Table 1 Open in new tab Overview of the...

Application

Application foundation

Classification

Refs.

Individual identification

Strong variations in community membership between individuals, some of these variations are stable over time

Main tissue origins: skin, oral, gut, and vaginal hair

[7,55,57,59,62–64,66–68]

The transfer of microbiomes: cohabitating individuals, direct and indirect transfer, sexual contact, single computer keys and mice, and smartphone

[7,57–60]

New markers: clade-specific markers and CRISPR spacers

[62–64,66]

Influencing factors: decay of microbiota traces with time and diurnal patterns of microbiota

[67,68]

Geolocation inference

Microbial communities exhibit a biogeographic pattern

Molecular technologies: TRFLP, DGGE, RISA, and NGS (16S rRNA gene, 18S rRNA gene, metabarcoding, and shotgun metagenomics)

[72–80]

Sample types: soil, shoe, dust, skin and body fluids, and gut

[60,72–79,81–85]

PMI estimation

The microbiomes that drive mammalian decomposition are somewhat similar and repeatable across different hosts and environments

Animal models: mice, rat, and swine

[20,88–91,93]

Human cadaver

[20,94]

Sample types: abdomen, skin, scalp, gut, bone, and gravesoil

[20,88–91,93]

External environments: aboveground, burial cadavers, freshwater, indoor, different seasons, and different sites

[20,84,85,88,90,91,93,94]

Table 1

Open in new tab

Overview of the application of microbiome in individual identification, geolocation inference, and PMI estimation

Application	Application foundation	Classification	Refs.
Individual identification	Strong variations in community membership between individuals, some of these variations are stable over time	Main tissue origins: skin, oral, gut, and vaginal hair	[7,55,57,59,62–64,66–68]
		The transfer of microbiomes: cohabitating individuals, direct and indirect transfer, sexual contact, single computer keys and mice, and smartphone	[7,57–60]
		New markers: clade-specific markers and CRISPR spacers	[62–64,66]
		Influencing factors: decay of microbiota traces with time and diurnal patterns of microbiota	[67,68]
Geolocation inference	Microbial communities exhibit a biogeographic pattern	Molecular technologies: TRFLP, DGGE, RISA, and NGS (16S rRNA gene, 18S rRNA gene, metabarcoding, and shotgun metagenomics)	[72–80]
Geolocation inference	Microbial communities exhibit a biogeographic pattern	Sample types: soil, shoe, dust, skin and body fluids, and gut	[60,72–79,81–85]
PMI estimation	The microbiomes that drive mammalian decomposition are somewhat similar and repeatable across different hosts and environments	Animal models: mice, rat, and swine	[20,88–91,93]
		Human cadaver	[20,94]
		Sample types: abdomen, skin, scalp, gut, bone, and gravesoil	[20,88–91,93]
		External environments: aboveground, burial cadavers, freshwater, indoor, different seasons, and different sites	[20,84,85,88,90,91,93,94]

Application	Application foundation	Classification	Refs.
Individual identification	Strong variations in community membership between individuals, some of these variations are stable over time	Main tissue origins: skin, oral, gut, and vaginal hair	[7,55,57,59,62–64,66–68]
		The transfer of microbiomes: cohabitating individuals, direct and indirect transfer, sexual contact, single computer keys and mice, and smartphone	[7,57–60]
		New markers: clade-specific markers and CRISPR spacers	[62–64,66]
		Influencing factors: decay of microbiota traces with time and diurnal patterns of microbiota	[67,68]
Geolocation inference	Microbial communities exhibit a biogeographic pattern	Molecular technologies: TRFLP, DGGE, RISA, and NGS (16S rRNA gene, 18S rRNA gene, metabarcoding, and shotgun metagenomics)	[72–80]
Geolocation inference	Microbial communities exhibit a biogeographic pattern	Sample types: soil, shoe, dust, skin and body fluids, and gut	[60,72–79,81–85]
PMI estimation	The microbiomes that drive mammalian decomposition are somewhat similar and repeatable across different hosts and environments	Animal models: mice, rat, and swine	[20,88–91,93]
		Human cadaver	[20,94]
		Sample types: abdomen, skin, scalp, gut, bone, and gravesoil	[20,88–91,93]
		External environments: aboveground, burial cadavers, freshwater, indoor, different seasons, and different sites	[20,84,85,88,90,91,93,94]

Note: PMI, post-mortem interval; CRISPR, clustered regularly interspaced short palindromic repeat; TRFLP, terminal restriction fragment length polymorphism; DGGE, denaturing gel electrophoresis; RISA, ribosomal intergenic spacer analysis; NGS, next-generation sequencing.

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