Monitoring the disturbance of the microbiota in Amazonian soils during conversion of forest to pasture and its consequences on cattle health

Pandemics of "swollen face", a bacterial-origin periodontitis disease afflicting ruminant livestock, have been correlated with deforested areas in Brazil (Dobereiner et al., 2000). This disease was commonly reported in Brazil during the 60s and 80s. New cases have recently been observed in sheep and goat flocks in the Amazonia, under the same epidemiological conditions and with the same characteristics observed in bovines. In such circumstances, the disease has destroyed herds of livestock, often up to 90% of the animals.We hypothesize a link between the "swollen face" disease and shifts in the soil microbial communities as a consequence of deforestation and pasture introduction based on previous scientific evidence that shows that this disease is triggered by deforestation, which in turn leads to significant changes in the soil communities, favoring specific populations such as actinomycetes. Our objective is to characterize correlations between the soil environment, changes in the microbial community due to deforestation, and the occurrence of this disease. Once more specific correlations are identified, we will experimentally test hypotheses (e.g., causation) generated through isolating key microbes and using culture-dependent and independent techniques. Answering these hypotheses is important to advance towards a cure for the disease, and design monitoring methods and alternative management to reduce its incidence. Additionally, confirming the link between the occurrence of diseases, deforestation and changes in biodiversity will contribute to the delineation of policies to hinder deforestation and to promote biodiversity conservation.We propose to leverage high-throughput microbiological characterization of environmental samples using next generation sequencing approaches, which are cultivation-free. These methods generate large amounts of data without the need for initially cultivating isolates. Since only 1% of the soil microorganisms can be cultivated, culture-independent approaches are powerful tools to assess microbial diversity. Our USG partner, Dr. James Cole, will provide training and support with bioinformatic analysis of these datasets. We will use tools that are currently under development from his current USG grant. Concurrently, co-PI Cole and his team may use our dataset to evaluate developed tools.