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You searched for: Journal name Journal of microbiological methods Remove constraint Journal name: Journal of microbiological methods Subject term digestive system Remove constraint Subject term: digestive system Text availability Citation in PubAg Remove constraint Text availability: Citation in PubAg
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1. Assessment of stool collection and storage conditions for in vitro human gut model studies

Author:
Grace A.I. Newland; Glenn R. Gibson; Frances L. Jackson; Anisha Wijeyesekera
Source:
Journal of microbiological methods 2021 v.185 pp. 106230
ISSN:
0167-7012
Subject:
batch fermentation; breast milk; culture media; digestive system; feces; humans; hybridization; ice; intestinal microorganisms; magnetism; oligosaccharides
Abstract:
... The role of the gut microbiota in health and disease is becoming increasingly apparent. Faeces is the most accessible sample to collect from human volunteers for studying the gut microbiota. However, the impact of stool collection and storage conditions on microbial and metabolic profiles have not been fully evaluated. By understanding the effect of different stool collection and storage condition ...
DOI:
10.1016/j.mimet.2021.106230

2. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags

Author:
Xin Peng; Ke-Qiang Yu; Guan-Hua Deng; Yun-Xia Jiang; Yu Wang; Guo-Xia Zhang; Hong-Wei Zhou
Source:
Journal of microbiological methods 2013 v.95 no.3 pp. 455-462
ISSN:
0167-7012
Subject:
DNA; bacterial communities; boiling; cost effectiveness; digestive system; environmental health; feces; high-throughput nucleotide sequencing; human health; metagenomics; microbiome; microorganisms; ribosomal RNA; species diversity
Abstract:
... Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present st ...
DOI:
10.1016/j.mimet.2013.07.015

3. Formalin-fixed paraffin-embedded tissues for microbiome analysis in rainbow trout (Oncorhynchus mykiss)

Author:
Roberto Cruz-Flores; Mónica Hernández Rodríguez; Jesús Salvador Olivier Guirado Flores; Arun K. Dhar
Source:
Journal of microbiological methods 2022 v.192 pp. 106389
ISSN:
0167-7012
Subject:
Oncorhynchus mykiss; digestive system; histology; intestinal microorganisms; microbiome
Abstract:
... The gut microbiomes of rainbow trout (Oncorhynchus mykiss) reared at 16° and 22 °C were determined using formalin-fixed paraffin-embedded tissues (FFPE) and compared to fresh frozen tissue. The data revealed microbiomes could be successfully determined using FFPE tissue opening a new horizon in studying intestinal microbiota using archived histological samples. ...
DOI:
10.1016/j.mimet.2021.106389

4. Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias

Author:
Michelle M. O'Donnell; Mary C. Rea; Órla O'Sullivan; Cal Flynn; Beth Jones; Albert McQuaid; Fergus Shanahan; R. Paul Ross
Source:
Journal of microbiological methods 2016 v.129 pp. 109-116
ISSN:
0167-7012
Subject:
biomass; cell viability; centrifugation; digestive system; feces; fermentation; freezing; glycerol; humans; inoculum; intestinal microorganisms; microbial communities; models; pelleting; phosphates; quantitative polymerase chain reaction; slurries
Abstract:
... In-vitro gut fermentation systems provide suitable models for studying gut microbiota composition and functionality. However, such methods depend on the availability of donors and the assumption of reproducibility between microbial communities before experimental treatments commence. The aim of this study was to develop a frozen standardised inoculum (FSI) which minimizes inter-individual variatio ...
DOI:
10.1016/j.mimet.2016.08.002

5. Protective effects of oral immunization with formalin-inactivated whole-cell Citrobacter rodentium on Citrobacter rodentium infection in mice

Author:
Keita Takahashi; Yuki Hanamura; Nagisa Tokunoh; Kohei Kassai; Masaru Matsunishi; Shiori Watanabe; Tsuyoshi Sugiyama; Naoki Inoue
Source:
Journal of microbiological methods 2019 v.159 pp. 62-68
ISSN:
0167-7012
Subject:
Citrobacter rodentium; animal models; antibodies; bacteria; blood serum; body weight changes; death; digestive system; edible vaccines; enterohemorrhagic Escherichia coli; enteropathogenic Escherichia coli; genes; hyperplasia; immunoglobulin G; mice; oral administration; oral vaccination; pathogens; protective effect; virulence
Abstract:
... Evaluation of the efficacy of vaccine candidates that prevent enteropathogenic and enterohemorrhagic Escherichia coli (EPEC/EHEC) infection in mouse models is difficult due to their limited pathogenicity in mice. Citrobacter rodentium, a murine pathogenic bacterium that shares its infection strategy and virulence genes with EPEC/EHEC, has been used as a model pathogen to develop novel vaccine stra ...
DOI:
10.1016/j.mimet.2019.02.016

6. Rapid differentiation of Lactobacillus species via metabolic profiling

Author:
Kundi Yang; Mengyang Xu; Fanyi Zhong; Jiangjiang Zhu
Source:
Journal of microbiological methods 2018 v.154 pp. 147-155
ISSN:
0167-7012
Subject:
Lactobacillus; data quality; digestive system; functional properties; humans; lactic acid; lactic acid bacteria; metabolites; metabolomics; monitoring; probiotics; spectrometers; sugars
Abstract:
... Lactobacillus, the major genus of lactic acid bacteria group, plays functional roles in the human body, for example, convert sugars to lactic acid. They are the significant microbiota which can be found at a number of human body sites, such as the digestive system, urinary system, and genital system. A number of Lactobacillus species are often used as probiotics and can benefit host health when ad ...
DOI:
10.1016/j.mimet.2018.10.013

7. Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model

Author:
Julie A.K. McDonald; Susana Fuentes; Kathleen Schroeter; Ineke Heikamp-deJong; Cezar M. Khursigara; Willem M. de Vos; Emma Allen-Vercoe
Source:
Journal of microbiological methods 2015 v.108 pp. 36-44
ISSN:
0167-7012
Subject:
biofilm; digestive system; humans; in vivo studies; intestinal microorganisms; models
Abstract:
... In vivo studies of human mucosal gut microbiota are often limited to end-point analyses and confounded by bowel cleansing procedures. Therefore, we used biofilm reactors to incorporate a simulated mucosal environment into an in vitro gut chemostat model. Communities developed were complex, reproducible, distinct, and representative of in vivo communities. ...
DOI:
10.1016/j.mimet.2014.11.007

8. Simulation of the mucosal environment in the re-construction of the synthetic gut microbial ecosystem

Author:
Humphrey A. Mabwi; Emmanuel Hitayezu; Intan Rizki Mauliasari; Kilaza Samson Mwaikono; Hyo Shin Yoon; Erick V.G. Komba; Cheol-Ho Pan; Kwang Hyun Cha
Source:
Journal of microbiological methods 2021 v.191 pp. 106351
ISSN:
0167-7012
Subject:
Bifidobacterium; Clostridium; Collinsella; Enterococcus; Roseburia; cell movement; digestive system; gels; gene expression; human health; humans; intestinal microorganisms; liquids; metabolism; microbial biomass; microbial communities; microbiome; prediction
Abstract:
... Human gut surface-attached mucosal microbiota plays significant roles in human health and diseases. This study sought to simulate the mucosal environment using mucin-agar gel and synthetic mucosal microbial community in vitro. To select suitable culture media, microbial communities were assembled and cultured in seven different media at 37 °C for 36 h. Among the seven media, Bryant & Burkey (BB) a ...
DOI:
10.1016/j.mimet.2021.106351

9. A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss)

Author:
Mathis Hildonen; Miyako Kodama; Lara C. Puetz; M. Thomas P. Gilbert; Morten T. Limborg
Source:
Journal of microbiological methods 2019 v.160 pp. 42-48
ISSN:
0167-7012
Subject:
DNA; Oncorhynchus mykiss; digestive system; dry ice; ethanol; fish; freezing; genomic libraries; intestinal microorganisms; labor; mammals; microbiome; new species; research programs; ribosomal RNA; sequence analysis; storage temperature; water content
Abstract:
... Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzyma ...
DOI:
10.1016/j.mimet.2019.03.010

10. An evaluation of the impact of clinical bacterial isolates on epithelial cell monolayer integrity by the electric Cell-Substrate Impedance Sensing (ECIS) method

Author:
Md A. Nahid; Carmen E. Campbell; Keith S.K. Fong; Jason C. Barnhill; Michael A. Washington
Source:
Journal of microbiological methods 2020 v.169 pp. 105833
ISSN:
0167-7012
Subject:
Enterococcus; Escherichia coli; Pseudomonas aeruginosa; bacteria; biosensors; capacitance; cell culture; cell structures; digestive system; dose response; epithelial cells; human cell lines; interleukin-13; interleukin-1beta; interleukin-8; methicillin-resistant Staphylococcus aureus; microelectrodes; virulence
Abstract:
... Virulence is the relative capacity of a pathogenic microorganism to cause damage in susceptible host cells such as those found in airway passages and the gut. In this study, the effect of clinical bacterial isolates on the monolayer integrity of cultured human alveolar basal epithelial cells (A549) was evaluated using the Electric Cell-Substrate Impedance Sensing (ECIS) system. ECIS is a morpholog ...
DOI:
10.1016/j.mimet.2020.105833