[Microbiome] 마이크로바이옴 연구에서 오염으로 판별된 Genus 목록
- 수정 2023.04.12
세 논문에 나오는 시약이나 air swab에서 얻어지는 오염 Genus를 표로 정리하였다.
꼭 아래에 나와있는 균을 오염으로 생각하여 제거할 필요는 없지만 어느 정도 참고의 기준으로 사용 가능하다. 추가적으로 본인이 사용하고 있는 Kit에서 오염으로 검출된 균도 찾아보면 도움 될 것이다.
Table1. OTUs removed from sequencing data prior to biostatical analysis [1]
| Phylum | List of constituent contaminant genera |
| Proteobacteria | Alpha-proteobacteria: |
| Acidovoraxc, Brevundimonasc, Phyllobacterium , Rhizobium, Mesorhizobium, Ochrobactrum, Devosia, Sphingomonas | |
| Beta-proteobacteria: | |
| Pelomonas, Ralstonia, Janthinobacterium, Achromobacter, Undibacterium, Variovorax | |
| Gamma-proteobacteria: | |
| Pseudomonas, Rhodanobacter, Stenotrophomonas | |
| Actinobacteria | Cellulosimicrobium, Clavibacter, Candidatus Planktoluna |
| Firmicutes | Turicibacter |
| Bacteroidetes | Bergeyella, Chryseobacterium, Flavobacterium, Gelidibacter, Pedobacter, Terrimonas |
Table2. Phylum List of constituent contaminant genera [2]
| Phylum | List of constituent contaminant genera |
| Proteobacteria | Alpha-proteobacteria: |
| Afipia, Aquabacteriume, Asticcacaulis, Aurantimonas, Beijerinckia, Bosea, Bradyrhizobiumd, Brevundimonasc, Caulobacter, Craurococcus, Devosia, Hoefleae, Mesorhizobium, Methylobacteriumc, Novosphingobium, Ochrobactrum, Paracoccus, Pedomicrobium, Phyllobacteriume, Rhizobiumc,d, Roseomonas, Sphingobium, Sphingomonasc,d,e, Sphingopyxis | |
| Beta-proteobacteria: | |
| Acidovoraxc,e, Azoarcuse, Azospira, Burkholderiad, Comamonasc, Cupriavidusc, Curvibacter, Delftiae, Duganellaa, Herbaspirilluma,c, Janthinobacteriume, Kingella, Leptothrixa, Limnobactere, Massiliac, Methylophilus, Methyloversatilise, Oxalobacter, Pelomonas, Polaromonase, Ralstoniab,c,d,e, Schlegelella, Sulfuritalea, Undibacteriume, Variovorax | |
| Gamma-proteobacteria: | |
| Acinetobactera,d,c, Enhydrobacter, Enterobacter, Escherichiaa,c,d,e, Nevskiae, Pseudomonasb,d,e, Pseudoxanthomonas, Psychrobacter, Stenotrophomonasa,b,c,d,e, Xanthomonas | |
| Actinobacteria | Aeromicrobium, Arthrobacter, Beutenbergia, Brevibacterium, Corynebacterium, Curtobacterium, Dietzia, Geodermatophilus, Janibacter, Kocuria, Microbacterium, Micrococcus, Microlunatus, Patulibacter, Propionibacteriume, Rhodococcus, Tsukamurella |
| Firmicutes | Abiotrophia, Bacillusb, Brevibacillus, Brochothrix, Facklamia, Paenibacillus, Streptococcus |
| Bacteroidetes | Chryseobacterium, Dyadobacter, Flavobacteriumd, Hydrotalea, Niastella, Olivibacter, Pedobacter, Wautersiella |
| Deinococcus-Thermus | Deinococcus |
| Acidobacteria | Predominantly unclassified Acidobacteria Gp2 organisms |
Table3. Taxa Previously Identified in Negative Controls from Multiple Studies [3]
| Phylum | List of constituent contaminant genera |
| Proteobacteria | Alpha-proteobacteria: |
| Rhizobium, Mesorhizobium, Bradyrhizobium, Brevundimonas, Afipia, Devosia, Methylobacterium, Phyllobacterium, Sphingomonas, Sphingobium, Novosphingobium, Roseomonas, | |
| Beta-proteobacteria: | |
| Massilia, Oxalobacter, Ralstonia, Janthinobacterium, Kingella, Leptothrix, Herbaspirillum, Duganella, Cupriavidus, Pelomonas, Curvibacter, Comamonas, Acidovorax, Burkholderia, Achromobacter, Neisseria, | |
| Gamma-proteobacteria: | |
| Acinetobacter, Xanthomonas, Stenotrophomonas, Escherichia, Haemophilus, | |
| Actinobacteria | Corynebacterium, Arthrobacter, Propionibacterium, Pseudomonas, Enhydrobacter, Actinomyces, Rothia, Atopobium, |
| Firmicutes | Bacillus, Geobacillus, Paenibacillus, Brevibacillus, Staphylococcus, Abiotrophia, Streptococcus, Granulicatella, Enterococcus, Lactobacillus, Clostridium, Coprococcus, Anaerococcus, Veillonella, Dialister, Megasphaera |
| Bacteroidetes | Chryseobacterium, Flavobacterium, Pedobacter, Sediminibacterium, Porphyromonas, Prevotella, Capnocytophaga |
| Saccharibacteria | UnclassifiedTM7 |
| Fusobacteria | Fusobacterium, Leptotrichia |
| 출처
[1] Jervis-Bardy J, Leong LE, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O'Leary S, Rogers GB, Marsh RL. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015 May 5;3:19. doi: 10.1186/s40168-015-0083-8. PMID: 25969736; PMCID: PMC4428251.
[2] Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z. PMID: 25387460; PMCID: PMC4228153.https://doi.org/10.1186/s12915-014-0087-z
[3] Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 2019 Feb;27(2):105-117. doi: 10.1016/j.tim.2018.11.003. Epub 2018 Nov 26. PMID: 30497919.