Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea

Abstract

Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of “healthy” (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa–function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella , Streptococcus , Dorea , uncultured Lachnospiraceae , Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate “healthy” and “unhealthy” (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

Parenteral Antimicrobial Treatment Diminishes Fecal Bifidobacterium Quantity but Has No Impact on Health in Neonatal Dairy Calves: Data From a Field Trial

“…A human neonatal study evaluating the impact of parenteral antimicrobials (ampicillin/gentamicin) on fecal Bifidobacterium showed a similar effect to those in our study ( 33 ). Using a different study design, Ma and others ( 7 ) investigated disturbances to the gut microbiome and reported that the use of antibiotics early in a calf's life delayed the development of microbial diversity. They noted that a gut microbiome with greater stability was more resistant to outside disturbances.…”

“…The transition to a stable GIT microbiota occurs early on in life; the exact age it occurs depends on the species. In dairy calves, there is an increase in the diversity and stability of the GIT microbiota over the first few months of age ( 7 ). This colonization is critical as interaction between the microbiota and the animal plays a key role in the development of the mucosal immune system ( 8 ) and is linked to resistance or susceptibility to diseases later in life.…”

Rumen and Hindgut Bacteria Are Potential Indicators for Mastitis of Mid-Lactating Holstein Dairy Cows

“…Despite the studies still being limited, the random forest model has been used for the successful prediction of diarrhea in dairy cows with high accuracy [ 14 ], suggesting the possibility for the model application in the discrimination of disease. Interestingly, the predicted incidence rate of mastitis in dairy cattle based on the rumen microbiome with the 24 selected genera was lower than when solely classifying based on SCC (6.29 vs. 30.24%).…”

“…In humans and nonhuman mammals, the suppression and over-colonization of certain bacterial species in the gastrointestinal tract result in increasing disease pathogenicity and emphasize the importance of understanding the interaction between a host and its inhabiting commensal microbes [ 12 ]. Thus, knowing the abundance of certain gastrointestinal bacteria can be used for the classification or prediction of the statuses of dairy cows [ 13 , 14 ]. Recently, Hu et al [ 15 ] demonstrated that gut microbiota act as protective factors in the host defense system against mastitis in mice and that the gut–mammary gland axis represents a new and promising therapeutic approach for the treatment of mastitis.…”

Preventive Effect of Depolymerized Sulfated Galactans from Eucheuma serra on Enterotoxigenic Escherichia coli-Caused Diarrhea via Modulating Intestinal Flora in Mice

“…It was reported that probiotic supplementation in children with acute infectious diarrhea caused by rotavirus infection caused the diarrhea symptoms to cease, and the maladjusted intestinal flora even returned to a normal state [ 17 ]. The observation results regarding the intestinal flora changes in newborn calves over time revealed that Ruminococcus 2 , Trueperella , Dorea , Streptococcus , and Erysipelatoclostridium could be used as key microbial markers to predict early diarrhea since the accuracy was as high as 84.3% [ 18 ]. During the treatment of antibiotic-related diarrhea in rats using herbal formula, the abundance of Sutterella was significantly suppressed, which was thought to be a pivotal phylotype in improving diarrhea [ 19 ].…”