Abstract
ABSTRACTDairy cows respond individually to stressful situations, even under similar feeding and housing conditions. The phenotypic responsiveness might trace back to their microbiome and its interactions with the host. This long-term study investigated the effects of calving, lipopolysaccharide (LPS)-induced inflammation, and l-carnitine supplementation on fecal bacteria and metabolites, dairy cow milk production, health, energy metabolism, and blood metabolites. Fifty-four multiparous Holstein dairy cows were examined over a defined period of life (168 days). The obtained data allowed a holistic analysis combining microbiome data such as 16S rRNA amplicon sequencing and fecal targeted metabolome (188 metabolites) with host parameters. The conducted analyses allowed the definition of three enterotype-like microbiome clusters in dairy cows which could be linked to the community diversity and dynamics over time. The microbiome clusters were discovered to be treatment independent, governed by Bifidobacterium (C-Bifi), unclassified (uncl.) Clostridiales (C-Clos), and unclassified Spirochaetaceae (C-Spiro). Animals between the clusters varied significantly in terms of illnesses, body weight, microbiome composition, and milk and blood parameters. C-Bifi animals were healthier and leaner with a less diverse but dynamic microbiome. C-Spiro animals were heavier, but the diversity of the static microbiome was higher. This pioneering study uncovered microbiome clusters in dairy cows, each contributing differently to animal health and productive performance and with a crucial role of Bifidobacterium.IMPORTANCE The health of dairy cows has to be carefully considered for sustainable and efficient animal production. The microbiome of animals plays an important role in the host’s nutrient supply and regulation of immune functions. We show that a certain composition of the fecal microbiome, called microbiome clusters, can be linked to an animal’s health at challenging life events such as calving and inflammation. Cows with a specific set of bacteria have coped better under these stressors than have others. This novel information has great potential for implementing microbiome clusters as a trait for sustainable breeding strategies.
Highlights
Dairy cows respond individually to stressful situations, even under similar feeding and housing conditions
Fecal samples were collected at 13 time points to obtain a representative overview of the microbiome changes in the host during two physiological challenges (Fig. 1; see Data Sets S1 to S3 at https://github.com/SebasSaenz/Troscher-Mussotter_Cow-enterotypes_2021/ tree/main/Datatsets). (Time points including a “2” or “1” indicate days antepartum or postpartum, and those including “h after the calving (hC)” or “hL” are samples taken at 12, 24, or 72 h after calving or LPS challenge, respectively.) The herd was randomly split into L-carnitine-supplemented (CAR) and nonsupplemented (CON) cows, defined hereafter as treatment
Before calving, the microbiomes show the highest within-time similarity, as greater variations among individual animal communities are seen at all other time points
Summary
Dairy cows respond individually to stressful situations, even under similar feeding and housing conditions. The phenotypic responsiveness might trace back to their microbiome and its interactions with the host This long-term study investigated the effects of calving, lipopolysaccharide (LPS)-induced inflammation, and L-carnitine supplementation on fecal bacteria and metabolites, dairy cow milk production, health, energy metabolism, and blood metabolites. CSpiro animals were heavier, but the diversity of the static microbiome was higher This pioneering study uncovered microbiome clusters in dairy cows, each contributing differently to animal health and productive performance and with a crucial role of Bifidobacterium. The latest studies have associated the aforementioned health issues with an impaired gut microbiome [9, 12], suggesting that the modern dairy industry should focus on maintaining gut health, including its complex ecosystem and integrity, to increase the cows’ well-being and performance [9] Additional stressors, such as calving or infection, can pose the final blow for the animal. The present work tested physiological and the microbial differences between individuals of the same herd during the calving, transition, and an LPS-induced inflammatory challenge with or without supplementation with rumen-protected L-carnitine
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