Global Change and the Soil Microbiome: A Human-Health Perspective

Abstract

The importance of the gut and the soil microbiomes as determinants of human and ecosystem health, respectively, is gaining rapid acceptation in the medical and ecological literatures. This suggests that there is a wealth of highly transferable knowledge about the microbial ecology of human and non-human ecosystems that is currently being generated in parallel, but mostly in isolation from one another. I suggest that effectively sharing this knowledge could greatly help at more efficiently understanding and restoring human health and the functioning of ecosystems, which are currently under wide-spread pressure. I illustrate this by comparing the effects of nitrogen deposition on ecosystem carbon sequestration with unhealthy dietary habits and human disease. The deposition of N, a key nutrient for plant growth, may increase carbon sequestration (equivalent to obesity) through several mechanisms, including a reduction in the ability of soil microbes to process organic matter, which some argue could help mitigate climate change. However, this usually results in a degradation of ecosystem health and, thus, cannot represent a real solution. Similarly, human obesity is linked to an alteration of the composition and functioning of microbial communities inhabiting the gut, which is often attributed to unhealthy dietary habits, including ingesting high amounts of simple sugars and processed foods. Finally, I advocate for the explicit recognition of the many commonalities between the functioning of the gut and ecosystems and a broader multidisciplinary collaboration among experts in ecology and human health, including the engineering of soil microbial communities designed ad-hoc to restore ecosystem health.

MetaNovo: a probabilistic approach to peptide discovery in complex metaproteomic datasets

“…We then showed that using an unbiased search of the entire release of UniProt (ca. 90 million protein sequences ) 1 MetaNovo was able to identify a similar bacterial taxonomic distribution compared to that found using a small, focused matched metagenome database, but now also simultaneously identified proteins present in the samples that are derived from other organisms missed by 16S or shotgun sequencing and by previous metaproteomic methods . Using MetaNovo to analyze a set of single-organism human neuroblastoma cell-line samples ( SH-SY5Y ) against Introduction Characterizing complex mass-spectrometry data from clinical or environmental samples allows for potential insights into the complex metabolic pathways involved in processes as diverse as carbon sequestration and climate change to the susceptibility and progression of human diseases.…”

Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture

“…The human microbiome includes all those bacteria, archaea, fungi, protists, and viruses that colonize, among others, human skin, placenta, uterus, seminal fluid, lungs, saliva, oral mucosa, conjunctiva, and especially the gastrointestinal tract. If we view the human as an integrated ecosystem with its microbiome [31] -a holobiont [32][33][34][35][36] then, the microbiome renders a vast array of ecosystem services. [37] By ecosystem services we mean that the human microbiome stimulates the immune system and shapes its development, [38][39][40] contributes to the development and functioning of the nervous system, [41][42][43] the synthesis of micronutrients, [44] nutrient digestion and absorption, and to energy regulation.…”

Insights into the soil microbiome and prospects for its manipulation for improved pasture resilience

“…If desired plant traits (e.g., drought tolerance) can be provided or enhanced by using a microbial partner, early collaboration would likely lead to greater success and save limited research resources. Broader multidisciplinary research is needed to fully understand the potential effect of new pasture cultivars/microbiome associations within the wider ecosystem (e.g., Duckworth et al 2017;Ochoa-Hueso 2017). Equally, as with any technological changes, questions around the unintended impacts will also need to be answered; for example, "what are the potential effects on other beneficial microbes in soil and plant?…”