The Cattle Microbiota and the Immune System: An Evolving Field

Exploring the effects of transport duration on the fecal microbial communities of surplus dairy calves

Transportation significantly affects the health and welfare of surplus dairy calves, largely due to the various stressors and pathogen exposures encountered during the process. Concurrently, an animal's microbiome is known to correlate with its health status, with stress-induced alterations in the microbiota potentially precipitating various diseases. This study aimed to compare the effects of transportation durations of 6, 12, or 16 h on the fecal microbiota in young surplus dairy calves. We used a randomized controlled design in which surplus dairy calves aged 1 to 19 d from 5 commercial dairy farms in Ontario were allocated into 1 of 3 transportation groups (6, 12, and 16 h of continuous transportation). Health assessments were conducted before, immediately after, and for 2 wk following transportation. Fecal samples were collected before, immediately after, and at 24 and 72 h after transportation and subjected to 16S rRNA sequencing. Alpha diversity metrics showed no significant differences between the 3 transportation groups at any of the sampling time points. Although β diversity metrics revealed no clustering by transportation groups, they indicated significant differences across sampling time points within each group. The overall analysis revealed a total of 22 phyla and 353 genera, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria being the most abundant phyla. Bacteroides, Escherichia/Shigella, Lactobacillus, Collinsella, and Bifidobacterium were the most abundant genera. The reduction in Fusobacteria abundance before and after transport was significantly larger in the 16-h transportation group when compared with the 6-h transportation group. We also identified several genus-level and amplicon sequence variation-level taxa that displayed significant differences in their abundances across various transportation groups, observed at all sampling time points investigated. This research identifies microbiota changes due to varying transportation durations in surplus dairy calves, providing a broad understanding of the microbial shifts in surplus dairy calves after transportation across varying durations. Although these variations may not directly correlate with overall calf health or indicate dysbiosis, these results emphasize the importance of further investigating transportation practices to enhance calf health and well-being. Further studies are warranted to elucidate the relationship between microbiota and calf health.

Characterization of the preweaned Holstein calf fecal microbiota prior to, during, and following resolution of uncomplicated gastrointestinal disease

Little is known about shifts in the fecal microbiome of dairy calves preceding and following the incidence of gastrointestinal disease. The objective of this cohort study was to describe the fecal microbiome of preweaned dairy calves before, during, and after gastrointestinal disease. A total of 111 Holstein dairy calves were enrolled on 2 dairies (D1 and D2) and followed until 5 weeks old. Health assessments were performed weekly and fecal samples were collected every other week. Of the 111 calves, 12 calves from D1 and 12 calves from D2 were retrospectively defined as healthy, and 7 calves from D1 and 11 calves from D2 were defined as diarrheic. Samples from these calves were sequenced targeting the 16S rRNA gene and compared based on health status within age groups and farms: healthy (0-1 week old) vs. pre-diarrheic (0-1 week old), healthy (2-3 weeks old) vs. diarrheic (2-3 weeks old), and healthy (4-5 weeks old) vs. post-diarrheic (4-5 weeks old) calves. Healthy and diarrheic samples clustered together based on age rather than health status on both farms. Based on linear discriminant analysis, a few species were identified to be differently enriched when comparing health status within age groups and farm. Among them, Bifidobacterium sp. was differently enriched in pre-diarrheic calves at D1 (0-1 week old) whereas healthy calves of the same age group and farm showed a higher abundance of Escherichia coli. Bifidobacterium sp. was identified as a biomarker of fecal samples from healthy calves (2-3 weeks old) on D1 when compared with diarrheic calves of the same age group and farm. Feces from diarrheic calves on D2 (2-3 weeks old) were characterized by taxa from Peptostreptococcus and Anaerovibrio genera whereas fecal samples of age-matched healthy calves were characterized by Collinsella aerofaciens and Bifidobacterium longum. After resolution of uncomplicated diarrhea (4-5 weeks old), Collinsella aerofaciens was more abundant in D2 calves whereas Bacteriodes uniformis was more abundant in D1 calves. Taken together, these findings suggest that the age of the preweaned calf is the major driver of changes to fecal microbiome composition and diversity even in the face of uncomplicated gastrointestinal disease.

Fecal Microbial Communities of Nellore and Crossbred Beef Calves Raised at Pasture

This study aimed to investigate the effect of age and genetics on the fecal microbiota of beef calves. Ten purebred Nellore (Bos taurus indicus) and ten crossbreed 50% Nellore-50% European breed (Bos taurus taurus) calves co-habiting on the same pasture paddock had fecal samples collected on days five (5 d), 14 d, 28 d, 60 d, 90 d, 180 d, 245 d (weaning) and 260 d after birth. All calves were kept with their mothers, and six Nellore dams were also sampled at weaning. Microbiota analysis was carried out by amplification of the V4 region of the 16S rRNA gene following high-throughput sequencing with a MiSeq Illumina platform. Results revealed that bacterial richness increased with age and became more similar to adults near weaning. Differences in microbiota membership between breeds were found at 60 d and 90 d and for structure at 60 d, 90 d, 245 d, and 260 d (p < 0.05). In addition, crossbreed calves presented less variability in their microbiota. In conclusion, the genetic composition significantly impacted the distal gut microbiota of calves co-habiting in the same environment, and further studies investigating food intake can reveal possible associations between microbiota composition and performance.

Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period

Introduction

Neonatal calf diarrhea is a multifactorial condition that occurs in early life when calves are particularly susceptible to enteric infection and dysbiosis of the gut microbiome. Good calf health is dependent on successful passive transfer of immunity from the dam through colostrum. There are limited studies on the developing gut microbiota from birth to weaning in calves.

Methodology

Therefore, the objective of this study was to examine the effect of immune status and diarrheal incidence on the development of the fecal microbiota in Jersey (n = 22) and Holstein (n = 29) heifer calves throughout the pre-weaning period. Calves were hand-fed a colostrum volume equivalent to 8.5% of their birthweight, from either the calf's dam (n = 28) or re-heated mixed colostrum (≤2 cows, ≤1d; n = 23) within 2 h of birth. All calves were clinically assessed using a modified Wisconsin-Madison calf health scoring system and rectal temperature at day (d) 0, d7, d21, or disease manifestation (DM) and weaning (d83). Weights were recorded at d0, d21, and d83. Calf blood samples were collected at d7 for the determination of calf serum IgG (sIgG). Fecal samples were obtained at d7, d21/DM [mean d22 (SE 0.70)], and at weaning for 16S rRNA amplicon sequencing of the fecal microbiota. Data were processed in R using DADA2; taxonomy was assigned using the SILVA database and further analyzed using Phyloseq and MaAsLin 2.

Results and discussion

Significant amplicon sequence variants (ASVs) and calf performance data underwent a Spearman rank-order correlation test. There was no effect (p > 0.05) of colostrum source or calf breed on serum total protein. An effect of calf breed (p < 0.05) was observed on sIgG concentrations such that Holstein calves had 6.49 (SE 2.99) mg/ml higher sIgG than Jersey calves. Colostrum source and calf breed had no effect (p > 0.05) on health status or the alpha diversity of the fecal microbiota. There was a relationship between health status and time interaction (p < 0.001), whereby alpha diversity increased with time; however, diarrheic calves had reduced microbial diversity at DM. No difference (p > 0.05) in beta diversity of the microbiota was detected at d7 or d83. At the genus level, 33 ASVs were associated (adj.p < 0.05) with health status over the pre-weaning period.

Uterine Disease in Dairy Cows: A Comprehensive Review Highlighting New Research Areas

Uterine disease is an intensely studied part of dairy cattle health management as it heavily affects many commercial dairy farms and has serious economic consequences. Forms of the disease, pathophysiology, pathogens involved and the effects of uterine disease on the health and performance of cows have already been well described by various authors. Lately, researchers' attention has shifted towards the healthy microbiome of the uterus and the vagina to put emphasis on prevention rather than treatment. This aligns with the growing demand to reduce the use of antibiotics or-whenever possible-replace them with alternative treatment options in farm animal medicine. This review provides a comprehensive summary of the last 20 years of uterine disease research and highlights promising new areas for future studies.

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen-protected Capsicum oleoresin

The microbiome has been linked to animal health and productivity, and thus, modulating animal microbiomes is becoming of increasing interest. Antimicrobial growth promoters (AGP) were once a common technology used to modulate the microbiome, but regulation and consumer pressure have decreased AGP use in food animals. One alternative to antimicrobial growth promoters are phytotherapeutics, compounds derived from plants. Capsaicin is a compound from the Capsicum genus, which includes chili peppers. Capsaicin has antimicrobial properties and could be used to manipulate the gastrointestinal microbiome of cattle. Both the rumen and fecal microbiomes are essential to cattle health and production, and modulation of either microbiome can affect both cattle health and productivity. We hypothesized that the addition of rumen-protected capsaicin to the diet of cattle would alter the composition of the fecal microbiome, but not the rumen microbiome. To determine the impact of rumen-protected capsaicin in cattle, four Holstein and four Angus steers were fed rumen-protected Capsicum oleoresin at 0 (Control), 5, 10, or 15 mg kg-1 diet dry matter. Cattle were fed in treatment groups in a 4 × 4 Latin Square design with a 21-d adaptation phase and a 7-d sample collection phase. Rumen samples were collected on day 22 at 0-, 2-, 6-, 12-, and 18-h post-feeding, and fecal swabs were collected on the last day of sample collection, day 28, within 1 h of feeding. Sequencing data of the 16s rRNA gene was analyzed using the dada2 pipeline and taxa were assigned using the SILVA database. No differences were observed in alpha diversity among fecal or rumen samples for either breed (P > 0.08) and no difference between groups was detected for either breed in rumen samples or for Angus steers in fecal samples (P > 0.42). There was a difference in beta diversity between treatments in fecal samples of Holstein steers (P < 0.01), however, a pairwise comparison of the treatment groups suggests no difference between treatments after adjusting for multiple comparisons. Therefore, we were unable to observe substantial overall variation in the rumen or fecal microbiomes of steers due to increasing concentrations of rumen-protected capsaicin. We do, however, see a trend toward increased concentrations of capsaicin influencing the fecal microbiome structure of Holstein steers despite this lack of significance.

Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis

BACKGROUND

Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites' biology and interactions with the host and microbiome in order to develop novel strategies against this infection. The age-dependent nature of symptomatic cryptosporidiosis suggests a link to the undeveloped immune response, the immature intestinal epithelium, and its associated microbiota. This led us to hypothesise that specific features of the early life microbiome could predict calf susceptibility to C. parvum infection.

RESULTS

In this study, a single faecal swab sample was collected from each calf within the first week of life in a cohort of 346 animals. All 346 calves were subsequently monitored for clinical signs of cryptosporidiosis, and calves that developed diarrhoea were tested for Rotavirus, Coronavirus, E. coli F5 (K99) and C. parvum by lateral flow test (LFT). A retrospective case-control approach was taken whereby a subset of healthy calves (Control group; n = 33) and calves that went on to develop clinical signs of infectious diarrhoea and test positive for C. parvum infection via LFT (Cryptosporidium-positive group; n = 32) were selected from this cohort, five of which were excluded due to low DNA quality. A metagenomic analysis was conducted on the faecal microbiomes of the control group (n = 30) and the Cryptosporidium-positive group (n = 30) prior to infection, to determine features predictive of cryptosporidiosis. Taxonomic analysis showed no significant differences in alpha diversity, beta diversity, and taxa relative abundance between controls and Cryptosporidium-positive groups. Analysis of functional potential showed pathways related to isoprenoid precursor, haem and purine biosynthesis were significantly higher in abundance in calves that later tested positive for C. parvum (q ≤ 0.25). These pathways are either absent or streamlined in the C. parvum parasites. Though the de novo production of isoprenoid precursors, haem and purines are absent, C. parvum has been shown to encode enzymes that catalyse the downstream reactions of these pathway metabolites, indicating that C. parvum may scavenge those products from an external source.

CONCLUSIONS

The host has previously been put forward as the source of essential metabolites, but our study suggests that C. parvum may also be able to harness specific metabolic pathways of the microbiota in order to survive and replicate. This finding is important as components of these microbial pathways could be exploited as potential therapeutic targets for the prevention or mitigation of cryptosporidiosis in bovine neonates.

Analysis of Fecal Microbial Changes in Young Calves Following Bovine Rotavirus Infection

The objective of the present study was to identify changes in fecal microbiota and predict the functional features of healthy calves and those infected with rotavirus over time. Six Holstein calves (average body weight 43.63 ± 1.19 kg, age-matched within 5-7 d) were randomly selected and distributed into two groups which contained three calves each. Fecal samples were taken 3 days before inoculation and on days 1 and 7 post-inoculation. The 16S rRNA gene amplicon sequencing was performed. Bacterial diversity tended to decrease in the rota group, as indicated by the alpha (evenness, p = 0.074 and Shannon, p = 0.055) and beta (Bray-Curtis dissimilarity, p = 0.099) diversity at 1 day post-inoculation. Differences in the bacterial taxa between healthy and rota-infected calves were detected using a linear discriminant analysis effect size (LDA > 2.0, p < 0.05). Rota calves had a higher abundance of certain bacterial taxa, such as Enterococcus, Streptococcus, and Escherichia-Shigella, and a lower abundance of bacteria that contribute to the production of short-chain fatty acids, such as Alistipes, Faecalibacterium, Pseudoflavonifractor, Subdoligranulum, Alloprevotella, Butyricicoccus, and Ruminococcus, compared to the healthy calves. The observed changes in the fecal microbiota of the rota-infected group compared to the healthy group indicated potential dysbiosis. This was further supported by significant differences in the predicted functional metagenomic profiles of these microbial communities. We suggest that calves infected with bovine rotavirus had bacterial dysbiosis, which was characterized by lower diversity and fewer observed genera than the fecal microbiota of healthy calves.

Combining 16S rRNA Sequencing and Metabolomics Data to Decipher the Interactions between Gut Microbiota, Host Immunity, and Metabolites in Diarrheic Young Small Ruminants

Diarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.

The fecal bacterial microbiota of healthy and sick newborn foals

BACKGROUND

The fecal bacterial microbiota of normal foals and foals with enterocolitis has been characterized using next-generation sequencing technology; however, there are no reports investigating the gut microbiota in foals hospitalized for other perinatal diseases.

OBJECTIVE

To describe and compare the fecal bacterial microbiota in healthy and sick foals using next-generation sequencing techniques.

ANIMALS

Hospitalized (17) and healthy foals (21).

METHODS

Case-control study. Fecal samples were collected from healthy and sick foals on admission. Sick foals were further divided into sick nonseptic (SNS, n = 9) and septic (n = 8) foals. After extraction of DNA, the V4 region of the 16 S rRNA gene was amplified using a PCR assay, and the final product was sequenced with an Illumina MiSeq.

RESULTS

Diversity was significantly lower in healthy than sick foals (P < .05). The bacterial membership (Jaccard index) and structure (Yue & Clayton index) of the fecal microbiota of healthy, septic, and SNS foals were similar (AMOVA, P > .05). Bacterial membership (AMOVA, P = .06) and structure (AMOVA, P = .33) were not different between healthy and sick foals. Enterobacteriaceae, Enterococcus, and Streptococcus were among the 5 more abundant taxa identified in both groups.

CONCLUSION AND CLINICAL IMPORTANCE

Higher fecal microbiota diversity in sick than healthy foals might suggest a high exposure to environmental microorganisms or an unstable colonic microbiota. The presence of microorganisms causing bacteremia in foals in a high relative abundance in the feces of foals suggests the intestine might play an essential role in the causation of bacteremia in foals.

Phyllanthus emblica (Amla) Fruit Powder as a Supplement to Improve Preweaning Dairy Calves' Health: Effect on Antioxidant Capacity, Immune Response, and Gut Bacterial Diversity

Disease is the main reason for the use of antimicrobials in calf rearing, and antibiotics are commonly used to treat calves, including for unknown diseases. This leads to antimicrobial resistance, which is a challenge to the livestock industry and public health. Plant products containing high levels of phytochemicals may improve the immunity and resistance of calves against infections, thereby reducing the use of antimicrobials. This study aimed to investigate the effect of Phyllanthus emblica (Amla) fruit powder (PE) supplementation on antioxidant capacity and immune response of preweaning dairy calves. One hundred, 2-day-old, male Holstein calves were randomly assigned into five treatment groups receiving 0, 5, 10, 20, and 40 g/d PE supplementation. Antioxidant and immune indices and pro- and anti-inflammatory cytokines were analyzed from serum samples, whereas 16S rRNA was analyzed from rumen fluid and fecal samples. PE supplementation, at 5 g/d, protected calves against oxidative stress and improved antioxidant enzymes and immune and anti-inflammatory responses, showing its immunity-enhancing and protective roles against infections. However, the antioxidant capacity and immune response decreased with increasing PE levels, illustrating the adverse effects of PE supplementation at higher doses. The analysis of ruminal and fecal bacterial community abundance detected higher proportions of Firmicutes at an early age, and a higher Bacteroidetes to Firmicutes ratio at weaning, in calves supplemented with 5 g/d PE. This contributed to the development of the immune system in early life, and improved immune and anti-inflammatory responses at a later age. The overall results suggest that PE could be supplemented at 5 g/d for preweaning dairy calves to protect against oxidative stress and infections while maintaining normal gut microbial hemostasis.

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.

Effect of an Immunomodulatory Feed Additive in Mitigating the Stress Responses in Lactating Dairy Cows to a High Concentrate Diet Challenge

Simple Summary

Dairy cows are often exposed to stressors during the lactation cycle. Nutritional stressors could be caused by rich-grain diet, leading to ruminal pH reduction and subsequent systemic inflammation. This metabolic pathology impacts animal health and productivity. Feed additives could provide beneficial effects on innate immune function in dairy cows, especially during stressing periods. The goal of this study was to determine the effect of OmniGen-AF on measures of immunity, inflammation, and liver function in lactating dairy cows fed a high-starch, low-fiber diet. Changes in rumination, pH, and volatile fatty acids were recorded. Treated cows resulted in better rumen volatile fatty acids profile and also showed shifts in hematological parameters compatible with a prompter regeneration of red blood cells, greater proportion of neutrophils, lower levels on GGT, PON, and BHB. These results show evidence of the nutritional stress induced by feeding a high-starch, low-fiber diet, and suggest that the fed additive tested modulates some of the metabolic and immunological responses to sub-acute ruminal acidosis.

Abstract

Dairy cows are often exposed to multiple stressors in a lactation-cycle, with sub-acute ruminal acidosis (SARA) a frequent example of nutritional stress. SARA affects ruminal and intestinal equilibrium resulting in dysbiosis with localized and systemic inflammation impacting animal health and productivity. OmniGen-AF (OMN, Phibro Animal Health Corporation, Teaneck, NJ, USA) is a feed product recognized for modulating innate immune function, especially during periods of stress. The objective of this study was to determine the effects of OMN in lactating dairy cows fed a high-starch, low-fiber diet. Twenty-four blocked cows were assigned to control or treatment (55 g/d). After the additive adaptation (49 d) cows were fed the challenge diet (28 d). Milk, rumination and pH were continuously recorded; components, rumen fluid, and blood were taken in multiple time-point and analyzed. Results showed that the challenge decreased the rumination, shifted ruminal fluid composition, decreased milk production and the components, and slightly increased the time below pH 5.5, with no differences between groups. The treatment produced greater rumen butyrate and lower lactate, prompter regeneration of red blood cells, increase of neutrophils, lower paraoxonase, gamma-glutamyl-transferase, and β-hydroxybutyrate, with no differences on other tested inflammatory markers. Results show that OMN helps modulating some of the metabolic and immunological responses to SARA.

Effects of Intrauterine Infusion of Micronised Purified Flavonoid Fraction (MPFF) in Metritis-Diagnosed Dairy Cows Naturally Infected by E. coli during the Early Postpartum

The occurrence of metritis during the postpartum period causes serious economic losses in dairy cattle. The Micronised Purified Flavonoid Fraction (MPFF) is a polyphenolic flavonoid compound which is considered to have many health-related properties such as antibiotic, anti-inflammatory, phlebotonic, and several vascular-protecting activities. The aim was to evaluate the effects of a new strategic therapy for metritis based on MPFF intrauterine infusions during the early postpartum in dairy cows naturally infected by Escherichia coli. The clinical effects on reproductive anatomical structures and chronological involution dynamics were monitored until day 24 postpartum by ultrasonography. Moreover, uterine bacteriological and cytological (polymorphonuclear neutrophils; PMNs) profiles were analysed before and after MPFF infusion. The results showed that the success rate (% cure) at day 24 postpartum was improved significantly when using higher MPFF doses (p < 0.05). Moreover, MPFF treatment acutely diminished the size of the cervix and uterus and improved the involution process during the first 24 days (p < 0.05). The prevalence of pathogenic bacteria found in in vitro cultures was significantly variable (p < 0.01), as were the antibiotic sensitivity patterns. Pathogenic bacteria isolates decreased after MPFF applications in a dose−response fashion (p < 0.01), while isolates obtained from controls and low-dose-MPFF-treated animals were stable and similar (p > 0.05). The sensitivity patterns of pathogenic bacteria isolated in in vitro cultures from MPFF-treated animals were variable, although resistance to E. coli, Staphylococcus aureus, Bacillus spp., and coliforms was shown irrespective of the MPFF doses used. However, MPFF-treated cows showed a dose−response effect regarding PMN rates (p < 0.05). The calving-first service, calving−conception interval, and conception rate improved significantly from using higher MPFF doses (p < 0.05). In conclusion, this study shows that MPFF treatment differentially affects uterine involution, bacteriological profiles, cytological traits, and reproductive performance in metritis-positive dairy cows naturally infected by E. coli.

Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes

The microorganisms inhabiting the gastrointestinal tract (GIT) of ruminants have a mutualistic relationship with the host that influences the efficiency and health of the ruminants. The GIT microbiota interacts with the host immune system to influence not only the GIT, but other organs in the body as well. The objective of this review is to highlight the importance of the role the gastrointestinal microbiota plays in modulating the health of a host through communication with different organs in the body through the microbiome-gut-organ axes. Among other things, the GIT microbiota produces metabolites for the host and prevents the colonization of pathogens. In order to prevent dysbiosis of the GIT microbiota, gut microbial therapies can be utilized to re-introduce beneficial bacteria and regain homeostasis within the rumen environment and promote gastrointestinal health. Additionally, controlling GIT dysbiosis can aid the immune system in preventing disfunction in other organ systems in the body through the microbiome-gut-brain axis, the microbiome-gut-lung axis, the microbiome-gut-mammary axis, and the microbiome-gut-reproductive axis.

Calf Diarrhea Is Associated With a Shift From Obligated to Facultative Anaerobes and Expansion of Lactate-Producing Bacteria

Diarrhea is the leading cause of morbidity, mortality and antimicrobial drug use in calves during the first month of age. Alteration in the bacterial communities of the gastrointestinal tract occurs during diarrhea. Diarrheic calves often develop anion gap (AG) acidosis associated with increased concentrations of unmeasured anions including D- and L-lactate. However, studies investigating the association between gut microbiota alterations and the development of acid-base disorders in diarrheic calves are lacking. We investigated the fecal bacterial alterations of calves with diarrhea and its association with changes in blood pH, and AG. Blood and fecal samples from healthy and diarrheic veal calves were taken 7 days after arrival to the farm. The fecal microbiota of healthy and diarrheic calves was assessed by sequencing of 16S ribosomal RNA gene amplicons. Blood gas analysis was completed using an i-Stat analyzer. In healthy calves, higher richness, evenness, and diversity were observed compared to diarrheic calves. Phocaeicola, Bacteroides, Prevotella, Faecalibacterium, Butyricicoccus, Ruminococcaceae and Lachnospiraceae were enriched in healthy compared with diarrheic calves. Enterococcus, Ligilactobacillus, Lactobacilus, Gallibacterium Streptococcus, and Escherichia/Shigella were enriched in diarrheic calves. In diarrheic calves, an increased abundance of lactate-producing bacteria including Lactobacillus, Streptococcus, Veillonella, Ligilactobacillus and Olsenella was detected. Diarrheic calves had a lower pH and bicarbonate concentration and a higher AG concentration than healthy calves. Together, these results indicate that calf diarrhea is associated with a shift from obligated to facultative anaerobes and expansion of lactate-producing bacteria which are related to acidemia, low bicarbonate and increase AG. Our results highlight the importance of the gastrointestinal microbiota on the clinicopathological changes observed in diarrheic calves.

Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease

Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4-21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli. Species of the genus Lactobacillus, such as an unclassified Lactobacillus, Lactobacillus reuteri, and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta, Bifidobacterium longum, and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E. coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.

Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves

Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected enrofloxacin on gut microbiota and resistome in calves. Thirty-five calves sourced for this study were divided into five groups: control (n = 7), two low dose groups (n = 14, 7.5 mg/kg), and two high dose groups (n = 14, 12.5 mg/kg). One group in the low and high dose groups was challenged with Mannheimia haemolytica to induce BRD. Both alpha and beta diversities were significantly different between pre- and post-treatment microbial communities (q < 0.05). The high dose caused a shift in a larger number of genera than the low dose. Using metagenomic ProxiMeta Hi-C, 32 unique antimicrobial resistance genes (ARGs) conferring resistance to six antibiotic classes were detected with their reservoirs, and the high dose favored clonal expansion of ARG-carrying bacterial hosts. In conclusion, enrofloxacin treatment can alter fecal microbiota and resistome irrespective of its dose. Hi-C sequencing provides significant benefits for unlocking new insights into the ARG ecology of complex samples; however, limitations in sample size and sequencing depth suggest that further work is required to validate the findings.

Effects of Dietary Supplementation of Bovine Lactoferricin on Rumen Microbiota, Lactation, and Health in Dairy Goats

This study aimed to investigate the biological effects of supplementation of bovine lactoferricin (BLFc) at the rate of 100 mg/kg/day (LF-1) or 200 mg/kg/day (LF-2) in lactating dairy goats. Dietary BLFc supplementation increased the concentration of lactoferrin (LF) in the milk and serum (p < 0.05) without affecting the feed intake. In the LF-1 group, serum Fe, total antioxidant (T-AOC), and immunoglobulin A (IgA) were increased (p < 0.05), while malondialdehyde (MDA) was decreased (p < 0.05). In the LF-2 group, ruminal fluid pH value was decreased (p < 0.05), and the composition of ruminal microflora on day 42 was more diversified. Firmicutes phylum in the LF-2 group was the most abundant phyla. In contrast, Bacteroidetes phylum in the control group and the LF-1 group were the most abundant. Lower milk somatic cell count and higher IgA were observed in the LF-1 group and the LF-2 group than those in the control group (p < 0.05). These results suggested beneficial effects of supplementation of 100 mg/kg/day BLFc on reducing the oxidative stress and altering diversity of ruminal microflora.

Bovine Immunology: Implications for Dairy Cattle

The growing world population (7.8 billion) exerts an increased pressure on the cattle industry amongst others. Intensification and expansion of milk and beef production inevitably leads to increased risk of infectious disease spread and exacerbation. This indicates that improved understanding of cattle immune function is needed to provide optimal tools to combat the existing and future pathogens and improve food security. While dairy and beef cattle production is easily the world's most important agricultural industry, there are few current comprehensive reviews of bovine immunobiology. High-yielding dairy cattle and their calves are more vulnerable to various diseases leading to shorter life expectancy and reduced environmental fitness. In this manuscript, we seek to fill this paucity of knowledge and provide an up-to-date overview of immune function in cattle emphasizing the unresolved challenges and most urgent needs in rearing dairy calves. We will also discuss how the combination of available preventative and treatment strategies and herd management practices can maintain optimal health in dairy cows during the transition (periparturient) period and in neonatal calves.

Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo

The microbiota of the gastrointestinal tract (GIT) are crucial for host health and production efficiency in ruminants. Its microbial composition can be influenced by several endogenous and exogenous factors. In the beef and dairy industry, the possibility to manipulate gut microbiota by diet and management can have important health and economic implications. The aims of this study were to characterize the different GIT site microbiota in water buffalo and evaluate the influence of diet on GIT microbiota in this animal species. We characterized and compared the microbiota of the rumen, large intestine and feces of water buffaloes fed two different diets with different non-structural carbohydrates/crude proteins (NSC/CP) ratios. Our results indicated that Bacteroidetes, Firmicutes and Proteobacteria were the most abundant phyla in all the GIT sites, with significant differences in microbiota composition between body sites both within and between groups. This result was particularly evident in the large intestine, where beta diversity analysis displayed clear clustering of samples depending on the diet. Moreover, we found a difference in diet digestibility linked to microbiota modification at the GIT level conditioned by NSC/CP levels. Diet strongly influences GIT microbiota and can therefore modulate specific GIT microorganisms able to affect the health status and performance efficiency of adult animals.

Probiotic effect of Bacillus subtilis B-2998D, B-3057D, and Bacillus licheniformis B-2999D complex on sheep and lambs

Objectives:

Probiotics are well documented for their health benefits by developing a balanced intestinal microbiota and boosting immunity. The present study was conducted to determine the effects of a probiotic preparation Enzimsporin^TM (consisting of spore-forming bacteria Bacillus subtilis B-2998D, B-3057D, and Bacillus licheniformis B-2999D) on the biochemical, hematological, immunological parameters, intestinal microbiota, and growth dynamics of sheep and lambs.

Materials and Methods:

Enzimsporin was fed to lambs and sheep at different doses to determine the bacteria’s probiotic effects. Sheep were divided into three groups (six each), which received 0, 1, and 3 gm of Enzimsporin/per head/day, respectively, and two groups of lambs (10 each), who received 0 gm and 1 gm of Enzimsporin/per head/day for 30 days in addition to their regular ration. On day 30, blood samples were collected, followed by the determination of biochemical, hematological, and natural resistance indicators. Fecal samples were examined to determine the intestinal microflora, and animals were weighed daily to determine their growth dynamics.

Results:

Supplementation of probiotics (Enzimsporin^TM) improved the lambs’ body weight gain by 18.8%. Analysis of the clinical parameters showed improvements in the levels of total protein, globulins, and urea by 5.3%, 10.8%, and 6.2%, respectively, in the blood of probiotic-supplemented lambs. Similarly, an increment in the total protein, albumins, and globulins was observed in the sheep with Enzimsporin^TM supplementation. The decrease in bilirubin and cholesterol levels in the blood and increased bactericidal and phagocytic index in the sheep and lambs with probiotic supplementation indicated a positive influence of Enzimsporin^TM on the liver function and natural resistance. Furthermore, an increase in Lactobacillus and Bifidobacterium and a decrease in the Escherichia coli, Enterococcus, and Yeast in the fecal contents of experimental sheep and lambs indicated the potentiality of Enzimsporin^TM on maintaining good gut health.

Conclusion:

Spore-forming bacteria B. subtilis B-2998D, B-3057D, and B. licheniformis B-2999D can be used in feeding sheep and lambs of 2 months of age to increase body weight gain, improve intestinal microbiota, strengthen the immune system, and maintain normal metabolic processes.

Short communication: Comparison of the fecal bacterial communities in diarrheic and nondiarrheic dairy calves from multiple farms in southeastern Pennsylvania

Diarrhea is a major cause of illness and death in preweaned calves and causes significant economic losses to producers. A better understanding of the fecal microbiota in diarrheic and nondiarrheic calves could lead to improved treatment and prevention strategies. The purpose of this study was to compare the fecal microbiota of diarrheic and nondiarrheic calves to improve our understanding of what constitutes a healthy fecal microbiota in preweaned calves. At each of 7 farms, fecal samples were obtained from 1 to 3 diarrheic Holstein dairy calves (2 to 17 d old at sampling time) and age-matched (within 5 d) nondiarrheic controls for a total of 20 samples. Calves were fed either acidified bulk milk, pasteurized or unpasteurized waste milk, or milk replacer depending on farm. 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 (Illumina Inc., San Diego, CA) platform, and analyzed using QIIME2. Firmicutes and Bacteroidetes were the most abundant phyla in both groups; Fusobacteria was numerically more abundant in the diarrheic group, whereas Proteobacteria and Actinobacteria were numerically more abundant in the nondiarrheic group. At the genus level, Bacteroides was the most abundant genus in both groups and was numerically more abundant in the nondiarrheic group. Results from the mixed-effects regression model showed that Faecalibacterium and Butyricimonas were more abundant in the nondiarrheic calves, whereas Clostridium and Peptostreptococcus were more abundant in the diarrheic calves. Our results indicate that commensal bacteria acquired in the neonatal period may have been replaced with potential pathogens in diarrheic calves, which may have contributed to the incidence of diarrhea either directly or indirectly.

Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets

A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina's MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.

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.

Streptococcus uberis strains originating from bovine uteri provoke upregulation of pro-inflammatory factors mRNA expression of endometrial epithelial cells in vitro

Streptococcus uberis is an opportunistic pathogen involved in various infections of cattle. It is a well-known etiological agent of bovine mastitis and has recently also been linked to postpartum endometritis in dairy cows. S. uberis is frequently isolated from the uterus of postpartum cows but its actual contribution to host pathophysiology is unknown and information on S. uberis virulence factors potentially involved in the disease is lacking. To gain first insights into the role of S. uberis in the pathology of bovine endometritis, a cell-culture-based infection model was employed to study inflammatory host responses and investigate cytotoxic effects. A comprehensive strain panel, comprising 53 strains previously isolated from bovine uteri, was compiled and screened for known virulence factor genes. Isolates showing distinct virulence gene patterns were used to study their impact on cellular viability and influence on mRNA expression of pro-inflammatory factors in endometrial epithelial cells. Our study revealed that S. uberis negatively impacts the viability of endometrial epithelial cells and provokes an upregulation of specific pro-inflammatory factors, although with certain strains having a greater effect than others. Especially, mRNA expression of IL1A and CXCL8 as well as CXCL1/2 and PTGS2 was found to be stimulated by S. uberis. These results suggest that S. uberis might indeed contribute to the establishment of bovine endometritis.