Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants

The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.

Impact of dairy calf management practices on the intestinal tract microbiome pre-weaning

Introduction. Microbiota in the gastrointestinal tract (GIT) consisting of the rumen and hindgut (the small intestine, cecum and colon) in dairy calves play a vital role in their growth and development. This review discusses the development of dairy calf intestinal microbiomes with an emphasis on the impact that husbandry and rearing management have on microbiome development, health and growth of pre-weaned dairy calves.Discussion. The diversity and composition of the microbes that colonize the lower GIT (small and large intestine) can have a significant impact on the growth and development of the calf, through influence on nutrient metabolism, immune modulation, resistance or susceptibility to infection, production outputs and behaviour modification in adult life. The colonization of the calf intestinal microbiome dynamically changes from birth, increasing microbial richness and diversity until weaning, where further dynamic and drastic microbiome change occurs. In dairy calves, neonatal microbiome development prior to weaning is influenced by direct and indirect factors, some of which could be considered stressors, such as maternal interaction, environment, diet, husbandry and weaning practices. The specific impact of these can dictate intestinal microbial colonization, with potential lifelong consequences.Conclusion. Evidence suggests the potential detrimental effect that sudden changes and stress may have on calf health and growth due to management and husbandry practices, and the importance of establishing a stable yet diverse intestinal microbiome population at an early age is essential for calf success. The possibility of improving the health of calves through intestinal microbiome modulation and using alternative strategies including probiotic use, faecal microbiota transplantation and novel approaches of microbiome tracking should be considered to support animal health and sustainability of dairy production systems.

Transition milk or milk replacer powder as waste milk supplements to cold-stressed neonatal Holstein dairy calves: Effects on performance, feeding behavior, and health

Young calves are more susceptible to cold than older animals due to their limited ability to regulate body temperature and lack of fat reserves and may have difficulty consuming the energy needed to cope with the cold by maintaining body temperature and meeting their metabolic needs, especially when fed constant levels of waste milk (WM) with less solids, which can be detrimental to health and future performance. An alternative to overcome this problem is increasing the milk's solids content to the existing volume by using different sources [milk replacer powder (MR) or transition milk (TM)]. Thus, we aimed to evaluate the effects of increasing the total solids of WM via MR (WM+MR) or TM (WM+TM) on the performance, feeding behavior, and health-related variables of cold-stressed dairy calves during pre- and post-weaning. We hypothesized that feeding WM supplemented with MR or TM as potential liquid feed enhancers would improve milk dry matter and energy intake of the calves with a positive impact on body development and have no negative impact on feeding behavior and health. Additionally, we hypothesized that MR would not differ from TM. As a sample size calculation at 80% power using power analysis (PROC POWER) in SAS 9.4, a total of 51 Holstein-Friesian vigorous male calves [vigor score 21-27; 17 per treatment; 4-d old; body weight (BW) = 40.0 ± 0.63 kg (mean ± SD)] were selected, assigned randomly to treatments, and housed in individual pens in an outdoor barn. Irrespective of the type of treatment, all calves were fed 6 kg/d liquid feed from d 1 to d 53 of the experiment. In a step-down weaning program, calves received 0.5 kg liquid feed from d 54 to d 60. All calves were weaned on d 61 and remained in the study until d 101 as post-weaning evaluation. The calves had ad libitum access to starter feed and fresh drinking water across the experiment. Intake, growth, and behavior data were analyzed using a general linear mixed model and health data were analyzed using mixed logistic regression, mixed linear regression, and survival analysis models in SAS. We found that supplementation was responsible for a greater dry matter intake (DMI; P = 0.004), superior average BW (P = 0.037), and increased crude protein (CP; P = 0.001) and crude fat (CF; P = 0.001) intakes, with the most favorable outcomes observed for the WM+TM group when compared with WM+MR. Animals fed WM (control group; CON) showed a smaller average daily gain during the first 40-d of life (P = 0.026), showing slight changes during the whole period of evaluation when compared with the supplemented groups (SUP; WM+MR and WM+TM). No difference between MR- and TM-SUP groups, probability of having abnormal appearance (P = 0.032) and pneumonia occurrence (P = 0.022) was reduced in the SUP than in CON animals, with no effect on diarrhea among treatment groups (P = 0.461). Using milk supplements added to WM is an alternative to improve the intake, performance, and health of young calves under cold stress. Our findings showed that SUP animals outperformed the CON group in terms of DMI, average BW, and intake of CP and CF, with the TM-SUP group displaying the most favorable outcomes. Moreover, the SUP groups demonstrated reduced odds of experiencing abnormal appearance and pneumonia, highlighting the positive impact of supplementation on calf health.

Effects of waste milk feeding on rumen fermentation and bacterial community of pre-weaned and post-weaned dairy calves

The objective of this study was to investigate the effect of waste milk with antibiotic residue on rumen fermentation and rumen bacterial composition of dairy calves during pre-weaned and post-weaned periods. A total of 24 Holstein male calves (43.4 ± 0.93 kg body weight, mean ± standard error) were allocated into four blocks based on birth date. Dairy calves were supplied 100% milk replacer (MR, n = 8), 50% milk replacer mixed with 50% waste milk (MM, n = 8), or 100% waste milk (WM, n = 8). Ruminal samples were collected at 49 and 63 days of age and then subjected to determinations of pH value, volatile fatty acids (VFA), ammonia nitrogen (NH₃-N) and 16S rRNA gene amplicon sequencing. The results showed that feeding WM had no effect on the pH value, the concentrations of VFA (acetic acid, propionic acid, butyric acid, isovaleric acid, valeric acid), and NH₃-N in dairy calves compared to feeding MR. However, from 49 to 63 days of age, the pH value (p < 0.001) was significantly increased, while the levels of total VFA (p = 0.004), acetic acid (p = 0.01), propionic acid (p = 0.003) and valeric acid (p < 0.001) were significantly decreased. For rumen microorganisms, there was no differences in bacterial diversity among the treatments. But the relative abundance of Veillonellaceae was significantly lower (p = 0.05) in the calves fed WM than that from MR group at 49 days of age; however, no difference was detected at 63 days of age. Feeding WM to calves tended to reduce family Veillonellaceae and genus Olsenella in the rumen at 49 days of age (p = 0.049). Analysis of temporal changes in rumen bacteria based on alpha-diversity and beta-diversity as well as the microbial relative abundances did not exhibit any difference. In addition, relative abundances of Clostridia_UCG-014, Prevotella, Syntrophococcus, Eubacterium_nodatum_group, Pseudoramibacter and Solobacterium were correlated with rumen pH value and the concentrations of TVFA, propionic acid, isovaleric acid, valeric acid and NH₃-N. In conclusion, compare to MR, calves supplied with WM had little changes on the rumen pH value, NH₃-N or VFAs contents. Additionally, limited effects could be found on rumen microbiota in the calves fed WM. However, further studies needed to explore if there exist any long-term effects of early-life rumen microbiota modulation on dairy cows.

Effects from supplementary feeding of bamboo powder in perinatal period on farrowing process, serum biochemical indexes, and fecal microbes of sows and offspring piglets

Introduction

This study was conducted to explore the effects of supplementary feeding of bamboo powder on the physical parameters of sows during the perinatal period of 7 days ± in parturition, including farrow duration, serum biochemical indexes, fecal physicochemical indexes, and microbial flora.

Methods

Thirty pregnant sows were randomly divided into three groups: the control group was fed a basal diet, TRE1 group and TRE2 group were fed a basal diet supplemented with 30 g d^-1 and 60 g d^-1 bamboo powder, respectively. Multiple parameters of sows and offspring piglets were determined.

Results

The contents of serum total cholesterol and triglyceride of sows in TRE2 group were significantly lower than those in the control group. The contents of serum malondialdehyde of sows in TRE2 and TRE1 groups were significantly lower than that in control group. The water content of sow feces in TRE2 group was significantly higher than that in control group, and the pH values of sows in TRE2 and TRE1 groups were significantly higher than that in control group. The richness index (Chao) of sow fecal bacterial community in TRE2 group was significantly lower than that of the control group, and the Ace and Sobs indexes tended to be lower than those of the control group. At the phylum level, the relative abundance of Actinobacteriota in the feces of sows in TRE2 group was significantly lower than that of the control group, while that of Fusobacteriota in the feces of suckling piglets in TRE2 group tended to be lower than that of the control group. At the genus level, among the Top10 dominant bacteria, the relative abundance of Tissierella in the feces of sows in TRE2 group was significantly lower than that of the control group while that of Fusobacterium in the feces of suckling piglets in TRE2 group tended to be lower than that of the control group. The relative abundance of Clostridium_sensu_stricto_1, Terrisporobacter, Turicibacter, and Tissierella in the feces of sows in TRE2 group was significantly lower than that of TRE1 group (p < 0.05), while Lactobacillus tended to be higher than that of TRE1 group (p < 0.10).

Discussion

The results suggested that supplementary feeding 60 g d^-1 bamboo powder could increase the water content in the feces of sows, reduce the oxidative damage, and tend to reduce the relative abundance of opportunistic pathogenic Fusobacterium for suckling piglets, while it reduced the fecal microbial diversity of sows.

Comparative study of different liquid diets for dairy calves and the impact on performance and the bacterial community during diarrhea

The liquid diet composition can affect dairy calves' performance and diarrhea incidence. The effect of three liquid diets on performance, incidence of diarrhea, and microbial community during diarrhea occurrence in dairy calves were evaluated. At birth, 35 dairy calves (20 male and 15 female) were randomly assigned to one of three treatments-refrigerated whole milk (WM), acidified whole milk (AWM), and milk replacer (MR). Intake, fecal score, and rectal temperature were evaluated daily, and performance and blood parameters were evaluated weekly during the preweaning period. Fecal samples from diarrheic calves were collected, and one initial and one final sample for each episode were selected. The bacterial community was assessed by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Calves fed WM had higher body weight at weaning, average daily gain, body measurements, and concentration of blood metabolites. The AWM-fed calves had a lower rectal temperature and fever days. Moreover, the MR-fed calves had lower beta-hydroxybutyrate concentration and a higher incidence of diarrhea. The fecal bacterial community of diarrheic calves showed dissimilarity among the AWM and the other treatments. At the compositional level, we observed a higher abundance of Fusobacterium and Ruminococcus genera (AWM), Prevotella (WM), and Lactobacillus (MR). In the AWM and MR diarrheic calves' feces, we also observed some beneficial bacterial genera. The performance and incidence of diarrhea of dairy calves were influenced by the liquid diet consumed and the bacterial composition of diarrhea.

Detection of Salmonella spp. by Traditional and PCR Assays in Raw Milk, Maysan, Iraq

Salmonella spp are characterized as rod- shaped, motile, gram- negative bacteria which has the ability to infect animals and human. Salmonella spp occasionally causes sickness while in most cases not lead to severe symptoms. Analyzing milk for Salmonella spp. is not routine but traditional culture methods are used to evaluate the health condition of the dairy products. However, the antibody-based and nucleic-acid- based methods are practical for identifying Salmonella spp. Therefore, this research was designed to evaluate the use of traditional culture methods and PCR in detection of the presence of Salmonella spp. in raw milk samples in, Maysan Iraq. A total number of 130 raw milk samples collected from Maysan Iraq. All the samples were analyzed for the presence of Salmonella spp. using traditional culture method and polymerase chain reaction (PCR). The culture method used in this experiment were done by using pre-enrichment, enrichment, selective plating and biochemical tests. The results of this traditional technique were compared with the results obtained from PCR method. The PCR was performed using a 284bp sequence of the invA gene. The results showed that 8 (7.07%) of samples were identified as salmonella positive using traditional culture technique but 14 (12.3%) samples were detected as salmonella positive by PCR method. The results of the current research revealed that the traditional culture based methods are generally time costuming and labor intensive but the development of new rapid methods including DNA based methods such as PCR are more sensitive and have dramatically decreased the time necessary for the detection of bacteria.

An Overview of Waste Milk Feeding Effect on Growth Performance, Metabolism, Antioxidant Status and Immunity of Dairy Calves

Waste milk (WM) is a part of the milk produced on dairy farms, which is usually unsuitable for human consumption. The WM contains transition milk, mastitis milk, colostrum, milk with somatic cells, blood (Hemolactia), harmful pathogens, pathogenic and antibiotic residues. Due to the high cost of milk replacer (MR), dairy farmers prefer raw WM to feed their calves. It has been well established that WM has a greater nutritive value than MR. Hence WM can contribute to improved growth, rumen development, and immune-associated parameters when fed to dairy calves. However, feeding raw WM before weaning has continuously raised some critical concerns. The pathogenic load and antibiotic residues in raw WM may increase the risk of diseases and antibacterial resistance in calves. Thus, pasteurization has been recommended as an effective method to decrease the risk of diseases in calves by killing/inhibiting the pathogenic microorganisms in the raw WM. Altogether, the current review provides a brief overview of the interplay between the positive role of raw WM in the overall performance of dairy calves, limitations of raw WM as a feed source and how to overcome these issues arising from feeding raw WM.

Effects of Milk Feeding Strategy and Acidification on Growth Performance, Metabolic Traits, Oxidative Stress, and Health of Holstein Calves

Effects of milk feeding strategy and acidification on calf growth, metabolic traits, oxidative stress, and health were evaluated in the first 78 days of life. Holstein calves (N = 48; 12 calves/treatment) were assigned to 1 of the 4 treatments in a 2 × 2 factorial arrangement of milk feeding strategy [6 L/d (MOD) or 12 L/d (HIGH) of milk] and acidification [non-acidified milk (NAM) or acidified milk (ACM)] on day 2. Calves were bucket-fed milk as follows: 6 L/d from days 2 to 49 for MOD and 6 L/d from days 2 to 49, 12 L/d from days 7 to 42, and 8 L/d from days 43 to 49 for HIGH calves. All calves were then fed 4 L/d from days 50 to 56. Starter and water were available ad libitum, while hay was fed at 5% of starter from day 64. Calves were weighed, measured, and blood (except days 14, 42 and 56) sampled on days 2, 14, 28, 42, 49, 56, 63 and 78. Data were analyzed using Mixed PROC of SAS with time as repeated measurements. Fecal scores, checked daily, were examined by the logistic regression using a binomial distribution in GLIMMIX procedure. There were no three-way interactions observed for all the parameters. We detected a milk feeding strategy × time interaction for starter intake, body weight, ADG, ADG/ME, FE, structural measurements, and glucose. Although, overall (558.0 vs. 638.6 g/d), HIGH calves tended to consume less starter compared to MOD, significant differences were only observed in week 8. The HIGH calves had greater ADG during days 2–14 (1.12 vs. 0.75 kg/d) and tended to have greater ADG on days 15–28 (0.79 vs. 0.55) and 29–42 (0.86 vs. 0.60) and lower on days 57–63 (0.11 vs. 0.38) compared to MOD calves. The HIGH calves had greater BW from days 28 to 78 compared to MOD, while NAM were bigger compared to ACM calves from days 49 to 78. The HIGH calves had lower overall feed and metabolizable energy efficiencies compared to MOD. Except for BW and heart girth, no milk acidification × time interaction was observed for starter intake, ADG, FE, or ADG/ME. Blood glucose in calves fed NAM-HIGH and ACM-HIGH were greater compared to those fed moderate milk volumes on day 28 only. Albeit, feeding strategy had no effect, calves fed ACM had lower likelihood of experiencing diarrhea (odds ratio = 1.32; 95% confidence interval: 1.018–1.698) compared to those fed NAM. Overall milk feeding strategy had no effect on growth, while milk acidification reduced growth in calves, despite lowering the likelihood of experiencing diarrhea.

Probiotic Lactobacilli Administration Induces Changes in the Fecal Microbiota of Preweaned Dairy Calves

Early microbial colonization is a determinant factor in animal health, and probiotic administration has been demonstrated to modulate intestinal microbiota and promote health in dairy calves. The objective of this study was to evaluate changes in calves' fecal microbiota after the administration of two probiotic lactobacilli strains that had previously exhibited beneficial effects in calves' health in relation to neonatal calf diarrhea. An in vivo assay was performed with 30 newborn male Holstein calves that were divided into three groups. Two groups were orally administered with two different lactobacilli strains (Lactobacillus johnsonii TP1.6 or Limosilactobacillus reuteri TP1.3B), and the third was the control group. Calves (5 to 9 days old) were administered with freeze-dried bacteria once a day for 10 consecutive days. Feces samples were taken before the first administration (day 0) and then again on days 10 and 21, and the V4 region of the bacterial 16S ribosomal gene was sequenced with an Illumina MiSeq 250 paired-end platform. The administration of both strains significantly affected the total bacterial community composition, and the effect lasted for 11 days after the last dose. In particular, amplicon sequence variants related to Bifidobacterium and Akkermansia genera were significantly higher in both treated groups. Therefore, modulation of the intestinal microbiota is a potential mechanism of action behind the beneficial effects of these probiotic strains.

Feeding Pre-weaned Calves With Waste Milk Containing Antibiotic Residues Is Related to a Higher Incidence of Diarrhea and Alterations in the Fecal Microbiota

The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence gastrointestinal health. We assessed the longitudinal effect of unpasteurized WM containing residual cefalexin on calf intestinal health and fecal microbiota in an 8-week trial. After 3 days of colostrum, six calves received WM and six calves received bulk tank milk (BM) for 2 weeks. For the following 6 weeks, all 12 calves received milk substitute and starter feed. Every week for the first 2 weeks and every 2 weeks for the remaining 6 weeks, we subjected all calves to clinical examination and collected rectal swabs for investigating the fecal microbiota composition. Most WM calves had diarrhea episodes in the first 2 weeks of the trial (5/6 WM and 1/6 BM), and their body weight was significantly lower than that of BM calves. Based on 16S rRNA gene analysis, WM calves had a lower fecal microbiota alpha diversity than that in BM calves, with the lowest p-value at Wk4 (p < 0.02), 2 weeks after exposure to WM. The fecal microbiota beta diversity of the two calf groups was also significantly different at Wk4 (p < 0.05). Numerous significant differences were present in the fecal microbiota taxonomy of WM and BM calves in terms of relative normalized operational taxonomic unit (OTU) levels, affecting five phyla, seven classes, eight orders, 19 families, and 47 genera. At the end of the trial, when 6 weeks had passed since exposure to WM, the phyla Bacteroidetes, Firmicutes, and Saccharibacteria were lower, while Chlamydiae were higher in WM calves. Notably, WM calves showed a decrease in beneficial taxa such as Faecalibacterium, with a concomitant increase in potential pathogens such as Campylobacter, Pseudomonas, and Chlamydophila spp. In conclusion, feeding pre-weaned calves with unpasteurized WM containing antibiotics is related to a higher incidence of neonatal diarrhea and leads to significant changes in the fecal microbiota composition, further discouraging this practice in spite of its short-term economic advantages.

Microbial colonization of the gastrointestinal tract of dairy calves - a review of its importance and relationship to health and performance

This review aims to explain how microbial colonization of the gastrointestinal tract (GIT) in young dairy calves is related to health and, consequently, to the performance of these animals. The review addresses everything from the fundamental aspects of microbial colonization to the current understanding about the microbiota manipulation to improve performance in adult animals. The ruminal microbiota is the most studied, mainly due to the high interest in the fermentative aspects, the production of short-chain fatty acids, and microbial proteins, and its effects on animal production. However, in recent years, the intestinal microbiota has gained space between studies, mainly due to the relationship to the host health and how it affects performance. Understanding how the GIT's microbiota looks like and how it is colonized may allow future studies to predict the best timing for dietary interventions as a way to manipulate it and, consequently, improve the health and performance of young ruminants.

The Liquid Diet Composition Affects the Fecal Bacterial Community in Pre-weaning Dairy Calves

Feeding a liquid diet to the newborn calf has considerable implications for developing the intestinal microbiota, as its composition can shift the population to a highly adapted microbiota. The present work evaluated 15 Holstein calves individually housed and fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9% CP; 16.2% fat; diluted to 14% solids; n = 5) and III – acidified whole milk to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at week 8 of life. Calves also had free access to water and starter concentrate. After weaning, all calves were grouped on pasture, fed with starter concentrate, and hay ad libitum. The fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8, and 10 of life. The bacterial community was assessed the through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Diversity indices were not affected by the liquid diets, but by age (P &lt; 0.001) with weeks 1 and 2 presenting lower diversity, evenness, and richness values. The bacterial community structure was affected by diet, age, and the interaction of these factors (P &lt; 0.01). Twenty-eight bacterial phyla were identified in the fecal samples, and the most predominant phyla were Firmicutes (42.35%), Bacteroidota (39.37%), and Proteobacteria (9.36%). The most prevalent genera were Bacteroides (10.71%), Lactobacillus (8.11%), Alloprevotella (6.20%). Over the weeks, different genera were predominant, with some showing significant differences among treatments. The different liquid diets altered the fecal bacterial community during the pre-weaning period. However, differences in the initial colonization due to different liquid diets are alleviated after weaning, when animals share a common environment and solid diet composition.

Clostridioides difficile on dairy farms and potential risk to dairy farm workers

Clostridioides difficile causes severe colitis in people and is a significant enteric pathogen in many species of animals, including swine, horses, and potentially cattle. C. difficile is shed in feces, and transmission occurs horizontally via the fecal-oral route. Livestock has been suggested as a potential reservoir for C. difficile, and while studies have shown that swine and farm workers can be colonized with identical clones of C. difficile, the zoonotic transmission of C. difficile from livestock to people has not been definitively demonstrated. The goal of this study was to determine whether dairy calves and dairy farm workers harbored genetically similar isolates of C. difficile. First, we validated a glove juice protocol for detecting C. difficile on farm workers' hands. We then visited 23 farms and collected 1) fecal samples from 92 dairy calves, 2) hand rinsates from 38 dairy farm workers, and 3) fecal samples from five of the dairy farm workers who were willing to submit them. All samples underwent anaerobic culture and qPCR to detect C. difficile. C. difficile was detected on 15 of the farms (65.2%, 95% confidence interval (CI) 42.7%-83.6%) and in 28 calves (30.4%, 95% CI 21.2-40.9%) but in none of the hand rinsates or human fecal samples. Thus, the zoonotic transmission of C. difficile on dairy farms could not be demonstrated, and dairy farmers did not appear to be at increased risk of acquiring C. difficile via the fecal-oral route.

The Effects of Feeding Waste Milk Containing Antimicrobial Residues on Dairy Calf Health

A number of studies have reported that there is a high prevalence of antimicrobial-resistant faecal bacteria excreted by dairy calves. Although faecal shedding is influenced by a variety of factors, such as the environment and calf age, feeding milk with antimicrobial residues contributes significantly to an increased prevalence of antimicrobial-resistant (AMR) bacteria, such as extended spectrum beta-lactamase (ESBL)-producing E. coli. As a follow-up to the European Food Safety Authority (EFSA) Scientific Opinion on the risk of AMR development in dairy calves published in January 2017, this review aims to illustrate more recent research in this area, focusing on the period 2016 to 2020. A total of 19 papers are reviewed here. The vast majority assess the commensal faecal bacteria, E. coli, isolated from dairy calves, in particular its antimicrobial-resistant forms such as ESBL-producing E. coli and AmpC-producing E. coli. The effect of waste milk feeding on the prevalence of pathogens such as Salmonella spp. has also been investigated. Current research findings include positive effects on daily liveweight gain and other advantages for calf health from feeding waste milk compared to milk replacer. However, the negative effects, such as the demonstrable selection for antimicrobial-resistant bacteria, the shift in the intestinal microbiome and the possible negative consequences that these could have on global public health, should always be taken into consideration.

Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet

The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period.

The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle

Improvement of the food value of rice straw is urgently required in rice crop growing areas to mitigate pollution caused by rice straw burning and enhance the supply of high-quality forages for ruminants. The aims of the present study were to compare the effects of fresh corn Stover and rice straw co-fermented with probiotics and enzymes on rumen fermentation and establish the feasibility of increasing the rice straw content in ruminant diets and, by extension, reducing air pollution caused by burning rice straw. Twenty Simmental hybrid beef cattle were randomly allotted to two groups with ten cattle per group. They were fed diets based either on rice straw co-fermented with probiotics and enzymes or fresh corn Stover for 90 days. Rumen fluid was sampled with an esophageal tube vacuum pump device from each animal on the mornings of days 30, 60, and 90. Bacterial diversity was evaluated by sequencing the V4–V5 region of the 16S rRNA gene. Metabolomes were analyzed by gas chromatography/time-of-flight mass spectrometry (GC–TOF/MS). Compared to cattle fed fresh corn Stover, those fed rice straw co-fermented with probiotics and enzymes had higher (P < 0.05) levels of acetic acid and propionate in rumen liquid at d 60 and d 90 respectively, higher (P < 0.05) abundances of the phyla Bacteroidetes and Fibrobacteres and the genera Ruminococcus, Saccharofermentans, Pseudobutyrivibrio, Treponema, Lachnoclostridium, and Ruminobacter, and higher (P < 0.05) concentrations of metabolites involved in metabolisms of amino acid, carbohydrate, and cofactors and vitamins. Relative to fresh corn Stover, rice straw co-fermented with probiotics and enzymes resulted in higher VFA concentrations, numbers of complex carbohydrate-decomposing and H₂-utilizing bacteria, and feed energy conversion efficiency in the rumen.

Antimicrobial resistance in E. coli isolated from dairy calves and bedding material

INTRODUCTION

E. coli is a ubiquitous bacterium commonly used as a sentinel in antimicrobial resistance studies. Here, E. coli was isolated from three groups (sick calves, healthy calves and bedding material), to assess the presence of antimicrobial resistance, describe resistance profiles, and compare these resistances among groups.

MATERIAL AND METHODS

Samples were collected from calves and calving pens from 20 dairy farms. Using the disc diffusion method, E. coli isolates were screened for antimicrobial resistance against seven antimicrobials: Amoxicillin, Ceftiofur, Gentamicin, Enrofloxacin, Trimethoprim-sulfamethoxazole, Florfenicol and Oxytetracycline. Isolates resistant to all these seven antimicrobials were tested again against an extended 19 antimicrobial drug panel and for the presence of the most common E. coli pathogenicity genes through PCR.

RESULTS & DISCUSSION

Three hundred forty-nine E. coli isolates were obtained; most isolates were resistant to a single antimicrobial, but 2.3% (8) were resistant to 16 to 19 of the antimicrobials tested. The group with the highest percentage of multiresistant isolates was the calves with diarrhea group. Younger calves provided samples with higher antimicrobial resistance levels.

CONCLUSIONS

There is a high rate of antimicrobial resistance in dairy farms calving pens. These bacteria could not only be a resistance gene reservoir, but also could have the potential to spread these determinants through horizontal gene transfer to other susceptible bacteria. Measures should be taken to protect colonization of younger calves, based on hygienic measures and proper management.

Effect of acidified milk feeding on the intake, average daily gain and fecal microbiological diversity of Holstein dairy calves

OBJECTIVE

To evaluate the effect of feeding acidified milk on the growth and fecal microbial diversity of dairy calves.

METHODS

Twenty healthy 3-day-old female Holstein calves with similar body weights were selected and randomly divided into two groups. One group was fed pasteurized milk (PM, Control), while the other was fed acidified milk (AM) ad libitum until weaned (day 60). The experiment lasted until day 180.

RESULTS

There was no difference in the nutritional components between PM and AM. The numbers of Escherichia coli and total bacteria in AM were lower than in PM. At 31 to 40 and 41 to 50 days of age, the milk intake of calves fed AM was higher than that of calves fed PM (p<0.05), and the solid feed intake of calves fed AM was higher than that of calves fed PM at 61 to 90 days (p<0.05). The average daily gain of calves fed AM was also higher than that of calves fed PM at 31 to 60, 61 to 180, and 7 to 180 days (p<0.05). The calves fed AM tended to have a lower diarrhea rate than those fed PM (p = 0.059). Bacteroides had the highest abundance in the feces of calves fed AM on day 50, while Ruminococcaceae_UCG_005 had the highest abundance in the feces of calves fed AM on day 90 and calves fed PM on days 50 and 90. At the taxonomic level, the linear discriminant analysis scores of 27 microorganisms in the feces of calves fed AM and PM on days 50 and 90 were higher than 4.0.

CONCLUSION

Feeding AM increased calf average daily gain and affected fecal bacterial diversity.

Early Feeding Regime of Waste Milk, Milk, and Milk Replacer for Calves Has Different Effects on Rumen Fermentation and the Bacterial Community

Simple Summary

The postnatal period may be the most critical window for rumen manipulation, and the early feeding regime may lead to permanent changes in the rumen microbial composition. The objective of this research was to investigate the effects of the most common liquid feeds (whole milk, waste milk, and milk replacer) on growth performance, rumen development, and the ruminal bacterial community during the weaning period, and to then follow calves to up to six months of age to determine the persistence of any ruminal imprinting effects. The results demonstrate that the early feeding regime impacts rumen development not only by dry matter intake, but also the type of liquid feed. Calves fed waste milk had a distinctly structured bacterial community at two months of age, but this difference diminished at six months of age. Calves fed milk replacer had a different rumen fermentation pattern at two months of age, which may induce a long-lasting effect on the rumen environment.

Abstract

We investigated the effects of different types of early feeding on rumen fermentation parameters and the bacterial community in calves. Fifty-four Holstein calves were assigned to three treatments and fed whole milk (M), pasteurized waste milk (WM), or milk replacer (MR). Male calves were slaughtered at the age of two months to measure the stomach masses. The female calves were followed for six months to determine the body weight, blood indices, rumen fermentation, and ruminal bacterial community. At the age of two months, the average daily gain was lower, but the concentration of total volatile fatty acids was greater in the MR group. Starter intake and stomach mass were lower, but the isovalerate molar proportion was greater in the WM group. The blood indices and ruminal bacterial community of the WM group differed from those of the other groups. At the age of six months, the ruminal propionate molar proportion was lower, but the ruminal pH and acetate/propionate ratio were greater in the MR group. In conclusion, calves fed WM had different rumen fermentation and bacterial community during the weaning period, whereas feeding MR produced a long-lasting effect on the rumen environment.

Feeding Pasteurized Waste Milk to Preweaned Dairy Calves Changes Fecal and Upper Respiratory Tract Microbiota

In the present study bacterial communities from both, the gastrointestinal and respiratory tract of pre-weaned dairy calves fed two different milk-feeding programs were characterized using 16S rRNA gene sequencing. Twenty female Holstein calves (38.8 ± 1.40 kg of BW) were fed pasteurized waste milk (pWM) containing residues of various antimicrobials. Twenty additional calves (38.1 ± 1.19 kg of BW) were fed milk replacer (MR) with similar nutrient composition (27.5% crude protein, 32.1% fat) compared to waste milk (28.6% crude protein, 30.0% fat) from day 1 to weaning at day 49 of study. Fecal samples and nasal swabs were collected on day 42 only from calves that were not treated with therapeutic antibiotics throughout the study, which were 8 MR and 10 pWM calves. To assess the impact of the two feeding regimes on the fecal and nasal microbiota, α and β-diversity measures were calculated, and the relative abundance of operational taxonomic units (OTUs) at different taxonomic levels was determined for each sample. In general, Chao1, PD Whole Tree, and Shannon diversity indices were similar for the fecal and nasal bacterial communities of calves regardless of the feeding regime. However, principal coordinate analysis based on unweighted Unifrac distances indicated differences in the structure of bacterial communities of calves fed milk replacer compared with those from calves fed pasteurized waste milk. The relative abundance of the Streptococcaceae family and the genus Histophilus was greater (P < 0.05) in the nasal microbiota of calves fed milk replacer than in those fed pasteurized waste milk. However, the genus Prevotella tended (P = 0.06) to be more relatively abundant in the respiratory tract of calves fed pasteurized waste milk than in those fed milk replacer. Differences in relative abundances of bacterial taxa in gut microbiota were only observed at the phylum level, suggesting that antimicrobial residues present in waste milk have a non-specific influence at a lower taxonomical level.

Effects of dietary leucine and phenylalanine on gastrointestinal development and small intestinal enzyme activities in milk-fed holstein dairy calves

This study was investigated the effects of dietary supplementation of leucine and phenylalanine on the development of the gastrointestinal tract and the intestinal digestive enzyme activity in male Holstein dairy calves. Twenty calves with a body weight of 38 ± 3 kg at 1 day of age were randomly divided into four groups: a control group, a leucine group (1.435 g·l⁻¹), a phenylalanine group (0.725 g·l⁻¹), and a mixed amino acid group (1.435 g·l⁻¹ leucine plus 0.725 g·l⁻¹ phenylalanine). The supplementation of leucine decreased the short-circuit current (Isc) of the rumen and duodenum (P<0.01); phenylalanine did not show any influence on the Isc of rumen and duodenum (P>0.05), and also counteracted the Isc reduction caused by leucine. Leucine increased the trypsin activity at the 20% relative site of the small intestine (P<0.05). There was no difference in the activity of α-amylase and of lactase in the small intestinal chyme among four treatments (P>0.05). The trypsin activity in the anterior segment of the small intestine was higher than other segments, whereas the α-amylase activity in the posterior segment of the small intestine was higher than other segments. Leucine can reduce Isc of the rumen and duodenum, improve the development of the gastrointestinal tract, and enhance trypsin activity; phenylalanine could inhibit the effect of leucine in promoting intestinal development.

Low Concentration of Antibiotics Modulates Gut Microbiota at Different Levels in Pre-Weaning Dairy Calves

The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), milk replacer plus low cocktail of antibiotics (LCA) concentration (penicillin 0.024 mg/L, streptomycin 0.025 mg/L, tetracycline 0.1 mg/L, ceftiofur 0.33 mg/L), and milk replacer plus a low concentration of single antibiotic (LSA; ceftiofur 0.33 mg/L). All the calves were harvested at 35-day-old, and the digesta from the ileum and colon was collected in addition to fecal samples. Samples were analyzed by 16S rRNA gene using Illumina MiSeq platform. Results showed that there were significant differences among treatments in the ileum, where LCA significantly reduced the relative abundance of Enterobacteriaceae (P = 0.02) especially Escherichia-coli (P = 0.02), while LSA significantly reduced the relative abundance of Comamonas (P = 0.02). In the colon and rectum, LSA treatment was significantly enriched with the class Bacilli, whereas the control group was significantly enriched with Alloprevotlla (P = 0.03). However, at the family level in the rectum LCA and LSA significantly reduced the relative abundance of Acidaminococcaceae (P = 0.01). Moreover, at the genera level in the colon, LSA significantly increased Prevotellaceae_Ga6A1_ group (P = 0.02), whereas in the rectum both of treatments reduced the relative abundance of Phascolarctobacterium (P = 0.01). In conclusion, the overall low cocktail of antibiotics concentration induced changes at different taxonomic levels; specifically the decrease in Escherichia-coli which might subsequently reduce the incidences of diarrhea in calves.

Dietary Corn Bran Altered the Diversity of Microbial Communities and Cytokine Production in Weaned Pigs

Corn bran (CB) has been used as an ingredient for pigs, but the underlying mechanisms that improve gut health is less clear. This study was conducted to investigate effects of dietary CB on growth performance, nutrient digestibility, plasma indices related to gut hormones and immunity, gut microbiota composition, and fermentation products in weaned pigs. A total of 60 weaned pigs were allocated to two dietary treatments, and piglets in each group received control (CON) diet or 5% CB diet for 28 days. Growth performance, nutrient digestibility, indices of gut hormones and immunity in plasma were evaluated. Microbiota composition in feces was determined using 16S rRNA amplicon sequencing, and fermentation products were measured by high-performance ion chromatography. The results showed that dietary CB did not affect growth performance, nutrient digestibility, gut hormones, or fermentation products in the trial (P > 0.05). There was an increased response to CB inclusion on interleukin-10 production (P < 0.05). On day 28, piglets fed dietary CB had a higher shannon index (P < 0.05). The population of the Firmicutes in CB treatment were decreased (P < 0.05), while the percentage of the Bacteroidetes were increased (P < 0.05). In particular, the populations of Eubacterium corprostanoligenes, Pevotella, and Fibrobacter related to polysaccharide fermentation of cereal bran were increased (P < 0.05). In conclusion, a post-weaning diet containing 5% CB increased intestinal microbial diversity, especially higher richness of fibrolytic bacteria, and promoted anti-inflammatory response to some extent in piglets, these changes should facilitate the adaptation of the digestive system of piglets in the subsequent growing phases.

Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers

Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.

Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs

Solid-state fermentation of feedstuffs by Bacillus subtilis MA139 can reduce insoluble dietary fiber content in vitro and improve growth performance in pigs. This study was conducted to investigate the effects of dietary corn bran (CB) fermented by B. subtilis on growth performance and gut microbiota composition in finishing pigs. A total of 60 finishing pigs were allocated to 3 dietary treatments consisting of a control (CON) diet, a 10% CB diet, and a 10% fermented CB (FCB) diet in a 21 d feeding trial. Growth performance and nutrient digestibility were evaluated. Fecal samples were determined for bacterial community diversity by 16S rRNA gene amplicon sequencing. The dietary CB and FCB did not affect growth performance of finishing pigs. The digestibility of organic matter was decreased in both CB and FCB treatments compared with CON group (P < 0.05). The α-diversity for bacterial community analysis of Chao 1 in FCB treatment was lower than CON treatment (P < 0.05). The Fibrobacteres phylum belongs to cellulolytic bacteria was isolated, and their relative abundance in CB group showed no difference between CON and FCB treatments. The abundance of Lachnospiraceae_NK4A136_group in CB treatment was higher than CON and FCB groups (P < 0.05), whereas the population of norank_f_Prevotellaceae was higher in FCB group compared to CON and CB groups (P < 0.05). In conclusion, dietary FCB decreased the abundance of bacterial communities, particularly the population of bacteria related to cellulolytic degradation.