Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding.

In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high-resolution whole genomic sequencing to examine the origin and distribution of Salmonella enterica after the 2018 Hurricane Florence flooding. We specifically asked whether S. enterica isolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independent S. enterica strains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmental Salmonella strains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmental S. enterica strains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18 S. enterica isolates. All ARGs were located on the Salmonella chromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic-resistant S. enterica after extreme flood events.

Host-specific signatures of the respiratory microbiota in domestic animals.

While the importance of respiratory microbiota in maintaining respiratory health is increasingly recognized, we still lack a comprehensive understanding of the unique characteristics of respiratory microbiota specific to individual hosts. This study aimed to address this gap by analyzing publicly available 16S rRNA gene datasets from various domestic animals (cats, dogs, pigs, donkeys, chickens, sheep, and cattle) to identify host-specific signatures of respiratory microbiota. The findings revealed that cattle and pigs exhibited the highest Shannon diversity index and observed features, indicating a greater microbial variety compared to other animals. Discriminant analysis demonstrated distinct composition of respiratory microbiota across different animals, with no overlapping abundant taxa. The linear discriminant analysis effect size highlighted prevalent host-specific microbiota signatures in different animal species. Moreover, the composition and diversity of respiratory microbiota were significantly influenced by various factors such as individual study, health status, and sampling sites within the respiratory tract. While associations between host and respiratory microbiota have been uncovered, the relative contributions of host and environment in the selection of respiratory microbiota and their impact on host fitness remain unclear. Further investigations involving diverse hosts are necessary to fully comprehend the significance of host-microbial coevolution in maintaining respiratory health.

Complete genome sequence of Candidatus Mycobacterium wuenschmannii, a nontuberculous mycobacterium isolated from a captive population of Amazon milk frogs.

A slow growing species of nontuberculous mycobacteria (NTM) was isolated from the liver of an Amazon milk frog. The complete genome of this isolate comprises 5,102,433 bp, exhibiting 66.86% GC content, 4,940 protein-coding sequences, 52 predicted RNA genes, and 39 repeat regions.

Diagnostic Evaluation of the IS1081-Targeted Real-Time PCR for Detection of Mycobacterium bovis DNA in Bovine Milk Samples.

The ability of Mycobacterium bovis (M. bovis) to survive in bovine milk has emerged as a serious public health concern. The first objective of this study was to evaluate the diagnostic utility of IS1081-targeted real-time PCR for the detection of M. bovis DNA in different fractions of bovine milk. In a model study, bovine milk samples were spiked with serially diluted M. bovis BCG to investigate the detection limit of M. bovis DNA in whole milk and milk fractions (cream, pellet, and pellet + cream combined) using IS1081 real-time PCR. The assay was then used to detect M. bovis DNA in whole milk and milk fractions from naturally infected animals. The results showed that the IS1081 real-time PCR was more sensitive when detecting M. bovis DNA in the cream layer alone and cream + pellet combined compared to whole milk or the pellet alone. While PCR-based diagnostic assays for the detection of M. bovis in milk samples provide a quicker diagnostic tool for bovine tuberculosis, safe processing, and handling of M. bovis-infected milk samples remain a challenge and pose a human health risk. PrimeStore Molecular Transport Medium (MTM) has been shown to rapidly inactivate infected specimens while preserving nucleic acid for subsequent Molecular analysis. Therefore, the secondary objective of this study was to evaluate the ability of MTM to inactivate M. bovis BCG in spiked milk samples as well as its ability to preserve BCG DNA for the PCR assay. The results showed that MTM can successfully inactivate BCG alone or in spiked milk samples while preserving DNA for the PCR assay. The CT values of M. bovis BCG alone and spiked milk samples aliquoted in MTM and without MTM were similar at various dilutions. Taken together, our results indicate that using DNA extracted from the milk cream fraction alone or combined milk cream and pellet improved the recovery rate of M. bovis DNA in bovine milk samples. MTM has the potential to provide a safe and rapid sample processing tool for M. bovis inactivation in milk samples and preserve DNA for molecular diagnostics.

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture.

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/µl to 0.1 pg/µl (10-1 to 10-4). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10-1 (mean Ct value: 20.3) and 10-2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

Effect of mango seeds as an untraditional source of energy on the productive performance of dairy Damascus goats.

Eighteen dairy Damascus goats weighing 38-45 kg live body weight and aged 3-4 years were divided into three groups according to their body weight, with six goats in each group. Yellow corn grain in their concentrate feed mixture was replaced with mango seeds (MS) at levels of 0% MS in group 1 (G1, control), 20% MS in group 2 (G2), and 40% MS in group 3 (G3). The digestibility coefficients of the organic matter, dry matter, crude fiber, crude protein, ether extract, nitrogen-free extract, and total digestible nutrients increased (P < 0.05) upon feeding MS to G2 and G3. The amounts of dry matter, total digestible nutrients, and digestible crude protein required per 1 kg 3.5% fat-corrected milk (FCM) were lower (P < 0.05) in G2 and G3 vs. G1. Actual milk and 3.5% FCM yield increased (P < 0.05) with the increasing MS dietary level. G2 and G3 had the highest significant (P < 0.05) total solids, total protein, non-protein nitrogen, casein, ash, fat, solids not fat, lactose, and calcium contents compared with G1. Replacing yellow corn grain with MS in G2 and G3 significantly (P < 0.05) decreased the cholesterol concentration and AST activity. Feeding MS increased the concentrations of caprioc, caprylic, capric, stearic, oleic, elaidic, and linoleic acids and decreased the concentrations of butyric, laueic, tridecanoic, myristic, myristoleic, pentadecanoic, heptadecanoic, cis-10-Heptadecanoic, cis-11-eicosenoic, linolenic, arachidonic, and lignoseric acids in the milk fat. The results show that the replacement of corn grain with MS improved the digestibility, milk yield, feed conversion, and economic efficiency, with no adverse effects on the performance of Damascus goats.

Beyond the Risk of Biofilms: An Up-and-Coming Battleground of Bacterial Life and Potential Antibiofilm Agents.

Microbial pathogens and their virulence factors like biofilms are one of the major factors which influence the disease process and its outcomes. Biofilms are a complex microbial network that is produced by bacteria on any devices and/or biotic surfaces to escape harsh environmental conditions and antimicrobial effects. Due to the natural protective nature of biofilms and the associated multidrug resistance issues, researchers evaluated several natural anti-biofilm agents, including bacteriophages and their derivatives, honey, plant extracts, and surfactants for better destruction of biofilm and planktonic cells. This review discusses some of these natural agents that are being put into practice to prevent biofilm formation. In addition, we highlight bacterial biofilm formation and the mechanism of resistance to antibiotics.

Complete Genome Sequence of Theileria equi NVSL354.

We are reporting the nearly complete genome of Theileria equi (Piroplasmida, Apicomplexa), which contains four nuclear chromosomes, a mitochondrial genome, and an apicoplast from the NVSL354 reference isolate. This report includes all six genetic molecules.

National Prevalence of Caprine Prion Protein Genetic Variability at Codons 146, 211, and 222 in Goat Herds in the United States.

Scrapie is a neurodegenerative disease that impacts sheep and goats, characterized by gradual and progressive changes in neurological function. Recent research shows that the scrapie incubation period is significantly influenced by specific variations in amino acids within the prion protein gene (PRNP). The objective of this study was to estimate the national prevalence of caprine PRNP genetic variability at codons 146, 211, and 222 in goat populations across the United States. A total of 3052 blood, ear tissue, and brain tissue samples were collected from goats from 50 states. The participating states were categorized into four Veterinary Service (VS) district regions. The samples underwent DNA extraction, and the PRNP variants corresponding to codons 146, 211, and 222 were amplified and sequenced. The analysis of PRNP variants, when compared to the PRNP reference sequence, revealed seven alleles in twelve genotypes. The homozygous 146NN, 211RR, and 222QQ alleles, which have been linked to an increased risk of scrapie, were found to be the most prevalent among all the goats. The heterozygous 222QK, 211RQ, 146SD, 146ND, and 146NS alleles and the homozygous 222KK, 146SS, and 146DD alleles, known to be associated with reduced scrapie susceptibility and a prolonged incubation period after experimental challenge, were found in 1.098% (222QK), 2.33% (211RQ), 0.58% (146SD), 3.13% (146ND), 20.68% (146NS), 0.005% (222KK), 3.31% (146SS), and 0.67% (146DD) of goats, respectively. The 222QK allele was found most frequently in goats tested from the east (VS District 1, 1.59%) and southwest (VS District 4, 1.08%) regions, whereas the 211RQ allele was found most often in goats tested from the Midwest (VS District 2, 8.03%) and east (VS District 1, 6.53%) regions. The 146NS allele was found most frequently in goats tested from the northwest (VS District 3, 29.02%) and southwest (VS District 4, 20.69%) regions. Our results showed that the prevalence of less susceptible genotypes at PRNP codon 146 may be sufficient to use genetic susceptibility testing in some herds. This may reduce the number of goats removed as part of a herd clean-up plan and may promote the selective breeding goats for less susceptible alleles in high-risk herds at the national level.

Bacterial and Fungal Adaptations in Cecum and Distal Colon of Piglets Fed With Dairy-Based Milk Formula in Comparison With Human Milk.

Exclusive breastfeeding is recommended to newborns during the first 6 months of life, whereas dairy-based infant formula is an alternative nutrition source offered to infants. Several studies demonstrated that breastfed infants have a different gut bacterial composition relative to formula-fed infants. In addition, animal models have shown that human milk (HM)-fed piglets had a distinct intestinal bacterial composition compared with milk formula (MF)-fed piglets. However, the gut fungal composition and the interactions with the bacterial community in breastfed compared with formula-fed infants remain to be investigated. In an attempt to evaluate such differences, we used an animal model to perform a shotgun metagenomics analysis on the cecal and distal colon contents of neonatal piglets fed with pasteurized HM or a dairy-based infant formula (MF) during the first 21 days of life. At postnatal day 21 (PND 21), a subset of piglets from each diet group (n = 11 per group) was euthanized. The remaining piglets in each group were weaned to a solid diet and euthanized at PND 51 (n = 13 per group). Large intestine contents (i.e., cecum and distal colon) were subjected to shotgun metagenomics analysis. The differential taxonomic composition of bacteria and fungi and the predicted functional gene profiling were evaluated. Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria are the most abundant bacterial phyla observed in piglets at PND 21 and PND 51. In the large intestine at PND 21 and PND 51, Proteobacteria phylum was significantly higher in MF-fed group, and species Burkholderiales bacterium of phyla was significantly higher in MF group relative to HM group. In addition, in HM group, several Lactobacillus spp. and Bacteroides spp. were higher relative to MF group in the large intestine at PND 21 and PND 51. Fungal genus Aspergillus was higher in MF, whereas Malassezia was lower relative to HM group. Persistent effects of the neonatal diets were observed at PND 51, where alpha- and beta-diversity differences were detected for bacterial and fungal species in the large intestine. Overall, our findings indicate that neonatal diet affects the large intestinal microbial community during the exclusive milk-feeding period, as well as after the introduction of the complementary food.

Large-scale survey of prion protein genetic variability in scrapie disease-free goats from the United States.

Scrapie is a slowly progressive neurodegenerative disease of small ruminants caused by an accumulation of an abnormal isoform of prion protein in the central nervous system. Polymorphisms of the prion protein gene (PRNP) strongly modulate scrapie resistance and incubation period in goats. The aim of this study was to identify PRNP genetic variability in goats across the United States. Blood from a total of 6,029 apparent scrapie disease-free goats from 654 operations and 19 breeds were analyzed. Sequencing of PRNP revealed 26 genotypes with different rates based on eight codons. The GG127, RR154, and QQ222 genotypes were predominant and showed a remarkably high rate across all goats. The QK222 and NS146 genotypes, known to be protective against scrapie, were found in 0.6% [with 95% CI = (0.3, 1.2)] and 22.0% [95% CI = (19.1, 25.2)] of goats, respectively. The QK222 genotype was found in 23.1% of Oberhasli goats tested, with 95%CI = (3.9, 68.7)] and 22.0% of Toggenburg goats tested with 95%CI = (9.7, 42.5)], while NS146 was found in 65.5% of Savannah goats tested, with 95%CI = (30.8, 89.9), 36.7% of Boer goats tested, with 95%CI = (33.1, 40.4), 36.3% of Nubian goats tested, with 95%CI = (27.0, 46.7)], and 35.6% of LaMancha goats tested, with 95%CI = (22.8, 50.8%). The MM142 and IM142 genotypes were found more frequently in goats on dairy operations, while the HR143, NS146, and ND146 genotypes were found more frequently in goats on meat operations. Goats in the east region had a higher percentage of goats with RH154, RQ211, and QK222 genotypes than goats in the west region. The results of this study showed high genetic variability of PRNP among the U.S. goat population, with differences by location and breed, and may serve as a rationale for development of goat breeding programs at the national level to mitigate the risk of scrapie.

Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis.

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet's fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

Distribution and Antibiotic Resistance Profiles of Salmonella enterica in Rural Areas of North Carolina After Hurricane Florence in 2018.

In this study, water samples were analyzed from a rural area of North Carolina after Hurricane Florence in 2018 and the distribution of the ttrC virulence gene of Salmonella enterica were investigated. We also examined the distribution of culturable S. enterica and determined their antibiotic resistance profiles. Antibiotic resistance genes (ARGs) in the classes of aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin B (MLSB) were targeted in this study. The ttrC gene was detected in 23 out of 25 locations. There was a wider and higher range of the ttrC gene in flooded water versus unflooded water samples (0-2.12 × 105 copies/L vs. 0-4.86 × 104 copies/L). Culturable S. enterica was isolated from 10 of 25 sampling locations, which was less prevalent than the distribution of the ttrC gene. The antibiotic resistance profiles were not distinct among the S. enterica isolates. The aminoglycoside resistance gene aac(6')-Iy had the highest relative abundance (around 0.05 copies/16S rRNA gene copy in all isolates) among all ARGs. These findings suggested that the 2018 flooding event led to higher copy numbers of the ttrC genes of S. enterica in some flooded water bodies compared to those in unflooded water bodies. The high ARG level and similar ARG profiles were observed in all S. enterica isolates from both flooded and unflooded samples, suggesting that the antibiotic resistance was prevalent in S. enterica within this region, regardless of flooding.

Applications, challenges, and strategies in the use of nanoparticles as feed additives in equine nutrition.

The rapid expansion of nanotechnology has been transforming the food industry by increasing market share and expenditure. Although nanotechnology offers promising benefits as feed additives, their usage in equines is primarily geared toward immunotherapy, hyper-immunization techniques, drug delivery systems, grooming activities, and therapeutic purposes. Nanoparticles could be engaged as alternatives for antibiotic feed additives to prevent foal diarrhea. Gold nanoparticles are proved to provide beneficial effects for racehorses by healing joint and tendon injuries. Because of the poor bioavailability of micro-sized mineral salts, the usage of nano-minerals is highly encourageable to improve the performance of racehorses. Nano-Vitamin E and enzyme CoQ10 for equines are no longer a simple research topic because of the increased commercial availability. Employing nanotechnology-based preservatives may offer a promising alternative to other conventional preservatives in preserving the quality of equine feed items, even during an extended storage period. While nanoparticles as feed additives may provide multitudinous benefits on equines, they could elicit allergic or toxic responses in case of improper synthesis aids or inappropriate dosages. The safety of nano-feed additives remains uninvestigated and necessitates the additional risk assessment, especially during their usage for a prolonged period. To adopt nano-feed additives in horses, there is an extreme paucity of information regarding the validity of various levels or forms of nanoparticles. Further, the currently available toxicological database on the topic of nano-feed additives is not at all related to equines and even inadequate for other livestock species. This review aims to provide new insights into possible future research pertaining to the usage of nano-feed additives in equines.

Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health.

Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.

Germline-dependent transmission of male reproductive traits induced by an endocrine disruptor, di-2-ethylhexyl phthalate, in future generations.

In males, defective reproductive traits induced by an exposure to an endocrine disruptor are transmitted to future generations via epigenetic modification of the germ cells. Interestingly, the impacted future generations display a wide range of heterogeneity in their reproductive traits. In this study, the role that the Y chromosome plays in creating such heterogeneity is explored by testing the hypothesis that the Y chromosome serves as a carrier of the exposure impact to future generations. This hypothesis implies that a male who has a Y chromosome that is from a male that was exposed to an endocrine disruptor will display a more severe reproductive phenotype than a male whose Y chromosome is from an unexposed male. To test this hypothesis, we used a mouse model in which F1 generation animals were exposed prenatally to an endocrine disruptor, di-2-ethylhexyl phthalate (DEHP), and the severity of impacted reproductive traits was compared between the F3 generation males that were descendants of F1 males (paternal lineage) and those from F1 females (maternal lineage). Pregnant dams (F0 generation) were exposed to the vehicle or 20 or 200 µg/kg/day of DEHP from gestation day 11 until birth. Paternal lineage F3 DEHP males exhibited decreased fertility, testicular steroidogenic capacity, and spermatogenesis that were more severely impaired than those of maternal lineage males. Indeed, testicular transcriptome analysis found that a number of Y chromosomal genes had altered expression patterns in the paternal lineage males. This transgenerational difference in the DEHP impact can be attributed specifically to the Y chromosome.

Effects of Tilmicosin Treatment on the Nasopharyngeal Microbiota of Feedlot Cattle With Respiratory Disease During the First Week of Clinical Recovery.

While the nasopharyngeal (NP) microbiota is believed to be a key player in bovine respiratory health, there is limited published information about the change of NP microbiota associated with clinical recovery from bovine respiratory disease (BRD). The objective of this study was to evaluate the effect of tilmicosin treatment on the NP microbiota composition and diversity of BRD-affected calves during the first week of clinical recovery. Deep NP swabs were collected from diseased calves at the initial diagnosis of BRD, and again 7 days after the administration of a single dose of tilmicosin. As an experimental control, samples were collected from clinically healthy, pen-matched calves at the time of initial BRD diagnosis. In general, the NP microbiota from the control calves were more diverse than the NP microbiota from tilmicosin treated and BRD-affected calves. Principle coordinate analysis (PCOA) of Bray-Curtis and Jaccard dissimilarity also revealed that the overall composition of NP microbial communities in tilmicosin-treated calves closely resembled that of BRD-affected calves but differed significantly from pen-matched healthy calves. Overall, it appeared that there were only minor changes in NP microbial communities following tilmicosin treatment and, during the early phase of clinical recovery the NP microbiota in treated animals was disparate from that observed in healthy control calves. Understanding the potential impact of this prolonged recovery in mucosal microbiota would be important in optimizing the use of antimicrobials in health management programs in the feedlot industry.

Residual feed intake divergence during the preweaning period is associated with unique hindgut microbiome and metabolome profiles in neonatal Holstein heifer calves.

BACKGROUND: Recent studies underscored that divergence in residual feed intake (RFI) in mature beef and dairy cattle is associated with changes in ruminal microbiome and metabolome profiles which may contribute, at least in part, to better feed efficiency. Because the rumen in neonatal calves during the preweaning period is underdeveloped until close to weaning, they rely on hindgut microbial fermentation to breakdown undigested diet components. This leads to production of key metabolites such as volatile fatty acids (VFA), amino acids, and vitamins that could potentially be absorbed in the hind-gut and help drive growth and development. Whether RFI divergence in neonatal calves is associated with changes in hindgut microbial communities and metabolites is largely unknown. Therefore, the objective of the current study was to determine differences in hindgut microbiome and metabolome in neonatal Holstein heifer calves retrospectively-grouped based on feed efficiency as most-efficient (M-eff) or least-efficient (L-eff) calves using RFI divergence during the preweaning period. METHODS: Twenty-six Holstein heifer calves received 3.8 L of first-milking colostrum from their respective dams within 6 h after birth. Calves were housed in individual outdoor hutches bedded with straw, fed twice daily with a milk replacer, and had ad libitum access to a starter grain mix from birth to weaning at 42 d of age. Calves were classified into M-eff [n = 13; RFI coefficient = - 5.72 ± 0.94 kg DMI (milk replacer + starter grain)/d] and L-eff [n = 13; RFI coefficient = 5.61 ± 0.94 kg DMI (milk replacer + starter grain)/d] based on a linear regression model including the combined starter grain mix and milk replacer DMI, average daily gain (ADG), and metabolic body weight (MBW). A deep sterile rectal swab exposed only to the rectum was collected immediately at birth before colostrum feeding (i.e., d 0), and fecal samples at d 14, 28, and 42 (prior to weaning) for microbiome and untargeted metabolome analyses using 16S rRNA gene sequencing and LC-MS. Microbiome data were analyzed with the QIIME 2 platform and metabolome data with the MetaboAnalyst 4.0 pipeline. RESULTS: No differences (P > 0.05) in body measurements including body weight (BW), body length (BL), hip height (HH), hip width (HW), and wither height (WH) were detected between M-eff and L-eff calves at birth and during preweaning. Although milk replacer intake did not differ between groups, compared with L-eff, M-eff heifers had lower starter intake (P < 0.01) between d 18 to 42 of age, whereas no differences (P > 0.05) for ADG, cumulative BWG, or body measurements were observed between RFI groups during the preweaning period. Microbiome and metabolome profiles through the first 42 d of age indicated greater hindgut capacity for the production of energy-generating substrates (butyrate and propionate) and essential nutrients (vitamins and amino acids) in heifers with greater estimated feed efficiency. CONCLUSION: Despite consuming approximately 54.6% less solid feed (cumulative intake, 10.90 vs. 19.98 ± 1.66 kg) from birth to weaning, the microbiome-metabolome changes in the hindgut of most-efficient heifers might have helped them maintain the same level of growth as the least-efficient heifers.

Supply of Methionine During Late-Pregnancy Alters Fecal Microbiota and Metabolome in Neonatal Dairy Calves Without Changes in Daily Feed Intake.

To our knowledge, most studies demonstrating the role of manipulating maternal nutrition on hindgut (i.e., large intestine) microbiota in the offspring have been performed in non-ruminants. Whether this phenomenon exists in cattle is largely unknown. Therefore, the objectives of the current study were to evaluate the impact of maternal post-ruminal supply of methionine during late-pregnancy in dairy cows on fecal microbiota and metabolome in neonatal calves, and their association with body development and growth performance during the preweaning period. To achieve this, heifer calves, i.e., neonatal female offspring, born to Holstein cows receiving either a control (CON) diet (n = 13) or CON plus rumen-protected methionine (MET; Evonik Nutrition & Care GmbH) during the last 28 days of pregnancy were used. Fecal samples from heifers were collected from birth until 6 weeks of age, i.e., the preweaning period. Fecal microbiota was analyzed with QIIME 2 whereas fecal metabolites were measured using an untargeted LC-MS approach. At birth, MET heifers had greater (P ≤ 0.05) BW, HH, and WH. During the preweaning period, no differences between groups were detected for starter intake (P = 0.77). However, MET heifers maintained greater (P ≤ 0.05) BW, HH and tended (P = 0.06) to have greater WH and average daily gain (ADG) (P = 0.10). Fecal microbiota and metabolome profiles through 42 days of age in MET heifers indicated greater capacity for hindgut production of endogenous antibiotics and enhanced hindgut functionality and health. Enhancing maternal post-ruminal supply of methionine during late-gestation in dairy cows has a positive effect on hindgut functionality and health in their offspring through alterations in the fecal microbiota and metabolome without affecting feed intake. Those alterations could limit pathogen colonization of the hindgut while providing essential nutrients to the neonate. Together, such responses contribute to the ability of young calves to achieve better rates of nutrient utilization for growth.