How low can we go? The implications of low bacterial load in respiratory microbiota studies

Marsh, Robyn L.; Nelson, Maria T.; Pope, Chris E.; Leach, Amanda J.; Hoffman, Lucas R.; Chang, Anne B.; Smith-Vaughan, Heidi C.

doi:10.1186/s41479-018-0051-8

Pneumonia

Table 1 Examples of genera detected previously as background contamination in negative controls from respiratory microbiota studies [4, 8, 11, 52]

From: How low can we go? The implications of low bacterial load in respiratory microbiota studies

Abiotrophia^a	Bifidobacterium	Curvibacter^a	Halocella	Microlunatus	Pseudoclavibacter	Staphylococcus
Acidocella	Blastococcus	Deinococcus	Herbaspirillum^a	Moryella	Pseudoflavonifractor	Stenotrophomonas^a
Acidovorax^a	Blautia	Delftia	Hoeflea	Neisseria	Pseudomonas^a	Streptococcus^a
Acinetobacter^a	Bosea	Devosia	Hydrotalea^a	Nevskia	Pseudorhodoferax	Sulfuritalea^a
Actionmyces	Bradyrhizobium^a	Dialister	Ilumatobacter	Niastella	Pseudoxanthomonas^a	Suttonella
Adhaeribacter	Brevibacillus^a	Dietzia^a	Intestinibacter	Nocardioides	Psychrobacter	Tericibacter
Aerococcus	Brevibacterium	Dorea	Janibacter	Novosphingobium	Quinella	Thauera
Aeromicrobium^a	Brevundimonas^a	Duganella	Janthinobacterium^a	Ochrobactrum^a	Ralstonia^a	tm7
Afipia^a	Brochothrix	Dyadobacter	Johnsonella	Olivibacter^a	Rhizobium^a	Treponema
Agrococcus	Brooklawnia	Dyella	Kingella^a	Oscillospira	Rhodococcus^a	Trichococcus
Alcaligenes	Burkholderia^a	Eggerthella	Klebsiella	Oxalobacter^a	Roseateles	Tsukamurella
Alcanivorax	Cadidatus pelagibacter	Elusimicrobium	Kocuria	Paenibacillus^a	Roseburia	Tumebacillus
Alicycliphilus	Cadidatus_alysiospaera	Enhydrobacter^a	Lachnoanaerobaculum	Papilibacter	Roseomonas^a	Tyzzerella
Alistipes	Campylobacter	Enterobacter	Lactobacillus	Parabacteroides	Rothia	Unclassified Gp 2 Acidobacteria
Aminobacter	Capnocytophagia	Enterococcus	Lactococcus	Paracoccus^a	Rubellimicrobium	Undibacterium^a
Anaerococcus	Cardiobacterium^a	Erysipelatoclostridium	Lanoclostidium	Parasutterella	Ruegeria	Vampirovibrio
Anaeromyxobacter	Catenibacterium	Escherichia_Shigella^a	Lanospira	Parvimonas	Ruminococcus	Variovorax^a
Anaerotrucus	Caulobacter^a	Eubacterium	Leptothrix	Patulibacter	Runiniclostridium	Veillonella^a
Anoxybacillus	Cellvibrio	Facklamia	Leptotrichia	Pedobacter^a	Saccharopolyspora	Wautersiella
Aquabacterium^a	Christensenella	Faecalibacterium	Limnobacter	Pedomicrobium	Salinicoccus	Xanthomonas
Arthrobacter^a	Chryseobacterium^a	Fastidiosipila	Massilia^a	Pelomonas^a	Schlegelella	Xlyanibacter
Asticcacaulis	Cloacibacterium	Flavobacterium	Megasphaera^a	Peptococcus	Seleomonas
Atopobium	Clostridium	Flavonifractor	Meiothermus	Petoniphilus	Serratia
Aurantimonas^a	Collinsella	Fusobacterium	Mesorhizobium^a	Phyllobacterium^a	Shewanella
Azoarcus	Comamonas^a	Gemella	Methylobacterium^a	Pilimelia	Slackia
Azospira	Coprococcus	Geobacillus	Methylophilus	Polaromonas	Solobacterium
Bacillus^a	Corynebacterium^a	Geodermatophilus	Methylopila	Porphyromonas	Sphingobacterium^a
Bacteroides	Craurococcus	Gordonia	Methyloversatilis	Prevotella^a	Sphingobium^a
Beijerinckia	Cupriavidus	Granulicatella^a	Microbacterium	Propionibacterium^a	Sphingomonas^a
Beutenbergia	Curtobacterium	Haemophilus	Micrococcus	Pseudobutyrivibrio	Sphinogpyxis

It is important that negative controls are included in all studies of the microbiota in low bacterial load specimens, as background contamination in sterile reagents and kits is likely to be batch-specific
^aIndicates genera detected as contaminants in multiple studies

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ISSN: 2200-6133

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