An integrated procedure is presented whereby gas chromatography-ion trap mass spectrometry is used to determine chemical markers of gram-negative bacterial lipopolysaccharide (3-hydroxy fatty acids with 10 to 18 carbon atoms), gram-positive bacteria (branched-chain fatty acids with 15 and 17 carbon atoms), bacterial peptidoglycan (muramic acid), and fungal biomass (ergosterol) in samples of settled house dust. A hydrolysate of 13 C-labeled cyanobacterial cells is used as an internal standard for the first three markers. These analyses require two dust samples, one for 3-OH fatty acids, branched-chain fatty acids, and muramic acid and another for ergosterol. The method may be used to characterize microbial communities in environmental samples.Inhalation of airborne microorganisms in indoor environments has been associated with the development of respiratory disorders. Substances such as endotoxins (lipopolysaccharides [LPS]) (14,17,18,28), peptidoglycan (9, 12), and various fungal components and products (3,6,21) are among the suspected causative agents. Culture-based methods are suitable for detection of culturable infectious agents and allow species identification; however, it is widely agreed that only a small fraction (0.1 to 10%) of the total microbial flora in an indoor environment is currently culturable (29). Direct microscopy is at best semiquantitative. Although the Limulus amebocyte lysate test is extremely sensitive to endotoxin and can detect glucans, it measures bioactivity rather than absolute amounts and its reproducibility and specificity have been questioned (5). Nucleic acid-based methods including PCR are very specific, and by using broad-range (universal) probes and primers sets based on 16S rDNA (20) and 18S rRNA (31), most bacteria and fungi present in a sample can be identified. To date, such universal probes and primers have not been used to characterize the microbiology of indoor environments; rather, PCR has been used to detect specific fungi and bacteria in such environments (4,11,22).In our laboratory we have developed and applied gas chromatography-mass spectrometry (GC-MS) methods to determine biomarker molecules in complex matrices including organic dust. Microorganisms contain unique compounds not found elsewhere in nature, which can be used as chemical markers of larger, bioactive structures (7). Endotoxins (LPS) are major constituents of the outer membrane of gram-negative bacteria. A backbone of lipid A, the toxic component of the LPS molecule, carries in general 4 mol of unique 3-hydroxy fatty acids (3-OH FAs) (23-26). Certain branched-chain FAs are found in most gram-positive bacteria (13,30). Muramic acid is a unique marker of peptidoglycan (2,8,9,15), which is the cross-linked macromolecular structure responsible for the rigidity of bacterial cell walls and is sometimes referred to as "gram-positive bacterial endotoxin" (27). Ergosterol is a common fungal membrane lipid that is widely used as a marker of fungal biomass, although the concentration depends on the species and ...