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Methods for Microbiota Analysis: Sample Collection and Laboratory Methods

  • Saleh Ibrahim
  • Meriem Belheouane
Chapter

Abstract

The human body hosts a myriad of complex and diversified microbial assemblages on various barrier organs. The symbiotic microbial communities impact several aspects of the host’s biology in health and disease. Nowadays, microbiota research has become a central area of investigation involving diverse fields such as immunology, nutrition, and genetics. Consequently, methods for microbiota studies, comprising study design and laboratory techniques, are central in addressing general and specific research questions and especially in providing clear and reliable insights. Fortunately, approaches that investigate different aspects of microbial communities have greatly improved and expanded allowing unprecedented levels of characterization of host-microbiota interactions.

Through this chapter, we aim to describe the diverse techniques available for researchers to examine bacterial communities associated with numerous human body sites. We describe various culture-based and sequencing methods, additional techniques that characterize several aspects of the entire bacterial community, as well as approaches that define the status of single cells. Moreover, we describe the advantageous strategy of combining distinct approaches in a microbiota study to collect different and complementary insights on the community and/or to confirm each different method’s outcome. Additionally, we thoroughly discuss the crucial steps of study design, sampling strategies, and sample collection and processing which influence the interpretation and conclusions of microbiota study. Overall, this chapter clarifies the critical steps and available investigation tools in a microbiota study and thus assists researchers in defining the experimental design and laboratory methods to conduct a microbiota study.

Keywords

Study design Laboratory methods Combination of several techniques Sampling strategies Sample collection 

Abbreviations

CD

Clostridium difficile

CD

Crohn’s disease

CDI

Clostridium difficile infection

DGGE

Denaturing gradient gel electrophoresis

FACS

Flow cytometry (FCM) fluorescence-activated cell sorting (FACS)

FISH

Fluorescence in situ hybridization

GC-MS

Gas chromatography-mass spectrometry

MAR

Microautoradiography

OTU

Operational taxonomic unit

RTF

Reduced transport fluid

SIMS

Secondary ion mass spectrometry

SIP

Isotope-labeled substrates

TGGE

Temperature gradient gel electrophoresis

T-RFLP

Terminal restriction fragment length polymorphism

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Lübeck Institute of Experimental DermatologyUniversity of LübeckLübeckGermany
  2. 2.College of Medicine and Sharjah Institute for Medical ResearchUniversity of SharjahSharjahUnited Arab Emirates
  3. 3.Max-Planck-Institute for Evolutionary BiologyPlönGermany
  4. 4.Institute for Experimental MedicineChristian-Albrechts-University of KielKielGermany

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