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Table 1 List of strains used for the extraction of the DNAs used to constitute the mock communities

From: rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

 

Taxonomic assignment based on Sanger sequencing of

Strain name

Phylum

The entire 16S rRNA gene1

The V3 V4 region2,3

The rpoB region2,3

F1

γ-Proteobacteria

X. nematophila

Xenorhabdus

X. nematophila

TT01

 

P. luminescens

Photorhabdus

P. luminescens

TUR03–22

 

S. liquefaciens

Serratia

S. liquefaciens

SW4

 

P. protegens

Pseudomonas

P. protegens

SK39-ApoA

 

P. chlororaphis

Pseudomonas

P. chlororaphis

SW5

 

P. putida

Pseudomonas

P. putida

B163

 

S. maltophilia

Stenotrophomonas

S. maltophilia

FR211A

 

Acinetobacter sp.

Acinetobacter

Acinetobacter

SC

β-Proteobacteria

A. faecalis

Alcaligenes

A. faecalis

SK39-ApoC

 

Achromobacter

Achromobacter

Achromobacter

MW8A4

 

Delftia sp.

Delftia

D. acidovorans

BS3–2-1

 

Variovorax sp.

Variovorax

V. paradoxus

173

 

Acidovorax sp.

Acidovorax

Acidovorax sp

Sphingo

ά-Proteobacteria

Sphingomonas sp.

Sphingomonas

Sphingomonas

TCH07-Apo2–4

 

Brevundimonas sp.

Brevundimonas

B. diminuta

SW2

 

O. anthropi

Brucellacae

O. anthropi

FR211C

Bacteroidetes

Sphingobacterium sp.

Sphingobacterium

Sphingobacterium

SK72–2

Fimicutes

Paenibacillus sp.

Paenibacillus

Paenibacillus

SG4

 

E. mundtii

Enterococcus

E. mundtii

  1. 1 based on NCBI Blast taxonomic assignment
  2. 2 based on RDP Classifier assignment (bootstrap confidence = 0.9)
  3. 3gene fragments used for metabarcoding analyses