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Respiratory Microbial Gene Catalogue

Introduction

Imbalanced respiratory microbiota have been demonstrated in pediatric pneumonia(PP), representing the most important causes of morbidity and mortality in Chinese children.

Here, we construct an integrated respiratory microbial gene catalogue(RMGC) based on metagenomic sequencing data of 334 respiratory samples in 171 healthy and 76 pneumonia children, as well as published respiratory bacterial genomes and small-sized RMGC in Human Microbiome Project(HMP). We also provide an easily accessible database to facilitate the utilization of the catalogue, including free download of the gene sets and online analysis pipeline.

Data summary

#ORFs Total length (bp) Average length (bp) Max length Min length % of genes assigned to a phylum % of genes assigned to a genus % of genes assigned to a species % of genes with KO annotation % annotated on eggNOG
2,245,343 1,708,322,497 760 32,241 100 57.08% 50.92% 27.52% 38.01% 53.95%

Metagenomic analysis. Well done is better than well said. Wanna know why?

Microbiome composition

Phylum Relative abundance(%)
Firmicutes 29.9228
Unclassified 23.0920
Bacteroidetes 21.9115
Proteobacteria 12.5073
Actinobacteria 9.4388
Fusobacteria 3.0082
Others 0.1194




Genus Relative abundance(%)
Unclassified 28.4830
Prevotella 18.7926
Streptococcus 13.2282
Veillonella 5.8526
Neisseria 5.5187
Rothia 3.5913
Actinomyces 3.2882
Staphylococcus 2.6362
Haemophilus 2.3148
Leptotrichia 1.4989
Peptoniphilus 1.2330
Acinetobacter 1.1911
Granulicatella 1.1634
Fusobacterium 1.1000
Atopobium 0.8463




Species Relative abundance(%)
Unclassified 55.5028
Prevotella melaninogenica 3.50319
Prevotella histicola 2.5744
Prevotella sp. 2.35983
Rothia mucilaginosa 2.13796
Streptococcus parasanguinis 1.95179
Prevotella pallens 1.80462
Streptococcus sp. 1.78913
Staphylococcus aureus 1.63875
Neisseria subflava 1.28294
Veillonella atypica 1.27725
Streptococcus pseudopneumoniae 1.1943
Neisseria flavescens 1.09725
Prevotella salivae 0.858959
Acinetobacter baumannii 0.753785

Phylum Relative abundance(%)
Firmicutes 56.4767
Proteobacteria 21.1863
Unclassified 10.9035
Actinobacteria 5.5105
Bacteroidetes 5.4922
Tenericutes 0.3619
Others 0.0689




Genus Relative abundance(%)
Staphylococcus 45.9709
Acinetobacter 15.9561
Unclassified 10.2326
Streptococcus 5.3611
Corynebacterium 4.0519
Bacteroides 3.3639
Mastadenovirus 2.7745
Prevotella 1.4743
Blautia 1.1702
Ralstonia 0.9084
Haemophilus 0.7787
Klebsiella 0.7625
Veillonella 0.7130
Escherichia 0.6237
Dolosigranulum 0.4774




Species Relative abundance(%)
Staphylococcus aureus 27.8951
Unclassified 19.3576
Staphylococcus epidermidis 7.6282
Staphylococcus haemolyticus 5.1094
Acinetobacter sp. DUT-2 3.7700
Acinetobacter calcoaceticus 3.3158
Acinetobacter baumannii 3.1810
Acinetobacter pittii 2.8416
Bacteroides vulgatus 2.0428
Human mastadenovirus B 1.9342
Corynebacterium accolens 1.9174
Streptococcus pneumoniae 1.6433
[Ruminococcus] gnavus 1.0971
Staphylococcus hominis 1.0664
Klebsiella pneumoniae 0.7455

Phylum Relative abundance(%)
Firmicutes 92.5185
Unclassified 5.0874
Proteobacteria 1.0917
Tenericutes 0.7414
Bacteroidetes 0.2451
Actinobacteria 0.1823
Others 0.1336




Genus Relative abundance(%)
Staphylococcus 75.8607
Bacillus 14.5496
Unclassified 5.4258
Streptococcus 0.9159
Mycoplasma 0.7408
Mastadenovirus 0.5650
Haemophilus 0.2816
Pseudomonas 0.2682
Enterobacter 0.1519
Bacteroides 0.1289
Microcystis 0.1123
Gemella 0.0999
Prevotella 0.0914
Escherichia 0.0647
Faecalibacterium 0.0613




Species Relative abundance(%)
Staphylococcus aureus 51.5443
Staphylococcus epidermidis 20.0261
Bacillus cereus 9.9344
Unclassified 9.6185
Bacillus anthracis 1.7322
Bacillus wiedmannii 1.1291
Staphylococcus hominis 0.7597
Mycoplasma pneumoniae 0.7314
Human mastadenovirus B 0.5399
Staphylococcus schweitzeri 0.3953
Bacillus thuringiensis 0.3327
Staphylococcus caprae 0.2892
Haemophilus influenzae 0.2455
Streptococcus agalactiae 0.2181
Streptococcus pneumoniae 0.2148

Membership