Glossary of terms related to microbiota studies
| Term . | Definition . | Reference . |
|---|---|---|
| Gnotobiology | The scientific investigation of organisms that are either free of microorganisms or are associated only with specified microorganisms. | 9 |
| Germ-free (axenic) mouse models | Mice free of all microorganisms, including those that are typically found in the gut. | 10 |
| Microbiota | The collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses. | 4 |
| Microbiome | Generally accepted to refer to the genomes (genetic material [DNA or RNA]) of the microbiota. | |
| Dysbiosis | A breakdown in the balance between putative species of “protective” vs “harmful” intestinal microorganisms. | 11 |
| Metagenomics | The study of a collection of genetic material (genomes) from a mixed community of organisms (ie, microbial communities). | |
| Monocolonization | Introduction of 1 bacterial species in axenic mice; alternatively, a clinical situation in which a single organism dominates the microbiota as a result of disease or treatment characteristics. | |
| Oligocolonization | Introduction of multiple bacterial species in axenic mice; alternatively, a clinical situation in which a small number (typically ∼2-5) of organisms dominate the microbiota as a result of disease or treatment characteristics. | |
| Fecal microbiota transfer | Introduction of a fecal suspension derived from a healthy donor into the gastrointestinal tract of a diseased individual. Fecal microbiota transfer can be performed via the introduction of an auto (self) or allo (other) source of stool or purified bacterial stool product via a multitude of methods, including administration by nasogastric tube, colonoscopy, or capsulized therapy. | 12 |
| Next-generation whole-genome sequencing | DNA is fragmented, amplified, and then sequenced in a massively parallel fashion. This sequence data can be compared to reference databases to infer the taxonomic community structure of a population of organisms; alternatively, novel organisms/strains can be discovered by de novo sequence assembly methods. | 13 |
| 16S ribosomal RNA/DNA sequencing | 16S ribosomal RNA/DNA of prokaryotes is amplified via polymerase chain reaction and sequenced to identify the genus or species of individual organisms. | 14 |
| Viral particle isolation and sequencing | Viral particles are separated from host contaminants using methods such as centrifugation and filtration. Viral particles can then be treated with DNase I to remove contaminating nucleic acids on the surface of these particles. A variety of molecular methods can be used to characterize the genomic sequence of the virions. | 15 |
| Term . | Definition . | Reference . |
|---|---|---|
| Gnotobiology | The scientific investigation of organisms that are either free of microorganisms or are associated only with specified microorganisms. | 9 |
| Germ-free (axenic) mouse models | Mice free of all microorganisms, including those that are typically found in the gut. | 10 |
| Microbiota | The collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses. | 4 |
| Microbiome | Generally accepted to refer to the genomes (genetic material [DNA or RNA]) of the microbiota. | |
| Dysbiosis | A breakdown in the balance between putative species of “protective” vs “harmful” intestinal microorganisms. | 11 |
| Metagenomics | The study of a collection of genetic material (genomes) from a mixed community of organisms (ie, microbial communities). | |
| Monocolonization | Introduction of 1 bacterial species in axenic mice; alternatively, a clinical situation in which a single organism dominates the microbiota as a result of disease or treatment characteristics. | |
| Oligocolonization | Introduction of multiple bacterial species in axenic mice; alternatively, a clinical situation in which a small number (typically ∼2-5) of organisms dominate the microbiota as a result of disease or treatment characteristics. | |
| Fecal microbiota transfer | Introduction of a fecal suspension derived from a healthy donor into the gastrointestinal tract of a diseased individual. Fecal microbiota transfer can be performed via the introduction of an auto (self) or allo (other) source of stool or purified bacterial stool product via a multitude of methods, including administration by nasogastric tube, colonoscopy, or capsulized therapy. | 12 |
| Next-generation whole-genome sequencing | DNA is fragmented, amplified, and then sequenced in a massively parallel fashion. This sequence data can be compared to reference databases to infer the taxonomic community structure of a population of organisms; alternatively, novel organisms/strains can be discovered by de novo sequence assembly methods. | 13 |
| 16S ribosomal RNA/DNA sequencing | 16S ribosomal RNA/DNA of prokaryotes is amplified via polymerase chain reaction and sequenced to identify the genus or species of individual organisms. | 14 |
| Viral particle isolation and sequencing | Viral particles are separated from host contaminants using methods such as centrifugation and filtration. Viral particles can then be treated with DNase I to remove contaminating nucleic acids on the surface of these particles. A variety of molecular methods can be used to characterize the genomic sequence of the virions. | 15 |