

10.5713/ajas.20.0137 ◽

2021 ◽

Vol 34 (2) ◽

pp. 243-255

Author(s):

Kondreddy Eswar Reddy ◽

Minji Kim ◽

Ki Hyun Kim ◽

Sang Yun Ji ◽

Youlchang Baek ◽

...

Keyword(s):

Immune Response ◽

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Intestinal Microflora ◽

Bacterial Flora ◽

Economic Losses ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Bacterial 16S Rrna Gene

Objective: Deoxynivalenol (DON) and zearalenone (ZEN) are mycotoxins that frequently contaminate maize and grain cereals, imposing risks to the health of both humans and animals and leading to economic losses. The gut microbiome has been shown to help combat the effects of such toxins, with certain microorganisms reported to contribute significantly to the detoxification process.Methods: We examined the cecum contents of three different dietary groups of pigs (control, as well as diets contaminated with 8 mg DON/kg feed or 0.8 mg ZEN/kg feed). Bacterial 16S rRNA gene amplicons were acquired from the cecum contents and evaluated by next-generation sequencing.Results: A total of 2,539,288 sequences were generated with ~500 nucleotide read lengths. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, occupying more than 96% of all three groups. Lactobacillus, Bacteroides, Megasphaera, and Campylobacter showed potential as biomarkers for each group. Particularly, Lactobacillus and Bacteroides were more abundant in the DON and ZEN groups than in the control. Additionally, 52,414 operational taxonomic units were detected in the three groups; those of Bacteroides, Lactobacillus, Campylobacter, and Prevotella were most dominant and significantly varied between groups. Hence, contamination of feed by DON and ZEN affected the cecum microbiota, while Lactobacillus and Bacteroides were highly abundant and positively influenced the host physiology.Conclusion: Lactobacillus and Bacteroides play key roles in the process of detoxification and improving the immune response. We, therefore, believe that these results may be useful for determining whether disturbances in the intestinal microflora, such as the toxic effects of DON and ZEN, can be treated by modulating the intestinal bacterial flora.

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