Research Topic

Gut Microbiome Modulation in Ruminants: Enhancing Advantages and Minimizing Drawbacks

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Historically, the gastrointestinal tract was considered an organ solely equipped for the digestion and absorption of nutrients. However, the gut harbours the largest population of immune cells and commensal microbes that outnumber the entire host cells. Therefore, there is a general consensus that a healthy ...

Historically, the gastrointestinal tract was considered an organ solely equipped for the digestion and absorption of nutrients. However, the gut harbours the largest population of immune cells and commensal microbes that outnumber the entire host cells. Therefore, there is a general consensus that a healthy gut leads to healthy ruminants with optimal performance.

The rumen is perhaps the most diverse and complex microbial ecosystem harboured in the gastrointestinal tract of animals. This microbial community consisting of symbiotic bacteria, archaea, protozoa, fungi and phages provides an evolutionary advantage for ruminants, which allows them to efficiently utilize lignocellulosic materials and low-quality protein sources to produce high quality foods. As a result, ruminants are capable of digesting a wide range of forages, decreasing the competition for human-edible foods. However, rumen microbial fermentation has some drawbacks: rumen proteolysis carried out by protozoa and certain bacterial species leads to low nitrogen efficiency and the excess of rumen ammonia is excreted to the environment. Similarly, methane formation in the rumen by the methanogenic archaea is wasteful in terms of energy and contributes to climate change. As antibiotics are being phased out of livestock production, novel and cost-effective strategies must be explored to modulate the rumen microbial fermentation in order to maximize its advantages and to minimize its drawbacks. In recent years, the exploration of bioactive phytochemicals as natural feed additives has gained interest to modify the rumen fermentation favourably, such as by minimizing protozoal levels, rumen methanogenesis and optimizing rumen function and product quality. Probiotics such as yeast, specific bacterial strains and even the direct inoculation of rumen microbiota have also been used to enhance fibre and starch digestion, to prevent rumen acidosis and to accelerate rumen microbial development. However, the effectiveness of these nutritional interventions is highly variable depending upon the interactions among the chemical structure of the compound, the diet and the rumen microbiota adaptability.

Unlike the rumen, the intestine is lined by a single layer of epithelial cells and a mucosa immune system that serves to facilitate absorption of nutrients and acts as a barrier to invading microorganism, toxins and dietary antigens. Appropriate early-life assembly of the gut microbiota is believed to play a key role in the immune system development but also in subsequent animal physiology and behavioural aspects as part of “Brain-Gut-Microbiota axis”. Thus, understanding the interactions between the gut microbiota, diet, host genetics and health are key to develop new strategies to meet consumers’ demands for a more environmentally friendly animal production.

This Research Topic would benefit of using a multidisciplinary approach combining omics-based techniques to characterize the gut microbial community and applied sciences to develop new nutritional strategies. Both in vitro and in vivo studies are welcomed to reveal the mode of action and the real impact on animal productivity. We would like to emphasize the use of novel strategies to modulate the gut microbiome which can lead to future research hypotheses. Original research, reviews and mini-reviews, perspectives, and hypothesis and theory manuscripts are all welcomed.


Keywords: Antibiotic Alternatives, Early Life Interventions, Feed Additives, Probiotics, Rumen Microbiome


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30 September 2019 Manuscript

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Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

30 September 2019 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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