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Abstract The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.

La mediastinitis es una complicación grave entre los pacientes sometidos a cirugía cardiaca. Los agentes etiológicos más frecuentes son los cocos Gram positivos y los Gram negativos son una causa poco común en la mayoría de las series publicadas. Presentamos nuestra experiencia con cuatro pacientes con mediastinitis debida a bacilos Gram negativos multirresistentes, los cuales fueron tratados con tigeciclina.Mediastinitis is a life-threatening complication among patients undergoing cardiac surgery. Gram-positives cocci are the most frequent pathogens associated with post-surgical mediastinitis, being the Gram-negative etiology uncommon in most of the published series. We present our experience with four patients with mediastinitis due to multidrug-resistant Gram-negative bacilli, who have been treated with tigecycline.