A metagenomics approach to characterize the footrot microbiome in Merino sheep

Usié, Ana; Leão, Célia; Gaspar, Daniel; Monteiro, Helena Serra Azul; Tábuas, Lino; Bettencourt, E.M.; Caetano, Pedro; Padre, Ludovina; Carolino, N.; Ramos, António Marcos; Matos, Claudino de; Branco, Sandra

doi:10.1016/j.vetmic.2023.109745

Cited by 3 publications

(6 citation statements)

References 25 publications

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“…The presence of bacterial coinfection is likely to be responsible for severe secondary symptoms associated with LSDV/SPV infection. This is in agreement, in part, with the research conducted by Usie et al who utilized shotgun metagenomics of skin lesions to reveal the multibacterial nature of sheep footrot ( 91 ). It is noteworthy that in the mentioned study the metagenome was analyzed under experimental conditions, enabling the evaluation of process dynamics.…”

Section: Discussionsupporting

confidence: 90%

“…Trueperella pyogenes, which was present in relatively small numbers but detected in more than half of the samples, is also a common commensal causing a variety of purulent infections in livestock ( 107 ). The correlation between the presence of this pathogen and F.necrophorum during the development of footrot disease in sheep, described by Usie et al ( 91 ), suggests the development of a complex co-infectious process in scabs.…”

Section: Discussionmentioning

confidence: 94%

“…In this study we characterized the microbial community composition of scabs developed in capripoxvirus-related infections and evaluated the presence of opportunistic pathogens. It should be noted that although various studies have investigated the microbiome and its possible contribution to coinfection development for various cattle diseases ( 90 , 91 ), most have been conducted in controlled experimental settings and never with capripoxvirus infections. Therefore, this study, which analyses the microbiome of skin lesions in viral infections of farm animals using real clinical specimens, is one of the first of its kind performed by shotgun sequencing ( 92 ).…”

Section: Discussionmentioning

confidence: 99%

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Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Sharko,

Mazloum,

Krotova

et al. 2024

Front. Vet. Sci.

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IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

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Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Sharko,

Mazloum,

Krotova

et al. 2024

Front. Vet. Sci.

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“…As a complementary diagnostic method, the presence of the main causal agent, i.e. D. nodosus , was monitored in ~ 18% and 15% of the animals included in our study by qPCR and metagenomic analyses, respectively [ 25 , 33 ]. Details on flock locations, number of animals sampled per flock and breed(s) are shown in Table S 2 .…”

Section: Methodsmentioning

confidence: 99%

“…Such studies have contributed to a better understanding of the complex biological processes of disease pathogenesis, leading to the identification of molecular markers tightly linked to resistance genes [ 19 , 20 ]. Extensive efforts have been made to investigate the pathogenesis and aetiology of footrot in sheep [ 21 – 25 ], but few studies were focused to understand innate genetic resistance. The first attempt to investigate the genetic association to footrot resistance/susceptibility in sheep resulted in the identification of genetic variants involved in the major histocompatibility complex (MHC) class II genes [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep

Gaspar,

Ginja,

Carolino

et al. 2024

BMC Genomics

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Background Ovine footrot caused by Dichelobacter nodosus (D. nodosus) is a contagious disease with serious economic and welfare impacts in sheep production systems worldwide. A better understanding of the host genetic architecture regarding footrot resistance/susceptibility is crucial to develop disease control strategies that efficiently reduce infection and its severity. A genome-wide association study was performed using a customized SNP array (47,779 SNPs in total) to identify genetic variants associated to footrot resistance/susceptibility in two Portuguese native breeds, i.e. Merino Branco and Merino Preto, and a population of crossbred animals. A cohort of 1375 sheep sampled across 17 flocks, located in the Alentejo region (southern Portugal), was included in the analyses. Results Phenotypes were scored from 0 (healthy) to 5 (severe footrot) based on visual inspection of feet lesions, following the Modified Egerton System. Using a linear mixed model approach, three SNPs located on chromosome 24 reached genome-wide significance after a Bonferroni correction (p < 0.05). Additionally, six genome-wide suggestive SNPs were identified each on chromosomes 2, 4, 7, 8, 9 and 15. The annotation and KEGG pathway analyses showed that these SNPs are located within regions of candidate genes such as the nonsense mediated mRNA decay associated PI3K related kinase (SMG1) (chromosome 24) and the RALY RNA binding protein like (RALYL) (chromosome 9), both involved in immunity, and the heparan sulfate proteoglycan 2 (HSPG2) (chromosome 2) and the Thrombospodin 1 (THBS1) (chromosome 7) implicated in tissue repair and wound healing processes. Conclusion This is the first attempt to identify molecular markers associated with footrot in Portuguese Merino sheep. These findings provide relevant information on a likely genetic association underlying footrot resistance/susceptibility and the potential candidate genes affecting this trait. Genetic selection strategies assisted on the information obtained from this study could enhance Merino sheep-breeding programs, in combination with farm management strategies, for a more effective and sustainable long-term solution for footrot control.

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Shotgun Metagenomics Reveals Minor Micro“bee”omes Diversity Defining Differences between Larvae and Pupae Brood Combs

Smutin,

Taldaev,

Lebedev

et al. 2024

IJMS

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Bees represent not only a valuable asset in agriculture, but also serve as a model organism within contemporary microbiology. The metagenomic composition of the bee superorganism has been substantially characterized. Nevertheless, traditional cultural methods served as the approach to studying brood combs in the past. Indeed, the comb microbiome may contribute to determining larval caste differentiation and hive immunity. To further this understanding, we conducted a shotgun sequencing analysis of the brood comb microbiome. While we found certain similarities regarding species diversity, it exhibits significant differentiation from all previously described hive metagenomes. Many microbiome members maintain a relatively constant ratio, yet taxa with the highest abundance level tend to be ephemeral. More than 90% of classified metagenomes were Gammaproteobacteria, Bacilli and Actinobacteria genetic signatures. Jaccard dissimilarity between samples based on bacteria genus classifications hesitate from 0.63 to 0.77, which for shotgun sequencing indicates a high consistency in bacterial composition. Concurrently, we identified antagonistic relationships between certain bacterial clusters. The presence of genes related to antibiotic synthesis and antibiotic resistance suggests potential mechanisms underlying the stability of comb microbiomes. Differences between pupal and larval combs emerge in the total metagenome, while taxa with the highest abundance remained consistent. All this suggests that a key role in the functioning of the comb microbiome is played by minor biodiversity, the function of which remains to be established experimentally.

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A metagenomics approach to characterize the footrot microbiome in Merino sheep

Cited by 3 publications

References 25 publications

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep

Shotgun Metagenomics Reveals Minor Micro“bee”omes Diversity Defining Differences between Larvae and Pupae Brood Combs

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