A clinician's guide to microbiome analysis

@article{Claesson2017ACG,
  title={A clinician's guide to microbiome analysis},
  author={Marcus J. Claesson and Adam G. Clooney and Paul W. O’Toole},
  journal={Nature Reviews Gastroenterology \&Hepatology},
  year={2017},
  volume={14},
  pages={585-595}
}
Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and… 
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References

SHOWING 1-10 OF 216 REFERENCES
Microbes, microbiota, and colon cancer.
TLDR
The roles of microbial metabolism as it relates to bile acids, xenobiotics, and diet in the etiology and therapeutics of CRC is explored and conceptual frameworks for evaluating the role of microbes in cancer causation are explored.
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
TLDR
Ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community, and support the hypothesis of functional redundancy in the human gut microbiota.
The vocabulary of microbiome research: a proposal
TLDR
This editorial aims to propose clear definitions of each of these terms such as microbiome, microbiota, metabolomic, and meetagenome and metagenomics among others, and to implore scientists in the field to adopt and perfect them.
The treatment-naive microbiome in new-onset Crohn's disease.
TLDR
Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.
The gut microbiota in IBD
TLDR
Dysbiosis (that is, abnormal microbiota composition) and decreased complexity of the gut microbial ecosystem are common features in patients with Crohn's disease or ulcerative colitis, and whether such changes are a cause or a consequence of the disease remains to be elucidated.
Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics
TLDR
The implementation of NGS in medical practice has been a slow process due to various challenges such as clinical trials, lack of applicable regulatory guidelines, and the adaptation of the technology to the clinical environment, so a colloquium to define issues was convened to begin to define these issues.
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
TLDR
This work determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.
Rectal Swabs for Analysis of the Intestinal Microbiota
TLDR
It is found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota, and may be ideally suited for clinical diagnostics and large-scale studies.
A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome
TLDR
Current scientific evidence does not support the existence of microbiomes within the healthy fetal milieu, which has implications for the development of clinical practices that prevent microbiome perturbations after birth and the establishment of future research priorities.
Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool
TLDR
It is found that stool subsampling resulted in large variability of gut microbiome data due to different microenvironments harbouring various taxa within an individual stool, and solutions for processing and storing human stool samples that reduce variability of microbiome data are provided.
...
1
2
3
4
5
...