TY - JOUR
T1 - Diversity and composition of gut microbiome of cervical cancer patients
T2 - Do results of 16S rRNA sequencing and whole genome sequencing approaches align?
AU - Biegert, Greyson
AU - El Alam, Molly B.
AU - Karpinets, Tatiana
AU - Wu, Xiaogang
AU - Sims, Travis T.
AU - Yoshida-Court, Kyoko
AU - Lynn, Erica J.
AU - Yue, Jingyan
AU - Medrano, Andrea Delgado
AU - Petrosino, Joseph
AU - Mezzari, Melissa P.
AU - Ajami, Nadim J.
AU - Solley, Travis
AU - Ahmed-Kaddar, Mustapha
AU - Klopp, Ann H.
AU - Colbert, Lauren E.
N1 - Funding Information:
This research was supported in part by the Radiological Society of North America Resident/Fellow Award (to L.E.C.), the National Institutes of Health (NIH) through MD Anderson's Cancer Center Support Grant P30CA016672, the Emerson Collective and the National Institutes of Health T32 grant #5 T32 CA101642–14 (T.T.S). This study was partially funded by The University of Texas MD Anderson Cancer Center HPV-related Cancers Moonshot (L.E.C and A.K.).
Publisher Copyright:
© 2021 Elsevier B.V.
PY - 2021/6
Y1 - 2021/6
N2 - Background: Next generation sequencing has progressed rapidly, characterizing microbial communities beyond culture-based or biochemical techniques. 16S ribosomal RNA gene sequencing (16S) produces reliable taxonomic classifications and relative abundances, while shotgun metagenome sequencing (WMS) allows higher taxonomic and functional resolution at greater cost. The purpose of this study was to determine if 16S and WMS provide congruent information for our patient population from paired fecal microbiome samples. Results: Comparative indices were highly congruent between 16S and WMS. The most abundant genera for 16S and WMS data did not overlap. Overlap was observed at the Phylum level, as expected. However, relative abundances correlated poorly between the two methodologies (all P-value>0.05). Hierarchical clustering of both sequencing analyses identified overlapping enterotypes. Both approaches were in agreement with regard to demographic variables. Conclusion: Diversity, evenness and richness are comparable when using 16S and WMS techniques, however relative abundances of individual genera are not. Clinical associations with diversity and evenness metrics were similarly identified with WMS or 16S.
AB - Background: Next generation sequencing has progressed rapidly, characterizing microbial communities beyond culture-based or biochemical techniques. 16S ribosomal RNA gene sequencing (16S) produces reliable taxonomic classifications and relative abundances, while shotgun metagenome sequencing (WMS) allows higher taxonomic and functional resolution at greater cost. The purpose of this study was to determine if 16S and WMS provide congruent information for our patient population from paired fecal microbiome samples. Results: Comparative indices were highly congruent between 16S and WMS. The most abundant genera for 16S and WMS data did not overlap. Overlap was observed at the Phylum level, as expected. However, relative abundances correlated poorly between the two methodologies (all P-value>0.05). Hierarchical clustering of both sequencing analyses identified overlapping enterotypes. Both approaches were in agreement with regard to demographic variables. Conclusion: Diversity, evenness and richness are comparable when using 16S and WMS techniques, however relative abundances of individual genera are not. Clinical associations with diversity and evenness metrics were similarly identified with WMS or 16S.
KW - 16S rRNA gene sequencing
KW - Cervical cancer
KW - Gut microbiome
KW - Whole genome shotgun sequencing
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U2 - 10.1016/j.mimet.2021.106213
DO - 10.1016/j.mimet.2021.106213
M3 - Article
C2 - 33785357
AN - SCOPUS:85105573311
SN - 0167-7012
VL - 185
JO - Journal of Microbiological Methods
JF - Journal of Microbiological Methods
M1 - 106213
ER -