Welcome back to Dispatches from ASM Microbe! Today weâ€™ll continue Microbe 2016 highlights of the microbiome, focusing on the non-human microbiome research being presented during the conference.
As mentioned Friday, commencement of the National Microbiome Initiative was met with great excitement by ASM. We are excited not only to delve more deeply into the role of the human microbiome on health impacts, but also to learn more about the numerous microbial communities that exist apart from people. Some of these microbiomes impact us through interaction with our urban environments or agriculture, while others may appear to impact us less directly but still play important global and local roles.
Microbiomes of Water Systems
Our built environment has a number of unique microbiomes, as illustrated by recent studies on the office microbiome and the urban transit microbiome. We spend the majority of our time inside these manmade structures, so characterizing and manipulating their microbial populations can help optimize our exposure to immunomodulatory or pathogenic microbes. And donâ€™t forget the water we use to drink, cook, and bathe. â€śMicroorganisms in the urban water cycle can enhance or diminish the quality of environment and infrastructure, and public health,â€ť says Ameet Pinto, who co-convenes a session on the urban water cycle this morning. â€śTheir impacts can range from established benefits such as pollution removal in wastewater bioreactors to emerging risks of antimicrobial resistance in water supply systems. The desire to effectively and efficiently manage these impacts is central to our motivation of understanding the inner workings of the urban water cycle microbiome.â€ť
The session kicked off with Lutgarde Raskin discussing the drinking water microbiome. Raskin has spearheaded some of the initial characterizations of the drinking water microbiome, characterizing the spatio-temporal patterns of water treatment facilities' bacterial microbiomes. These studies establish a baseline seasonal variation of these communities to identify when contaminants reach levels of concern. Her research also looks at the drinking water microbiome as a potential source of respiratory pathogens aerosolized during sink or shower usage. Inhalation of certain aerosolized microbes is particularly dangerous for those with impaired immunity, such as cystic fibrosis patients.
Tom Curtis presented his work on improving wastewater treatment systems, an important task given their role in clearing bacteria harboring drug resistance genes, including pathogens. His research focuses on applying relatively new microbiological methods toward engineered biological systems involved in wastewater treatment. These important applications build a safe infrastructure for water treatment and transport, which are vital for a healthy urban environment. The recent Academy FAQ report and Twitter Chat further discuss the impacts of these structural and infrastructural microbes. But unlike built structures, our water systems are not contained, and interact with natural waterways. Research on the interaction between the urban coastal areas and the natural water systems that surround them was discussed by Sandra McLellan in her presentation.
Waterways have their own natural microbiomes even in the absence of people, of course, and several oceanic microbiome research studies were presented at Friday afternoonâ€™s symposium on new discoveries in marine microbiology. Peer Bork presented his computational analyses of marine viral, prokaryotic, and picoeukaryotic content, using algorithms to better predict community function. Borkâ€™s work also demonstrates that the oceanic microbial core shares 73% of its gene abundance with the human gut microbiome ($). Generating tools like these that predict and characterize genomic function is a goal of the Kavli Microbiome Ideas Challenge.
Yesterdayâ€™s oceanic microbe session also saw Pia Moisander present the microbiome of copepods. Her sequence-based research shows that the most prominent stable microbiome members are taxa within Gammaproteobacteria, particularly Pseudoalteromonas species. This association seems more important than Vibrio species, which cultivation-dependent studies have identified as an important microbiome member and dangerous potential pathogens. Moisanderâ€™s research emphasizes yet again the importance of using multiple methods in measuring microbial population structures.
Marcel Kuypers' presentation in last nightâ€™s Distinguished Lecture continued the oceanic theme. Kuypersâ€™ research focuses on the pathways, interactions, and environmental regulation of microbial processes that control oceanic nutrient cycling. His presentation focused on the novel type of symbiotic relationship of the cyanobacterium UCYN-A to its diatom host, in which the host relies on UCYN-A for nitrogen and UCYN-A relies on its host for carbon. These important global processes are being impacted by climate change (as discussed in a previous ASM Cultures issue) and a combination of chemical, molecular, microbiological, and mathematical modeling techniques are necessary to make predictions for the ocean systems as the climate changes.
[While not related to oceanic research, the Distinguished Lecture also featured Graham Hatfull, presenting research derived from the SEA Phage Hunters Advancing Genomics and Evolutionary Science, or SEA PHAGES, citizen science-based undergraduate science courses. The evening ended with a talk from Jennifer Doudna, whose work on CRISPR is likely well known to readers, on aspects of CRISPR biology related to Cas9 function, genome defense, and genome engineering.]
Microbiomes in Agriculture
Thereâ€™s no denying the role microbes play in plant growth, and optimizing the microbes used in our agricultural systems is important for issues ranging from plant immunity to crop yield to food safety. These issues were addressed at Saturday's morning session on agribiomes. The session began with a presentation from Jos Raaijmakers on the root microbiome, a community that affects plant growth and stress tolerance, but also is itself affected by the host plant species.
E. Toby Kiers presented research on competition as a stabilizing force in plant-microbe mutualism, while Benjamin Wolfe presented one of the tastiest ideas of the session: using fermented foods as means to explore microbiome patterns and processes. These foods provide both a tractable system to study microbiome interactions and an accessible way to teach systems concepts using safe, hands-on tools.
Tomorrowâ€™s Dispatches from ASM Microbe will focus on the pressing issue of antimicrobial resistance.