scholarly journals Characterization of bacterial DNA identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest

2021 ◽  
Author(s):  
Miranda K Stotz ◽  
Darren D Henry ◽  
Whitney L Crossland
Keyword(s):  
Liver Tissue ◽  
Bovine Liver ◽  
Fusobacterium Necrophorum ◽  
Laboratory Culture ◽  
Hepatic Tissue ◽  
Rrna Gene ◽  
Pathogenic Potential ◽  
Bacterial Dna ◽  
Cultural Methods

Abstract Bacteriological characterization of bovine liver abscesses has been accomplished by cultural methods but DNA methods are still needed, as many bacteria are not conducive to laboratory culture. In addition to this gap in research, there have been no studies which identify the bacterial presence within healthy, non-abscessed liver tissue. The objective of this study was to compare the bacteriome of both abscessed and non-abscessed bovine livers in an observational case-control study design. Fifty-six livers, obtained from Holstein steers, were scored according to a modified Elanco liver abscess score description where A- was partitioned into active abscesses or scarred where only scars were present. Parenchyma tissue was collected from non-abscessed livers (n=22), and scarred livers (n=7), and purulent material was collected from abscessed livers (n=24), and DNA was extracted for 16s rRNA gene sequence-based bacterial analysis. Across liver samples, 21 total phyla were identified with a mean of 14. Predominant phyla, accounting for > 98% of reads, were Fusobacteria (51.7%), Bacteroidetes (26.9%), Proteobacteria (8.03%), Firmicutes (5.39%), Cyanobacteria (3.85 %) and Actinobacteria (2.21%). Proteobacteria, Cyanobacteria and Firmicutes were greater in non-abscessed and scarred livers, whereas Fusobacteria and Bacteroidetes prevailed in abscessed livers. Non-abscessed livers shared 3,059 operational taxonomic units (OTU) with abscessed livers (total OTU of all livers= 4,167), but non-abscessed livers had greater richness and evenness whereas abscessed livers had greater dominance (P ≤ 0.0014). Liver score affected the relative abundance of OTU (R = 0.463; P = 0.001) but abscessed livers shared ≥ 40% similarity and were not different from each other (P ≥ 0.370). Of the predominant OTU (top 10 as a % of reads), three OTU (Fusobacteria necrophorum, Bacteroides spp., and Trueperella pyogenes) were shared across both abscessed and non-abscessed livers. Fusobacterium necrophorum was the dominant OTU regardless of liver score, and the single most abundant OTU, even among non-abscessed livers. We describe bacterial DNA detected in non-abscessed bovine liver tissue for the first time, which indicates possible presence of viable bacteria with pathogenic potential in apparently healthy liver tissue.

Revisiting theAcanthamoebaspecies that form star-shaped cysts (genotypes T7, T8, T9, and T17): characterization of seven new Brazilian environmental isolates and phylogenetic inferences

Parasitology ◽  
2011 ◽  
Vol 139 (1) ◽  
pp. 45-52 ◽  
Author(s):  
ANA C. M. MAGLIANO ◽  
MARTA M. G. TEIXEIRA ◽  
SILVIA C. ALFIERI
Keyword(s):  
Opportunistic Infections ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
Pathogenic Potential ◽  
Morphological Group ◽  
Isolation And Characterization ◽  
Group I ◽  
Group 2

SUMMARYFree-living amoebae of the genusAcanthamoebaare the agents of both opportunistic and non-opportunistic infections and are frequently isolated from the environment. Of the 17 genotypes (T1–T17) identified thus far, 4 (T7, T8, T9, and T17) accommodate the rarely investigated species of morphological group I, those that form large, star-shaped cysts. We report the isolation and characterization of 7 new Brazilian environmentalAcanthamoebaisolates, all assigned to group I. Phylogenetic analyses based on partial (∼1200 bp) SSU rRNA gene sequences placed the new isolates in the robustly supported clade composed of the species of morphological group I. One of the Brazilian isolates is closely related toA. comandoni(genotype T9), while the other 6, together with 2 isolates recently assigned to genotype T17, form a homogeneous, well-supported group (2 0% sequence divergence) that likely represents a newAcanthamoebaspecies. Thermotolerance, osmotolerance, and cytophatic effects, features often associated with pathogenic potential, were also examined. The results indicated that all 7 Brazilian isolates grow at temperatures up to 40°C, and resist under hyperosmotic conditions. Additionally, media conditioned by each of the newAcanthamoebaisolates induced the disruption of SIRC and HeLa cell monolayers.

scholarly journals Microbiota Profile with Stunting Children in West Sumatera Province, Indonesia

2020 ◽  
Vol 8 (E) ◽  
pp. 334-340
Author(s):  
Masrul Masrul ◽  
Doddy Izwardy ◽  
Ikhwan Resmala Sudji ◽  
Idral Purnakarya ◽  
Syahrial Syahrial ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bioinformatic Analysis ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
West Sumatra ◽  
Dominant Bacteria ◽  
Microbial Dna ◽  
Bacterial Dna Extraction

BACKGROUND: Microbiota profile plays an important role in the growth of children. Recently, a number of microbiota profile studies have illustrated association with child stunting. AIM: Here, this study applied microbiota profile for stunting children in Indonesia to know a framework for future activities toward further characterization of microbiota profile contribution to stunting. METHODS: In this case–control study, we collected 96 samples with 48 stunting children and 48 non-stunting children in Pasaman and West Pasaman district as stunting locus areas in West Sumatra Province, Indonesia. All study subjects met the inclusion criteria: Children ≤3 years of age and they did not suffer from gastrointestinal disorders. Samples collected were then carried out by intestinal bacterial DNA extraction. All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a child fecal sample. Bioinformatic analysis of microbiota DNA sequencing results compared with the intestinal microbiota profile of infants. RESULTS: This study found in intestinal of stunting children identified 61 species of bacteria which were only found in the intestines of stunting children and not found in non-stunting children. The dominant bacteria in intestinal microbiota profile of Pasaman and West Pasaman district, West Sumatera Province, Indonesia, among stunting children were Firmicutes (47.52%), Proteobacteria (21.12%), and Bacteroidetes (16.15%). The high number of these microbiota associated with high amount of carbohydrate intake among stunting children than dietary protein. CONCLUSION: This study confirmed the role of microbiota profile in the incidence of stunting children.

scholarly journals Characterization of PaxA and Its Operon: a Cohemolytic RTX Toxin Determinant from Pathogenic Pasteurella aerogenes

2000 ◽  
Vol 68 (1) ◽  
pp. 6-12 ◽  
Author(s):  
Peter Kuhnert ◽  
Bénédicte Heyberger-Meyer ◽  
Jacques Nicolet ◽  
Joachim Frey
Keyword(s):  
Sequence Similarity ◽  
Opportunistic Pathogen ◽  
Toxin Gene ◽  
Rrna Gene ◽  
Commensal Bacterium ◽  
Pathogenic Potential ◽  
Newborn Piglets ◽  
Toxin Genes ◽  
Rtx Toxin

ABSTRACT Pasteurella aerogenes is known as a commensal bacterium or as an opportunistic pathogen, as well as a primary pathogen found to be involved in abortion cases of humans, swine, and other mammals. Using broad-range DNA probes for bacterial RTX toxin genes, we cloned and subsequently sequenced a new operon namedpaxCABD encoding the RTX toxin PaxA in P. aerogenes. The pax operon is organized analogous to the classical RTX operons containing the activator genepaxC upstream of the structural toxin genepaxA, which is followed by the secretion protein genespaxB and paxD. The highest sequence similarity of paxA with known RTX toxin genes is found withapxIIIA (82%). PaxA is structurally similar to ApxIIIA and also shows functional analogy to ApxIIIA, since it shows cohemolytic activity with the sphingomyelinase of Staphylococcus aureus, known as the CAMP effect, but is devoid of direct hemolytic activity. In addition, it shows to some extent immunological cross-reactions with ApxIIIA. P. aerogenes isolated from various specimens showed that the pax operon was present in about one-third of the strains. All of the pax-positive strains were specifically related to swine abortion cases or septicemia of newborn piglets. These strains were also shown to produce the PaxA toxin as determined by the CAMP phenomenon, whereas none of thepax-negative strains did. This indicated that the PaxA toxin is involved in the pathogenic potential of P. aerogenes. The examined P. aerogenes isolates were phylogenetically analyzed by 16S rRNA gene (rrs) sequencing in order to confirm their species. Only a small heterogeneity (<0.5%) was observed between the rrs genes of the strains originating from geographically distant farms and isolated at different times.

scholarly journals Development of a robust protocol for the characterization of the pulmonary microbiota

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Nathan Dumont-Leblond ◽  
Marc Veillette ◽  
Christine Racine ◽  
Philippe Joubert ◽  
Caroline Duchaine
Keyword(s):  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Validity Of Results ◽  
Healthy Human ◽  
Bacterial Dna ◽  
Starting Point ◽  
Sampling Procedures ◽  
Negative Controls ◽  
The Impact

AbstractThe lack of methodological standardization diminishes the validity of results obtained and the conclusions drawn when studying the lung microbiota. We report the validation of a complete 16S rRNA gene amplicon sequencing workflow, from patient recruitment to bioinformatics, tailored to the constrains of the pulmonary environment. We minimize the impact of contaminants and establish negative controls to track and account for them at every step. Enzymatic and mechanical homogenization combined to commercially available extraction kits allow for a fast and reliable extraction of bacterial DNA. The DNA extraction kits have a significant impact on the bacterial composition of the controls. The bacterial signatures of extracted cancerous and healthy human tissues from 5 patients are highly distinguishable from methodological controls. Our work expands our understanding of low microbial burdened environments analysis. This article is to be a starting point towards methodological standardization and the implementation of proper sampling procedures in the study of lung microbiota.

Viscohyperelastic Material Modeling of Liver Tissue

2007 ◽  
Author(s):  
Kumar Vemaganti ◽  
Esra Roan
Keyword(s):  
Soft Tissue ◽  
Liver Tissue ◽  
Critical Role ◽  
Experimental Studies ◽  
Strain Energy Function ◽  
Bovine Liver ◽  
Disease Diagnosis ◽  
Strain Rates ◽  
The Continuum

Mechanical characterization of soft tissue plays a critical role in applications such as automated surgery, disease diagnosis and tissue engineering. Soft tissue is often modeled as an isotropic incompressible and hyperelastic material. However, it is well known that viscoelasticity plays an important role in determining the response of soft tissue to mechanical loads [1]. This work is concerned with the development of hyperviscoelastic models of soft tissue in general and liver tissue in particular. Experimental studies in uniaxial compression are conducted on bovine liver tissue at strain rates between 0.001 s−1 and 0.04 s−1. The response of liver tissue is modeled using the continuum mechanics framework using an exponential form of the strain energy function.

scholarly journals Cloning and characterization of cDNA for mitochondrial GTP:AMP phosphotransferase of bovine liver

1989 ◽  
Vol 264 (32) ◽  
pp. 19192-19199
Author(s):  
M Yamada ◽  
M Shahjahan ◽  
T Tanabe ◽  
F Kishi ◽  
A Nakazawa
Keyword(s):  
Bovine Liver

scholarly journals Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Konrad Egli ◽  
Anna Roditscheff ◽  
Ursula Flückiger ◽  
Martin Risch ◽  
Lorenz Risch ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
23S Rrna ◽  
Rrna Gene ◽  
Limited Information ◽  
Specific Pcr ◽  
Appropriate Treatment ◽  
23S Rrna Gene ◽  
Allele Type ◽  
Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene
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