[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. 

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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.