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Table 1 Summary findings of the included studies, published from 2012 to 2016

From: The respiratory microbiota: new insights into pulmonary tuberculosis

Study

Respiratory microbiota

Method

Sequencing region of 16 s RNA

TB patients

Healthy Controls

Phyla

Genera

Phyla

Genera

Cheung et al

Proteobacteria*, Bacteroidetes*, Actinobacteria, Fusobacteria, Firmicutes

Neisseria* Streptococcus Prevotella*, Lactococcus, Pseudomonas, Enterobacteria

Proteobacteria Bacteroidetes,

ActinobacteriaFusobacteria

Firmicutes*

Streptococcus Neisseria Prevotella, Lactococcus*, Pseudomonas*, Enterobacter*

Roche/454

V1-V2

Wu et al

Firmicutes* Actinobacteria*, Spirochaetes*, Bacteroidetes, Fusobacteria, Cyanobacteria−Thermi−Acidobacteria−

Prevotella, LeptotrichiaTreponema, Catonella

Neisseria, Coprococcus

Streptococcus*,Gramulicatella*, Pseudomonas*, Haloplasma*,Bergeyella**

Sharpea**

Firmicutes, Actinobacteria Spirochaetes

Bacteroidetes* Fusobacteria*

Cyanobacteria − Thermi − Acidobacteria-

Prevotella*, Leptotrichia*Treponema*Catonella*

Coprococcus*

Streptococcus

Neisseria, Gramulicatella Pseudomonas, Haloplasma

Roche/454

V1-V2

Krishna et al

Firmicutes*, Actinobacteria*

Bacteriodes, Proteobacteria, Fusobacteria

Streptococcus, Neisseria, Veillonella

Unclassified-Gammaproteobacteria

Haemophilus, Actinobacillus

Rothia *, Leuconosto*

Lactobacillus*, Corynebacterium*, Atopobium*, Bacillus*, Acinetobacter*

Firmicutes, Actinobacteria

Bacteriodes, Proteobacteria*

Fusobacteria*

Streptococcus

, Neisseria, Veillonella

Unclassified-Gammaproteobacteria

Haemophilus, Actinobacillus*, Rothia

Leuconostoc, Lactobacillus

Corynebacterium, Atopobium, Bacillus

Acinetobacter*

Ion Torrent

V6-V7

Cui et al

Firmicutes, Bacteroidetes, ProteobacteriaCrenarchaeota Actinobacteria, Chlamydiae

Chloroflexi, Cyanobacteria/Chloroplast

Deinococcus-Thermus*, Elusimicrobia, Euryarchaeota

SR1, Spirochaetes, Synergistetes, Tenericute

Fusobacteria, Aquificae**

Caldiserica**, Gemmatimonadetes**, Lentisphaerae** Planctomycetes**

Thermodesulfobacteria**, Verrucomicrobia**

Phenylobacterium* Stenotrophomona*, Cupriavidus*

Sphingomonas*, Mobilicoccus* Brevundimonas* Brevibacillus*

Diaphorobacter*

Thermus**, Pelomonas**

Methylobacterium**, Comamonas**, Lactobacillus** Thermobacillus**, Aur tidibacter**, Lapillicoccus**

Devriesea**

Firmicutes

Bacteroidetes*ProteobacteriaCrenarchaeota Actinobacteria

Chlamydiae, Chloroflexi, Cyanobacteria/Chloroplast

Deinococcus-Thermus Elusimicrobia, Euryarchaeota

SR1, Spirochaetes, Synergistetes, Tenericute

Fusobacteria*

Phenylobacterium, Stenotrophomonas

Cupriavidus

SphingomonasMobilicoccusBrevundimonasBrevibacillus

Diaphorobacter

Roche/454

V3

Botero et al

Firmicutes, BacteroidetesProteobacteria, Actinobacteria*. Fusobacteria, Spirochaetes

SR1, Gemmatimonadetes**

Chloroflexi, Acidobacteria**

Tenericutes, Unclassified bacteria

Ascomycota, Unclassified fungi

 

Firmicutes, BacteroidetesProteobacteria, Actinobacteria, Fusobacteria, Spirochaetes

SR1, Chloroflexi

Tenericutes, Unclassified bacteria, Ascomycota

Unclassified fungi

 

Roche/454

V1-V2

  1. Key: * abundant microbiome either in TB cases or healthy controls, ** unique microbiome in TB cases