VLP Extraction from Fecal Samples v2

2021 ◽  
Author(s):  
Frej Larsen
Keyword(s):  
Fecal Matter ◽  
Fecal Samples ◽  
Viral Particles

This protocol is for isolation of bacteriophages from fecal matter. It is based on the protocol used for the COPSAC10 cohort and was originally described by Ling Deng in doi:10.3390/v11070667. Extraction is performed using centrifugation and ultrafiltration to isolate viral particles and get rid of contaminants.

Virome Extraction v1

2021 ◽  
Author(s):  
Frej Larsen
Keyword(s):  
Fecal Matter ◽  
Viral Particles

This protocol is for isolation of bacteriophages from fecal matter. It is based on the protocol used for the COPSAC10 cohort and was originally described by Ling Deng in doi:10.3390/v11070667. Extraction is performed using centrifugation and ultrafiltration to isolate viral particles and get rid of contaminants.

scholarly journals Food habits of indian crested porcupine (Hystrix indica) (Kerr 1792), in district Bagh, Azad Jammu and Kashmir

2022 ◽  
Vol 82 ◽  
Author(s):  
M. B. Khan ◽  
N. Irshad ◽  
B. Ahmed ◽  
M. R. Khan ◽  
R. A. Minhas ◽  
...  
Keyword(s):  
Plant Species ◽  
Diversity Index ◽  
Melia Azedarach ◽  
Pest Species ◽  
Fecal Matter ◽  
Jammu And Kashmir ◽  
Fecal Samples ◽  
Diet Preference ◽  
Crested Porcupine ◽  
Summer Time

Abstract The Indian Crested Porcupine (Hystrix indica) is classified as an agricultural pest species. It feeds on plants and crops; hence, it is responsible for massive financial losses worldwide. The current study was conducted to assess the diet composition of Indian Crested Porcupine in District Bagh, Azad Jammu and Kashmir (AJ&K). Thus, fecal samples were collected and examined from different sampling sites. Reference slides of the material collected from the study area were prepared for identification of dietary components in fecal pellets. A total of 80 fecal samples were collected and processed. Percent relative frequencies (P.R.F.) were calculated for each plant species recovered from pellets. Data revealed that Indian Crested Porcupine consumed 31 plant species in its diet, among them Zea mays (34.31±7.76) was the most frequently selected species followed by Rumex obtusifolius (15.32±2.57) and Melia azedarach (12.83±4.79). The study revealed that the greatest diversity of (n=20) plant species were consumed in summer season while minimum (n=13) species were used during winter. Among the parts of plants, stem was highly consumed in spring (57.2%) as compared to seed in fall (36.7%) while spikes and leaf were the least recovered parts from the fecal matter. The Berger-Parker diversity index showed highly diversified food (10.92) in the summer time of the year as compared to the autumn season (2.95). This study provides a baseline for the diet preference of this pest in the study area. Based on current findings, a detailed investigation on damage assessment, exploration, habitat use and management of Indian Crested Porcupine in AJ&K has been recommended.

scholarly journals Stool pattern is associated with not only the prevalence of tumorigenic bacteria isolated from fecal matter but also plasma and fecal fatty acids in healthy Japanese adults

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Daiki Watanabe ◽  
Haruka Murakami ◽  
Harumi Ohno ◽  
Kumpei Tanisawa ◽  
Kana Konishi ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Polyketide Synthase ◽  
Significant Negative Correlation ◽  
Factorial Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Valuable Insight ◽  
Fecal Matter ◽  
Fecal Samples ◽  
E Coli ◽  
Validated Questionnaire

Abstract Background Colibactin-producing Escherichia coli containing polyketide synthase (pks+E. coli) has been shown to be involved in colorectal cancer (CRC) development through gut microbiota analysis in animal models. Stool status has been associated with potentially adverse gut microbiome profiles from fecal analysis in adults. We examined the association between stool patterns and the prevalence of pks+E. coli isolated from microbiota in fecal samples of 224 healthy Japanese individuals. Results Stool patterns were determined through factorial analysis using a previously validated questionnaire that included stool frequency, volume, color, shape, and odor. Factor scores were classified into tertiles. The prevalence of pks+E. coli was determined by using specific primers for pks+E. coli in fecal samples. Plasma and fecal fatty acids were measured via gas chromatography-mass spectrometry. The prevalence of pks+E. coli was 26.8%. Three stool patterns identified by factorial analysis accounted for 70.1% of all patterns seen (factor 1: lower frequency, darker color, and harder shape; factor 2: higher volume and softer shape; and factor 3: darker color and stronger odor). Multivariable-adjusted odds ratios (95% confidence intervals) of the prevalence of pks+E. coli for the highest versus the lowest third of the factor 1 score was 3.16 (1.38 to 7.24; P for trend = 0.006). This stool pattern exhibited a significant positive correlation with fecal isobutyrate, isovalerate, valerate, and hexanoate but showed a significant negative correlation with plasma eicosenoic acid and α-linoleic acid, as well as fecal propionate and succinate. No other stool patterns were significant. Conclusions These results suggest that stool patterns may be useful in the evaluation of the presence of tumorigenic bacteria and fecal fatty acids through self-monitoring of stool status without the requirement for specialist technology or skill. Furthermore, it may provide valuable insight about effective strategies for the early discovery of CRC.

scholarly journals Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces

2021 ◽  
Author(s):  
Marie Bunker ◽  
Mark Martin ◽  
Stacey Weiss
Keyword(s):  
Cloacal Swab ◽  
Gi Tract ◽  
Microbial Composition ◽  
Fecal Matter ◽  
Tissue Samples ◽  
Fecal Samples ◽  
Community Function ◽  
Lower Intestine ◽  
Specialized Function ◽  
Sceloporus Virgatus

Microbial diversity and community function are related, and can be highly specialized in different gut regions. The cloacal microbiome of Sceloporus virgatus provides antifungal protection to eggshells during oviposition – a specialized function that suggests a specialized microbial composition. Here, we describe the S. virgatus cloacal microbiome from tissue and swab samples, and compare it to tissue samples from the gastrointestinal (GI) tract and oviduct, adding to the growing body of evidence of microbiome localization in reptiles. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these microbial communities and whether feces might “seed” the cloacal microbiome or impact the accuracy of cloacal swab sampling. We found that different regions of the gut had unique microbial community structures. The cloacal community, in particular, showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues, but fecal samples had much higher diversity and a distinct composition (62% Firmicutes and 39% Lachnospiraceae) relative to all gut regions. Finally, we found that feces and cloacal swabs recover different communities, but cloacal swabs may be contaminated with fecal matter if taken immediately after defecation. These results serve as a caution against the assumption that fecal samples provide an accurate representation of the gut, and that although cloacal swabs can reflect a portion of the lower GI tract microbiome, they may also result in a mixed community of gut and fecal microbes.

scholarly journals Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes

2021 ◽  
Author(s):  
Maud Billaud ◽  
Quentin Lamy-Besnier ◽  
Julien Lossouarn ◽  
Elisabeth Moncaut ◽  
Moira B. Dion ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genetic Maps ◽  
Human Pathogens ◽  
Bacterial Dna ◽  
Fecal Samples ◽  
Viral Particles ◽  
First Time ◽  
Animal Reservoirs

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

A rapid method for negative staining of fecal samples for diagnosis of viral-induced gastroenteritis by Transmission Electron Microscopy

1994 ◽  
Vol 52 ◽  
pp. 314-315
Author(s):  
J. P. Barrish ◽  
MJ Hicks ◽  
LC Leer ◽  
ES Hayes ◽  
MK Estes ◽  
...  
Keyword(s):  
Rapid Method ◽  
Negative Staining ◽  
Particle Identification ◽  
Viral Gastroenteritis ◽  
Norwalk Virus ◽  
Screening Process ◽  
Fecal Samples ◽  
Transmission Electron ◽  
Etiologic Agents ◽  
Viral Particles

The most common etiologic agents for viral gastroenteritis are rotavirus, adenovirus, and members of the “small round structure virus” category (enterovirus, norwalk virus, calicivirus, astrovirus). A rapid diagnosis of viral infection can avoid unnecessary antibiotic therapy, extensive and costly medical workups and reduce the patient’s hospital stay. Pseudoreplication has been the preparation method of choice at many institutions, because of its concentrating effect on viral particles. Unfortunately, in addition to concentrating viral particles, this method also concentrates fecal debris, making the screening process quite difficult at times and time consuming.A rapid method of negative staining for viral particle identification in fecal samples is presented. The method first described by Cubitt et al has been modified, resulting in a reduction in the amount of debris and improved staining quality of the viral particles, while still concentrating the number of viral particles. This method requires less than 1 ml of stool specimen and may be prepared in less than three minutes.

A Rapid Method for Viral Particle Detection in Viral-Induced Gastroenteritis: A TEM Study

1995 ◽  
Vol 1 (5) ◽  
pp. 185-189
Author(s):  
M. John Hicks ◽  
James P. Barrish ◽  
Elizabeth S. Hayes ◽  
Laurie C. Leer ◽  
Mary K. Estes ◽  
...  
Keyword(s):  
Staining Method ◽  
Pediatric Population ◽  
Staining Technique ◽  
Negative Staining ◽  
Viral Gastroenteritis ◽  
Particle Detection ◽  
Fecal Samples ◽  
Infectious Gastroenteritis ◽  
Viral Particles ◽  
Tem Method

Infectious gastroenteritis is a common cause of hospitalization in the pediatric population. The most frequent cause of gastroenteritis is viral in origin. The purpose of this study was to compare a rapid modified negative-staining TEM method with the conventional pseudoreplica technique in detection of viral particles in fecal samples from children with viral gastroenteritis. The modified negative-staining method resulted in a significantly higher (2.5 ± 0.5, p = 0.02) viral rating score than that for the conventional pseudoreplica technique (1.7 ± 0.4). In addition, the preparation time for the negative-staining method was approximately one fifth that for the conventional pseudoreplica technique. Rapid diagnosis of viral gastroenteritis may be made by ultrastructural detection of viral particles in fecal samples using the negative staining technique.

Transmission Of ESBL Producing Klebsiella Ozaenae Between Wildlife And Domesticated Animals

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S136-S137
Author(s):  
G M Leu-Burke ◽  
B Hernandez
Keyword(s):  
Antimicrobial Resistance ◽  
Contaminated Soil ◽  
Human Interaction ◽  
Resistant Bacteria ◽  
Shared Environment ◽  
Fecal Matter ◽  
Fecal Samples ◽  
Domesticated Animals ◽  
Extended Spectrum Beta Lactamase ◽  
Urban City

Abstract Introduction/Objective Animal and human interaction can result in zoonotic transmission, colonization and risk for infectious disease. However wildlife exposure to humans through domesticated animals is not fully understood. Alaska’s largest urban city, Anchorage, is home to approximately one thousand moose migrating into city parks and suburban backyards with an environmental impact from fecal contamination. As domesticated canines inhabit the same environment there is a potential public health for microbial transfer from wildlife to humans. Methods In order to determine potential risk of zoonosis from wildlife to domesticated animals, we ground collected fecal samples from three related canines (Chico, Kali, Chubs), moose habituating the canine’s backyard and from an unrelated canine (Odin) who lived nearby, but did not inhabit the same backyard environment. Observation of canine outdoor activity, including rolling and digging in the soil, was also evaluated. Using standard microbial techniques, all fecal samples were cultured for enterobacteriaceae and further identified by biochemical testing, along with antimicrobial resistance using conventional minimum inhibition concentration antibiotic panels. Phenotypic evaluation for extended spectrum beta-lactamase enzyme was performed using antibiotic disc diffusion. Results Fecal samples from the moose contained identical biotype and antimicrobial resistance of ESBL producing Klebsiella ozaenae with related canines Chico and Chubs. Chico and Chubs consistently exposed themselves to moose fecal matter by digging in contaminated soil, indicating aerosol transmission. Although Kali and Odin interacted with Chico and Chubs, they were not colonized suggesting a lack of microbial transmission between domesticated animals. Conclusion Close proximity to moose in urban Anchorage draws our attention to their commensal microbiome and potential for infectious transfer. Domesticated animals inhabit shared environment and are at risk for colonization during exposure to wildlife fecal contaminated soil and water. In a limited study, we found transfer of ESBL Klebsiella ozaenae from moose to domesticated animals in a shared urban residence. Human contact with infected domesticated animals, along with aerosol soil exposure during gardening or landscaping activities, presents opportunity for zoonosis from urban wildlife and a risk for colonization of multi-drug resistant bacteria.

scholarly journals PCR Detection of Group A Bovine Rotaviruses in Feces

1993 ◽  
Vol 5 (4) ◽  
pp. 516-521 ◽  
Author(s):  
Jarasvech Chinsangaram ◽  
Geoffrey Y. Akita ◽  
Anthony E. Castro ◽  
Bennie I. Osburn
Keyword(s):  
Ethidium Bromide ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Pcr Assay ◽  
Fecal Samples ◽  
Bovine Rotavirus ◽  
Viral Particles ◽  
Pcr Inhibitor ◽  
Group A

A polymerase chain reaction (PCR) protocol has been developed for identification of bovine group A rotavirus infection in feces. Primers (20mers) complementary to 3′ ends of double-stranded RNA genome segment 6 of bovine rotavirus NCDV strain were synthesized and used in PCR. Bovine rotavirus RNA from infected cell culture was employed to optimize the PCR protocol. Rotavirus-negative fecal samples were spiked with known quantities of bovine rotavirus, and the sensitivity of the PCR assay was determined. Fecal samples were extracted with phenol and treated to eliminate unidentified PCR inhibitor(s) in feces, and PCR was performed. PCR products were either visualized on ethidium bromide-stained agarose gels or detected by chemiluminescent hybridization. The sensitivity of the assay was 6 × 104 viral particles/ml of feces with ethidium bromide-stained agarose gel visualization or 6 × 102 viral particles/ml of feces with chemiluminescent hybridization. The PCR assay was applied to 18 fecal specimens from clinical cases. All 16 clinical samples that were positive for rotavirus by enzyme-linked immunosorbent assay (ELISA) or by ELISA and electron microscopy (EM) were positive by PCR. The 2 samples that were rotavirus negative by ELISA or by ELISA and EM were also negative on PCR analysis.

Two Cases of Hemorrhagic Diarrhea Caused by Cronobacter sakazakii in Hospitalized Nursing Infants Associated with the Consumption of Powdered Infant Formula

2011 ◽  
Vol 74 (12) ◽  
pp. 2177-2181 ◽  
Author(s):  
J. PARRA FLORES ◽  
S. ARVIZU MEDRANO ◽  
J. SILVA SÁNCHEZ ◽  
E. FERNÁNDEZ-ESCARTÍN
Keyword(s):  
Infant Formula ◽  
Enterotoxigenic Escherichia Coli ◽  
Most Probable Number ◽  
Powdered Infant Formula ◽  
Cronobacter Sakazakii ◽  
Fecal Matter ◽  
Probable Number ◽  
Fecal Samples ◽  
Mother And Child ◽  
Child Hospital

Two cases of acute gastroenteritis occurred in 5-month-old infants hospitalized in a mother-and-child hospital in Queretaro, Mexico, on 24 January 2010. C. sakazakii was recovered from the powdered infant formula (PIF), rehydrated PIF (R-PIF) fed to infants, and their fecal samples. The microorganism was present at levels of 0.33 most probable number (MPN)/g and 24 MPN/ml in PIF and R-PIF, respectively. The total ingested dose for the day before the onset of the diarrheic syndrome ranged between 2,160 and 3,600 MPN/ml. All strains of C. sakazakii recovered from the three sources (R-PIF, PIF, and fecal matter) showed identical biotypes, adhesion and invasiveness factors, and pulsed-field gel electrophoresis profiles. No deaths were observed. Salmonella, Shigella, and enterotoxigenic Escherichia coli were not found in food or fecal samples.

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