scholarly journals The microbiota of the surface, dermis and subcutaneous tissue of dog skin

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Rocío García-Fonticoba ◽  
Lluís Ferrer ◽  
Olga Francino ◽  
Anna Cuscó
Keyword(s):  
Subcutaneous Tissue ◽  
Dna Amplification ◽  
Skin Surface ◽  
Molecular Techniques ◽  
The Other ◽  
Rrna Gene ◽  
Culture Methods ◽  
Bacterial Dna ◽  
Microbiological Culture ◽  
Two Samples

Abstract Background Studies using highly sensitive molecular techniques have detected bacterial communities below the human epidermis. Depending on their abundance and composition, this finding could be clinically relevant. The aim of this study was to determine if bacteria can be detected in the dermis and subcutaneous tissue of dogs without cutaneous disease using two different approaches: traditional cultures and DNA sequencing of the V4 region of bacterial 16S rRNA gene using next-generation sequencing (NGS). Results Seven healthy dogs were included in the study, and two sets of samples were collected from each subject. Sample sets were composed of a 6-mm abdominal skin biopsy, including epidermis, dermis, and subcutis, a skin surface swab, and an environmental blank sample for contamination control. One set of samples from each dog was submitted for bacterial culture and the other one for bacterial DNA amplification and sequencing. Five different bacterial genera (Staphylococcus, Bacillus, Corynebacterium, Streptococcus, and Enterococcus) were isolated in five out of the seven skin surface swab samples with aerobic microbiological culture methods, while no growth was obtained from the other two samples. Although some DNA could be amplified from epidermal, dermal, and subcutaneous tissue samples, the results of the NGS were similar to those of the blanks. Conclusion When investigated with aerobic microbiological culture methods, the dermis and subcutaneous tissue of dogs are sterile. NGS techniques lead to the detection of some bacterial DNA, similar to the signal detected in blanks, which does not support the presence of a microbiota in dermis or subcutaneous tissue.

scholarly journals The microbiota of the surface, dermis and subcutaneous tissue of dog skin

2020 ◽  
Author(s):  
Rocío García-Fonticoba ◽  
Lluis Ferrer ◽  
Olga Francino ◽  
Anna Cusco
Keyword(s):  
Subcutaneous Tissue ◽  
Dna Amplification ◽  
Skin Surface ◽  
Molecular Techniques ◽  
The Other ◽  
Rrna Gene ◽  
Culture Methods ◽  
Bacterial Dna ◽  
Microbiological Culture ◽  
Two Samples

Abstract Background. Studies using highly sensitive molecular techniques have detected bacterial communities below the human epidermis. Depending on their abundance and composition, this finding could be clinically relevant. The aim of this study was to determine if bacteria can be detected in the dermis and subcutaneous tissue of dogs without cutaneous disease using two different approaches: traditional cultures and DNA sequencing of the V4 region of bacterial 16S rRNA gene using next-generation sequencing (NGS).Results. Seven healthy dogs were included in the study, and two sets of samples were collected from each subject. Sample sets were composed of a 6-mm abdominal skin biopsy, including epidermis, dermis, and subcutis, a skin surface swab, and an environmental blank sample for contamination control. One set of samples from each dog was submitted for bacterial culture and the other one for bacterial DNA amplification and sequencing. Five different bacterial genera (Staphylococcus, Bacillus, Corynebacterium, Streptococcus, and Enterococcus) were isolated in five out of the seven skin surface swab samples with aerobic microbiological culture methods, while no growth was obtained from the other two samples. Although some DNA could be amplified from epidermal, dermal, and subcutaneous tissue samples, the results of the NGS were similar to those of the blanks.Conclusion. When investigated with aerobic microbiological culture methods, the dermis and subcutaneous tissue of dogs are sterile. NGS techniques lead to the detection of some bacterial DNA, similar to the signal detected in blanks, which does not support the presence of a microbiota in dermis or subcutaneous tissue.

scholarly journals The microbiota of the surface, dermis and subcutaneous tissue of dog skin

2020 ◽  
Author(s):  
Rocío García-Fonticoba ◽  
Lluis Ferrer ◽  
Olga Francino ◽  
Anna Cusco
Keyword(s):  
Subcutaneous Tissue ◽  
Skin Surface ◽  
Molecular Techniques ◽  
The Other ◽  
Rrna Gene ◽  
Culture Methods ◽  
Bacterial Dna ◽  
Microbiological Culture ◽  
Two Samples ◽  
Healthy Dogs

Abstract Background. Studies using highly sensitive molecular techniques have detected bacterial communities below the human epidermis. Depending on their abundance and composition, this finding could be clinically relevant. This possibility, however, has not been investigated in the dog so far. The aim of this study was to determine if bacteria can be detected in the dermis and subcutaneous tissue of healthy dogs using two different approaches: traditional cultures and DNA sequencing of the V4 region of bacterial 16S rRNA gene using next-generation sequencing (NGS). Results. Seven healthy dogs were included in the study, and two sets of samples were collected from each subject. Sample sets were composed of a 6-mm abdominal skin biopsy, including epidermis, dermis, and subcutis, a skin surface swab, and an environmental blank sample for contamination control. One set of samples from each dog was submitted for bacterial culture and the other one for bacterial DNA amplification and sequencing. Five different bacterial genera (Staphylococcus, Bacillus, Corynebacterium, Streptococcus, and Enterococcus) were isolated in five out of the seven skin surface swab samples with aerobic microbiological culture methods, while no growth was obtained from the other two samples. Although some DNA could be amplified from epidermal, dermal, and subcutaneous tissue samples, the results of the NGS were similar to those of the blanks. Conclusion. When investigated with aerobic microbiological culture methods, the dermis and subcutaneous tissue of dogs are sterile. NGS techniques lead to the detection of some bacterial DNA, similar to the signal detected in blanks, which does not support the presence of a microbiota in dermis or subcutaneous tissue.

scholarly journals Skin microbiome in healthy dogs: from the surface to the inner layers

2020 ◽  
Author(s):  
Rocío García-Fonticoba ◽  
Lluis Ferrer ◽  
Olga Francino ◽  
Anna Cusco
Keyword(s):  
Subcutaneous Tissue ◽  
Traditional Culture ◽  
Skin Surface ◽  
Molecular Techniques ◽  
The Other ◽  
Skin Microbiome ◽  
Culture Methods ◽  
Bacterial Dna ◽  
Two Samples ◽  
Healthy Dogs

Abstract Background. Studies using highly sensitive molecular techniques have detected bacterial communities below the human epidermis. Depending on their abundance and composition, this finding could be clinically relevant. This possibility, however, has not been investigated in the dog so far. The aim of this study was to determine if bacteria can be detected in the dermis and subcutaneous tissue of healthy dogs using two different approaches: traditional cultures and massive DNA sequencing of the V4 region of bacterial 16S rRNA gene using next-generation sequencing (NGS).Results. Seven healthy dogs were included in the study, and two sets of samples were collected from each subject. Sample sets were composed of a 6-mm abdominal skin biopsy, including epidermis, dermis, and subcutis, a skin surface swab, and an environmental blank sample for contamination control. One set of samples from each dog was submitted for bacterial culture and the other one for bacterial DNA amplification and sequencing. Five different bacterial genera (Staphylococcus, Bacillus, Corynebacterium, Streptococcus, and Enterococcus) were isolated in five out of the seven skin surface swab samples with traditional culture methods, while no growth was obtained from the other two samples. Although some DNA could be amplified from epidermal, dermal, and subcutaneous tissue samples, the results of the NGS were similar to those of the blanks.Conclusion. When investigated with traditional culture methods, the dermis and subcutaneous tissue of healthy dogs are sterile. NGS techniques lead to the detection of some bacterial DNA which, although similar to the signal detected in blanks, does not support the presence of a microbiome in dermis or subcutaneous tissue.

PCR Analysis of Nasal Polyps, Chronic Sinusitis, and Hypertrophied Turbinates for DNA Encoding Bacterial 16S rRNA

2002 ◽  
Vol 16 (3) ◽  
pp. 169-173 ◽  
Author(s):  
Gerald A Bucholtz ◽  
Sherry A. Salzman ◽  
Fernando B. Bersalona ◽  
Timothy R. Boyle ◽  
Victor S. Ejercito ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Nasal Polyps ◽  
Chronic Sinusitis ◽  
Consensus Sequence ◽  
Rrna Gene ◽  
Dna Encoding ◽  
Bacterial Dna ◽  
Two Samples ◽  
The 16S Rrna Gene

Background Nasal polyps are considered to result from chronic inflammation, but the initial or persisting stimulus for the inflammation is not known. A variety of bacteria and fungi have been cultured from nasal polyps, but ∼35% have sterile cultures. Previously, Mycoplasma pneumoniae–specific DNA was detected in human nasal polyps using polymerase chain reaction (PCR) techniques, suggesting M. pneumoniae as a causative agent in the etiology of nasal polyps. Methods In this study, we tested for the presence of bacterial DNA in nasal polyps resected from 40 patients, in nasal mucosa membrane from 9 patients undergoing turbinectomy for hypertrophy, and in sinus mucosa membrane from 6 patients undergoing endoscopic surgery for chronic sinusitis. Tissue DNA was extracted and analyzed by PCR using M. pneumoniae specific primers for DNA that encode the 16S rRNA gene in 41 specimens (31 polyps, 6 turbinates, and 4 sinus), and by consensus sequence-based PCR using broad range primers for most eubacterial DNA encoding the 16S rRNA gene in 38 specimens (26 polyps, 7 turbinates, and 5 sinuses). Results Only two samples were positive for bacterial DNA encoding 16S rRNA: Streptococcus sp. DNA was isolated from one polyp specimen and Pseudomonas aeruginosa DNA was isolated in one maxillary sinusitis specimen. No evidence of M. pneumoniae–specific DNA encoding 16S rRNA was found in any of the tissues. Conclusions This study suggests that chronic bacterial infection is not a major component of nasal polyp etiology.

scholarly journals The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

2020 ◽  
Vol 3 (2) ◽  
pp. 39 ◽  
Author(s):  
Anna Ojo-Okunola ◽  
Shantelle Claassen-Weitz ◽  
Kilaza S. Mwaikono ◽  
Sugnet Gardner-Lubbe ◽  
Heather J. Zar ◽  
...  
Keyword(s):  
Human Milk ◽  
Dna Extraction ◽  
Bacterial Population ◽  
Illumina Miseq ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Dna Recovery ◽  
Culture Independent ◽  
Zymo Research

Culture-independent molecular techniques have advanced the characterization of environmental and human samples including the human milk (HM) bacteriome. However, extraction of high-quality genomic DNA that is representative of the bacterial population in samples is crucial. Lipids removal from HM prior to DNA extraction is common practice, but this may influence the bacterial population detected. The objective of this study was to compare four commercial DNA extraction kits and lipid removal in relation to HM bacterial profiles. Four commercial DNA extraction kits, QIAamp® DNA Microbiome Kit, ZR Fungal/Bacterial DNA MiniPrep™, QIAsymphony DSP DNA Kit and ZymoBIOMICS™ DNA Miniprep Kit, were assessed using milk collected from ten healthy lactating women. The kits were evaluated based on their ability to extract high quantities of pure DNA from HM and how well they extracted DNA from bacterial communities present in a commercial mock microbial community standard spiked into HM. Finally, the kits were evaluated by assessing their extraction repeatability. Bacterial profiles were assessed using Illumina MiSeq sequencing targeting the V4 region of the 16S rRNA gene. The ZR Fungal/Bacterial DNA MiniPrep™ and ZymoBIOMICS™ DNA Miniprep (Zymo Research Corp., Irvine, CA, USA) kits extracted the highest DNA yields with the best purity. DNA extracted using ZR Fungal/Bacterial DNA MiniPrep™ best represented the bacteria in the mock community spiked into HM. In un-spiked HM samples, DNA extracted using the QIAsymphony DSP DNA kit showed statistically significant differences in taxa prevalence from DNA extracted using ZR Fungal/Bacterial DNA MiniPrep™ and ZymoBIOMICS™ DNA Miniprep kits. The only difference between skim and whole milk is observed in bacterial profiles with differing relative abundances of Enhydrobacter and Acinetobacter. DNA extraction, but not lipids removal, substantially influences bacterial profiles detected in HM samples, emphasizing the need for careful selection of a DNA extraction kit to improve DNA recovery from a range of bacterial taxa.

scholarly journals The Presence of Toxic and Non-toxic Cyanobacteria in the Sediments of the Limpopo River Basin: Implications for Human Health

2018 ◽  
Author(s):  
Murendeni Magonono ◽  
Paul Johan Oberholster ◽  
Shonhai Addmore ◽  
Makumire Stanley ◽  
Jabulani Ray Gumbo
Keyword(s):  
Human Health ◽  
River Basin ◽  
Bottom Sediments ◽  
Algal Blooms ◽  
River Sediments ◽  
Molecular Techniques ◽  
Cylindrospermopsis Raciborskii ◽  
Rrna Gene ◽  
Toxic Cyanobacteria ◽  
Two Samples

The presence of harmful algal blooms (HABs) and cyanotoxins in drinking water sources poses a great threat to human health. The current study employed molecular techniques to determine the occurrence of non-toxic and toxic cyanobacteria species in the Limpopo River basin based on the phylogenetic analyses of 16S rRNA gene. The bottom sediments samples were collected from selected rivers: Limpopo, Crocodile, Mokolo, Mogalakwena, Nzhelele, Lephalale, Sand Rivers (South Africa); Notwane (Botswana), Shashe River and Mzingwane River (Zimbabwe). The physical-chemical analysis of the bottom sediments showed the availability of nutrients, nitrates and phosphates, in excess of 0.5 mg/l for most of river sediments, alkaline pH and salinity in excess of 500 mg/l. The FlowCam showed the dominant cyanobacteria species identified from the samples were Microcystis species, followed by Cylindrospermopsis raciborskii, Phormidium and Planktothrix species and this was confirmed by molecular techniques. Nevertheless, two samples showed the amplification of cylindrospermopsin polyketide synthetase gene (S3 and S9) while two samples showed amplification for microcystin/nodularin synthetase gene (S8 and S13). Thus these findings may imply the presence of toxic cyanobacteria species in the river sediments. The presence of cyanobacteria may be hazardous to human because rural communities and farmers who abstract water from Limpopo river catchment for human consumption, livestock and wildlife watering and irrigation.

Meningitis Following Spinal Anesthesia: 6 Cases in 5 Years

2007 ◽  
Vol 28 (10) ◽  
pp. 1187-1190 ◽  
Author(s):  
Lisa Rubin ◽  
Hannah Sprecher ◽  
Ahmed Kabaha ◽  
Gabriel Weber ◽  
Nava Teitler ◽  
...  
Keyword(s):  
Spinal Anesthesia ◽  
Short Interval ◽  
The Other ◽  
Rrna Gene ◽  
Streptococcus Salivarius ◽  
Aseptic Technique ◽  
Bacterial Dna ◽  
Culture Positive ◽  
Culture Negative ◽  
The 16S Rrna Gene

We describe 6 cases of meningitis after spinal anesthesia associated with a single anesthesiologist over the course of 5 years. The earliest case occurred in 2000, and the other 5 cases occurred over the course of 14 months in 2004-2005. The case identified in 2000 was culture-positive for Streptococcus salivarius. The other 5 cases were culture-negative for this organism but in 2 cases, the cerebrospinal fluid was found to be positive for bacterial DNA that was identified as belonging to S. salivarius by sequencing of the 16S rRNA gene. The association with a single anesthesiologist and a single hospital during a relatively short interval, however, lead us to believe that these occurrences are part of a series associated with possible violations of aseptic technique.

scholarly journals Bartonella quintana Aortitis in a Man with AIDS, Diagnosed by Needle Biopsy and 16S rRNA Gene Amplification

2015 ◽  
Vol 53 (8) ◽  
pp. 2773-2776 ◽  
Author(s):  
Sulggi A. Lee ◽  
Sara K. Plett ◽  
Anne F. Luetkemeyer ◽  
Gina M. Borgo ◽  
Michael A. Ohliger ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Back Pain ◽  
Needle Biopsy ◽  
Dna Amplification ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Newly Diagnosed ◽  
Content Type ◽  
Bartonella Quintana ◽  
Biopsy Tissue

A man with newly diagnosed AIDS presented with months of back pain and fever. Computed tomography (CT) results demonstrated aortitis with periaortic tissue thickening. DNA amplification of biopsy tissue revealed Bartonella quintana , and Bartonella serologies were subsequently noted to be positive. The patient improved with prolonged doxycycline and rifabutin treatment. This case illustrates how molecular techniques are increasingly important in diagnosing Bartonella infections.

scholarly journals Serological and molecular techniques applied for identification of Plasmodium spp. in blood samples from nonhuman primates

2018 ◽  
Author(s):  
Mayra Araguaia Pereira Figueiredo ◽  
Silvia Maria Di Santi ◽  
Wilson Gómez Manrique ◽  
Marcos Rogério André ◽  
Rosangela Zacarias Machado
Keyword(s):  
Nonhuman Primates ◽  
Fluorescent Antibody ◽  
Antibody Test ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Soluble Antigen ◽  
Blood Samples ◽  
Two Samples ◽  
Dot Elisa

Abstract The aim of this study was to identify Plasmodium spp. in blood samples from nonhuman primates (NHPs) in the state of Maranhão, using classical and alternative techniques for examination of human malaria. A total of 161 blood samples from NHPs were analyzed: 141 from captive animals at a Wildlife Screening Center (CETAS) and 20 from free-living animals in a private reserve. The techniques used were microscopy, rapid diagnostic test (RDT), Indirect fluorescent antibody test (IFAT) and molecular techniques (semi-nested PCR, quantitative real-time PCR and LAMP). Two serological methods (dot-ELISA and indirect ELISA) were also standardized with rhoptry protein-soluble antigen of P. falciparum and P. berghei. Trophozoite forms of Plasmodium sp. were identified on slides from five different animals. No samples were positive through RDT and LAMP. Four samples were seropositive for P. malariae through IFAT. The samples showed low reactivity to ELISA. Plasmodium sp. was detected in 34.16% (55/161) of the samples using qPCR based on the 18S rRNA gene. After sequencing, two samples showed 100% identityl to P. malariae, one showed 97% identity to Plasmodium sp. ZOOBH and one showed 99% identity to P. falciparum . PCR was shown to be the most sensitive technique for diagnosing Plasmodium in NHP samples.

scholarly journals Association of Different Genetic Types of Francisella-Like Organisms with the Rocky Mountain Wood Tick (Dermacentor andersoni) and the American Dog Tick (Dermacentor variabilis) in Localities Near Their Northern Distributional Limits

2011 ◽  
Vol 78 (4) ◽  
pp. 965-971 ◽  
Author(s):  
Shaun J. Dergousoff ◽  
Neil B. Chilton
Keyword(s):  
Tick Species ◽  
Horizontal Transmission ◽  
Dermacentor Variabilis ◽  
Molecular Techniques ◽  
The Other ◽  
Rrna Gene ◽  
Sympatric Populations ◽  
Dermacentor Andersoni ◽  
Content Type ◽  
Distributional Limits

ABSTRACTDermacentor andersoniandDermacentor variabilisfrom allopatric and sympatric populations near their northern distributional limits were examined for the presence ofFrancisellaspecies using molecular techniques that targeted 373 bp of the 16S rRNA gene. Although there was no evidence for the presence ofFrancisella tularensisin any tick,Francisella-like endosymbionts (FLEs) were common inD. andersoniandD. variabilisadults and immatures. A significantly greater proportion of female ticks contained FLEs compared to male ticks. In addition, significantly moreD. variabilisadult individuals contained multiple FLE sequence types than didD. andersoniadults. Ten different types of FLEs were identified based on the sequence data, which has implications for diagnostic tests and epidemiological studies ofF. tularensisin tick populations in Canada. The three most prevalent types of FLEs have been detected previously inD. andersoniorD. variabilisfrom other parts of their distributional ranges, whereas the other seven FLE types have not been reported previously. A comparison of the FLEs from both allopatric and sympatric populations of these two tick species provided insight into the relative host-specificity and the modes of transmission of these tick-borne bacteria. In general, each FLE type was specific for one tick species, suggesting vertical transmission of each bacterium. However, there were a few instances of potential cross-transfer of two FLE types to the other tick species at locations whereD. andersoniandD. variabilisoccurred in sympatry, suggesting that there may be occasional horizontal transmission of some FLEs.

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