Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

Weimer, Paul J.

doi:10.3389/fmicb.2015.00296

Cited by 487Ruminant Nutrition and Digestive PhysiologyGut microbiota and healthAnaerobic Digestion and Biogas Production

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

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Weimer, Paul J.·2015·Frontiers in Microbiology

DOI 10.3389/fmicb.2015.00296PMC PMC4392294

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Abstract

The ruminal microbial community is remarkably diverse, containing 100s of different bacterial and archaeal species, plus many species of fungi and protozoa. Molecular studies have identified a "core microbiome" dominated by phyla Firmicutes and Bacteroidetes, but also containing many other taxa. The rumen provides an ideal laboratory for studies on microbial ecology and the demonstration of ecological principles. In particular, the microbial community demonstrates both redundancy (overlap of function among multiple species) and resilience (resistance to, and capacity to recover from, perturbation). These twin properties provide remarkable stability that maintains digestive function for the host across a range of feeding and management conditions, but they also provide a challenge to engineering the rumen for improved function (e.g., improved fiber utilization or decreased methane production). Direct ruminal dosing or feeding of probiotic strains often fails to establish the added strains, due to intensive competition and amensalism from the indigenous residents that are well-adapted to the historical conditions within each rumen. Known exceptions include introduced strains that can fill otherwise unoccupied niches, as in the case of specialist bacteria that degrade phytotoxins such as mimosine or fluoroacetate. An additional complicating factor in manipulating the ruminal fermentation is the individuality or host specificity of the microbiota, in which individual animals contain a particular community whose species composition is capable of reconstituting itself, even following a near-total exchange of ruminal contents from another herd mate maintained on the same diet. Elucidation of the interactions between the microbial community and the individual host that establish and maintain this specificity may provide insights into why individual hosts vary in production metrics (e.g., feed efficiency or milk fat synthesis), and how to improve herd performance.

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Rumen microbes possess genes coding for a high level of functional redundancy.
“given that rumen microbes possess genes coding for a high level of functional redundancy (Edwards et al., 2008; Weimer, 2015).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Weimer, 2015

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Authors: Weimer, P. J.
Affiliations: Agricultural Research Service (US)
Corresponding author: Weimer, Paul J.
ORCID: Weimer, Paul J.
Venue: Frontiers in Microbiology
Publisher: Frontiers Media SA
Published: 2015-04-10
Volume: 6
Pages: 296-296
ISSN: 1664-302X (ISSN-L)
DOI: 10.3389/fmicb.2015.00296
PMC: PMC4392294
OpenAlex: W2064490992
Cited by: 487
References: 147
Citations by year: 2026: 53 · 2025: 38 · 2024: 47 · 2023: 56 · 2022: 53 · 2021: 50 · 2020: 50 · 2019: 33 · 2018: 40 · 2017: 38 · 2016: 24 · 2015: 5
FWCI: 6.22
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: Frontiers in Microbiology (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics: Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
Keywords: rumen microbiota, microbial resilience, host specificity, core microbiome, Firmicutes, Bacteroidetes, probiotics, microbial competition, niche occupation, mimosine, fluoroacetate, feed efficiency, methane mitigation, fiber applications

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Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

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