Research Tracks
Microbial communities impact food quality and safety at all stages of the food production chain. The Food Systems Biotechnology group utilizes integrated "omics" approaches to examine the interconnection of biotic and abiotic factors, microbiomes, and characteristics of regional food products and food production systems, with the ultimate goal of reverse engineering these systems to improve food quality, safety, and sustainability. This includes characterizing microbial properties of food products that underpin regional quality characteristics ("microbial terroir"), as well as studying the temporospatial organization of microbiomes in food production systems both in the field and during food processing, to better predict and control microbial activity during food production.
Microbial communities are shaped by host factors, environmental conditions, and human influences, and have a strong impact on food quality and safety at every stage of the food production chain. This is particularly of interest in vineyards, since regionally varying factors, including associated microbiota (microbial terroir), produce wines with distinct sensory qualities. Yet the complex interactions underpinning these local differences are poorly understood. Therefore, the Food Systems Biotechnology Group utilizes integrated "omics" approaches to disentangle biotic and abiotic factors and to gain a more holistic insight into plant-microbiome-environment interactions. This includes characterizing microbial properties of food products that underpin regional quality characteristics ("microbial terroir"), as well as studying the temporospatial organization of microbiomes in food production systems both in the field and during food processing, to better predict and control microbial activity during food production.
This includes investigation of microbial ecosystems of wine production, encompassing both vineyard and winery environments, and the role of climate, human management practices, and plant genotype in regulating the microbial and chemical composition of wine and other foods; factors that can be harnessed for quality improvement. This same model is applied to other fermented foods on a broad scale, using both culture-independent untargeted “omics” technologies, as well as high-throughput culturomics for microbial isolation and characterization.
The human body is inhabited by trillions of microbial cells (outnumbering the cells of the host!), forming complex microbiomes that are intimately tied to human health and disease at various body sites. The Food Systems Biotechnology group utilizes integrated multi-omics approaches to study the assembly and development of these microbial communities, to provide a predictive understanding of their behavior and interactions with human diet. This includes studies of the establishment of gut microbiota during infancy and childhood, the interaction of the gut microbiome with diet, and the role of the microbiome in microenvironment and carcinogenesis at different human body sites.
Microbiome and cancer treatment
The human microbiome has been implicated in cancer risk (or protection) by numerous research studies. We investigate microbial dysbiosis in different solid and liquid cancers to identify potential strategies for risk detection and treatment. In a collaboration with University of Basel and University of Zurich, we are examining interactions between the gut/skin microbiomes, metabolomes, and personalized responses to allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT is the only effective treatment for certain blood cancers and disorders; while life-saving, the procedure also carries a high occurrence of side effects including infection and graft-versus-host-disease (GVHD). We seek to understand how the human gut microbiome interacts with the immune system and influences morbidity risks in allo-HSCT. Understanding individualized features affecting patient response will guide drug treatment, improve quality of care, and improve patient survival rate following allo-HSCT.
Microbiome development during early childhood
The first years of life are characterized by rapid development of the human microbiome from being essential sterile at birth to reaching an adult-like stable composition. The maturation of the microbiome parallels critical milestones in physiological, immunological, and neurobehavioral development, with evidence for significant bi-lateral interactions with microbiome development. We use multi-omics and machine learning methods to investigate microbiome and host development during early life, with particular interest in longitudinal causative relationships between functional microbiome development and host developmental, behavioral, and health outcomes.
The Microbiota Vault
Numerous ecosystems on earth are experiencing unprecedented loss of biodiversity, due to climate change, lifestyle change, and various other anthropogenic impacts. This includes degradation of microbial communities that critically support diverse aspects of human, plant, animal, and environmental health. The Microbiota Vault aims to establish a backup biobank infrastructure in Switzerland for long-term storage of microbiomes important for sustaining life on this planet. FSB is co-leading the Launch phase of the Microbiota Vault launch together with University of Lausanne and University of Zurich. FSB is leading efforts for establishing analytical standards, open data, and bioinformatics analysis. In addition, FSB leads a subproject for collection and preservation of culturally important fermented foods in the Microbiota Vault.
Advances in DNA sequencing technologies enable acquisition of metagenomic datasets at an unprecedented scale. More accurate methods are needed to analyze and interpret these high-dimensional data, and integrate "omics" datasets to gain detailed insight into host–microbial interactions. The Food Systems Biotechnology group develops open-source bioinformatics software and machine-learning methods to explore microbiomes and other omics datasets in diverse ecosystems, including development of diverse plugins for the QIIME 2 (external page https://qiime2.org) microbiome multi-omics platform. This includes open-source bioinformatics tools for genome and metagenome assembly, enabling in silico reconstruction of whole microbial genomes to provide information about species composition and functional genetic potential of complex microbiomes. Activities in the group since 2020 have focused on development of open-source software packages for infectious disease and microbial biosurveillance using shotgun metagenome sequence data, traceable and reproducible bioinformatics workflows, machine learning approaches for microbial classification and longitudinal prediction, and software for reproducible FAIR reuse of open research datasets. To see our latest projects visit external page https://github.com/bokulich-lab.
