The calf’s gastrointestinal tract (GIT) microbiome undergoes rapid shifts during early post-natal life, which can directly affect calf performance. The objectives of this study were to characterise and compare differences in the establishment and succession of GIT microbiota, GIT morphological changes, and the growth of dairy calves from birth until weaned. Forty-four newborn Holstein-Friesian calves were randomly selected and assigned to Treatment (TRT) and Control (CON) groups. The TRT group calves received a once-daily dose of a direct-fed microbial (DFM) liquid product containing Lacticaseibacillus paracasei, Lentilactobacillus buchneri, and Lacticaseibacillus casei, all formerly known as Lactobacillus. Fresh faecal samples were manually taken from the rectum of all calves, and gross necropsy was performed on the forestomachs and gastrointestinal tracts. Bacterial DNA was extracted from frozen faecal samples for 16S rRNA gene amplicon sequencing. Calves in the TRT group had greater live weights (p = 0.02) at weaning compared with calves in the CON group (mean = 69.18 kg, SD = 13.37 kg). The average daily live weight gain (ADG) and total feed intake were similar between the two groups. Calves in the TRT group had greater duodenum, abomasum, and reticulum weights (p = 0.05). Rumen and intestinal development (p < 0.05) and faecal microbial diversity (p < 0.05) were more pronounced in the TRT group. The relative abundances of eight genera differed (p < 0.001) between the groups. Supplementing calves with the LAB-based DFM increased live weight at weaning and had a more pronounced effect on the development of rumen and the gastrointestinal tract and on microbiota diversity and evenness. Future work is needed to better understand the potential association of LAB-DFM products on gut mucosa-associated microbiota.

Summary: Above: Illustration of the impact of a lactobacilli-based direct-fed microbial (DFM) supplement on dairy calves. The centerpiece displays 2 calves, highlighting notable differences in live weight between the treatment (TRT; n = 22) and control (CON; n = 22) groups. This difference was associated with a more developed gastrointestinal tract (GIT) and the microbial community. This study demonstrates the potential of targeted microbial interventions in improving dairy calf performance and overall health, suggesting a promising avenue for enhancing livestock productivity through microbiota intervention.

The rumen microbiota of dairy cows plays a crucial role in fermenting fibrous material, essential for nutrient extraction and overall productivity, detoxification of anti-nutritional toxic compounds, synthesis of vital nutrients, and is essential for optimal animal health. This study investigated the impact of Lentilactobacillus-, Lactocaseibacillus-, and Lacticaseibacillus-based direct-fed microbial (DFM) supplementation on dairy cows’ faecal microbial composition and diversity. The study was carried out on a commercial dairy farm using 50 Holstein-Friesian cows randomly assigned into control (CON) and treatment (TRT) groups. Faecal samples were collected directly from the rectum every two months from September 2021 to January 2023. The bacterial 16S rRNA gene and fungal ITS-1 regions were amplified, sequenced, and analysed. Microbial diversity was assessed through alpha- and beta-diversity metrics. Linear discriminant analysis effect size (LEfSe) was performed to identify which taxa were driving the changes seen in the microbiota over time and treatment. Bacteroidaceae were the most prevalent bacterial family, followed by Lachnospiraceae and Muribaculaceae in both CON and TRT cows. Ascomycota, Basidiomycota, and Mucoromycota were the dominant three fungal phyla in the faeces of both CON and TRT cows. Bacterial genera Fructilactobacillus was abundant in the CON and Absicoccus in the TRT groups. Fungal taxa Chaetothryriales_incertae_sedis and Pseudomentella were absent in the faeces of TRT cows. Significant temporal and specific taxonomic differences were observed between the CON and TRT groups. The study’s findings underscore the dynamic nature of microbial communities and the importance of targeted dietary interventions. Further research is necessary to elucidate these microbial shifts, long-term impacts, and functional implications, aiming to optimise ruminant nutrition and enhance dairy cow performance.

The current study examined the effects of lactobacilli-based direct-fed microbial (DFM) supplementation on the microbiota composition and diversity in ruminal fluid samples collected from dairy cows. Over 18 months (September 2021 through January 2023), the rumen bacterial and archaeal communities of fifty cows, supplemented with the DFM (DFM; n = 25) or serving as un-supplemented controls (CON; n = 25), were examined using 16S rRNA gene amplification and sequence analysis of DNA extracted from ruminal samples. Microbial diversity was assessed through alpha- and beta-diversity metrics (p<0.05). Linear discriminant analysis effect size (LEfSe) analysis was performed to identify taxa driving the changes seen in the microbiota between experimental groups and temporally within each group (p<0.05). Bacillota and Bacteroidota were the major bacterial phyla, while Methanobacteriaceae was the predominant archaeal family. Bacterial genera such as Eubacterium_Q, Atopobium sp. UBA7741, and Sharpea were significantly more abundant in the DFM group, while Bacillus_P_294101 and SFMI01 had higher abundance in the CON group. The results also indicated significant temporal variations in ruminal microbial diversity, with specific taxa exhibiting different abundances between the DFM and CON groups. This study provides insights into how DFM feed additives can modulate the ruminal microbiota in dairy cows, revealing specific microbial shifts in response to supplementation.

Previous studies of direct-fed microbial (DFM) supplements showed variable effects on the microbiota and physiology of dairy cows. The main aims of this study were to investigate the milk microbiota of cows supplemented with a lactobacilli-based DFM compared to untreated cows; describe the changes; and quantify the association between the taxa and cow productivity. The study followed seventy-five Holstein–Friesian dairy cows supplemented with a DFM over 16 months compared to seventy-five non-supplemented cows. Twenty-five cows from each group were sampled for microbiota analysis. The top taxa significantly associated with the variables were as follows: Age (Mammaliicoccus_319276, Turicibacter), milk production (Turicibacter, Bifidobacterium_388775), DIM (Stenotrophomonas_A_615274, Pedobacter_887417), milk fat percentage (Pseudomonas_E_647464, Lactobacillus), calendar month (Jeotgalicoccus_A_310962, Planococcus), milk protein percentage (Tistrella, Pseudomonas_E_650325), experimental group (Enterococcus_B, Aeromonas), SCC (Paenochrobactrum, Pseudochrobactrum), and trimester of pregnancy (Dyadobacter_906144, VFJN01 (Acidimicrobiales)). These were identified using multivariable analysis. Twenty-six genera were associated with the differences between experimental groups, including Pseudomonas, Lactococcus and Staphylococcus. Microbial taxa that changed in relative abundance over time included Atopostipes, Brevibacterium and Succinivibrio. Many of these genera were also part of the core microbiota. Supplementation with the DFM significantly altered the milk microbiota composition in the dairy cows, highlighting the impact of long-term DFM supplementation on microbial communities.