Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Genes

Klas I. Udekwu¹  Valquiria C. A. Martins²  Katia L. Torres²  Luiz P. Kowalski³  Laura C. L. Claro⁴  Stephania M. Bezerra⁴  Fábio A. Alves⁵  Stênio C. Zequi⁶  Felipe J. F. Coimbra⁷  Adriane G. Pelosof⁸  Claudia Z. Sztokfisz⁸  Lais L. S. Abrantes⁹  Israel T. Silva^1,10  Alexandre Defelicibus^1,10  Bruno S. Moda^1,10  Gabriela P. Branco^1,11  Emmanuel Dias-Neto^1,11  Isabella K. T. M. Takenaka^1,11  Marianna S. Serpa^1,11  Thais F. Bartelli^1,11  Diana N. Nunes^1,11  Gabriela E. de Albuquerque^1,11  Elizabeth C. Miola^1,11  Maria G. de Amorim^1,11 

[1] Department of Aquatic Sciences and Assessment, Swedish University of Agriculture, P.O. Box 7050, 75007 Uppsala, Sweden;Department of Education and Research, Fundação Centro de Controle de Oncologia do Estado do Amazonas, Manaus 69040-010, AM, Brazil;Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;Department of Pathology, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;Department of Stomatology, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;Department of Urology, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;Director Department of Abdominal Surgery, Head Upper GI Oncology Reference Center, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;Endoscopy, A.C.Camargo Cancer Center, Sao Paulo 01509-001, SP, Brazil;International Research Center, A.C.Camargo Cancer Center, Sao Paulo 01508-010, SP, Brazil;Laboratory of Computational Biology and Bioinformatics, A.C.Camargo Cancer Center, Sao Paulo 01508-010, SP, Brazil;Laboratory of Medical Genomics, A.C.Camargo Cancer Center, Sao Paulo 01508-010, SP, Brazil;

关键词: microbiome;    mycobiome;    metagenomics;    16S;    qPCR;    shotgun;   

DOI  :  10.3390/genes13020237

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown