Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs

Rekindling old friendships in new landscapes: The environment–microbiome–health axis in the realms of landscape research

1. Humans are spending less time in biodiverse environments, and according to the Old Friends and Biodiversity hypotheses, this has led to fewer interactions with diverse immunoregulatory micro‐organisms or ‘old friends’. 2. Non‐communicable diseases such as asthma and inflammatory bowel disease are on the rise, and the development and progression of these ‘modern’ diseases may be attributed in part, to the breakdown of this evolutionary relationship between humans and environmental microbiota. 3. There is a growing interest in the environment–microbiome–health axis as a mechanism to explain some of the health benefits linked to spending time in nature. 4. This may provide a platform for proposing a new, holistic and transdisciplinary approach to public and environmental health. 5. The field of landscape research—which combines social and natural sciences—responds to emerging socioecological issues and can make a significant contribution towards this approach. 6. This paper explores innovative, landscape research‐based approaches to understanding the complex relationships between the environment, the microbiome and human health. 7. Transdisciplinarity will play an important role moving forward. This forms a major discussion point in this paper, along with future research directions, key research questions and novel concepts supported by recent technological advancements. 8. The development of a new field of study—Microbioscape Research as a crossover between microbiome science and landscape research—is also discussed

Creating a 3D microbial and chemical snapshot of a human habitat

Kapono CA, Morton JT, Bouslimani A, et al. Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports. 2018;8(1): 3669

A 454 survey of the community composition and core microbiome of the common bed bug, Cimex lectularius, reveals significant microbial community structure across an urban landscape

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius, known as the common bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of bed bug microbial communities by amplifying the V4-V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight natural populations collected from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs identified as the {\alpha}-proteobacterium Wolbachia and an unnamed {\gamma}-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host populations for measures of community diversity and exhibited significant population structure. We also uncovered a strong negative correlation in the abundance of the two dominant OTUs, suggesting they may fulfill similar roles as nutritional mutualists. This broad survey represents the most comprehensive assessment, to date, of the microbes that associate with bed bugs, and uncovers evidence for potential antagonism between the two dominant members of the bed bug microbiome