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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, CyanobacteriaThermiAcidobacteria 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
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