Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol Collector (ABC) for NASA's C-20A that can make collections for microbiological research investigations up to altitudes of 13.7 km. Herein we report results from the first set of science flights—four consecutive missions flown over the United States (US) from 30 October to 2 November, 2017. To ascertain how the concentration of airborne bacteria changed across the tropopause, we collected air during aircraft Ascent/Descent (0.3 to 11 km), as well as sustained Cruise altitudes in the lower stratosphere (~12 km). Bioaerosols were captured on DNA-treated gelatinous filters inside a cascade air sampler, then analyzed with molecular and culture-based characterization. Several viable bacterial isolates were recovered from flight altitudes, including Bacillus sp., Micrococcus sp., Arthrobacter sp., and Staphylococcus sp. from Cruise samples and Brachybacterium sp. from Ascent/Descent samples. Using 16S V4 sequencing methods for a culture-independent analysis of bacteria, the average number of total OTUs was 305 for Cruise samples and 276 for Ascent/Descent samples. Some taxa were more abundant in the flight samples than the ground samples, including OTUs from families Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae as well as the following genera: Clostridium, Mogibacterium, Corynebacterium, Bacteroides, Prevotella, Pseudomonas, and Parabacteroides. Surprisingly, our results revealed a homogeneous distribution of bacteria in the atmosphere up to 12 km. The observation could be due to atmospheric conditions producing similar background aerosols across the western US, as suggested by modeled back trajectories and satellite measurements. However, the influence of aircraft-associated bacterial contaminants could not be fully eliminated and that background signal was reported throughout our dataset. Considering the tremendous engineering challenge of collecting biomass at extreme altitudes where contamination from flight hardware remains an ever-present issue, we note the utility of using the stratosphere as a proving ground for planned life detection missions across the solar system.

Manipulation of cellular motility using a target signal can facilitate the development of biosensors or microbe-powered biorobots. Here, we engineered signal-dependent motility in Escherichia coli via the transcriptional control of a key motility gene. Without manipulating chemotaxis, signal-dependent switching of motility, either on or off, led to population-level directional movement of cells up or down a signal gradient. We developed a mathematical model that captures the behaviour of the cells, enables identification of key parameters controlling system behaviour, and facilitates predictive-design of motility-based pattern formation. We demonstrated that motility of the receiver strains could be controlled by a sender strain generating a signal gradient. The modular quorum sensing-dependent architecture for interfacing different senders with receivers enabled a broad range of systems-level behaviours. The directional control of motility, especially combined with the potential to incorporate tuneable sensors and more complex sensing-logic, may lead to tools for novel biosensing and targeted-delivery applications.

ObjectiveInflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary.MethodsWe sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data.ResultsWe identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level.ConclusionWe propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions.

The gut microbiota has emerged as an important player in cancer pathology, and increasing evidence supports its role in clinical response to immune checkpoint inhibitor (ICI) therapy. However, the specific microbiome-derived factors responsible for the improved response to ICI therapy remain unknown. Second Genome has developed a unique discovery platform to identify, screen, and validate microbiome-derived peptides that promote response to cancer immunotherapy. Using our multitechnology meta-analysis of published datasets and characterizing the baseline microbiome of melanoma patients treated with anti-PD-1, we have identified gut microbiome strains differentially abundant in responders versus nonresponders that are concordant across multiple cohorts. Next, peptides from strains associated with responder signatures were predicted from their genome sequences. In addition, we predicted peptides from assembled metagenomes that were associated with responders. The predicted peptides were screened using phage display technology to identify binders to immune cells known to play a role in the tumor microenvironment (TME). Peptides that bound to specific immune cells were then evaluated for activity in cell-based assays using isolated primary human T cells, dendritic cells (DCs), and macrophages. We have demonstrated that several microbiome-derived peptides induce secretion of proinflammatory cytokines and chemokines such as CXCL10 and TNF-α by primary human monocyte-derived dendritic cells (moDCs), as well as secretion of effector cytokines such as IFNγ and IL-2 by primary human T cells. We have also identified microbiome-derived peptides with the capacity to inhibit an M2-like phenotype in macrophages (decreased LPS-induced IL-10 secretion). These effects were dose dependent and evident across immune cells derived from multiple human blood donors. In a coculture assay using allogeneic moDCs and T cells from human donors, combination of our DC-activating peptides with CD40 agonistic antibody and/or anti-PD-L1 induced secretion of proinflammatory cytokines such as IFNγ and TNF-α. In vivo, peritumoral administration of a candidate DC-activating peptide into RENCA tumor-bearing mice led to a significant reduction in tumor volume as compared to the control-treated mice. Collectively, these data demonstrate the potential of the microbiome-derived peptides identified by Second Genome’s discovery platform to modulate immune-cell effector functions in vitro and promote antitumor immunity in vivo. These results validate the unique approach of Second Genome’s discovery platform to identify novel microbiome-derived agents with potential for use as therapeutics in cancer immunotherapy. This abstract is also being presented as Poster B19. Citation Format: Dhwani D. Haria, Jayamary Divya Ravichandar, Lynn Yamamoto, Bernat Baeza-Raja, Ashil Bans, Cheryl-Emiliane Chow, Jill Desnoyer, Joanna Dreux, Shoko Iwai, Sabina Lau, Jina Lee, Michelle Lin, Paul Loriaux, Nicole Narayan, Eskedar Nigatu, Erica Rutherford, Michi Wilcoxon, Yonggan Wu, Todd DeSantis, Toshihiko Takeuchi, Karim Dabbagh, Helena Kiefel. Novel microbiome-derived peptides modulate immune cell activity and the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR08.

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