VetBiomeX's Research and Development team is a collaborative group of biologists who thrive working at the forefront of innovation.
VetBiomeX portfolio showcases various projects created throughout our career.
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.
- Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture.
- Frontiers in Microbiology.
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.
- Metabolomics and Proteomics Signatures in Feed-Efficient Beef and Dairy Cattle
- Sustainable Agriculture Reviews.
Feed accounts for 40–60% of total expenses of beef and dairy cattle production costs. Therefore, feed-efficient cattle have a great potential to reduce production costs without compromising meat or milk production levels, resulting in a greater profit margin for producers. Many approaches for measuring feed efficiency are available with residual feed intake being one of the most common. The residual feed intake is defined as the difference between actual dry matter intake and expected dry matter intake based on animal size and production level. Therefore, compared with a least-efficient animal, the most-efficient animal would have a negative residual feed intake coefficient value, indicating that it consumed less dry matter intake while maintaining the same level of production. Recent studies have focused on investigating changes in key metabolites and proteins that would shift metabolic pathways to support better feed efficiency. Recent reports highlighted that in most-efficient cattle metabolic pathways associated with energy, vitamins, and amino acid metabolism in rumen and skeletal muscle are upregulated to provide extra energy, thus, allowing for a similar level of production despite lower dry matter intake. Other studies demonstrated that most-efficient cattle reduce protein turnover in skeletal muscle including upregulation of key protein synthesis pathways, such as mechanistic target of rapamycin signaling, and the downregulation of key proteins in protein degradation such as ubiquitin-proteasome pathway, resulting in greater protein deposition in muscle. In this chapter, we discuss applications of novel comprehensive techniques for protein and metabolite profiling in rumen, intestine, blood, liver, and skeletal muscle to elucidate adaptive biological functions that support better feed efficiency in beef and dairy cattle.
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. 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.
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.
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.
- Contribution of the mucosal microbiota to bovine respiratory health.
- Trends in microbiology journal.
Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock.
While the antimicrobial resistance profiles of cultured pathogens have been characterized in swine, the fluctuations in antimicrobial resistance genes (ARGs) associated with the developing gastrointestinal microbiota have not been elucidated. The objective of this study was to assess the impact of perinatal tulathromycin (TUL) metaphylaxis on the developmental dynamics of fecal microbiota and their accompanying antimicrobial resistome in pre-weaned piglets. Sixteen litters were given one of two treatments [control group (CONT; saline 1cc IM) and TUL group (TUL; 2.5 mg/kg IM)] directly after birth. Deep fecal swabs were collected at day 0 (prior to treatment), and again at days 5 and 20 post treatment. Shotgun metagenomic sequencing was performed on the extracted DNA, and the fecal microbiota structure and abundance of ARGs were assessed. Collectively, the swine fecal microbiota and their accompanying ARGs were diverse and established soon after birth. Across all samples, a total of 127 ARGs related to 19 different classes of antibiotics were identified. The majority of identified ARGs were observed in both experimental groups and at all-time points. The magnitude and extent of differences in microbial composition and abundance of ARGs between the TUL and CONT groups were statistically insignificant. However, both fecal microbiota composition and ARGs abundance were changed significantly between different sampling days. In combination, these results indicate that the perinatal TUL metaphylaxis has no measurable benefits or detriment impacts on fecal microbiota structure and abundance of ARGs in pre-weaned piglets.
The limited understanding of the interaction between rearing environment of the growing pig and the pig’s microbial community impedes efforts to identify the optimal housing system to maximize animal health and production. Accordingly, we characterized the impact of housing complexity on shaping the respiratory and gut microbiota of growing pig. A total of 175 weaned pigs from 25 litters were randomly assigned within liter to either simple slatted-floor (S) or complex straw-based rearing ecosystem (C). Beside the floor swabs samples, fecal swabs and mucosal scraping samples from bronchus, ileum, and colon were collected approximately 164 days post-weaning at the time of slaughter. The S ecosystem seems to increase the α-diversity of respiratory and gut microbiota. Moreover, the C-raised pigs showed 35.4, 89.2, and 60.0% reduction in the Firmicutes/Bacteroidetes ratio than the S-raised pigs at bronchus, ileum, and colon, respectively. The unfavorable taxa Psychrobacter, Corynebacterium, Actinobacteria, and Neisseria were the signature taxa of C environment-associated microbial community. Therefore, the microbiota of S-raised pigs seems to show higher density of the most essential and beneficial taxa than the C-raised pigs. We preliminarily conclude that increasing the physical complexity of rearing environment seems to provide suboptimal conditions for establishing a healthy microbial community in the growing pigs.
Optimization of antimicrobial use in swine management systems requires full understanding of antimicrobial-induced changes on the developmental dynamics of gut microbiota and the prevalence of antimicrobial resistance genes (ARGs). The purpose of this study was to evaluate the impacts of early life antimicrobial intervention on fecal microbiota development, and prevalence of selected ARGs (ermB, tetO, tetW, tetC, sulI, sulII, and blaCTX–M) in neonatal piglets. A total of 48 litters were randomly allocated into one of six treatment groups soon after birth. Treatments were as follows: control (CONT), ceftiofur crystalline free acid (CCFA), ceftiofur hydrochloride (CHC), oxytetracycline (OTC), procaine penicillin G (PPG), and tulathromycin (TUL). Fecal swabs were collected from piglets at days 0 (prior to treatment), 5, 10, 15, and 20 post treatment. Sequencing analysis of the V3-V4 hypervariable region of the 16S rRNA gene and selected ARGs were performed using the Illumina Miseq platform. Our results showed that, while early life antimicrobial prophylaxis had no effect on individual weight gain, or mortality, it was associated with minor shifts in the composition of fecal microbiota and noticeable changes in the abundance of selected ARGs. Unifrac distance metrics revealed that the microbial communities of the piglets that received different treatments (CCFA, CHC, OTC, PPG, and TUL) did not cluster distinctly from CONT piglets. Compared to CONT group, PPG-treated piglets exhibited a significant increase in the relative abundance of ermB and tetW at day 20 of life. Tulathromycin treatment also resulted in a significant increase in the abundance of tetW at days 10 and 20, and ermB at day 20. Collectively, these results demonstrate that the shifts in fecal microbiota structure caused by perinatal antimicrobial intervention are modest and limited to particular groups of microbial taxa. However, early life PPG and TUL intervention could promote the selection of ARGs in herds. While additional investigations are required to explore the consistency of these findings across larger populations, these results could open the door to new perspectives on the utility of early life antimicrobial administration to healthy neonates in swine management systems
- Antimicrobial effects on swine gastrointestinal microbiota and their accompanying antibiotic resistome.
- Frontiers in microbiology journal.
Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.
Optimization of antimicrobial use in swine management systems requires full understanding of antimicrobial-induced changes on the developmental dynamics of gut microbiota and the prevalence of antimicrobial resistance genes (ARGs). The purpose of this study was to evaluate the impacts of early life antimicrobial intervention on fecal microbiota development, and prevalence of selected ARGs (ermB, tetO, tetW, tetC, sulI, sulII, and blaCTX–M) in neonatal piglets. A total of 48 litters were randomly allocated into one of six treatment groups soon after birth. Treatments were as follows: control (CONT), ceftiofur crystalline free acid (CCFA), ceftiofur hydrochloride (CHC), oxytetracycline (OTC), procaine penicillin G (PPG), and tulathromycin (TUL). Fecal swabs were collected from piglets at days 0 (prior to treatment), 5, 10, 15, and 20 post treatment. Sequencing analysis of the V3-V4 hypervariable region of the 16S rRNA gene and selected ARGs were performed using the Illumina Miseq platform. Our results showed that, while early life antimicrobial prophylaxis had no effect on individual weight gain, or mortality, it was associated with minor shifts in the composition of fecal microbiota and noticeable changes in the abundance of selected ARGs. Unifrac distance metrics revealed that the microbial communities of the piglets that received different treatments (CCFA, CHC, OTC, PPG, and TUL) did not cluster distinctly from CONT piglets. Compared to CONT group, PPG-treated piglets exhibited a significant increase in the relative abundance of ermB and tetW at day 20 of life. Tulathromycin treatment also resulted in a significant increase in the abundance of tetW at days 10 and 20, and ermB at day 20. Collectively, these results demonstrate that the shifts in fecal microbiota structure caused by perinatal antimicrobial intervention are modest and limited to particular groups of microbial taxa. However, early life PPG and TUL intervention could promote the selection of ARGs in herds. While additional investigations are required to explore the consistency of these findings across larger populations, these results could open the door to new perspectives on the utility of early life antimicrobial administration to healthy neonates in swine management systems.
- Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration.
- Frontiers in microbiology journal.
- Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs.
- Microbial pathogenesis journal.
- Synergetic action between the rumen microbiota and bovine health.
- Microbial pathogenesis journal.
- Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea.
- Microbial pathogenesis journal.
The bovine gastrointestinal microbiota is a complex polymicrobial ecosystem that plays an important role in maintaining mucosal health. The role of mucosal microbial populations in the pathogenesis of gastrointestinal diseases has been well established in other species. However, limited information is available about changes in the fecal microbiota that occur under disease conditions, such as hemorrhagic diarrhea in feedlot cattle. The objectives of this study were to characterize the differences in fecal microbiota composition, diversity and functional gene profile between feedlot calves with, and without, hemorrhagic diarrhea. Deep fecal swabs were collected from calves with hemorrhagic diarrhea (n = 5) and from pen matched healthy calves (n = 5). Genomic DNA was extracted, and V1-V3 hypervariable region of 16S rRNA gene was amplified and sequenced using the Illumina MiSeq sequencing. When compared to healthy calves, feedlot cattle with hemorrhagic diarrhea showed significant increases in the relative abundance of Clostridium, Blautia and Escherichia, and significant decreases in the relative abundance of Flavobacterium, Oscillospira, Desulfonauticus, Ruminococcus, Thermodesulfovibrio and Butyricimonas. Linear discriminant analysis effect size (LEfSe) also revealed significant differences in bacterial taxa between healthy calves and hemorrhagic diarrhea calves. This apparent dysbiosis in fecal microbiota was associated with significant differences in the predictive functional metagenome profiles of these microbial communities. In summary, our results revealed a bacterial dysbiosis in fecal samples of calves with hemorrhagic diarrhea, with the diseased calves exhibiting less diversity and fewer observed species compared to healthy controls. Additional studies are warranted in a larger cohort of animals to help elucidate the trajectory of change in fecal microbial communities, and their predictive functional capacity, in calves with other gastrointestinal diseases.
- Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease.
- Veterinary microbiology journal.
- Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model.
- Microbial pathogenesis journal.
The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract. Consequently, we have little understanding of the relationship between upper and lower respiratory tract microbiota in healthy cattle. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Nasopharyngeal swabs (NPS), and bronchoalveolar lavage (BAL) fluid, were collected from clinically healthy feedlot calves (n = 8). Genomic DNA from each sample was extracted, and the V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using Illumina Miseq platform. Across all samples, the most predominant phyla were Proteobacteria, Actinobacteria and Firmicutes. The most common genera were Rathayibacter, Mycoplasma, Bibersteinia and Corynebacterium. The microbial community structure was distinct between these two biogeographical sites. Most of the bacterial genera identified in the BAL samples were also present in the NPS, but biogeographical-specific genera were enriched in both the NPS (Rathayibacter) and BAL (Bibersteinia) samples. There were strong associations between the presence of certain taxa at each specific location, and strong correlations between the presence of specific taxa in both the NPS and BAL samples. The correlation between the presence of specific taxa in both the NPS and BAL samples, supports the notion of a mutualistic interrelationship between these microbial communities. Future studies, in large cohorts of animals, are needed to determine the role and clinical importance of the relationships of respiratory tract microbial communities with health, productivity, and susceptibility to the development of respiratory disease, in growing cattle.