Fig 3 - available from: Microbiome
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Principal coordinates analysis (PCoA) 3D images. PCoA was performed using Bray-Curtis dissimilarity (a), unweighted UniFrac (b), and weighted UniFrac (c) distance matrices. Each sample is represented by a point with nasal swabs (NS = 11) in blue and trans-tracheal aspiration (TTA = 17) in red. The clustering observed between the NS and TTA samples indicates differences in the microbial compositions of these sampling sites
Source publication
Background:
The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characteri...
Context in source publication
Context 1
... was compared by Bray-Curtis dissimilarity, weighted UniFrac, and unweighted UniFrac phylogenetic distances. The difference between the two bacterial com- munities was statistically significant as assessed by Adonis (P = 0.001), based on the three different distance matrices. Principal coordinates analysis (PCoA) plots of the methods are shown in Fig. 3. The type I error with a significance at 0.05 was < 0.001, as was the type II error, providing a power > ...
Citations
... Despite its detection in diverse settings, its potential to cause or prevent disease remains unknown [48]. Furthermore, the genus Psychrobacter has been recognized as a commensal of the bovine nasal microbiome but is occasionally detected in nasal samples from animals with BRD [11,43,49,50]. However, some studies have even suggested that Psychrobacter may have an antagonistic effect on Mycoplasma abundance [11,30,35]. ...
Background
Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.
Results
Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.
Conclusions
Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.
... These differences underscore the significance of microbial profiles in distinguishing between the two groups. The prevalent families Moraxellaceae, Enterobacteriaceae, and Flavobacteriaceae in Fig. 2 Hierarchical clustering analysis heatmap at the family level of the LRT microbiota among the healthy and BRD-affected calves the cattle's lower respiratory tract align with previous studies, emphasizing their importance in the cattle respiratory microbiome (Chai et al. 2022;Nicola et al. 2017). In line with other studies, we observed significant differences in their relative abundances between healthy and BRD-infected groups, indicating a disrupted microbiota in BRD-affected calves (Klima et al. 2019;Nicola et al. 2017). ...
... The prevalent families Moraxellaceae, Enterobacteriaceae, and Flavobacteriaceae in Fig. 2 Hierarchical clustering analysis heatmap at the family level of the LRT microbiota among the healthy and BRD-affected calves the cattle's lower respiratory tract align with previous studies, emphasizing their importance in the cattle respiratory microbiome (Chai et al. 2022;Nicola et al. 2017). In line with other studies, we observed significant differences in their relative abundances between healthy and BRD-infected groups, indicating a disrupted microbiota in BRD-affected calves (Klima et al. 2019;Nicola et al. 2017). Notably, certain genera such as Acinetobacter, and Pseudomonas were markedly more prevalent in the lower respiratory tract of BRD-infected calves. ...
The advent of next-generation sequencing technologies has uncovered the importance of commensal microbial populations in the lower respiratory tract (LRT) for mucosal health and their role in the development of bovine respiratory disease (BRD). In this study, we aimed to characterize and compare the LRT microbiota in healthy and BRD-affected calves in Egypt. After assessing clinical respiratory scores in both groups, post-mortem lung samples from the cranial lobes of six clinically healthy calves and six calves affected by BRD were collected following slaughter. The most prevalent bacterial families in all samples were Moraxellaceae (11.06%), Enterobacteriaceae (8.23%), and Flavobacteriaceae (8.13%). The most common bacterial genera across all samples were Acinetobacter (13.1%), Gracilibacillus (7.9%), and Pseudomonas (5.0%). Notably, the overall microbial community structures differed significantly between healthy and BRD-affected calves. Alpha diversity analysis revealed significant differences in the Shannon (p = 0.0043) and Chao1 (p = 0.0001) indices between the two groups. This study highlights the substantial impact of BRD on the LRT microbiota of calves, highlighting the intricate relationship between host health and the LRT microbial ecosystem. Further investigations involving a larger sample size are necessary to establish the clinical significance of LRT microbiota in maintaining bovine respiratory health.
... While Psychrobacter species have been recovered from mammalian hosts, including marine mammals, birds, and fish, their capability to cause disease is rare, and the factors influencing infection remain unclear [27]. This microbe has occasionally been associated with BRD occurrences [9,[28][29][30]. But studies have also suggested that it possesses antagonistic effect on Mycoplasma abundance [9,31]. ...
Background
Bovine respiratory disease (BRD) remains a significant health and economic problem to the dairy cattle industry. Multiple risk factors contribute to BRD susceptibility including the bacterial pathobionts Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Studies have characterized and quantified the abundance of these bacteria in the nasal cavity of cattle to infer and help disease diagnosis; nonetheless, there is still discrepancy in the results observed of when these microbes are commensal or pathogenic. Additionally, some of these studies are limited to a specific farm. The goal of this study is to compare the nasal microbiome community (diversity and composition) and the abundance of the four bacterial pathogens (by qPCR) in the nasal cavity to identify differences between dairy calves that are apparently healthy and those identified to have BRD. Nasal swabs were collected from approximately 50 apparently healthy and 50 BRD-affected calves sampled from five different dairy farms in the US (CA, IN, NY (two farms), and TX).
Results
Calves diagnosed with BRD in NY, and TX had lower nasal microbiome diversity compared to the apparently healthy calves. Differences in the nasal microbiome composition were observed between the different farms predicted by Bray-Curtis and weighted UniFrac dissimilarities. Commensal and pathobiont genera Acinetobacter, Moraxella, Psychrobacter, Histophilus, Mannheimia, Mycoplasma, and Pasteurella were prevalent in the bovine nasal microbiome regardless of farm or disease status. The BRD-pathobiont H. somni was the most prevalent pathobiont among all the samples and M. bovis the least prevalent. Only in CA was the abundance of a pathobiont different according to disease status, where M. haemolytica was significantly more abundant in the BRD-affected animals than apparently healthy animals.
Conclusions
This study offers insight into the nasal microbiome community composition in both animals diagnosed with BRD and healthy animals, and shows that the farm effect plays a more significant role in determining the microbiome community than disease status in young dairy calves.
... While there were minimal overlaps between differentially abundant taxa among each respiratory tract site and across sampling times, there were taxa present in more than one site of the respiratory tract. This overlap has been observed in other studies (Nicola et al., 2017;Zeineldin et al., 2017;Timsit et al., 2018;Howe et al., 2023). ...
Introduction
Probiotics are a promising intervention for modulating the microbiome and the immune system, promoting health benefits in cattle. While studies have characterized the calf lung bacterial profile with and without oral probiotics, simultaneous probiotic effects on the bacterial populations of multiple sites along the respiratory tract have not been characterized.
Methods
This study utilized the same pre-weaning diary calf group from our previous studies to characterize the bacterial populations present in the nostril and tonsil across control and treatment groups and nine sampling time points. DNA was exacted from the nostril and tonsil swabs and lung lavage fluids, and 16S ribosomal RNA gene hypervariable regions 1-3 were subsequently sequenced.
Results
Temporal variation in alpha bacterial diversity within the nostril, tonsil, and lung samples was observed, indicating distinct bacterial compositions among sampling time points. Oral probiotic treatment did not change alpha diversity in any respiratory tissue, however, spatial variability in bacterial taxa composition was observed among the three respiratory tract regions. While the majority of differentially abundant taxa in probiotic treated calves were unique to their anatomical location, a few were common to two anatomical locations and one Finegoldia amplicon sequence variant was differentially abundant in all three anatomical locations.
Discussion
In conclusion, these findings contribute to the understanding of the dynamic nature of bacterial diversity and the potential effects of probiotics within the bovine respiratory tract and provides insight for future studies of probiotics on animal health, disease prevention, and management.
... Based on the limited published case reports, Psychrobacter sanguini strains are considered to be highly susceptible to antimicrobial drugs. Although Psychrobacter species have mainly been isolated from marine environments and cold habitats, a study reported that P. sanguinis (1.1% of total operational taxonomic units) was the most abundant species in the upper respiratory microbiota in Piedmontese calves [15]. We report a case of P. sanguinis infection in a pediatric patient with craniopharyngioma. ...
Psychrobacter species are gram‐negative bacteria in the Moraxellaceae family. These bacteria are considered rare opportunistic human pathogens, and the infection sites include blood, cerebral spinal fluid, wounds, urine, the ears, and the eyes. Few cases of human infection by these species have been described previously. We report a case of a 10‐year‐old boy with postneurosurgical bacteremia due to Psychrobacter sanguinis infection. This infection was difficult to identify using routine biochemical phenotypical tests. Sequencing of 16S rRNA was performed to identify this pathogen. The patient was successfully treated with antibiotics. In conclusion, P. sanguinis infections are rare but should be considered when cultures remain negative for common pathogens.
... As a crucial organ of the respiratory system, variations in the indigenous microbiota inside the lung correspond to shifts in other areas of the body, like the oral cavity, upper respiratory tract, and intestinal tract. These changes can impact the lung microbiota in multiple ways [63,64]. ...
The human body harbors a diverse microbiota across various anatomical sites, including the lungs, which play a crucial role in maintaining respiratory health and influencing disease outcomes. This review synthesizes current research on the lung microbiota's impact on pulmonary diseases, emphasizing its interactions with microbiota from other body regions, such as the gut and oral cavity. Emerging evidence suggests that lung microbiota dysbiosis is intricately linked to the pathogenesis of various pulmonary diseases, including idiopathic pulmonary fibrosis, lung cancer, pneumonia, asthma, and chronic obstructive pulmonary disease (COPD). The review highlights the significance of understanding these microbial interactions to advance diagnostic, preventive, and therapeutic strategies for respiratory diseases. By elucidating the mechanisms through which microbiota influence lung health, this review underscores the potential of microbiome-based diagnostics and therapeutics in revolutionizing the management of pulmonary diseases, paving the way for personalized medicine and innovative treatment approaches.
... Under normal physiological conditions, commensal microorganisms maintain a mutualistic relationship with the host by regulating the airway's innate and adaptive immune functions (Mach et al. 2021). Classifying healthy versus diseased animals based on their respiratory tract microbiomes has been done successfully for ruminants (Holman et al. 2015;Nicola et al. 2017;Gaeta et al. 2017;Zeineldin et al. 2017;Timsit et al. 2017;McMullen et al. 2019;Zeineldin et al. 2020;McMullen et al. 2020;Chai et al. 2022;Mariadassou et al. 2023), pigs (Correa-Fiz et al. 2016;Wang et al. 2018;Correa-Fiz et al. 2019;Mahmmod et al. 2020), horses (UCVM Class of 2019, 2020), and chickens (Yitbarek et al. 2018;Ngunjiri et al. 2019;Yitbarek et al. 2019). However, mucus is an often forgotten aspect of the complex respiratory system in animals. ...
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
... The microbiota has been shown to play a pivotal role in various aspects of host health, for example by providing critical support in immune system maturation, nutrient utilization 2,3 , and defense against pathogen invasion 3,4 . In the case of respiratory pathogens, one of the first lines of defense is the nasal microbiota 5 , and many recent studies have focused on characterizing the commensal nasal microbiota and its relationship with respiratory pathogens in humans 5,6 and various animal species [7][8][9][10][11] . These studies have identified a variety of taxa that are frequently found in the nasal microbiota of different host species, including members from different genera such as Moraxella, Lactobacillus, Streptococcus, Haemophilus/Glaesserella, and Staphylococcus [6][7][8][9][10][11] . ...
... In the case of respiratory pathogens, one of the first lines of defense is the nasal microbiota 5 , and many recent studies have focused on characterizing the commensal nasal microbiota and its relationship with respiratory pathogens in humans 5,6 and various animal species [7][8][9][10][11] . These studies have identified a variety of taxa that are frequently found in the nasal microbiota of different host species, including members from different genera such as Moraxella, Lactobacillus, Streptococcus, Haemophilus/Glaesserella, and Staphylococcus [6][7][8][9][10][11] . ...
The nasal microbiota is a key contributor to animal health, and characterizing the nasal microbiota composition is an important step towards elucidating the role of its different members. Efforts to characterize the nasal microbiota composition of domestic pigs and other farm animals frequently report the presence of bacteria that are typically found in the gut, including many anaerobes from the Bacteroidales and Clostridiales orders. However, the in vivo role of these gut-microbiota associated taxa is currently unclear. Here, we tackled this issue by examining the prevalence, origin, and activity of these taxa in the nasal microbiota of piglets. First, analysis of the nasal microbiota of farm piglets sampled in this study, as well as various publicly available data sets, revealed that gut-microbiota associated taxa indeed constitute a substantial fraction of the pig nasal microbiota that is highly variable across individual animals. Second, comparison of herd-matched nasal and rectal samples at amplicon sequencing variant (ASV) level showed that these taxa are largely shared in the nasal and rectal microbiota, suggesting a common origin driven presumably by the transfer of fecal matter. Third, surgical sampling of the inner nasal tract showed that gut-microbiota associated taxa are found throughout the nasal cavity, indicating that these taxa do not stem from contaminations introduced during sampling with conventional nasal swabs. Finally, analysis of cDNA from the 16S rRNA gene in these nasal samples indicated that gut-microbiota associated taxa are indeed active in the pig nasal cavity. This study shows that gut-microbiota associated taxa are not only present, but also active, in the nasal cavity of domestic pigs, and paves the way for future efforts to elucidate the function of these taxa within the nasal microbiota.
... Bovine respiratory disease (BRD) is a widespread disease and one of the greatest challenges in the livestock industry. It is a leading cause of morbidity, mortality, and economic loss in cattle (1), accounting for approximately 70%-80% of total morbidity in feedlots, especially among newborn calves (2,3). Over 90% of feedlots in the United States report BRD as the most prevalent disease, with an estimated annual cost ranging from USD 1 to 3 billion (4,5); in Australia, the documented morbidity and mortality rates for BRD were 18% and 2.1%, respectively, with an average net loss of AUD 1647.53 per death (6). ...
... However, some pathogenic microorganisms appear to be conditionally pathogenic, especially in newly weaned calves, whose many stressors can disrupt the respiratory system and promote development of BRD (19,20). Pathogenic microorganisms associated with common BRD pathogens such as M. bovis, Mh, and Pm have been observed in nasal and pharyngeal swabs from both healthy and BRD-infected cattle (1,21). Common respiratory pathogens have also been recently identified in the lungs of both healthy and affected cattle. ...
Bovine respiratory disease (BRD) is one of the most common diseases in the cattle industry worldwide; it is caused by multiple bacterial or viral coinfections, of which Mycoplasma bovis (M. bovis) and bovine herpesvirus type 1 (BoHV-1) are the most notable pathogens. Although live vaccines have demonstrated better efficacy against BRD induced by both pathogens, there are no combined live and marker vaccines. Therefore, we developed an attenuated and marker M. bovis-BoHV-1 combined vaccine based on the M. bovis HB150 and BoHV-1 gG-/tk- strain previously constructed in our lab and evaluated in rabbits. This study aimed to further evaluate its safety and protective efficacy in cattle using different antigen ratios. After immunization, all vaccinated cattle had a normal rectal temperature and mental status without respiratory symptoms. CD4⁺, CD8⁺, and CD19⁺ cells significantly increased in immunized cattle and induced higher humoral and cellular immune responses, and the expression of key cytokines such as IL-4, IL-12, TNF-α, and IFN-γ can be promoted after vaccination. The 1.0 × 10⁸ CFU of M. bovis HB150 and 1.0 × 10⁶ TCID50 BoHV-1 gG-/tk- combined strain elicited the most antibodies while significantly increasing IgG and cellular immunity after challenge. In conclusion, the M. bovis HB150 and BoHV-1 gG-/tk- combined strain was clinically safe and protective in calves; the mix of 1.0 × 10⁸ CFU of M. bovis HB150 and 1.0 × 10⁶ TCID50 BoHV-1 gG-/tk- strain was most promising due to its low amount of shedding and highest humoral and cellular immune responses compared with others. This study introduces an M. bovis-BoHV-1 combined vaccine for application in the cattle industry.
... Bovine respiratory disease (BRD) is a widespread cause of morbidity, mortality, and economic loss in beef and dairy cattle farming [1]. BRD may also be responsible for up to 70% of morbidity and mortality in U.S. feedlot cattle [2,3], and BRD is recognized as the primary disease affecting cattle in over 90% of feedlots across the United States, with an estimated annual cost ranging from 1 to 3 billion USD [4,5]. ...
... In Australia, the recorded rates of illness and death for BRD were 18% and 2.1%, respectively, with an average financial loss of $1076.17 per death [7]. BRD is a multifactorial disease, and its etiology involves bacterial and viral coinfections with high re-infection rates [8]; also, the susceptibility of cattle to this disease can be influenced by a complex interaction between stress, management practices, physiological conditions, and the host immune response [1,9,10]. Moreover, immunosuppression caused by viral infections is also significantly associated with the risk of severe secondary bacterial infections. ...
Bovine respiratory disease (BRD) is one of the most common diseases in the cattle industry; it is a globally prevalent multifactorial infection primarily caused by viral and bacterial coinfections. In China, Mycoplasma bovis (M. bovis) and bovine herpesvirus type 1 (BoHV-1) are the most notable pathogens associated with BRD. Our previous study attempted to combine the two vaccines and conducted a preliminary investigation of their optimal antigenic ratios. Based on this premise, the research extended its investigation by administering varying vaccine doses in a rabbit model to identify the most effective immunization dosage. After immunization, all rabbits in other immunization dose groups had a normal rectal temperature without obvious clinical symptoms. Furthermore, assays performed on the samples collected from immunized rabbits indicated that there were increased humoral and cellular immunological reactions. Moreover, the histological analysis of the lungs showed that immunized rabbits had more intact lung tissue than their unimmunized counterparts after the challenge. Additionally, there appears to be a positive correlation between the protective efficacy and the immunization dose. In conclusion, the different immunization doses of the attenuated and marker M. bovis HB150 and BoHV-1 gG-/tk- combined vaccine were clinically safe in rabbits; the mix of 2.0 × 108 CFU of M. bovis HB150 and 2.0 × 106 TCID50 BoHV-1 gG-/tk- strain was most promising due to its highest humoral and cellular immune responses and a more complete morphology of the lung tissue compared with others. These findings determined the optimal immunization dose of the attenuated and marker M. bovis HB150 and BoHV-1 gG-/tk- combined vaccine, laying a foundation for its clinical application.
