Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.

Context: Improving feed efficiency in livestock production is of great importance to reduce feeding costs. Aims: To examine the relationship between ruminal microbiota and variation in feed efficiency in beef cattle fed concentrate-based diets. Methods: Residual feed intake of 389 fattening bulls, supplied with corn-based concentrate and forage ad libitum, was used to estimate animals’ feed efficiency. Faeces and ruminal fluid samples, from 48 bulls chosen at random, were collected to estimate their forage intake and to determine their apparent digestibility, ruminal fermentation and microbiota. Those animals with extreme values of feed efficiency (high-efficiency (HE, n = 12) and low-efficiency (LE, n = 13)) were subjected to further comparisons. Alpha biodiversity was calculated on the basis of the normalised sequence data. Beta diversity was approached through performing a canonical correspondence analysis based on log-transformed sequence data. Genera differential abundance was tested with an ANOVA-like differential expression analysis and genera interactions were determined applying the sparse correlations for compositional data technique. Key results: No differences in dry matter intake were found between the two categories of feed efficiency (P = 0.699); however, HE animals had higher apparent digestibility of dry matter (P = 0.002), organic matter (P = 0.003) and crude protein (P = 0.043). The concentration of volatile fatty acids was unaffected by feed efficiency (P = 0.676) but butyrate proportion increased with time in LE animals (P = 0.047). Ruminal microbiota was different between HE and LE animals (P = 0.022); both α biodiversity and genera network connectance increased with time in LE bulls (P = 0.005 for Shannon index and P = 0.020 for Simpson index), which suggests that LE animals hosted a more robust ruminal microbiota. Certain genera usually related to high energy loss through methane production were found to establish more connections with other genera in LE animals’ rumen than in HE ones. Microbiota function capability suggested that methane metabolism was decreased in HE finishing bulls. Conclusions: Rumen microbiota was associated with feed efficiency phenotypes in fattening bulls fed concentrate-based diets. Implications: The possible trade-off between feed efficiency and robustness of ruminal microbiota should be taken into account for the optimisation of cattle production, especially in systems with intrinsic characteristics that may constitute a disturbance to rumen microbial community.

Characterization of intestinal microbiota is of great interest due to its relevant impact on growth, feed efficiency and pig carcass quality. Microbial composition shifts along the gut, but it also depends on the host (i.e., age, genetic background), diet composition and environmental conditions. To simultaneously study the effects of producing type (PT), production phase (PP) and dietary crude protein (CP) content on microbial populations, 20 Duroc pigs and 16 crossbred pigs (F2), belonging to growing and fattening phases, were used. Half of the pigs of each PT were fed a moderate CP restriction (2%). After sacrifice, contents of ileum, cecum and distal colon were collected for sequencing procedure. Fattening pigs presented higher microbial richness than growing pigs because of higher maturity and stability of the community. The F2 pigs showed higher bacterial alpha diversity and microbial network complexity (cecum and colon), especially in the fattening phase, while Duroc pigs tended to have higher Firmicutes/Bacteroidetes ratio in cecum segment. Lactobacillus was the predominant genus, and along with Streptococcus and Clostridium, their relative abundance decreased throughout the intestine. Although low CP diet did not alter the microbial diversity, it increased interaction network complexity. These results have revealed that the moderate CP restriction had lower impact on intestinal microbiota than PP and PT of pigs.