Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves

Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies

This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.

Antimicrobial use and its association with the isolation of and antimicrobial resistance in Campylobacter spp. recovered from fecal samples from Canadian dairy herds: A cross-sectional study

Campylobacteriosis is one of the most common zoonotic diseases in North America. As opposed to humans, animal infections caused by Campylobacter spp. are often asymptomatic. In this study, data collected through the Canadian Dairy Network for Antimicrobial Stewardship surveillance system were used to determine the proportion of Campylobacter spp. and antimicrobial resistant isolates recovered from dairy cattle herds. Additionally, the association of antimicrobial use (AMU) with fecal carriage and antimicrobial resistance (AMR) of Campylobacter spp. were investigated. Pooled fecal samples from 5 animals from each production phase (pre-weaned calves, post-weaned heifers, lactating cows), and a manure storage sample were collected from 140 dairy herds across Canada. Samples were cultured using selective media, and Campylobacter isolates were speciated using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibilities were determined using the minimum inhibitory concentration test, and interpretation was made according to the Clinical and Laboratory Standards Institute. Two multilevel logistic regression models were used to investigate the association between the AMU with the isolation and antimicrobial resistance in Campylobacter spp. Of 560 samples, 63.8% were positive for Campylobacter spp., and 96% of the participating farms had at least one sample source (i.e., calves, heifers, lactating cows, or manure storage) positive for Campylobacter spp. Overall, 54.3% of the Campylobacter spp. isolates were resistant to at least one antimicrobial. Resistance to tetracycline was observed in 49.7% of the Campylobacter spp. isolates, followed by ciprofloxacin (19.9%) and nalidixic acid (19.3%). The proportion of multi-drug resistant (≥3 antimicrobial classes) Campylobacter spp. isolates was low (0.3%); however, 15.6% were resistant to two different classes of antimicrobials. Samples collected from lactating cows, heifers, and manure storage were more likely to be positive for Campylobacter spp. compared to calves. Total AMU was associated with a decreased probability of recovering Campylobacter spp. In addition, AMR to either tetracycline or ciprofloxacin had an interaction with antimicrobial use. The probability of resistance to tetracycline increased for each unit increase in the total AMU (Defined Course Dose/100 animal-years), while the probability of resistance to ciprofloxacin decreased. Campylobacter coli isolates were more likely to be resistant to ciprofloxacin and tetracycline when compared to C. jejuni. Our study demonstrated that Campylobacter spp. is widespread among Canadian dairy farms, and a higher proportion of resistance to tetracycline was identified. The total AMU was associated with increased resistance to tetracycline in Campylobacter spp. isolates; however, for ciprofloxacin the AMU was associated with decreased resistance.

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.

An Evaluation of Nutritional and Therapeutic Factors Affecting Pre-Weaned Calf Health and Welfare, and Direct-Fed Microbials as a Potential Alternative for Promoting Performance—A Review

The priority for calf rearing has been to maintain good health and welfare in order to promote and sustain future production. However, there have been numerous reports of undesirable levels of morbidity and mortality amongst pre-weaned calves. This may be mitigated or exacerbated by nutritional management practices. Some areas of concern include colostrum feeding, utilization of waste milk, and restrictive milk feeding regimes. Antibiotics may be prescribed at lethal or sub-inhibitory doses to treat or prevent disease. However, extensive antibiotic use may disrupt the gastrointestinal microbiota and aid in expanding the antibiotic resistant gene pool. In an attempt to reduce the use of antibiotics, there is a demand to find alternative performance enhancers. Direct-fed microbials, also known as probiotics, may comply with this role. A DFM consists of live microorganisms that are biologically active and able to confer health benefits onto the host. Lactic acid bacteria have been the most frequently investigated; however, this field of research has expanded to include spore-forming bacteria and live yeast preparations. This review aims to provide a comprehensive evaluation of the nutritional management strategies that may increase a calf’s susceptibility to morbidity and mortality, the efficacy and sustainability of antibiotics as a tool for managing calf health and welfare, and the potential for DFMs as a supportive strategy for promoting calf wellbeing.

Antibiotics in Dairy Production: Where Is the Problem?

Antibiotics have long been used for the prevention and treatment of common diseases and for prophylactic purposes in dairy animals. However, in recent decades it has become a matter of concern due to the widespread belief that there has been an abuse or misuse of these drugs in animals and that this misuse has led to the presence of residues in derived foods, such as milk and dairy products. Therefore, this review aims to compile the scientific literature published to date on the presence of antibiotic residues in these products worldwide. The focus is on the reasons that lead to their presence in food, on the potential problems caused by residues in the characteristics of dairy products and in their manufacturing process, on the development and spread of antibiotic-resistant bacteria, and on the effects that both residues and resistant bacteria can cause on human and environmental health.

Wellness Management in Beef Feeder Cattle: Changing Mental Models to Support Beneficial Emergent System Behaviors

Despite evidence-based "improvements" in animal health products and management, losses to bovine respiratory disease have increased with associated animal wastage, welfare concerns, and antimicrobial use; questioning the fitness of current disease-centric paradigms for improving critical outcomes in complex adaptive systems. Systems thinking is used to model a paradigm shift from mental models based on management of failure outcomes in a flawed pass/fail dichotomy to one of managing success outcomes on a continuum. In the proposed wellness paradigm, the notion of health as absence of disease is rejected and replaced with perspective of disease as symptomatic of systems insufficiently supporting wellness.

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.

Outbreak of Multidrug-Resistant Salmonella Heidelberg Infections Linked to Dairy Calf Exposure, United States, 2015-2018

In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease.

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.

Prevalence and Risk Factors for ESBL/AmpC-E. coli in Pre-Weaned Dairy Calves on Dairy Farms in Germany

The objectives of this study were to ascertain the fecal ESBL/AmpC-E. coli prevalence and to detect risk factors for their occurrence in young pre-weaned calves and their dams on large dairy farms in Germany. From 2018-2019 we investigated 2816 individual fecal samples from pre-weaned dairy calves and their dams, representing seventy-two farms (mean = 667 milking cows) from eight German federal states. To assess possible risk factors associated with ESBL/AmpC-E. coli prevalence in calves and dams, a questionnaire was performed, collecting management data. We observed an ESBL/AmpC-E. coli prevalence of 63.5% (95% CI: 57.4-69.5) among the sampled calves and 18.0% (95% CI: 12.5-23.5) among the dams. On all farms, at least one positive sample was obtained. To date, this is the highest ESBL/AmpC-E. coli prevalence observed in dairy herds in Europe. Feeding with waste milk was identified as a significant risk factor for a high prevalence of ESBL/AmpC-E. coli in calves. Many calves at large dairies in Germany are fed with waste milk due to the large amounts generated as a result of antibiotic dry-off routines and mastitis treatment with antibiotics. Other notable risk factors for high ESBL/AmpC-E. coli in calves were the general fitness/health of dams and calves, and the quality of farm hygiene. Taken together, these findings suggest that new or improved approaches to animal health management, for example, antibiotic dry cow management (selective dry cow therapy) and mastitis treatment (high self-recovery), as well as farm hygiene, should be researched and implemented.

Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

A Narrative Review on the Unexplored Potential of Colostrum as a Preventative Treatment and Therapy for Diarrhea in Neonatal Dairy Calves

Diarrhea is the leading cause of morbidity and mortality in pre-weaned dairy calves and, as such, represents a significant animal health and welfare concern. Furthermore, digestive disease early in life is associated with several long-term consequences such as reduced growth rate and decreased milk yield during the first lactation, thus generating severe economic losses. The majority of diarrheic cases in young calves are treated with antimicrobials; however, it is necessary to develop alternative treatments, as excessive antimicrobial usage can lead to antimicrobial resistance and can negatively impact the gut microflora of a calf. Bovine colostrum is abundant in immune and bioactive factors that improve immune function and development. This rich and natural combination of immunoglobulins, natural antimicrobial factors, growth factors, anti-inflammatories and nutrients may be an attractive alternative to antimicrobials in the treatment of diarrhea in young dairy calves. There is evidence that supports the use of colostrum as an early treatment for diarrhea in young calves. Future research should investigate its therapeutic and economic effectiveness.

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.

Differences in the fecal microbiota of dairy calves reared with differing sources of milk and levels of maternal contact

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We compared fecal microbiota in dam-reared and conventionally reared dairy calves, which were fed whole milk and waste milk, respectively.

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Dairy calves reared with dam contact had higher relative abundance of Lactobacillus.

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Conventionally reared calves had higher concentrations of taxa such as Bacteroides.

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Dam-reared calves were predicted to have higher levels of l-tryptophan biosynthesis.

The practice of rearing cows and calves together is gaining popularity on dairy farms, with different systems currently under assessment in mainland Europe, the United Kingdom, and Oceania. Research into the effects of cow–calf rearing has primarily focused on direct health and welfare implications, and little work has examined the role of different rearing paradigms on calf microbiota. We trialed a cow–calf rearing system on a Canadian dairy farm and compared fecal microbiota of these calves with the microbiota of calves reared according to the conventional practice of the same farm (separated from the dam and fed waste milk). At 4 wk, the conventionally reared calves had reduced relative abundance of Lactobacillus and higher relative abundance of other taxa, including Sutterella, Prevotella, and Bacteroides. We also detected predicted functional differences, such as reduced l-tryptophan biosynthesis in conventionally reared calves. These results suggest that maternal contact may influence the calf microbiota, but the observed differences are also likely related to other aspects of the rearing environment independent of maternal contact (e.g., potential exposure to antibiotic residues in waste milk). These findings provide preliminary evidence of the effects of early rearing environments on the establishment of the dairy calf fecal microbiota. This research is needed, given the critical role of the bovine gut microbiome in behavioral, metabolic, and immune development.

A multidisciplinary approach to reduce and refine antimicrobial drugs use for diarrhoea in dairy calves

This study evaluated the impact of a multidisciplinary intervention to reduce and refine antimicrobial drug use for treatment of diarrhoea in dairy calves. The intervention consisted of modification of management practices for disease prevention, health evaluation training of farm staff, implementation of an algorithm directed at antimicrobial therapy for diarrhoeic calves, and monthly farm visits. A combination of retrospective (before intervention period [BP], 1 year) and prospective (immediately after intervention period [AP], 1 year) cohorts were used. Health outcomes measured included incidence of diarrhoea and overall mortality. Antimicrobial treatment rates for diarrhoea and total mass of antimicrobial drugs used at the calf and farm level were also evaluated. Outcomes were assessed using the χ² or Fisher's exact test, and odds ratios and 95% confidence intervals (95% CI) were calculated. Records of 2049 and 2251 calves from 10 farms were available in the BP and AP, respectively. Reduced antimicrobial treatment rates occurred on seven farms (P < 0.01), but not on three farms in the AP. A total of 85% (1303/1573) and 18% (310/1698) of diarrhoeic calves were treated with antimicrobial drugs in the BP and AP (P < 0.001), respectively. There were no differences in the incidence of diarrhoea or mortality between periods. In the AP, the use sulfamethazine and trimethoprim decreased on eight farms, one farm discontinued use of lincomycin and spectinomycin, while two farms discontinued use and one reduced use of cephalosporins. This multidisciplinary approach was effective in reducing antimicrobial drug use for calf diarrhoea on dairy farms without negative impacts on calf health.

Calf health from birth to weaning - an update

Research on calf health and welfare has intensified in the past decades. This is an update on a review series on calf health from birth to weaning published ten years ago.

Good colostrum management is still recognised as the single most important factor to preventing calf morbidity and mortality, however, it is now known that immunoglobulins are only one of many components of colostrum that are vital for the calf’s development. Other non-nutrient factors like leucocytes, hormones and growth factors, oligosaccharides as well as microRNAs have significant effects on the development and maturation of the intestinal and systemic immune functions. They also promote the maturation and function of the intestine, thus enabling the calf to digest and absorb the nutrients provided with colostrum and milk. The improved energetic status of colostrum-fed neonates is reflected by an accelerated maturation of the somatotropic axis, which stimulates body growth and organ development. Colostrum oligosaccharides are presumed to play a major role in the development of a healthy intestinal flora.

A biologically normal (intensive) milk-feeding programme is subsequently necessary for optimal body growth, organ development and resistance to infectious diseases. Ad-libitum or close to ad-libitum feeding in the first three to four weeks of life also leaves calves less hungry thus improving calf welfare. Only calves fed intensively with colostrum and milk are able to reach their full potential for performance throughout their life.

Public interest in farm animal welfare is growing in past decades, which makes it necessary to have a closer look at contentious management practices in the dairy industry like early separation of the dairy calf from the dam with subsequent individual housing. Public objection to these practices cannot be mitigated through educational efforts. Contrary to common opinion there is no evidence that early cow-calf separation is beneficial for the health of calf or cow. There is evidence of behavioural and developmental harm associated with individual housing in dairy calves, social housing improves feed intake and weight gains, and health risks associated with grouping can be mitigated with appropriate management.

In conclusion, there are still many management practices commonly applied, especially in the dairy industry, which are detrimental to health and welfare of calves.

Dynamic progression of the calf's microbiome and its influence on host health

The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.

Temporal dynamics of the fecal microbiota in veal calves in a 6-month field trial

BACKGROUND

Little is known about maturation of calves' gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance.

RESULTS

There was high heterogeneity between calves' microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (- 0.17 CI95%[-0.27; - -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (- 0.37 log10 (E. coli/g) CI95%[- 0.66; - 0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (rs ≥ 0.40; Bonferroni corrected p < 0.05).

CONCLUSIONS

This observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of microbial diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.

Population physiologically based modeling of pirlimycin milk concentrations in dairy cows

Predictions of drug residues in milk are critical in food protection and are a major consideration in the economics of treatment of mastitis in dairy cows. Nonlinear mixed-effects modeling (NLME) has been advocated as a suitable pharmaco-statistical method for the study of drug residues in milk. Recent developments in physiologically based pharmacokinetic (PBPK) modeling of intramammary drugs allow the combination of a mechanistic description of milk pharmacokinetics with NLME methods. The PBPK model was applied to NLME analysis of a data set consisting of milk drug concentrations from 78 healthy cows and 117 with clinical mastitis. Pirlimycin milk pharmacokinetics were adequately described by the model across the range of observed concentrations. Mastitis was characterized by increased variance in milk production volume. Udder residual volume was larger in cows with 1, or 2 or greater diseased mammary glands than in the healthy cows. Low-producing cows had a greater risk of prolonged milk residues. With the exclusion of the low-production cows, the model predicted that healthy cows required a milk discard time 12 h longer than that indicated by the label, and the diseased cows 36 h longer than indicated by the label. More pirlimycin was systemically absorbed in the gram-positive infected compared with the gram-negative infected or healthy cows, suggesting a greater risk of violative meat residues in gram-positive infected cows. Using NLME and PBPK models, we identified factors associated with changes in pirlimycin milk residues that may affect food safety. This model extends the verification of a simple physiologically based framework for the study of intramammary drugs.

Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds

Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10⁰ ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10^-1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves

The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative abundance of "Resistance to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and "Erythromycin resistance", of relevance given the study groups, were not statistically different in relative abundance between study groups. "Resistance to fluoroquinolones" increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.

Evaluation of four commercial tests for detecting ceftiofur in waste milk bulk tank samples

The objective of this study was to identify factors affecting the accuracy of four commercial tests for ceftiofur drug residue in milk samples from bulk tank waste milk (WM). WM samples were collected from 12 California dairy farms which were initially tested using liquid chromatography (LC-MS/MS) to confirm their negative status for drug residues above the FDA established tolerance/safe levels. The milk samples were also tested for fat, protein, lactose, solids non-fat (SNF), somatic cell count (SCC), coliform count, and standard plate count (SPC). Each WM sample was divided into two aliquots, one labeled as negative for drug residues (WMN) and the second spiked with ceftiofur as positive for ceftiofur residues (WMPos). Both types of WM samples were tested to evaluate the performance of 4 commercially available tests: Penzyme® Milk Test, SNAP® β-lactam, BetaStar® Plus and Delvo SP-NT®. Three assays in triplicates for the WMN and WMPos were conducted for each WM sample. Test were evaluated using sensitivity, specificity, positive predictive value, negative predictive value and positive likelihood ratio. Kruskal-Wallis method was used to evaluate the effect of milk quality parameters on true positive (TP) and false negative (FN) test results. All WMPos samples were identified as positive by all four tests, rendering 100% sensitivity for each test. The specificity for Penzyme, BetaStar, Delvo, and SNAP tests were 59.2, 55.5, 44.4, and 29.6, respectively. Overall, all tests correctly identified samples with ceftiofur residues (WMPos), as shown by 100% sensitivity. Greater variability was observed regarding identification of samples free of any drug residue, with Penzyme and BetaStar having the highest risk for correctly identifying TN samples. Our findings indicate that when selecting commercial tests to detect drug residues in WM, milk quality parameters must be considered if the aim is to reduce FP test results.

Antibiogram, virulotyping and genetic diversity of Escherichia coli and Salmonella serovars isolated from diarrheic calves and calf handlers

Antimicrobial resistance profile of E. coli and Salmonella serovars isolated from diarrheic calves and handlers in Egypt is unknown due to the absence of monitoring. Therefore, this study aimed to determine the virulence, genetic and antimicrobial resistance profiles of E. coli and Salmonella serovars associated with diarrhea in calves and handlers in intensive dairy farms in Egypt. A total of 36 bacterial strains (20 E. coli and 16 Salmonella) were isolated from fecal samples of 80 diarrheic Holstein dairy calves (10 E. coli and 13 Salmonella) and hand swabs of 35 handlers (10 E. coli and 3 Salmonella) in two intensive dairy farms in Sharkia Governate in Egypt. E. coli strains belonged to six different serogroups and O114:K90 was the most prevalent serogroup (30%). However, Salmonella strains were serotyped into four different serogroups and S. Kiel was the most prevalent serotype (50%). Thirteen (65%) E. coli isolates were harbouring either stx2, eaeA and/or astA virulence-associated genes. However, stn and spvC virulence genes were detected in 2 (12.5%) and 4 (25%) of Salmonella isolates, respectively. E. coli isolates showed marked resistance to ampicillin (75%), while Salmonella strains exhibited high resistance to amikacin (100%), gentamicin (93.75%) and tobramycin (87.5%). Results of the present study showed that E. coli and Salmonella serovars isolated from diarrheic calves and handlers in intensive dairy farms in Egypt exhibited resistance to multiple classes of antimicrobials, which may pose a public health hazard. Thus, the continuous monitoring of antimicrobial resistance is necessary for both humans and veterinary medicine to decrease the economic losses caused by antimicrobial-resistant strains in animals as well as the zoonotic risk.

Invited Review: Nutritional regulation of gut function in dairy calves: From colostrum to weaning

Purpose

Published literature regarding calf nutrition was reviewed to create an information base for the implementation of proper nutritional management to maximize health and productivity.

Sources

The main source of data and information for this review was peer-reviewed literature.

Synthesis

Feeding a sufficient volume of colostrum during the first hours of life is crucial to calf health and survival; however, less is known about transition milk feeding and the potential benefits of the myriad of bioactive compounds it contains. After feeding colostrum and transition milk, calves are susceptible to diarrhea when moved onto high amounts of milk, and antibiotic use is often necessary to decrease disease. Feeding an elevated plane of milk nutrition results in increased ADG and, in some studies, increased future milk production. Thus, this nutritional strategy is recommended; however, weaning calves from high volumes of milk represents massive changes in the structure and microbiology of the gastrointestinal tract.

Conclusions and Applications

Colostrum and transition milk contain an abundance of bioactive molecules that can positively affect gut development and microbiota. There is significant potential for the use of novel feeding strategies and microbial-based products as alternatives to antibiotics. Calves fed an elevated plane of nutrition in the first month of life have greater productivity and growth. However, weaning should take place later in life. Moreover, applying a proper step-down feeding protocol is recommended, as it allows calves to intake and digest sufficient solid feed for growth and minimize distress at weaning.

A Novel Animal Model for Regional Microbial Dysbiosis of the Pioneer Microbial Community

Pioneer microbiota colonizing the newborn gastrointestinal tract has long-lasting effects on host health. Restoration of the gut microbial community, following dysbiosis during the neonatal period, may be one strategy to prevent undesirable health outcomes linked to an altered neonatal gut microbiome. Without appropriate animal models that recreate the prolonged human neonatal developmental period it is not possible to effectively analyze interventions designed to restore regional microbial populations. Our study used a lamb model in which intestinal segments were surgically isolated (blind-ended) in fetal lambs to create early microbial dysbiosis by delaying post-natal exposure to intestinal ingesta. Intestinal segments isolated in utero retained blood flow, innervation, and lymphatic drainage through the mesenteric attachment. Continuity of the fetal gastro-intestinal tract was re-established by side-to-side anastomosis of intestine proximal and distal to each isolated intestinal segment. Microbial restoration was then implemented in neonatal lambs by reconnecting a portion of the in utero isolated intestinal segments to adjacent intestinal tract 1 and 7 days after birth. Bacterial communities colonizing the adjacent intestine, in utero isolated intestinal segments, and reconnected intestinal segments were profiled using 16S amplicon sequencing on days 1, 7, and 56 of age. The in utero isolated intestinal segments were colonized 1 day after birth but the density of active bacteria was reduced and community composition altered when compared to adjacent intestine. Proteobacteria dominated the adjacent small intestine at early time points (day 1 and day 7) with a shift to primarily Firmicutes on day 56, consistent with establishment of an anaerobic bacterial community. In contrast, Proteobacteria persisted as the predominant community for 56 days in the in utero isolated intestinal segments. There was, however, almost full restoration of the microbial community composition in the in utero isolated intestinal segments following reconnection to the adjacent intestine. The density of beneficial bacteria, especially Bifidobacterium, remained significantly lower in the reconnected intestinal segments at 56 days when compared to adjacent intestine. Post-natal persistence of a stable pioneer community (Proteobacteria) in the in utero isolated intestinal segments provides a model system to study the temporal effects of regional microbial dysbiosis throughout a prolonged neonatal period.

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 antibiotic residues in milk on growth, ruminal fermentation, and microbial community of preweaning dairy calves

The aim of this study was to evaluate the effects of antibiotic residues in milk on growth, ruminal fermentation, and microbial community of dairy calves in their first 35 d of age. Twenty newborn Holstein bull calves were assigned to 1 of 2 treatments equally: milk replacer without antibiotics (control) and milk replacer plus 4 antibiotics: 0.024 mg/L of penicillin, 0.025 mg/L of streptomycin, 0.1 mg/L of tetracycline, and 0.33 mg/L of ceftiofur (ANT). Starter intake and fecal consistency scores of each calf were recorded on a daily basis. Body weight, withers height, body length, and heart girth were measured on d 1, 7, 14, 21, 28, and 35 before feeding in the morning. Rumen fluid was collected on d 15, 25, and 35 to determine ruminal pH, volatile fatty acids (VFA), and NH₃-N concentrations. A total of 10 (5 per treatment) samples of rumen fluid taken on d 35 were analyzed for microbial community. Rumen tissues from the cranial ventral sac and cranial dorsal sac were collected from 8 calves of each group for morphology analysis on d 35 after being harvested. The results showed that calves in 2 treatments had similar starter intake, body weight, withers height, body length, heart girth, and average daily gain. The ANT group showed a lower diarrhea frequency in wk 4, and no differences were found for other weeks. Calves in the ANT group exhibited a greater concentration of acetic acid in the rumen and no differences for other VFA, total VFA, rumen pH, or NH₃-N. As for rumen morphology, the length of papillae from cranial ventral sac of the ANT group was longer than that of the control group. The results of ruminal microbial community showed that antibiotic residues had minor effects on bacteria phyla and bacteria diversity. At the genus level, calves in the ANT group showed lower richness of Prevotella and higher richness of Acetitomaculum. In conclusion, antibiotic residues stimulated the development of ruminal papillae and increased the production of acetic acid in rumen, which might be caused by the influence of antibiotics on the ruminal microbial community.

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome

BACKGROUND

Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the long term effects of sub-inhibitory levels of antibiotics on the gut microbiota composition and resistome of veal calves in vivo. Forty-two veal calves were randomly assigned to three groups. The first group (OTC-high) received therapeutic oral dosages of 1 g oxytetracycline (OTC), twice per day, during 5 days. The second group (OTC-low) received an oral dose of OTC of 100-200 μg per day during 7 weeks, mimicking animal exposure to environmental contamination. The third group (CTR) did not receive OTC, serving as unexposed control. Antibiotic residue levels were determined over time. The temporal effects on the gut microbiota and antibiotic resistance gene abundance was analysed by metagenomic sequencing.

RESULTS

In the therapeutic group, OTC levels exceeded MIC values. The low group remained at sub-inhibitory levels. The control group did not reach any significant OTC levels. 16S rRNA gene-based analysis revealed significant changes in the calf gut microbiota. Time-related changes accounted for most of the variation in the sequence data. Therapeutic application of OTC had transient effect, significantly impacting gut microbiota composition between day 0 and day 2. By metagenomic sequence analysis we identified six antibiotic resistance genes representing three gene classes (tetM, floR and mel) that differed in relative abundance between any of the intervention groups and the control. qPCR was used to validate observations made by metagenomic sequencing, revealing a peak of tetM abundance at day 28-35 in the OTC-high group. No increase in resistance genes abundance was seen in the OTC-low group.

CONCLUSIONS

Under the conditions tested, sub-therapeutic administration of OTC did not result in increased tetM resistance levels as observed in the therapeutic group.

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.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

Multidrug residues and antimicrobial resistance patterns in waste milk from dairy farms in Central California

Waste milk (WM) is a common source of feed for preweaned calves in US dairy farms. However, limited information is available about characteristics of this product, including concentration of drug residues and potential hazards from antibiotic-resistant bacteria present in the milk. The aims of this cross-sectional study were to (1) identify and measure the concentration of antimicrobial residues in raw WM samples on dairy farms in the Central Valley of California, (2) survey farm management practices for factors associated with the occurrence of specific antimicrobial residues in raw WM, (3) characterize the antimicrobial resistance patterns of E. coli cultured from raw WM samples, and (4) evaluate the potential association between WM quality parameter and risk of identifying drug residues in milk. A single raw bulk tank WM sample was collected from dairy farms located in California's Central Valley (n = 25). A questionnaire was used to collect information about farm management practices. Waste milk samples were analyzed for a multidrug residue panel using liquid chromatography-tandem mass spectrometry. Bacteria were cultured and antimicrobial resistance was tested using standard techniques; milk quality parameters (fat, protein, lactose, solids-not-fat, somatic cell count, coliform count, and standard plate count) were also measured. Of the 25 samples collected, 15 (60%) contained detectable concentrations of at least 1 antimicrobial. Of the drug residue-positive samples, 44% (11/25) and 16% (4/25) had detectable concentrations of β-lactams and tetracycline, respectively. The most prevalent drug residues were ceftiofur (n = 7, 28%), oxytetracycline (n = 4, 16%), and cephapirin (n = 3, 12%). No significant associations were identified between farm characteristics or management practices and presence of drug residues in WM. In this study, 20% of farms did not pasteurize WM before feeding to calves. Two of the 10 Escherichia coli isolated from WM samples were multidrug resistant. Streptococcus spp. (n = 21, 84%) was the most common genus cultured from WM samples, followed by Staphylococcus spp. (n = 20, 80%) and E.coli (n = 10, 40%). Mycoplasma spp. was cultured from 2 WM samples (n = 2, 8%). The presence of drug residues in WM at concentrations that increase selection of resistant bacteria indicates the need for additional studies targeting on-farm milk treatments to degrade drug residues before feeding to calves. The presence of multidrug-resistant E. coli in WM urges the need for on-farm practices that reduce calf exposure to resistant bacteria, such as pasteurization.

Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016

Nontyphoidal Salmonella infections contribute to approximately 1.2 million annual illnesses in the United States. Historical and recent outbreaks have been associated with dairy products, ground beef, and direct contact with cattle. Salmonella antimicrobial resistance (AMR) is a serious concern that can reduce successful treatment of infections, increasing recovery time, medical costs, and mortality rates in humans and animals. This highlights the need to track AMR in Salmonella isolated from cattle to improve treatment plans, manage trends in AMR, and prevent future AMR development. A total of 242 Salmonella isolates were retrieved from 9,162 cattle fecal samples submitted to the University of California, Davis Veterinary Medical Teaching Hospital from 2002 to 2016. These isolates were tested for antimicrobial susceptibility using a standardized broth dilution panel. Multidrug resistance (MDR) to three or more classes of antimicrobials was observed in 50.8% of isolates, and the most common MDR pattern was amoxicillin-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-tetracycline (23.2%). There were significantly greater odds for antimicrobial resistance to aminoglycosides (OR: 2.03, 95% CI: 1.1–3.7), penicillins (OR: 1.87, 95% CI: 1.007–3.5), and tetracyclines (OR: 1.87, 95% CI: 1.017–3.4) for the 2002–2009 period when compared to the 2010–2016 period. The most prevalent MDR serotypes were Newport (100% MDR, n = 52), Typhimurium (100%, n = 20), and Dublin (71% MDR, n = 46). Risk factors associated with higher odds for isolating MDR Salmonella included isolates from calves when compared to adult cattle (OR: 22.0; 95% C.I.: 3.9–125.7), and isolates obtained from cattle suspect of having salmonellosis versus from the infectious disease control surveillance program (OR:13.7; 95%C.I.: 2.8–66.8). Despite a temporal trend for reduced AMR to most antimicrobial drug classes, a lack of this observed in the 2002–2009 period when compared to the 2010–2016 period for important drug classes such as cephalosporins (OR: 1.6, 95% CI: 0.87–3.1), and a trend for temporal increase in resistant to quinolones drugs (P value 0.004) highlight the relevance of AMR surveillance in cattle with Salmonella infections with the aim of targeting future prophylactic interventions.

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota

Feeding drug residue-containing milk to calves is common worldwide and no information is currently available on the impact on the functional profile of the fecal microbiota. Our objective was to characterize the functional profile of the fecal microbiota of preweaned dairy calves fed raw milk with residual concentrations of antimicrobials commonly found in waste milk from birth to weaning. Calves were assigned to a controlled feeding trial being fed milk with no drug residues or milk with antibiotic residues. Fecal samples collected from each calf once a week starting at birth, prior to the first feeding in the trial, until 6 weeks of age. Antibiotic residues resulted in a significant difference in relative abundance of microbial cell functions, especially with genes linked with stress response, regulation and cell signaling, and nitrogen metabolism. These changes could directly impacts selection and dissemination of virulence and antimicrobial. Our data also identified a strong association between age in weeks and abundance of Resistance to Antibiotics and Toxic Compounds. Findings from this study support the hypothesis that drug residues, even at very low concentrations, impact the gut microbiota of calves and result in changes in the functional profile of microbial populations.

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health

Early gut microbiota plays a vital role in the long-term health of the host. However, understanding of these microbiota is very limited in livestock species, especially in dairy calves. Neonatal calves are highly susceptible to enteric infections, one of the major causes of calf death, so approaches to improving gut health and overall calf health are needed. An increasing number of studies are exploring the microbial composition of the gut, the mucosal immune system, and early dietary interventions to improve the health of dairy calves, revealing possibilities for effectively reducing the susceptibility of calves to enteric infections while promoting growth. Still, comprehensive understanding of the effect of dietary interventions on gut microbiota-one of the key aspects of gut health-is lacking. Such knowledge may provide in-depth understanding of the mechanisms behind functional changes in response to dietary interventions. Understanding of host-microbial interactions with dietary interventions and the role of the gut microbiota during pathogenesis at the site of infection in early life is vital for designing effective tools and techniques to improve calf gut health.

Food additives, contaminants and other minor components: effects on human gut microbiota-a review

Gut bacteria play an important role in several metabolic processes and human diseases, such as obesity and accompanying co-morbidities, such as fatty liver disease, insulin resistance/diabetes, and cardiovascular events. Among other factors, dietary patterns, probiotics, prebiotics, synbiotics, antibiotics, and non-dietary factors, such as stress, age, exercise, and climatic conditions, can dramatically impact the human gut microbiota equilibrium and diversity. However, the effect of minor food constituents, including food additives and trace contaminants, on human gut microbiota has received less attention. Consequently, the present review aimed to provide an objective perspective of the current knowledge regarding the impacts of minor food constituents on human gut microbiota and consequently, on human health.

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

BACKGROUND

Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea.

OBJECTIVES

To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.

METHODS

Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).

RESULTS

Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.

CLINICAL RELEVANCE

The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Risk for the development of Antimicrobial Resistance (AMR) due to feeding of calves with milk containing residues of antibiotics

EFSA was requested to: 1) assess the risk for the development of antimicrobial resistance (AMR) due to feeding on farm of calves with colostrum potentially containing residues of antibiotics; 2) assess the risk for the development of AMR due to feeding on farm of calves with milk of cows treated during lactation with an antibiotic and milked during the withdrawal period, and 3) propose possible options to mitigate the risk for the development of AMR derived from such practices. Treatment of dairy cows during the dry period and during lactation is common in the EU Member States. Penicillins, alone or in combination with aminoglycosides, and cephalosporins are most commonly used. Residue levels of antimicrobials decrease with the length of the dry period. When the interval from the start of the drying-off treatment until calving is as long as or longer than the minimum specified in the Summary of Product Characteristics of the antimicrobial, faecal shedding of antimicrobial-resistant bacteria will not increase when calves are fed colostrum from treated cows. Milk from cows receiving antimicrobial treatment during lactation contains substantial residues during the treatment and withdrawal period. Consumption of such milk will lead to increased faecal shedding of antimicrobial-resistant bacteria by calves. A range of possible options exist for restricting the feeding of such milk to calves, which could be targeting the highest priority critically important antimicrobials. β-Lactamases can reduce the concentration of β-lactams which are the most frequently used antimicrobials in milking cows. Options to mitigate the presence of resistant bacteria in raw milk or colostrum are mainly based on thermal inactivation.

Antimicrobial usage and resistance in beef production

Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.

Assessment of the Fecal Microbiota in Beef Calves

Background

There is increasing interest in the fecal microbiota, but study in calves has been limited.

Hypothesis/Objectives

To evaluate the fecal microbiota of beef calves and cows on different farms, and to preliminarily explore the impact of antimicrobial exposure.

Animals

A total of 172 animals, 156 (91%) calves and 16 (9.3%) cows, were enrolled from 5 cow‐calf farms.

Methods

The fecal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V4 region) amplicons.

Results

There were significant differences in the relative abundances of numerous phyla between calves on different farms. Farms could be separated into 2 groups: 1 (farms B and C) dominated by Firmicutes and 1 (farms A, D, and E) with predominance of Proteobacteria and Actinobacteria. Richness (median 2,974 versus 1,477, P = .008), diversity (51.4 versus 29.1, P = .0029), and evenness (0.73 versus 0.68, P = .006) were higher in cows. Over‐represented operational taxonomic units (OTUs) in cows tended to be from the classes Bacilli and Bacteroidia, whereas Clostridia and Actinobacteria were most prominently over‐represented in calves. There were differences in community membership (P = .028) and structure (P = .029) in calves that had a history of antimicrobial exposure compared those that did not. Eight (89%) over‐represented OTUs in the untreated group were Firmicutes (7 from the order Clostridiales), compared to only 3 (38%) (2 Clostridiales) in the untreated group.

Conclusions and Clinical Importance

Interfarm variation should be investigated to determine the causes and potential implications for health and production. Antimicrobial exposure may have an impact on the fecal microbiota at individual and farm levels.

The bovine milk microbiota: insights and perspectives from -omics studies

Recent findings and future perspectives of -omics studies on the bovine milk microbiota, focusing on its impact on animal health.