Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer.

Autor: Fouladi F; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA., Glenny EM; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Bulik-Sullivan EC; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Tsilimigras MCB; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Sioda M; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA., Thomas SA; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Wang Y; Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Djukic Z; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Tang Q; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Tarantino LM; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.; Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Bulik CM; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden., Fodor AA; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA. afodor@uncc.edu., Carroll IM; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. ian_carroll@med.unc.edu.; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. ian_carroll@med.unc.edu.
Jazyk: angličtina
Zdroj: The ISME journal [ISME J] 2020 Jul; Vol. 14 (7), pp. 1809-1820. Date of Electronic Publication: 2020 Apr 20.
DOI: 10.1038/s41396-020-0645-z
Abstrakt: Transplanting human gut microbiotas into germ-free (GF) mice is a popular approach to disentangle cause-and-effect relationships between enteric microbes and disease. Algorithm development has enabled sequence variant (SV) identification from 16S rRNA gene sequence data. SV analyses can identify which donor taxa colonize recipient GF mice, and how SV abundance in humans is replicated in these mice. Fecal microbiotas from 8 human subjects were used to generate 77 slurries, which were transplanted into 153 GF mice. Strong correlations between fecal and slurry microbial communities were observed; however, only 42.15 ± 9.95% of SVs successfully transferred from the donor to the corresponding recipient mouse. Firmicutes had a particularly low transfer rate and SV abundance was poorly correlated between donor and recipient pairs. Our study confirms human fecal microbiotas colonize formerly GF mice, but the engrafted community only partially resembles the input human communities. Our findings emphasize the importance of reporting a standardized transfer rate and merit the exploration of other animal models or in silico tools to understand the relationships between human gut microbiotas and disease.
Databáze: MEDLINE
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