Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Nov 27;14(23):3437.
doi: 10.3390/ani14233437.

Temporal Changes in Faecal Microbiota Composition and Diversity in Dairy Cows Supplemented with a Lactobacillus-Based Direct-Fed Microbial

Bronwyn E Campbell  1 , Mohammad Mahmudul Hassan  2 , Robert J Moore  1 , Timothy Olchowy  3 , Shahab Ranjbar  2 , Martin Soust  4 , Orlando Ramirez-Garzon  4 , Rafat Al Jassim  5 , John I Alawneh  2
Affiliations

Temporal Changes in Faecal Microbiota Composition and Diversity in Dairy Cows Supplemented with a Lactobacillus-Based Direct-Fed Microbial

Bronwyn E Campbell et al. Animals (Basel). .

Abstract

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.

Keywords: DFM; dairy cows; faecal microbiota; microbial diversity; temporal changes.

PubMed Disclaimer

Conflict of interest statement

M.S. and O.R.-G. were employed by Terragen Biotech Pty Ltd., which funded this study and assisted in the administrative component of this multiyear study. All remaining co-authors declare no conflicts of interest. The funders had no role in the design of the study, in the analyss or interpretation of the data, in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Relative abundance of bacterial families in faeces for control (CON) and DFM-treated (TRT) groups throughout the study period.
Figure 2
Figure 2
Bacterial alpha diversity analysis (genus level) over time in faeces from Control (CON) and DFM-treated (TRT) experimental groups. Observed (A) and Chao1 (B) for Shannon index (C). Pooled data for overall differences between experimental groups disregarding the effect of the calendar month: Observed and Chao1, p-value: <0.001, t-test: 46.5; Shannon, p-value: <0.001, t-test: −25.2. Asterisk (*) on x-axis below experimental group denotes p < 0.05 between experimental groups for a given calendar month.
Figure 3
Figure 3
Bacterial beta-diversity (genus level) analysis via (A) principal component analysis and (B) non-metric multidimensional scaling of faeces across eight time points from September 2021 to January 2023. Microbial diversity differed significantly over the 16 months of the trial.
Figure 4
Figure 4
Linear discriminant analysis effect size (LEfSe) analysis of the top twenty genera from faeces from Control (CON) compared with DFM-supplemented (TRT) experimental group. LDAscore refers to the linear discriminant analysis scores.
Figure 5
Figure 5
Relative abundance of fungal classes in faeces for control (CON) and treatment (TRT) groups throughout the study period.
Figure 6
Figure 6
Alpha-diversity analysis (genus-level) of the fungal composition of faeces over time from Control (CON) compared with DFM-treated (TRT) cows. Observed (A) and Chao1 (B) for Shannon index (C). Pooled data for overall differences between experimental groups disregarding the effect of the calendar month: Observed and Chao1, p-value 0.32, t-test: 0.99; Shannon, p-value: 0.23, t-test: −1.2. Asterisk (*) on x-axis below experimental group denotes p < 0.05 between experimental groups for a given calendar month.
Figure 7
Figure 7
Bacterial beta-diversity (genus level) analysis of fungi of faeces across eight time points from September 2021 to January 2023 (A,B), using Microbial diversity differed significantly over the 16 months of the trial.
Figure 8
Figure 8
Prevalences of fungal genera found as the core microbiota of the faeces of Control (CON) and DFM-supplemented (TRT) cows.
See this image and copyright information in PMC

References

    1. Henderson G., Cox F., Ganesh S., Jonker A., Young W., Janssen P.H. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 2015;5:14567. doi: 10.1038/srep14567. - DOI - PMC - PubMed
    1. Kumar S., Indugu N., Vecchiarelli B., Pitta D.W. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows. Front. Microbiol. 2015;6:781. doi: 10.3389/fmicb.2015.00781. - DOI - PMC - PubMed
    1. Samtiya M., Aluko R.E., Dhewa T. Plant food anti-nutritional factors and their reduction strategies: An overview. Food Prod. Process. Nutr. 2020;2:6. doi: 10.1186/s43014-020-0020-5. - DOI
    1. Bickhart D., Weimer P. Symposium review: Host–rumen microbe interactions may be leveraged to improve the productivity of dairy cows. J. Dairy Sci. 2018;101:7680–7689. doi: 10.3168/jds.2017-13328. - DOI - PubMed
    1. Zeineldin M., Barakat R., Elolimy A., Salem A.Z., Elghandour M.M., Monroy J.C. Synergetic action between the rumen microbiota and bovine health. Microb. Pathog. 2018;124:106–115. doi: 10.1016/j.micpath.2018.08.038. - DOI - PubMed

LinkOut - more resources