Batch effects;
Decontam;
Colonization in utero;
16S rRNA;
MICROCOCCUS-LUTEUS;
D O I:
10.1186/s40168-020-00949-z
中图分类号:
Q93 [微生物学];
学科分类号:
071005 ;
100705 ;
摘要:
A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.
引用
收藏
页数:7
相关论文
共 17 条
[1]
Antwerpen MH, 2017, MBIO, V8, DOI [10.1128/mBio.00440-17, 10.1128/mbio.00440-17]
机构:
Stanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Davis, Nicole M.
;
Proctor, Diana M.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA
Univ Calif San Francisco, Sch Dent, Dept Orofacial Sci, San Francisco, CA 94143 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Proctor, Diana M.
;
Holmes, Susan P.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Stat, Stanford, CA 94305 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Holmes, Susan P.
;
Relman, David A.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA
Vet Affairs Palo Alto Hlth Care Syst, Infect Dis Sect, Palo Alto, CA 94304 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Relman, David A.
;
Callahan, Benjamin J.
论文数: 0引用数: 0
h-index: 0
机构:
North Carolina State Univ, Dept Populat Hlth & Pathobiol, Coll Vet Med, 456 Res Bldg,1060 William Moore Dr, Raleigh, NC 27607 USA
North Carolina State Univ, Bioinformat Res Ctr, Raleigh, NC 27695 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
机构:
Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Univ Adelaide, Ctr Excellence Australian Biodivers & Heritage CA, ARC, Adelaide, SA, AustraliaUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Eisenhofer, Raphael
;
Minich, Jeremiah J.
论文数: 0引用数: 0
h-index: 0
机构:
Scripps Inst Oceanog, Marine Biol Res Div, La Jolla, CA USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Minich, Jeremiah J.
;
Marotz, Clarisse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Marotz, Clarisse
;
论文数: 引用数:
h-index:
机构:
Cooper, Alan
;
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA
Univ Calif San Diego, Jacobs Sch Engn, Ctr Microbiome Innovat, La Jolla, CA 92093 USA
Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Knight, Rob
;
Weyrich, Laura S.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Univ Adelaide, Ctr Excellence Australian Biodivers & Heritage CA, ARC, Adelaide, SA, AustraliaUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Univ Calif San Francisco, Biomed Sci Grad Program, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Rackaityte, E.
;
Halkias, J.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Pediat, Div Neonatol, San Francisco, CA USA
Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Halkias, J.
;
Fukui, E. M.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Fukui, E. M.
;
Mendoza, V. F.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Pediat, Div Neonatol, San Francisco, CA USA
Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Mendoza, V. F.
;
Hayzelden, C.
论文数: 0引用数: 0
h-index: 0
机构:
San Francisco State Univ, Coll Sci & Engn, San Francisco, CA 94132 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Hayzelden, C.
;
Crawford, E. D.
论文数: 0引用数: 0
h-index: 0
机构:
Chan Zuckerberg Biohub, San Francisco, CA USA
Univ Calif San Francisco, Dept Microbiol & Immunol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Crawford, E. D.
;
Fujimura, K. E.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Genentech Inc, San Francisco, CA 94080 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Fujimura, K. E.
;
Burt, T. D.
论文数: 0引用数: 0
h-index: 0
机构:
Duke Univ, Sch Med, Durham, NC USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Burt, T. D.
;
Lynch, S. V.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
机构:
Stanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Davis, Nicole M.
;
Proctor, Diana M.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA
Univ Calif San Francisco, Sch Dent, Dept Orofacial Sci, San Francisco, CA 94143 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Proctor, Diana M.
;
Holmes, Susan P.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Stat, Stanford, CA 94305 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Holmes, Susan P.
;
Relman, David A.
论文数: 0引用数: 0
h-index: 0
机构:
Stanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA
Vet Affairs Palo Alto Hlth Care Syst, Infect Dis Sect, Palo Alto, CA 94304 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
Relman, David A.
;
Callahan, Benjamin J.
论文数: 0引用数: 0
h-index: 0
机构:
North Carolina State Univ, Dept Populat Hlth & Pathobiol, Coll Vet Med, 456 Res Bldg,1060 William Moore Dr, Raleigh, NC 27607 USA
North Carolina State Univ, Bioinformat Res Ctr, Raleigh, NC 27695 USAStanford Univ, Dept Microbiol & Immunol, Sch Med, Stanford, CA 94305 USA
机构:
Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Univ Adelaide, Ctr Excellence Australian Biodivers & Heritage CA, ARC, Adelaide, SA, AustraliaUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Eisenhofer, Raphael
;
Minich, Jeremiah J.
论文数: 0引用数: 0
h-index: 0
机构:
Scripps Inst Oceanog, Marine Biol Res Div, La Jolla, CA USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Minich, Jeremiah J.
;
Marotz, Clarisse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Marotz, Clarisse
;
论文数: 引用数:
h-index:
机构:
Cooper, Alan
;
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA
Univ Calif San Diego, Jacobs Sch Engn, Ctr Microbiome Innovat, La Jolla, CA 92093 USA
Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USAUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Knight, Rob
;
Weyrich, Laura S.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
Univ Adelaide, Ctr Excellence Australian Biodivers & Heritage CA, ARC, Adelaide, SA, AustraliaUniv Adelaide, Australian Ctr Ancient DNA, Adelaide, SA, Australia
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Univ Calif San Francisco, Biomed Sci Grad Program, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Rackaityte, E.
;
Halkias, J.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Pediat, Div Neonatol, San Francisco, CA USA
Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Halkias, J.
;
Fukui, E. M.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Fukui, E. M.
;
Mendoza, V. F.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Pediat, Div Neonatol, San Francisco, CA USA
Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Mendoza, V. F.
;
Hayzelden, C.
论文数: 0引用数: 0
h-index: 0
机构:
San Francisco State Univ, Coll Sci & Engn, San Francisco, CA 94132 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Hayzelden, C.
;
Crawford, E. D.
论文数: 0引用数: 0
h-index: 0
机构:
Chan Zuckerberg Biohub, San Francisco, CA USA
Univ Calif San Francisco, Dept Microbiol & Immunol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Crawford, E. D.
;
Fujimura, K. E.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Genentech Inc, San Francisco, CA 94080 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Fujimura, K. E.
;
Burt, T. D.
论文数: 0引用数: 0
h-index: 0
机构:
Duke Univ, Sch Med, Durham, NC USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA
Burt, T. D.
;
Lynch, S. V.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USAUniv Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA