Abstract:
:Gut microbiota can provide great insight into host health, and studies of the gut microbiota in wildlife are becoming more common. However, the effects of field conditions on gut microbial samples are unknown. This study addresses the following questions: 1) How do environmental factors such as sunlight and insect infestations affect fecal microbial DNA? 2) How does fecal microbial DNA change over time after defecation? 3) How does storage method affect microbial DNA? Fresh fecal samples were collected, pooled, and homogenized from a family group of 6 spider monkeys, Ateles geoffroyi. Samples were then aliquoted and subjected to varying light conditions (shade, sun), insect infestations (limited or not limited by netting over the sample), and sample preservation methods (FTA - Fast Technology for Analysis of nucleic acid - cards, or freezing in liquid nitrogen then storing at -20°C). Changes in the microbial communities under these conditions were assessed over 24h. Time and preservation method both effected fecal microbial community diversity and composition. The effect size of these variables was then assessed in relation to fecal microbial samples from 2 other primate species (Rhinopithecus bieti and R. brelichi) housed at different captive institutions. While the microbial community of each primate species was significantly different, the effects of time and preservation method still remained significant indicating that these effects are important considerations for fieldwork.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Hale VL,Tan CL,Niu K,Yang Y,Cui D,Zhao H,Knight R,Amato KRdoi
10.1016/j.mimet.2016.09.017subject
Has Abstractpub_date
2016-11-01 00:00:00pages
180-188eissn
0167-7012issn
1872-8359pii
S0167-7012(16)30267-6journal_volume
130pub_type
杂志文章abstract::One of the known limitations for biosensor assays is the high limit of detection for target cells within complex samples (e.g., Escherichia coli at 10(4) to 10(5) CFU/mL) due to poor capture efficiencies. Currently, researchers can only estimate the cell capture efficiency necessary to produce a positive signal for an...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.11.004
更新日期:2008-01-01 00:00:00
abstract::A protein database was constructed and validated with identification rate over 90% for the 4 most common Gram-negative bacteria on agar plates. By protein masses comparison, 120 bacteria of the 4 species from blood culture bottles were identified. The concordance was high (Kappa=0.906) between our method and conventio...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.07.021
更新日期:2014-10-01 00:00:00
abstract::Alternaria tenuissima is a fungus widely present in the environment and causes diseases in plants and humans in the world. In this study, we constructed an A. tenuissima cDNA expression library in a centromeric yeast vector that allows the isolation of functional cDNA sequences from this environmental and pathogenic f...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.12.021
更新日期:2007-04-01 00:00:00
abstract::A sensitive, selective, and rapid protocol for detecting Ralstonia solanacearum from soil and plant tissues was developed based on the integration of the rapid self-replicating ability of bacteriophages with quantitative PCR (q-PCR). Six bacteriophages were isolated and selected for their ability to specifically infec...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.11.008
更新日期:2009-03-01 00:00:00
abstract::Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of paratuberculosis, a chronic granulomatous enteric disease of ruminants. MAP detection by faecal culture provides the definitive diagnosis of the infection. Automated liquid systems for MAP culture are more sensitive and rapid than culture on s...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2011.01.019
更新日期:2011-03-01 00:00:00
abstract::An updated dataset of in silico specificities for 54 previously published 16S rRNA-targeted oligonucleotides was assembled to provide guidance for reliable fluorescence in situ hybridization (FISH) analysis of sulfate-reducing bacteria. Additionally, six new FISH probes were developed for major deltaproteobacterial ta...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.02.009
更新日期:2007-06-01 00:00:00
abstract::Mycobacterium tuberculosis (MTB) is the causative agent of pulmonary tuberculosis. Rapid and accurate diagnosis is crucial to tuberculosis control and prevention. A series of diagnostic methods has been available for MTB detection; however, new rapid, simple and affordable methods are needed. In this study, a multiple...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.11.003
更新日期:2018-02-01 00:00:00
abstract::Confocal microscopy-based monitoring of pH in biofilms is gaining increasing interest, as it allows for a quick assessment of horizontal pH gradients without mechanically perturbing the biofilm. Ratiometric monitoring of pH with the fluorescent dye C-SNARF-4 has been used to reliably map extracellular pH in the basal ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.08.007
更新日期:2018-09-01 00:00:00
abstract::AFLP is a selective restriction fragment amplification method generating DNA fingerprints for microbial isolates. We present high-throughput AFLP (htAFLP) to characterize molecular markers associated with bacterial phenotypes. Methicillin-resistant and -susceptible isolates of Staphylococcus aureus have been used for ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.07.013
更新日期:2007-10-01 00:00:00
abstract:OBJECTIVES:Galactomannan (GM) and Aspergillus DNA detection are useful tools for the diagnosis of invasive pulmonary aspergillosis (IPA), primarily in blood and bronchoscopy samples. This study aimed to evaluate the utility of both markers for detection of Aspergillus in sputum from patients with allergic bronchopulmon...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.06.016
更新日期:2017-09-01 00:00:00
abstract::A method for rapidly and selectively isolating Salmonellae from buffer solutions and concentrating the bacteria by a factor of approximately 500 was developed. Anti-Salmonellae antibody was covalently linked to 40 microm polyacrylamide beads to prepare a solid phase with affinity for the bacteria. The beads were packe...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00163-5
更新日期:2003-10-01 00:00:00
abstract::A pair of polymerase chain reaction (PCR) primers was designed on the basis of the nucleotide sequence homology of dextranase genes (dex) of Streptococcus mutans, S. sobrinus and S. downei. The primer pair amplified a 530-bp DNA fragment on the dex genes of mutans streptococcal species: S. mutans, S. sobrinus, S. down...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(01)00263-9
更新日期:2001-08-01 00:00:00
abstract::Two rapid in situ enumeration methods using fluorescent probes were used to assess the physiological activities of Klebsiella pneumoniae biofilms on stainless steel. Fluorescent dyes, 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) and rhodamine 123 (Rh 123), were chosen to perform this study. CTC is a soluble redox ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/0167-7012(94)90058-2
更新日期:1994-01-01 00:00:00
abstract::The performance of 3 blood culture bottles (BACTEC Plus Aerobic/F, Plus Anaerobic/F, and Anaerobic Lytic/F) were analyzed with clinical specimens collected from 688 Emergency Department patients. A total of 270 strains belonging to 33 species were identified, with E. coli and S. aureus as the most frequently detected....
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2016.09.008
更新日期:2016-11-01 00:00:00
abstract::Thermophilic strains of Geobacillus, Anoxybacillus and Bacillus that are able to grow at 55 degrees C and above are recognized as commonly occurring contaminants during the production of milk powders. In particular, Anoxybacillus flavithermus strain C and Bacillus licheniformis strain F are often the most prevalent. W...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2004.09.008
更新日期:2005-02-01 00:00:00
abstract::Quantitative PCR is becoming the method of choice for the detection of pathogenic microorganisms and other targets in the environment. A major obstacle when amplifying DNA is the presence of inhibiting substances like humic acids that decrease the efficiency of PCR. We combined the polymeric adsorbent Supelite™ DAX-8 ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.12.027
更新日期:2011-04-01 00:00:00
abstract::Lactobacillus animalis NP51 is a direct-fed microbial strain (DFM) extensively used as a pre-harvest food safety mitigation in feedlot cattle due to its antagonistic effects against human foodborne pathogens such as Salmonella and Escherichia coli O157:H7. NP51 not only promotes overall gut health but interferes with ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.04.012
更新日期:2018-06-01 00:00:00
abstract::Counting colonies is usually used in microbiological analysis to assess if samples meet microbiological criteria. Although manual counting remains gold standard, the process is subjective, tedious, and time-consuming. Some developed automatic counting methods could save labors and time, but their results are easily af...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.09.004
更新日期:2018-10-01 00:00:00
abstract::Leptospirosis is an emerging worldwide zoonosis with a changing epidemiology responsible for an acute disease in humans and dogs. A better knowledge of the responsible bacterium Leptospira and in particular its various serovars and serogroups prevalence is essential for better diagnosis and prevention of the disease. ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2020.106007
更新日期:2020-09-01 00:00:00
abstract::Laser desorption-time of flight (LD-TOF) mass spectrometry-based detection of hemozoin was assessed for its performance characteristics as a rapid screening test for malaria. In spite of good specificity of >95%, poor sensitivity of 80.2% for microscopically positive samples makes the easy-to-apply and rapid approach ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2019.04.002
更新日期:2019-05-01 00:00:00
abstract::Laccase is a key enzyme in the degradation of lignin by fungi. Reports indicate that the activity of this enzyme ranges from 3.5 to 484,000 U L(-1). Our aim was to analyze how laccase activity is calculated in the literature, and to determine statistically whether variations in activity are due to biological propertie...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.10.007
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:Fluorescence in situ hybridization (FISH) is not adapted for the detection of bacterial spores because of their resistance to conventional permeabilization treatments. Since spore-forming bacteria have important ecological, economical, and medical roles, their in situ detection needs to be improved. The aim ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.12.009
更新日期:2009-04-01 00:00:00
abstract::Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.07.009
更新日期:2010-09-01 00:00:00
abstract::Phenotypic differentiation between Campylobacter fetus (C. fetus) subspecies fetus and C. fetus subspecies venerealis is hampered by poor reliability and reproducibility of biochemical assays. AFLP (amplified fragment length polymorphism) and MLST (multilocus sequence typing) are the molecular standards for C. fetus s...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.06.005
更新日期:2013-10-01 00:00:00
abstract::Flow cytometry was used to characterize bacterioplankton from two tropical environments in Brazil: the eutrophic Guanabara Bay and the oligotrophic southwest Atlantic Ocean. Bacterial abundance was evaluated by flow cytometry, and cells were stained with SYTO 13, allowing demonstration of differences in nucleic acid c...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2003.08.002
更新日期:2003-12-01 00:00:00
abstract::Several studies have been conducted to develop rapid methods for quantification of lipid content in microalgae, as an alternative for time consuming gravimetric methods. Different studies showed that lipid staining with Nile Red in whole cell suspensions and subsequently quantification by the use of a spectrofluoromet...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.09.009
更新日期:2015-11-01 00:00:00
abstract::A novel fluorescent microbead immunoassay (FMIA) using the recombinant polypeptide SpaA415 was developed for detection of anti-Erysipelothrix spp. IgG in pig sera. The diagnostic performance of the FMIA was evaluated on samples from pigs with known and unknown Erysipelothrix spp. exposure and compared to an in-house e...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.07.014
更新日期:2012-10-01 00:00:00
abstract::A new method was established for fine visualization of bacterial subcelluar filamentous structures by freezing the bacterial cells to displace cytoplasmic matrix granules to the periphery. This method was successfully applied in immunoelectron microscopy and electron microscopic tomography, and should be applicable fo...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.03.016
更新日期:2012-07-01 00:00:00
abstract::Activated charcoal is a carbonaceous adsorbent with a high internal porosity, and hence a large internal surface area. Cells of a strain of Escherichia coli O157:H7 seeded into oyster tissue homogenates were completely bound to untreated charcoal after an incubation period of 15 min at room temperature. In contrast, a...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.09.012
更新日期:2007-02-01 00:00:00
abstract::Neuraminidase was produced by 32.1% and 28.5% of Porphyromonas from dogs with and without periodontitis, respectively; and by 31.8% of bacteria from humans. The presence of neuraminidase in Porphyromonas spp. suggests that this enzyme can be involved with the pathogenesis of the periodontal disease, and the use of thi...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.06.017
更新日期:2013-09-01 00:00:00