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Research article - Peer-reviewed, 2022

Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

de Albuquerque, Gabriela E.; Moda, Bruno S.; Serpa, Marianna S.; Branco, Gabriela P.; Defelicibus, Alexandre; Takenaka, Isabella K. T. M.; de Amorim, Maria G.; Miola, Elizabeth C.; Martins, Valquiria C. A.; Torres, Katia L.; Bezerra, Stephania M.; Claro, Laura C. L.; Pelosof, Adriane G.; Sztokfisz, Claudia Z.; Abrantes, Lais L. S.; Coimbra, Felipe J. F.; Kowalski, Luiz P.; Alves, Fabio A.; Zequi, Stenio C.; Udekwu, Klas I.;
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Abstract

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types.

Keywords

microbiome; mycobiome; metagenomics; 16S; qPCR; shotgun

Published in

Genes
2022, volume: 13, number: 2, article number: 237
Publisher: MDPI

Authors' information

de Albuquerque, Gabriela E.
A.C.Camargo Cancer Center
Moda, Bruno S.
A.C.Camargo Cancer Center
Serpa, Marianna S.
A.C.Camargo Cancer Center
Branco, Gabriela P.
A.C.Camargo Cancer Center
Defelicibus, Alexandre
A.C.Camargo Cancer Center
Takenaka, Isabella K. T. M.
A.C.Camargo Cancer Center
de Amorim, Maria G.
A.C.Camargo Cancer Center
Miola, Elizabeth C.
A.C.Camargo Cancer Center
Martins, Valquiria C. A.
Fundação Centro de Controle de Oncologia do Estado do Amazonas
Torres, Katia L.
Fundação Centro de Controle de Oncologia do Estado do Amazonas
Bezerra, Stephania M.
A.C.Camargo Cancer Center
Claro, Laura C. L.
A.C.Camargo Cancer Center
Pelosof, Adriane G.
A.C.Camargo Cancer Center
Sztokfisz, Claudia Z.
A.C.Camargo Cancer Center
Abrantes, Lais L. S.
A.C.Camargo Cancer Center
Coimbra, Felipe J. F.
A.C.Camargo Cancer Center
Kowalski, Luiz P.
Universidade de Sao Paulo
Kowalski, Luiz P.
A.C.Camargo Cancer Center
Alves, Fabio A.
A.C.Camargo Cancer Center
Zequi, Stenio C.
A.C.Camargo Cancer Center
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UKÄ Subject classification

Microbiology in the medical area

Publication Identifiers

DOI: https://doi.org/10.3390/genes13020237

URI (permanent link to this page)

https://res.slu.se/id/publ/120594