Environmental Chemicals, the Human Microbiome, and Health Risk A Research Strategy (2018) / Chapter Skim
Currently Skimming:
4 Current Methods for Studying the Human Microbiome
4 Current Methods for Studying the Human Microbiome
Pages 49-70
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 49... ...
The most common tardreds of strains that differ nearly completely from geted assays might involve gnotobiotic transfer of one site to another throughout the body (HMP Con- human microbiome samples into controlled modsortium 2012a,b)
|
From page 50... ...
Each sampling method for hurisks are possible. Animal models can rarely pre- man-associated microbial community types has cisely recapitulate human-associated microbial strengths and weaknesses that are driven by the community structure (Chung et al.
|
From page 51... ...
-- above with the skin, the respiratory tract is less miand require more extensive sequencing and care crobially dense, and it is essential to use protocols during analysis. Because of the low biomass of that have carefully controlled elements to miniskin microbiome samples and the challenges as- mize sample contamination by nontarget tissue sociated with collecting them, assays that evalu- (Charlson et al.
|
From page 52... ...
First, crobial community or strain is to introduce it diit is much easier to manipulate animal models than rectly into conventionally reared animals that are human subjects experimentally. Animal studies already colonized with a microbiota (a probiotic allow the careful control of experimental vari- or super-colonization approach)
|
From page 53... ...
The donor microbial communities can be derived from various sources; Engineered Systems for Studying "humanized" animal models that are more rel- Host–Microbiome Interactions evant to the human condition are produced when In Vitro and Ex Vivo a human source is used (Ridaura et al.
|
From page 54... ...
Changes in the quality of alized organoid lines from different clinical donors the epithelial layer can be measured by assessing or animal models to be generated. Several protopermeability, transmembrane resistance (used to cols have been developed and generally introduce measure how tightly connected neighboring cells specialized factors into cell-culture media to difare)
|
From page 55... ...
Organoid cultures and prolonged culture times are being explored. offer moderate experimental throughput, moder Analogous tools are available to study host– ate to high physiologic relevance, and moderate microbiome interactions in the respiratory tract.
|
From page 56... ...
2012) is a model dium has a lower concentration of gelatin, which of the small and large intestines that contains sta- allows the detection of mobile microorganisms -- ble and functional microbial communities similar can be used to encourage the growth of difficult to those found in the human (Joly et al.
|
From page 57... ...
, which is Nucleotide Sequencing almost universal among bacteria, whereas the 18S rRNA gene and internal transcribed spacer (ITS) The decreasing cost and increasing accessi- sequence variants are increasingly common for eubility of nucleotide sequencing unquestionably karyotic profiling6 (Findley et al.
|
From page 58... ...
be cautious to avoid destroying sensitive subsets of microorganisms while still extracting genomic Other Culture-Independent material from more hardy or resistant organisms. Molecular Profiling Techniques If RNA is the desired genetic material, extra caution will be needed to avoid destroying the RNA Metabolomic and metaproteomic techniques during sample processing.
|
From page 59... ...
Fluorescence in situ hybridization metabolomic surveys and quantification of small (FISH) can be used to evaluate the taxonomy, lomolecules from biofluids include gas chromatogra- cation, and organization of microbial community phy, liquid chromatography, capillary electropho- members in fixed microbiome samples.
|
From page 60... ...
in animal systems, or comprehensive transforma Finally, genetic screens and modifications can tion of community members in situ, all of which be used to observe microbial communities. Func- are technically challenging to conduct and verify.
|
From page 61... ...
among microorganisms, cells, or molecules. They Multivariate statistical modeling techniques -- might target molecular-interaction networks or such as generalized linear modeling, factor anal- ecologic structures in microbial communities diysis, variations on ordination, correspondence rectly (Faust et al.
|
From page 62... ...
. Be- microbiome transplant studies in animal models, cause nearly all molecular assays measure relative experiments that include chemical treatment and abundance (compositions)
|
From page 63... ...
nisms provide appropriate experimental environ ments for controlled manipulation of host-as Analyses sociated microbial communities, although none mimics humans perfectly. Analysis of human microbiome data, regard- • Gnotobiotic animal models are particularless of their source or assay method, can benefit ly amenable to studies of the effect of microbialfrom the approaches that have been developed over community composition on host phenotype.
|
From page 64... ...
2012. Defining a healthy human gut microbiome: 2016.
|
From page 65... ...
:478-488. and metagenome of the human gut.
|
From page 66... ...
2015. Systems best: The universality of maternal microbial transmis- modeling approaches for microbial community studies sion.
|
From page 67... ...
:2726-2734. of the human gut microbiota through culture-enriched Kaiko, G.E., S.H.
|
From page 68... ...
2014. Animal models of ex vivo lung biotics shape the physiology and gene expression of the perfusion as a platform for transplantation research.
|
From page 69... ...
Walker. meta'omics for microbial community studies.
|
From page 70... ...
Cell Host Microbe 17(3)
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.