Microbiomes associated with bovine periodontitis and oral health

Gingivitis- and periodontitis-associated microbiota in bovine deciduous incisor teeth - A preliminary study

As ruminants are frequently affected by periodontal diseases, understanding their microbial communities is crucial. In this pilot study, we analyzed subgingival biofilm samples of young cattle across different states: clinically healthy (n = 5), gingivitis (n = 5), and periodontitis (n = 5) using 16S rRNA gene sequencing and co-occurrence network analysis. The findings revealed that Proteobacteria was the predominant phylum across all conditions, with Fusobacteriota constituting 27.6 % of the microbiota in periodontitis-affected sites. In healthy sites, Moraxella (21.11 %), Neisseria (13.16 %), and Lautropia (7.69 %) were the predominant genera; in gingivitis-affected sites, the leading genera were Neisseria (23.65 %), Moraxella (18.95 %), and Conchiformibius (10.79 %); and in periodontitis sites, Caviibacter (19.78 %), Moraxella (16.13 %), and Fusobacterium (7.56 %) were most prevalent. Richness and dissimilarity analyses did not show significant differences across the clinical states, but differences were found between gingivitis and periodontitis sites (p = 0.01) in diversity. The co-occurrence networks highlighted significant variances in the central phyla across the phenotypes, with a higher number of positive interactions observed in periodontitis-affected sites. Consequently, this study demonstrated that the microbiota associated with periodontitis in young cattle exhibits greater diversity compared to gingivitis. Notably, in the deciduous dentition of cattle, the genera Caviibacter and Moraxella are pivotal in the context of periodontitis and periodontal health, respectively.

Effects of Toothpaste Containing 2% Zinc Citrate on Gingival Health and Three Related Bacteria-A Randomized Double-Blind Study

OBJECTIVES

Gingivitis is the initial stage of periodontitis, one of the most common oral diseases and the primary cause of tooth loss. This study aims to evaluate the effect of toothpaste containing 2% zinc citrate on gingival health and the abundance of three bacteria related to gingivitis and periodontitis.

METHODS AND MATERIALS

Eleven volunteers with the same oral health status were randomly assigned to the treatment (n = 5) and control (n = 6) groups. The control group used fluoride toothpaste, while the treatment group used fluoride toothpaste supplemented with 2% zinc citrate for 3 months. The plaque index, gingival index, and bleeding index were measured at baseline (0 day), 3 weeks, and 3 months. Dental plaque from four areas of the mouth (FDI criteria) was collected at the same timepoints. A total of 132 dental plaque samples were analyzed using quantitative PCR (qPCR) to monitor the abundance of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythia.

RESULTS

Toothpaste containing 2% zinc citrate significantly lowered the gingival index and reduced gum bleeding but did not affect the plaque index. It also reduced the total abundance of the three bacteria related to gingivitis and periodontitis in dental plaque over a long-term period.

CONCLUSIONS

Toothpaste with 2% zinc citrate persistently improves gingival health and reduces the presence of gingivitis-associated bacteria in dental plaque.

TRIAL REGISTRATION

Chinese Clinical Trial Registry (Clinical trial registration no.: ChiCTR1900020592) (09/01/2019).

Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color

Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial community, offering potential for broad-scale population-based studies on the rumen microbiome. The swabs collected from dairy cows often vary widely with respect to sample quality, likely due to several factors such as time of sample collection and cow rumination behavior, which may limit the ability of a given swab to accurately represent the ruminal microbiome. One such factor is the color of the swab, which can vary significantly across different cows. Here, we hypothesize that darker-colored swabs contain more rumen contents, thereby better representing the ruminal bacterial community than lighter-colored swabs. To address this, we collected oral swabs from 402 dairy cows and rumen samples from 13 cannulated cows on a research farm in Wisconsin, United States and subjected them to 16S rRNA sequencing. In addition, given that little is known about the ability of oral swabs to recapitulate the ruminal fungal community, we also conducted ITS sequencing of these samples. To correlate swab color to the microbiota we developed and utilized a novel imaging approach to colorimetrically quantify each swab from a range of light to dark. We found that swabs with increasing darkness scores were significantly associated with increased bacterial alpha diversity (p < 0.05). Lighter swabs exhibited greater variation in their community structure, with many identified amplicon sequence variants (ASVs) categorized as belonging to known bovine oral and environmental taxa. Our analysis of the fungal microbiome found that swabs with increasing darkness scores were associated with decreased alpha diversity (p < 0.05) and were also significantly associated with the ruminal solids fungal community, but not with the ruminal liquid community. Our study refines the utility of oral swabs as a useful proxy for capturing the ruminal microbiome and demonstrates that swab color is an important factor to consider when using this approach for documenting both the bacterial and fungal communities.

The oral microbiome as a proxy for feed intake in dairy cattle

Genetic material from rumen microorganisms can be found within the oral cavity, and hence there is potential in using the oral microbiome as a proxy of the ruminal microbiome. Feed intake (FI) influences the composition of rumen microbiota and might directly influence the oral microbiome in dairy cattle. Ruminal content samples (RS) from 29 cows were collected at the beginning of the study and also 42 d later (RS0 and RS42, respectively). Additionally, 18 oral samples were collected through buccal swabbing at d 42 (OS42) from randomly selected cows. Samples were used to characterize and compare the taxonomy and functionality of the oral microbiome using nanopore sequencing and to evaluate the feasibility of using the oral microbiome to estimate FI. Up to 186 taxonomical features were found differentially abundant (DA) between RS and OS42. Similar results were observed when comparing OS42 to RS collected on different days. Microorganisms associated with the liquid fraction of the rumen were less abundant in OS42 because these were probably swallowed after regurgitation. Up to 1,102 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were found to be DA between RS and OS42, and these results differed when comparing time of collection, but DA KEGG pathways were mainly associated with metabolism in both situations. Models based on the oral microbiome and rumen microbiome differed in their selection of microbial groups and biological pathways to predict FI. In the rumen, fiber-associated microorganisms are considered suitable indicators of FI. In contrast, biofilm formers like Gammaproteobacteria or Bacteroidia classes are deemed appropriate proxies for predicting FI from oral samples. Models from RS exhibited some predictive ability to estimate FI, but oral samples substantially outperformed them. The best lineal model to estimate FI was obtained with the relative abundance of taxonomical feature at genera level, achieving an average R2 = 0.88 within the training data, and a root mean square error of 3.46 ± 0.83 (±SD) kg of DM, as well as a Pearson correlation coefficient between observed and estimated FI of 0.48 ± 0.30 in the test data. The results from this study suggest that oral microbiome has potential to predict FI in dairy cattle, and it encourages validating this potential in other populations.

Characterization of the Hoof Bacterial Communities of Active Digital Dermatitis Lesions in Feedlot Cattle

Digital dermatitis (DD) is a costly hoof infection, causing lameness and pain in feedlot cattle. DD lesions can develop nonlinearly through a series of clinical stages, which can be classified by Dopfer's M-stage scoring system. This widely adopted lesion scoring system recognizes five DD stages, where M1 (early lesion), M2 (acute ulcerative lesion), and M4.1 (chronic proliferative lesion with new developing lesion) are considered active but separate stages of the disease. This study assessed the skin surface microbiota of the active DD lesions of feedlot cattle. The DD lesions from three commercial feedlots were swabbed and then scored according to Dopfer's M-stage scoring system. Swab samples were collected from 12 M2- and 15 M4.1-stage lesions. A total of 21 control swab samples from healthy contralateral feet (DD control) were classified as stage M0. An additional six skin swabs (M0) were collected from completely healthy (CH control) cattle with no lesions. The bacterial communities of active DD lesions (M2 and M4.1) and healthy skin (M0) were profiled using 16S amplicon sequencing. Diversity analyses showed that the hoof bacterial communities of M2 and M4.1 lesions were each distinct from those of M0 skin. However, the bacterial communities between the two active lesion stages were not different from each other. A significant increase in the relative abundance of Spirochaetota and Fusobacteriota and an overall decrease in bacterial diversity contributed to the altered bacterial communities in M2 and M4.1 lesions compared to those of healthy skin (M0). Although stages M2 and M4.1 are considered clinically different stages, the lesion-associated bacterial community is similar between the two active stages.

The effects of ambient temperature and feeding regimens on cecum bacteria composition and circadian rhythm in growing rabbits

Seasonal environmental shifts and improper eating habits are the important causes of diarrhea in children and growing animals. Whether adjusting feeding time at varying temperatures can modify cecal bacterial structure and improve diarrhea remains unknown. Three batches growing rabbits with two groups per batch were raised under different feeding regimens (fed at daytime vs. nighttime) in spring, summer and winter separately, and contents were collected at six time points in 1 day and used 16S rRNA sequencing to investigate the effects of feeding regimens and season on the composition and circadian rhythms of cecum bacteria. Randomized forest regression screened 12 genera that were significantly associated with seasonal ambient temperature changes. Nighttime feeding reduced the abundance of the conditionally pathogenic bacteria Desulfovibrio and Alistipes in summer and Campylobacter in winter. And also increases the circadian rhythmic Amplicon Sequence Variants in the cecum, enhancing the rhythm of bacterial metabolic activity. This rhythmic metabolic profile of cecum bacteria may be conducive to the digestion and absorption of nutrients in the host cecum. In addition, this study has identified 9 genera that were affected by the combination of seasons and feeding time. In general, we found that seasons and feeding time and their combinations affect cecum composition and circadian rhythms, and that daytime feeding during summer and winter disrupts the balance of cecum bacteria of growing rabbits, which may adversely affect cecum health and induce diarrhea risk.

Co-occurrence of periodontal lesions and dental wear in incisor and masticatory teeth in two sheep flocks in Brazil

BACKGROUND

Periodontitis and tooth wear are multifactorial diseases with distinct etiopathogenesis that affect the health, feed efficiency and welfare of sheep.

METHODS

This study evaluated the co-occurrence of tooth wear and periodontal lesions in 129 ewes from two Brazilian flocks, clinically classified the lesions and presence of dental calculus, and identified potential pathogens in the dental biofilm of 63 ewes by polymerase chain reaction.

RESULTS

Of the 129 ewes included in the study, 75 presented periodontal lesions, while all animals presented tooth wear and dental calculus. Of the animals with periodontal lesions, 16.2% had lesions in incisor teeth and 52.7% in masticatory teeth. Regarding excessive tooth wear, 38.6% had severe wear on the incisor teeth and 89.1% on the masticatory teeth. Ewes older than 36 months had a higher frequency of periodontal lesions in incisor teeth (p < 0.001) and a greater amount of dental calculus (p < 0.001), but there was no association between tooth wear and animal age. Fusobacterium nucleatum, Tannerella forsythia and Fusobacterium necrophorum predominated in periodontal lesions.

LIMITATION

This study is limited by the small sample size and lack of diagnostic imaging to assess periodontal disease.

CONCLUSION

The co-occurrence of periodontal lesions and excessive dental wear involving both the incisor and masticatory teeth suggests that although the two diseases have different aetiologies, they likely have common risk factors.

The Oral Microbiome across Oral Sites in Cats with Chronic Gingivostomatitis, Periodontal Disease, and Tooth Resorption Compared with Healthy Cats

Feline chronic gingivostomatitis (FCGS) is a chronic mucosal and gingival inflammatory disease in which pathogenesis remains unclear. Interactions between the host inflammatory process, the host immune response, and the oral microbiome are implicated in this pathogenesis. To begin to understand this disease and the impact of the microbiome to host inflammatory disease states, we collected sterile noninvasive plaque biofilm samples from ten distinct sites within the oral cavity in cats with stomatitis (n = 12), healthy cats (n = 9), and cats with tooth resorption or periodontitis (n = 11). Analysis of full-length 16S rRNA gene sequences indicated that the microbiomes of cats with FCGS presented marked dysbiosis at multiple oral sites. Additionally, microbiome beta diversity varied with oral condition, indicating that stomatitis, periodontitis, and/or tooth resorption influence the microbiome differently. Lastly, we found that the microbiomes of swabs taken from the oral cavity were comparable to those taken from plaque using endodontic paper points, validating this as another sampling method. Collectively, our work furthers our understanding of the dysbiosis and composition of bacteria in the oral microbiome in FCGS, with hopes of contributing to the prevention, diagnosis, and treatment of this challenging condition in felines.

The spatial dissimilarities and connections of the microbiota in the upper and lower respiratory tract of beef cattle

Bovine respiratory disease (BRD) causes morbidity and mortality in cattle. The critical roles of the respiratory microbiota in BRD have been widely studied. The nasopharynx was the most popular sampling niche for BRD pathogen studies. The oral cavity and other niches within the respiratory tract, such as nostrils and lung, are less assessed. In this study, oropharyngeal swabs (OS), nasal swabs (NS), nasopharyngeal swabs (NP), and bronchoalveolar lavage (BAL) were collected from calves located in four countries and analyzed for investigation of the dissimilarities and connections of the respiratory microbiota. The results showed that the microbial diversity, structure, and composition in the upper and lower respiratory tract in beef cattle from China, the USA, Canada, and Italy were significantly different. The microbial taxa for each sampling niche were specific and associated with their local physiology and geography. The signature microbiota for OS, NS, NP, and BAL were identified using the LEfSe algorithm. Although the spatial dissimilarities among the respiratory niches existed, the microbial connections were observed in beef cattle regardless of geography. Notably, the nostril and nasopharynx had more similar microbiomes compared to lung communities. The major bacterial immigration patterns in the bovine respiratory tract were estimated and some of them were associated with geography. In addition, the contribution of oral microbiota to the nasal and lung ecosystems was confirmed. Lastly, microbial interactions were characterized to reveal the correlation between the commercial microbiota and BRD-associated pathogens. In conclusion, shared airway microbiota among niches and geography provides the possibility to investigate the common knowledge for bovine respiratory health and diseases. In spite of the dissimilarities of the respiratory microbiota in cattle, the spatial connections among these sampling niches not only allow us to deeply understand the airway ecosystem but also benefit the research and development of probiotics for BRD.

The recovery of the microbial community after plaque removal depends on periodontal health status

Plaque accumulation and microbial community changes are important causes of periodontal disease. Cleaned plaque microorganisms will reattach to form biofilms, but the recovery and outcome of plaque microbial communities in different periodontal health states remain unknown. In this study, we tracked the biofilm remodeling process in 206 dental plaque samples from 40 healthy periodontal, gingivitis and periodontitis volunteers at 6 time points before and after supragingival scaling. We found that microbial communities of different periodontal states changed asynchronously during the process, and the more severe the periodontal disease condition, the more lagged the recovery of plaque microorganisms to their original state after cleaning; this reflected a higher degree of plaque development in periodontitis samples. The plaque index and bleeding index were significantly correlated with plaque recovery, especially the recovery of bacteria such as Abiotrophia and Capnocytophaga. Meanwhile, we found that the microbial community structure of different periodontal health states was most similar at the Day 3 after plaque cleaning, and the communities gradually differentiated and developed in different directions. Abiotrophia and other bacteria might play an important role in determining the development trend of plaque biofilms. The discovery of specific time points and bacteria was of great value in clarifying the pathogenesis of periodontal disease and in seeking targets for prevention and treatment.

Periodontitis Disease in Farmed Ruminants-Current State of Research

Periodontal disease in ruminants is common and occurs in farmed and wild animals. Periodontal lesions can result from the secretion of endotoxins by pathogenic bacteria and as consequences of immune system activity. Three main types of periodontitis have been described. The first is chronic inflammation involving mainly premolars and molars-periodontitis (PD). The second type is an acute inflammatory reaction occurring with calcification of the periosteum of the jawbone and swelling of the surrounding soft tissues (Cara inchada, CI-"swollen face"). Finally, a third type, similar to the first but located in the incisor area, is called "broken mouth" (BM). Etiological variation between the different types of periodontitis is indicated. This particularly manifests in the composition of the microbiome, which is characteristic of the different forms of periodontitis. The widespread detection of lesions has drawn attention to the current nature of the problem.

Dysbiosis and predicted function of dental and ruminal microbiome associated with bovine periodontitis

Extensive cattle livestock is advancing in Amazonia and its low productivity, with consequent pressure to open new areas, is partly due to sanitary problems and, among them, the periodontal diseases, whose environmental triggers or modifying factors are unknown. In this study, we used high-throughput sequencing, network analysis and predicted functions to investigate the dental and ruminal microbiota of cattle raised in new livestock areas in the Amazon and identify possible keystone pathogens and proteins associated with the disease. Ninety-three genera were common in dental and ruminal fluid microbiomes and among them periodontal pathogens such as Fusobacterium, Prevotella, Porphyromonas and Actinomyces were recognized. Network analysis showed that dental microbiomes of clinically healthy animals tend to comprise a group of OTUs in homeostasis and when analyzed together, dental and ruminal fluid microbiomes of animals with periodontitis had almost twice the number of negative edges, indicating possible competition between bacteria and dysbiosis. The incisor dental and ruminal fluid microbiomes were dominated by a core community composed of members of the phyla Firmicutes and Bacteroidetes. Network results showed that members of the Prevotella genus stood out among the top five OTUs, with the largest number of hubs in the dental and ruminal microbiota of animals with periodontitis. Protein families linked to an inflammatory environment were predicted in the dental and ruminal microbiota of cattle with periodontitis. The dissimilarity between dental microbiomes, discriminating between healthy cattle and those with periodontitis and the identification of possible key pathogens, represent an important reference to elucidate the triggers involved in the etiopathogenesis of bovine periodontitis, and possibly in the development of measures to control the disease and reduce the pressures for deforestation.

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys’ oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis

Periodontitis is a polymicrobial biofilm-induced inflammatory disease associated with a dysbiotic microbial community and severely affects the health and welfare of animals. However, little is known regarding the dental microbiota associated with this disease in goats. In this study, we used high-throughput sequencing, network analysis, and predicted functions to investigate the microbiota of clinically healthy goats and those with periodontitis and identify possible pathogens and proteins associated with the disease. Dental microbiomes of goats with periodontitis were richer, and network analyses showed that the number of negative interactions was higher in the networks of animals with periodontitis. Based on the interrelationships, Porphyromonas, Fusobacterium, and Prevotella were suggested to play an important role in the dental microbiota associated with goat periodontitis. Protein families linked to translation, cytoplasmatic translation, and rRNA processing were more abundant in the dental microbiota of goats with periodontitis. In conclusion, the dental biofilm microbiota associated with goat periodontitis seems to be dysbiotic and has significant antagonistic interactions, which discriminate healthy animals from diseased animals and highlight the importance of key bacteria. Thus, these novel findings contribute to the evolution of knowledge regarding the etiopathogenesis of goat periodontitis and possibly to the development of periodontitis control measures.

The Plaque Microbiota Community of Giant Panda (Ailuropoda melanoleuca) Cubs With Dental Caries

Dental caries severely hinders efficient access to adequate energy in wildlife. Different food supplies will develop characteristic plaque, and the microorganisms of these plaque are closely related to dental health. Here, plaque samples from panda cubs with caries and caries-free were collected for 16S rRNA high-throughput sequencing. All sequences clustered into 337 operational taxonomic units (OTUs; 97% identity), representing 268 independent species belonging to 189 genera, 98 families, 51 orders, 24 classes, and 13 phyla. Two groups shared 218 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in plaques with caries exceeded that of caries-free. The dominant phyla of plaque microbiota included Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. The dominant genera included unclassified Neisseriaceae, Actinobacillus, Lautropia, Neisseria, Porhyromonas, unclassified Pasteurellaceae, Moraxella, Streptococcus, Bergeywlla and Capnocytophaga. β diversity analysis showed that the plaque microbial community structure was different between two groups. Using LEfSe analysis, 19 differentially abundant taxa were identified as potential biomarkers. Finally, function predictions analysis showed All the energy related metabolic pathways on KEGG level 2 were enriched in caries-active group. Consistent with the mainstream caries-causing narrative, our results illuminate the lack of information regarding the oral microflora composition and function within giant panda cubs.

Bovine respiratory microbiota of feedlot cattle and its association with disease

Bovine respiratory disease (BRD), as one of the most common and costly diseases in the beef cattle industry, has significant adverse impacts on global food security and the economic stability of the industry. The bovine respiratory microbiome is strongly associated with health and disease and may provide insights for alternative therapy when treating BRD. The niche-specific microbiome communities that colonize the inter-surface of the upper and the lower respiratory tract consist of a dynamic and complex ecological system. The correlation between the disequilibrium in the respiratory ecosystem and BRD has become a hot research topic. Hence, we summarize the pathogenesis and clinical signs of BRD and the alteration of the respiratory microbiota. Current research techniques and the biogeography of the microbiome in the healthy respiratory tract are also reviewed. We discuss the process of resident microbiota and pathogen colonization as well as the host immune response. Although associations between the microbiota and BRD have been revealed to some extent, interpreting the development of BRD in relation to respiratory microbial dysbiosis will likely be the direction for upcoming studies, which will allow us to better understand the importance of the airway microbiome and its contributions to animal health and performance.

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing

Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order "Unclassified Clostridiales" when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations.

Neutrophils Orchestrate the Periodontal Pocket

The subgingival biofilm attached to tooth surfaces triggers and maintains periodontitis. Previously, late-onset periodontitis has been considered a consequence of dysbiosis and a resultant polymicrobial disruption of host homeostasis. However, a multitude of studies did not show "healthy" oral microbiota pattern, but a high diversity depending on culture, diets, regional differences, age, social state etc. These findings relativise the aetiological role of the dysbiosis in periodontitis. Furthermore, many late-onset periodontitis traits cannot be explained by dysbiosis; e.g. age-relatedness, attenuation by anti-ageing therapy, neutrophil hyper-responsiveness, and microbiota shifting by dysregulated immunity, yet point to the crucial role of dysregulated immunity and neutrophils in particular. Furthermore, patients with neutropenia and neutrophil defects inevitably develop early-onset periodontitis. Intra-gingivally injecting lipopolysaccharide (LPS) alone causes an exaggerated neutrophil response sufficient to precipitate experimental periodontitis. Vice versa to the surplus of LPS, the increased neutrophil responsiveness characteristic for late-onset periodontitis can effectuate gingiva damage likewise. The exaggerated neutrophil extracellular trap (NET) response in late-onset periodontitis is blameable for damage of gingival barrier, its penetration by bacteria and pathogen-associated molecular patterns (PAMPs) as well as stimulation of Th17 cells, resulting in further neutrophil activation. This identifies the dysregulated immunity as the main contributor to periodontal disease.

Insights into the Oral Bacterial Microbiota of Sows

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs.

Dental biofilm and its ecological interrelationships in ovine periodontitis

Introduction. Periodontitis, one of the most common oral disorders in sheep, is caused by a mixed and opportunistic microbiota that severely affects the health and welfare of animals. However, little is known about the ecological processes involved and the composition of the microbiota associated with the development of the disease.Hypothesis/Gap Statement. Using high-throughput sequencing of the 16S ribosomal RNA gene and network analysis it would be possible to discriminate the microbiomes of clinically healthy sheep and those with periodontitis and possibly identify the key microorganisms associated with the disease.Aim. The present study aimed to characterise the composition of dental microbiomes and bacterial co-occurrence networks in clinically healthy sheep and animals with periodontitis.Methodology. Dental biofilm samples were collected from ten sheep with periodontitis and ten clinically healthy animals. Bacteria were identified using high-throughput sequencing of the 16S ribosomal RNA gene.Results. The most prevalent genera in the dental microbiota of sheep with periodontitis were Petrimonas, Acinetobacter, Porphyromonas and Aerococcus. In clinically healthy animals, the most significant genera were unclassified Pasteurellaceae, Pseudomonas, and Neisseria. Fusobacterium was found at high prevalence in the microbiomes of both groups. The dental microbiota of sheep in the two clinical conditions presented different profiles and the diversity and richness of bacteria was greater in the diseased animals. Network analyses showed the presence of a large number of antagonistic interactions between bacteria in the dental microbiota of animals with periodontitis, indicating the occurrence of a dysbiotic community. Through the interrelationships, members of the Prevotella genus are likely to be key pathogens, both in the dental microbiota of healthy animals and those with periodontitis. Porphyromonas stood out among the top three nodes with more centrality and the largest number of hubs in the networks of animals with periodontitis.Conclusion. The dental biofilm microbiota associated with ovine periodontitis is dysbiotic and with significant antagonistic interactions, which discriminates healthy animals from diseased animals and highlights the importance of key bacteria, such as Petrimonas, Porphyromonas, Prevotella and Fusobacterium species.

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

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

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

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

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

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

Risk factors for bovine periodontal disease - a preliminary study

The work presented in this pilot study aimed to identify potential risk factors associated with bovine periodontitis development. Bovine periodontitis is a multifactorial polymicrobial infectious disease for which the aetiopathogenesis and risk factors are not fully understood. From cattle slaughtered in an abattoir in Scotland, 35 dental arcades with periodontal lesions and 40 periodontally healthy arcades were selected over seven visits for study. Multivariable logistic regression analysis was used to evaluate the association between periodontitis and the independent variables, gender, age and breed. For every increase in year of age, cattle were 1.5 times more likely to have periodontitis. A graphical analysis indicated that within the limits of this study, we could not detect any major influence of breed on the age-effect. Although logistic regression analysis demonstrated that periodontitis lesions are more prevalent with increasing age of cattle the underlying mechanisms remain unclear. It is likely that periodontitis is an important cause of oral pain in older cattle and can contribute to reduced productivity/performance. Further studies with a larger sample size are necessary to elucidate the associations between potential risk factors and periodontitis in cattle and to define its effects on animal welfare and productivity.

Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing

The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.

Effects of Fermented Soybean Meal Supplementation on the Growth Performance and Cecal Microbiota Community of Broiler Chickens

Simple Summary

Microbial fermentation is considered an economically viable processing technique to reduce the content of anti-nutritional factors and improve the nutritional quality of soybean meal (SBM). Fermented soybean meal (FSBM) exerts beneficial effects on the growth performance, carcass traits, and meat quality of broilers. However, there is very little information on the effects of FSBM on cecal microbial composition and diversity in broilers. Hence, this trial is conducted to investigate the effects of the partial replacement of SBM with FSBM in the diet on growth performance and cecal microflora of broilers. Replacing 25% of the SBM in the diet of broilers with FSBM promoted average daily gain and feed conversion ratio during the growth and whole phases. Both dietary treatment (25% or 50% of the SBM in the basal diet was replaced with FSBM) influenced the serum immunity, diversity and composition of cecal microbiota in broilers. FSBM supplementation in the diet shifted the cecal microbial community of broilers towards a healthier balance by increasing the abundance of beneficial bacteria and reducing the abundance of potentially harmful bacteria.

Abstract

This study investigated the growth performance, serum immunity, and cecal bacterial microbiota of broilers fed a diet in which soybean meal (SBM) was partially replaced with fermented soybean meal (FSBM) for 36 days. A total of 180 one-day-old male Cobb 500 broilers were randomly divided into three dietary groups (six replicates per group): corn-SBM diet (CC); 25% SBM replaced by FSBM (SC); 50% SBM replaced by FSBM (TC). The average daily gain (ADG) and feed conversion rates (FCR) were higher in SC than CC and TC groups (p < 0.05) during the growth (d 22–36) and whole (d 1–36) phases. No significant difference was observed in ADG and average daily feed intake (ADFI) between CC and TC groups during any phases. Dietary treatments increased serum IgA, IgG, and IgM, Chao 1, observed species, and the abundance of the phylum Fimicutes but decreased the proportion of Proteobacteria (p < 0.05). Dietary treatments increased the abundance of the genera Lachnospiraceae, Lachnoclostridium, Gastranaerophilales, and Lactobacillus but decreased the abundance of Escherichia-Shigella and Clostridiales (p < 0.05). Spearman’s correlations showed that the abundance of Gastranaerophilales was positively correlated with ADG and serum immunity, and the abundance of Lactobacillus was strongly positively with IgM. Thus, replacing 25% of SBM with FSBM improves the growth performance and serum immunity of broilers, possibly due to altered cecal microbial composition.

Metataxonomic and Histopathological Study of Rabbit Epizootic Enteropathy in Mexico

Simple Summary

Epizootic rabbit enteropathy (ERE) is a worldwide-distributed dysbiotic syndrome that affects young rabbits. In Mexico, ERE represents 32% of the enteropathies that occur in rabbit production farms. The etiology of this syndrome has not been clarified yet; however, it has been associated with nutritional, environmental, and microbial factors. A metataxonomic and histopathology study of ERE was carried out to compare the lesions and gastrointestinal microbiota of healthy and positive-ERE rabbits. The results revealed a difference in the diversity and abundance of the gastrointestinal microbiota in rabbits with ERE. The genus Clostridium and the species. Cloacibacillus porcorum and Akkermansia muciniphila were associated with the presentation of ERE. Histopathologic analysis showed smaller crypt sizes in the colon of ERE rabbits.

Abstract

Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal microbiota and histopathological lesions of healthy and positive-ERE rabbits. The metataxonomic study was done using an Illumina MiSeq (MiSeq^® system, Illumina, San Diego California, USA) massive segmentation platform, and a Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm) was used to obtain Shannon and Simpson diversity indices as well as the relative abundance of the identified communities. For the histopathological study, paraffin sections of the cecum, ileo-cecal valve, and colon were stained with eosin and hematoxylin. AxioVision 4.9 software (Carl Zeiss MicroImaging GmbH, Jena, Germany) was used to measure the crypt depths. Statistical analysis was done using PERMANOVA analysis for the metataxonomic study and ANOVA for the histopathology study. Histopathologic analysis showed smaller sizes of crypts in the colon of ERE rabbits. Differences were observed in the diversity and abundance of the gastrointestinal microbiota between the analyzed groups. The genus Clostridium and the species Cloacibacillus porcorum and Akkermansia muciniphila were associated with ERE. The results obtained from this study can provide information for future clarification of the etiology and proposals of effective treatments.

Identification of uncultured bacteria from abscesses of exotic pet animals using broad-range nested 16S rRNA polymerase chain reaction and Sanger sequencing

Background:

The Sanger sequencing technique has been questioned and challenged by advanced high-throughput sequencing approaches. Sanger sequencing seems to be an obsolete technology. However, there are still research problems that could be answered using the Sanger sequencing technology. Fastidious obligate anaerobic bacteria are mostly associated with abscesses in animals. These bacteria are difficult to isolate from abscesses and are frequently excluded due to the bias of conventional bacterial culturing.

Aim:

This study demonstrated the usefulness of a broad-range polymerase chain reaction (PCR) with Sanger sequencing to identify the majority population of bacteria in abscesses from exotic pet animals.

Materials and Methods:

This study performed a pilot investigation of abscesses from 20 clinical cases (17 rabbits, 2 hedgehogs, and 1 sugar glider) using standard culture methods for both aerobes and anaerobes and broad-range nested PCR targeting the 16S rRNA gene followed by the Sanger sequencing technique.

Results:

The standard culture and PCR techniques detected bacteria in 9 and 17 of 20 samples, respectively. From the 17 sequencings of the 16S rRNA, 10 PCR products were found to be closely related with obligate anaerobes including Bacteroides spp., Fusobacterium spp., Prevotella spp. Phylogenetic analysis using the rpoB gene revealed that the species for the Bacteroides was thetaiotaomicron and for the Fusobacterium was varium and nucleatum. However, the amplification of the rpoB gene for the Prevotella spp. was unsuccessful. Correlations between the standard culture and PCR techniques were found in 9 (6 positive and 3 negative samples) of 20 samples. Eleven samples were discordant between the standard culture and PCR techniques which were composed of eight samples negative by culture but positive by PCR and three samples had different bacteria by the culture and PCR techniques.

Conclusion:

According to this study, broad-range PCR combined with Sanger sequencing might be useful for the detection of dominant anaerobic bacteria in abscesses that were overlooked based on conventional bacterial culture.

The microbiome of the footrot lesion in Merino sheep is characterized by a persistent bacterial dysbiosis

Footrot is prevalent in most sheep-producing countries; the disease compromises sheep health and welfare and has a considerable economic impact. The disease is the result of interactions between the essential causative agent, Dichelobacter nodosus, and the bacterial community of the foot, with the pasture environment and host resistance influencing disease expression. The Merino, which is the main wool sheep breed in Australia, is particularly susceptible to footrot. We characterised the bacterial communities on the feet of healthy and footrot-affected Merino sheep across a 10-month period via sequencing and analysis of the V3-V4 regions of the bacterial 16S ribosomal RNA gene. Distinct bacterial communities were associated with the feet of healthy and footrot-affected sheep. Infection with D. nodosus appeared to trigger a shift in the composition of the bacterial community from predominantly Gram-positive, aerobic taxa to predominantly Gram-negative, anaerobic taxa. A total of 15 bacterial genera were preferentially abundant on the feet of footrot-affected sheep, several of which have previously been implicated in footrot and other mixed bacterial diseases of the epidermis of ruminants. Some, including Porphyromonas, can trigger a shift in the composition of bacterial communities and may therefore be of significance to the expression of footrot. A comparison of the communities in footrot lesions of different scores and at different times revealed that this state of dysbiosis is persistent at the active margins of lesions, irrespective of their severity.

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics

Liver abscesses in feedlot cattle form secondary to high concentrate feeds and rumen acidosis. Antimicrobial drugs are commonly included in cattle feed for prevention of liver abscesses, but concerns regarding antimicrobial resistance have increased the need for alternative treatments. A block randomized clinical trial was conducted to evaluate the effects of a Saccharomyces cerevisiae fermentation product (SCFP) on liver abscesses, fecal microbiomes, and resistomes in cattle raised without antibiotics in a Colorado feedlot. At enrollment, steers (n = 4,689) were sorted, by weight and source, into 2 pens comprising a block (n = 14 blocks, 28 pens); pens were randomly allocated to either the control group or the treatment group, where the diet was supplemented with SCFP. Prior to harvest, composited feces were collected for characterization of the microbiome and resistome using 16S rRNA gene and shotgun sequencing. At harvest, liver abscess severity was quantified for individual cattle. There were no statistical differences detected by treatment group in animal health, liver abscess prevalence or severity. Organisms classified to phylum, Elusimicrobia were more abundant in the feces of treated cattle, however, there were no differences in the resistome by treatment group. Both microbiome and resistome varied significantly among enrollment blocks.

Efficacy of virginiamycin for the control of periodontal disease in calves

ABSTRACT: Periodontal diseases are multifactorial infectious processes caused by complexes of microorganisms, with damage to health, production, and animal welfare. The aim of the present study was to evaluate the efficacy of virginiamycin in the prevention and control of two early forms of periodontal disease: gingivitis and necrotizing gingivitis. Ten weaned calves, aged four to six months, were permanently kept in a single lot under the same rotational grazing regime in a newly reformed area of Panicum maximum. Five of the calves were orally administered 340mg of virginiamycin (Virginiamycin Group) daily for a period of 18 weeks, while the remaining five calves (Control Group) remained under the same food management but did not receive virginiamycin. During this period, animals underwent 18 weekly evaluations regarding periodontal health, with monitoring and recording of clinical parameters of the eight deciduous incisor teeth on the labial and lingual faces. At approximately two-week intervals, nine collections of subgingival sulcus material from five sites of the four right incisor teeth of each animal were performed and subjected to microbiological evaluation using polymerase chain reaction with primers of 25 microorganisms considered potentially pathogenic. After 1440 periodontal clinical evaluations of incisor teeth of the 10 calves, a total of 395 episodes of gingivitis were recorded, of which 267 occurred in the Control Group and 128 in the Virginiamycin Group. Similarly, 89 episodes of necrotizing gingivitis were recorded; 58 in the Control Group and 31 in the Virginiamycin Group. Comparison of between-group means found significant differences for teeth with gingivitis and necrotizing gingivitis (t test; p<0.05). The total number of teeth with gingivitis (p<0.01) and necrotizing gingivitis (p<0.01) in Control Group was significantly higher than that of gingivitis (p<0.01) and necrotizing gingivitis (p<0.05) in the Virginiamycin Group. There was a positive correlation between total occurrence of gingivitis and necrotizing gingivitis in the Virginiamycin Group by Pearson’s test. Virginiamycin had a protective effect on treated animals compared with the Control Group (OR = 0.36: CI (95%) = 0.27-0.43). In the Control Group, Actinomyces israelli (4.74%), domain Archaea (1.58%), Eikenella corrodens (1.05%), Fusobacterium nucleatum (27.37%), class Mollicutes (5.26%); Porphyromonas endodontalis(5.26%); Porphyromonas gulae(0.53%), Prevotella buccae (6.32%), Prevotella loescheii (3.68%), Prevotella nigrescens (8.42%), Prevotella oralis (1.58%), Tannerella forsythia (0.53%), and Treponema denticola (4.21%) were detected at healthy sites, and gingivitis or necrotizing gingivitis samples. In the Virginiamycin Group, A. israelli (3.41%), domain Archaea (0.98%), F. nucleatum (9.27%), class Mollicutes(4.39%), P. endodontalis (4.39%), P. gulae (0.49%), P. buccae (8.29%), P. loescheii (6.83%), P. nigrescens (15.61%), P. oralis (1.46%), Selenomonas sputigena (0.49%), T. forsythia (0.49%), and T. denticola (2.44%) were detected. In conclusion, virginiamycin administered at a dosage of 340mg/animal/day significantly reduced the occurrence of gingivitis and necrotizing gingivitis in cattle maintained on reformed pastures, and was revealed to have action against periodontal bacterial microbiota considered to be potentially pathogenic.