Abstract
The human upper respiratory tract is the reservoir of a diverse community of commensals and potential pathogens (pathobionts), including Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus, which occasionally turn into pathogens causing infectious diseases, while the contribution of many nasal microorganisms to human health remains undiscovered. To better understand the composition of the nasal microbiome community, we create a workflow of the community model, which mimics the human nasal environment. To address this challenge, constraint-based reconstruction of biochemically accurate genome-scale metabolic models (GEMs) networks of microorganisms is mandatory. Our workflow applies constraint-based modeling (CBM), simulates the metabolism between species in a given microbiome, and facilitates generating novel hypotheses on microbial interactions. Utilizing this workflow, we hope to gain a better understanding of interactions from the metabolic modeling perspective. This article presents nasal community modeling workflow (NCMW)—a python package based on GEMs of species as a starting point for understanding the composition of the nasal microbiome community. The package is constructed as a step-by-step mathematical framework for metabolic modeling and analysis of the nasal microbial community. Using constraint-based models reduces the need for culturing species in vitro, a process that is not convenient in the environment of human noses. Availability: NCMW is freely available on the Python Package Index (PIP) via pip install NCMW. The source code, documentation, and usage examples (Jupyter Notebook and example files) are available at https://github.com/manuelgloeckler/ncmw.
Highlights
The human nose community is far more than a convenient model system, while it plays vital roles in human health and global nutrient cycles (Widder et al, 2016)
Like OptCom (Zomorrodi and Maranas, 2012), a multilevel optimization framework for the metabolic modeling, we considered species-level and community-level criteria in defining the objective function
The cultural capability of strains in microbial communities in the laboratory remains limited. Since this community research in the human nose provides explicit, testable hypotheses and potential targets for experimental verification, it provides a basis to examine the therapeutic potential of individual species as a typical nasal probiotic and possible novel discoveries
Summary
The human nose community is far more than a convenient model system, while it plays vital roles in human health and global nutrient cycles (Widder et al, 2016). The previous work focusing on ecological interactions can identify whether the interacting partners promote or hinder each other’s growth (Carrara et al, 2015). Studying these interactions on their own does not reveal the NCMW: Nasal Community Modeling Workflow mechanistic details of the nasal microbiome community or its composition and structure. Understanding the pair-wise or multispecies interactions in the human nose community is a starting point for manipulating microbiomes for therapeutic and prophylactic purposes This is often made difficult due to the inability to culture and co-culture the various species of human nasal microbiota in vitro
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