The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

Ribeiro, David M.; Salama, A. A. K.; Vítor, Ana C. M.; Argüello, A.; Moncau, Cristina Tschorny; Santos, Edson Mauro; Caja, G.; Oliveira, Juliana; Balieiro, J. C. C.; Hernández-Castellano, Lorenzo E.; Zachut, Maya; Poleti, Mirele Daiana; Castro, N.; Alves, Susana P.; Almeida, André M.

doi:10.1016/j.jprot.2020.103905

Cited by 31 publications

(14 citation statements)

References 190 publications

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“…Environmental conditions pose various health and production constraints to the optimal production of small ruminants in different climatic zones, i.e., tropical versus temperate climatic zones [ 13 ]. For example, in tropics and subtropics, ticks and tick-borne diseases (TTBDis) such as anaplasmosis, babesiosis, ehrlichiosis and theileriosis constitute one of the major health challenges for the production of sheep and goats [ 14 , 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Systematic Review of Ticks and Tick-Borne Pathogens of Small Ruminants in Pakistan

et al. 2020

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Ticks and tick-borne diseases (TTBDis) are a major constraint to the health and production of small ruminants in Pakistan. Despite being the subject of intermittent studies over the past few decades, comprehensive information on the epidemiology and control of TTBDis is lacking. Herein, we have systematically reviewed the current knowledge on TTBDis of small ruminants in Pakistan. Critical appraisal of the selected 71 articles published between 1947 to 2020 revealed that morphological examination had been the most widely used method for the identification of TTBDis in Pakistan. Tick fauna comprise at least 40 species, mainly belonging to Haemaphysalis, Hyalomma and Rhipicephalus. The prevalence of ticks is the highest in summer (June–September) and it is also higher in goats than sheep. Anaplasma, Babesia and Theileria spp. are the major tick-borne pathogens (TBPs), and their prevalence is usually higher in sheep than goats. Spatio-temporal distribution, genetic diversity and control of ticks and TBPs of small ruminants as well as the competence of tick vectors for various TBPs remain to be explored. Therefore, coordinated and focused investigations are required to fill knowledge gaps in these areas to maximise the health, production and welfare of small ruminants and minimise economic losses associated with TTBDis in Pakistan.

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Section: Introductionmentioning

confidence: 99%

Systematic Review of Ticks and Tick-Borne Pathogens of Small Ruminants in Pakistan

et al. 2020

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“…Keystone nodes (M00049 and Desulfobulbus ) in the exclusive network of PE(+) calves were positively associated each other and this interaction need to be understood within protozoa-harboring rumen microbiome. Purine metabolism is related to the cell growth and death [ 62 ], and this might be associated with bacterial predation activity of rumen protozoa inoculated by PE. In addition to its differential abundance in PE(+) calves, sulfate-reducing Desulfobulbus and its association with rumen protozoa is yet to be determined.…”

Section: Discussionmentioning

confidence: 99%

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

et al. 2022

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Background Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing. Results Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3–6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets was significantly different (P = 0.024), 21 out of 31 shared major bacterial genera differed in their relative abundance between the two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeota that differed for BE based on the Bray–Curtis dissimilarity matrix (P = 0.009). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic genera significantly correlated to various fermentation and animal measurements including butyrate proportion, body weight, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE (P < 0.05), and this might be supported by the individual KEGG module and CAZymes profile differences. Exclusive networks between major active microbial (bacterial and archaeal genera) and functional features (KEGG modules) were determined which were differed by microbial inoculations. Conclusions This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentations and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other parts of the gastrointestinal tract (e.g., abomasum, omasum, and small intestine) using metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.

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“…Over the last decade, the use of proteomics has of course exponentially increased worldwide [75]. Proteomics has provided complementary information to the well-established biochemical procedures used in animal science [76,77]. Some of the main negative aspects affecting the exponential development and use of several proteomics techniques are the high cost of the required infrastructure as well as the complexity of the data obtained when different approaches are combined [15].…”

Section: Domestic Animal Proteomics In Europe In Recent Years: North and Southmentioning

confidence: 99%

“…Proteomics is particularly suitable to address this challenge as it is used much more frequently in environmental sciences than in animal and veterinary sciences. Applications could include for instance the use of alternative feedstuffs such as algae [94] or insect meal, monitoring ruminal fermentation manipulation through the animal diets [76] or contribute to a more sustainable extensive production system highlighting the benefits also for product quality [8]. These, together with improvements towards the increase of animal welfare for instance in damaging behavior of pigs [93] or in cattle by characterizing heat stress effects [52,53], are areas where the contributions of proteomics is crucial.…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Almeida

Ali

Ceciliani

et al. 2021

Journal of Proteomics

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Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. Significance: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the

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The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

Cited by 31 publications

References 190 publications

Systematic Review of Ticks and Tick-Borne Pathogens of Small Ruminants in Pakistan

Systematic Review of Ticks and Tick-Borne Pathogens of Small Ruminants in Pakistan

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

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