Bacteria are cosmopolitan organisms that in recent years have demonstrated many roles in maintaining host equilibrium. In this review, we discuss three roles bacteria can occupy in a host: pathogenic, symbiotic, and transient, with a specific focus on how bacterial small molecules contribute to homeostasis or dysbiosis. First, we will dissect how small molecules produced by pathogenic bacteria can be used as a source for communication during colonization and as protection against host immune responses. The ability to achieve a higher level of organization through small molecule communication gives pathogenic bacteria an opportunity for increased virulence and fitness. Conversely, in symbiotic relationships with hosts, small molecules are used in the initial acquisition, colonization, and maintenance of this beneficial population. Chemical signals can come from both the host and symbiont, and it is often observed that these interKingdom symbioses result in coevolution of both species involved. Furthermore, the transition from transient to commensal or opportunistic likely relies on molecular mechanisms. The small molecules utilized and produced by transient bacteria are desirable for both the immune and nutritional benefits they provide to the host. Finally, the advantages and disadvantages of modern analytical techniques that are available to researchers in order to study small molecules in situ is an important aspect of this review. It is our opinion that small molecules produced by bacteria are central to many biological processes and a larger focus on uncovering the function and identity of these small molecules is required to gain a deeper understanding of host-microbe associations.

Imaging mass spectrometry (IMS) has proven to be a useful tool when investigating the spatial distributions of metabolites and proteins in a biological system. One of the biggest advantages of IMS is the ability to maintain the 3D chemical composition of a sample and analyze it in a label-free manner. However, acquiring the spatial information leads to an increase in data size. Due to the increased availability of commercial mass spectrometers capable of IMS, there has been an exciting development of different statistical tools that can help decipher the spatial relevance of an analyte in a biological sample. To address this need, software packages like SCiLS and the open source R package Cardinal have been designed to perform unbiased spectral grouping based on the similarity of spectra in an IMS data set. In this note, we evaluate SCiLS and Cardinal compatibility with MALDI-TOF IMS data sets of the Gram-negative pathogen Pseudomonas aeruginosa PA14. Both software were able to perform unsupervised segmentation with similar performance. There were a few notable differences which are discussed related to the identification of statistically significant features which required optimization of preprocessing steps, region of interest, and manual analysis.

Biofilm inhibition by exogenous molecules has been an attractive strategy for the development of novel therapeutics. We investigated the biofilm inhibitor taurolithocholic acid (TLCA) and its effects on the specialized metabolism, virulence, and biofilm formation of the clinically relevant bacterium Pseudomonas aeruginosa strain PA14. Our study shows that TLCA alters the specialized metabolism, thereby affecting P. aeruginosa colony biofilm physiology. We observed an upregulation of metabolites correlated to virulence such as the siderophore pyochelin. A wax moth virulence assay confirmed that treatment with TLCA increases the virulence of P. aeruginosa. On the basis of our results, we believe that future endeavors to identify biofilm inhibitors must consider how a putative lead alters the specialized metabolism of a bacterial community to prevent pathogens from entering a highly virulent state.

There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.