An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickensAbstract
The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices
Keywords:
animal microbiome; microbiome; chicken microbiome; animal welfare; metagenomics; 16S rRNA sequencing
Resumo
O microbioma animal desempenha um papel crucial na determinação da saúde, produtividade e bem-estar das espécies pecuárias, incluindo ovelhas, cavalos, gado, camelo e frango. Essas espécies animais foram selecionadas por causa do alto consumo de seus produtos no Cazaquistão. Aumentar sua produtividade, mantendo a segurança e a qualidade da carne e do leite derivados deles, representa uma prioridade de pesquisa. Este artigo de revisão inclui pesquisas atuais sobre a composição, diversidade e finalidades da microbiota encontrada em diferentes sistemas orgânicos dessas espécies. Este estudo se concentra em avanços recentes na tecnologia de sequenciamento, incluindo metagenômica, sequenciamento de rRNA 16S e métodos multiômicos, para combinar dados sobre diversidade microbiana, composição e funcionalidade dentro do trato gastrointestinal e outros órgãos. As principais descobertas mostram diferenças nas comunidades microbianas associadas à raça, idade e dieta, o impacto da microbiota nas emissões de metano e eficiência alimentar em ruminantes e a possibilidade de usar técnicas de manejo do microbioma (por exemplo, probióticos, prebióticos e aditivos alimentares) para melhorar a produção pecuária. O microbioma influencia várias espécies, estendendo seus efeitos para além da digestão e imunidade, para a saúde reprodutiva e comportamento. Apesar dos avanços, a tradução dos dados do microbioma em intervenções acionáveis é dificultada pela variabilidade resultante de fatores genéticos, ambientais e de manejo. Integrar a pesquisa do microbioma mais de perto com a genética animal e os métodos de produção pecuária pode levar a abordagens inovadoras para melhorar a saúde, a eficiência e o bem-estar dos animais de produção, apoiando, em última análise, práticas pecuárias sustentáveis.
Palavras-chave:
microbioma animal; microbioma; microbioma de frango; bem-estar animal; metagenômica; sequenciamento de rRNA 16S
1. Introduction
The animal microbiome, comprising microorganisms that colonize various body regions, plays a crucial role in host health, immunity, and productivity (Hoffmann et al., 2016; Lourenco and Welch, 2022). Recent advancements in non-culturing methodologies have facilitated a more profound comprehension of the microbiome's complexity and its interactions with host organisms (Lourenco and Welch, 2022). Researchers are investigating microbiome management strategies to enhance animal health and conservation, including fecal microbiota transplantation, prebiotics, probiotics, and targeted approaches such as phage therapy (Song et al., 2013). The influence of the microbiome extends to marine animals, potentially affecting their adaptation to climatic and anthropogenic changes in the oceanic environment (Apprill, 2017). As this field progresses, the integration of microbiome data with other domains of animal science may lead to more precise comparative studies and broader beneficial outcomes (Lourenco and Welch, 2022). Nonetheless, unresolved issues persist regarding factors that may transition host-microbiome associations from a symbiotic to a dissociated state (Apprill, 2017). Investigations into the microbiome of livestock have garnered significant attention due to their potential impact on livestock productivity and health. The intestinal microbiome influences feed intake through metabolites and the stimulation of host hormones, which affect appetite regulation and potentially even taste perception (Wessels, 2022).
Metagenomics has become an effective tool in the field of animal husbandry, offering valuable insights into the diversity and roles of microbes in livestock environments. This method allows for the analysis of microorganisms that cannot be cultured, thus providing a thorough understanding of the microbiome in farm animals (Singh et al., 2008). Metagenomics has been used to study the gut microbiota, discover new genes and enzymes, and create probiotics for livestock and poultry (Pawar et al., 2021). In addition, recent studies have also identified the potential role of the gut microbiome in respiratory diseases, extending its influence beyond the gastrointestinal tract and underscoring its significance for livestock production and productivity (Niederwerder, 2017).
Furthermore, research underscores the significant role of microbiomes in animal welfare and behavior. The intestinal microbiome, comprising a diverse array of microorganisms, contributes to the maintenance of host homeostasis, nutrition, growth, and protection from pathogens (Peixoto et al., 2021). Investigations reveal a close relationship between gastrointestinal microbiota and animal behavior, suggesting potential implications for ethology and veterinary medicine (Gorzelanna and Miszczak, 2024).
Moreover, there is a two-way interaction between animal behavior and microbiomes: the behavior of the host influences the makeup of the microbial community, while the microbes, in turn, affect the host's behavior (Ezenwa et al., 2012). Understanding these interactions presents opportunities for novel therapeutic approaches and more sustainable animal husbandry practices, highlighting the importance of microbiome research in maintaining animal health and welfare (Gorzelanna and Miszczak, 2024; Peixoto et al., 2021).
Recent advancements in sequencing technologies have facilitated a deeper exploration of the complex microbial communities residing in the gastrointestinal tract, particularly in ruminants (Lourenco and Welch, 2022; Mizrahi and Jami, 2018) The rumen microbiome, one of the most diverse ecosystems on Earth, fulfills up to 90% of the metabolic needs of ruminants and significantly influences methane emissions (Mizrahi and Jami, 2018).
Researchers emphasize the importance of proper sample collection, data analysis, and integration with other areas of animal science to maximize the potential of microbiome research (Lourenco and Welch, 2022). Future research should focus on examining the natural variations of microbial communities and their effects on animal productivity to develop targeted intervention methods (Mizrahi and Jami, 2018).
This review was prepared based on a literature analysis conducted using the Scopus, Web of Science, and Google Scholar databases over recent years. It includes information on the microbiome of four major groups of livestock animals - sheep, horses, cattle, camels, and poultry. Unlike works focused on individual species or specific organ systems, this review considers both gastrointestinal and extraintestinal microbiota, including skin and reproductive tract communities, across these species. The article may serve as a foundation for future research in the field of animal microbiome studies, including the selection of analytical methods, with the eventual goal of promoting sustainable livestock production and advancing animal health management.
A comparative overview of livestock gut microbiomes, including dominant phyla, characteristic genera, and species-specific features, is presented in Table 1. An analysis of the dynamics of publications on the microbiome of farm animals shows that the systematic growth of interest in this topic began in 2016, with a peak in publication activity in 2017 and 2021 (see Figure 1). Scientific research covers a wide range of countries, including USA, Europe, Asia and the Middle East, which indicates the global nature of the studied issues. The largest contribution was made by the USA, UK, China and a number of European countries. The stable level of publications that has been maintained in recent years reflects the sustained interest of the research community in the microbiome of farm animals and emphasizes their importance for ensuring productivity and welfare.
2. Microbiome Studies in Livestock
2.1. Sheep (Ovis aries Linnaeus, 1758) microbiome
Globally, there are approximately 1.2 billion sheep, primarily raised for their meat, milk, and wool. Sheep farming continues to be a significant focus in agriculture worldwide, as shown by the consistent yearly expansion of the dairy sheep industry (Pulina et al., 2018).
In recent years, there has been a marked increase in interest in researching the sheep microbiome, primarily due to its crucial role in enhancing animal health and productivity. Numerous studies indicate that the microbiota in sheep is integral to various physiological functions, such as improving feeding efficiency and bolstering disease resistance. For instance, investigation utilizing bacterial 16S rRNA analysis has verified that the microbial communities within the host can affect feeding efficiency (McLoughlin et al., 2020). As well as feeding strategies are significant as they can encourage the development of more diverse microbial communities (Fu et al., 2020; Yu et al., 2020).
Research indicates that the microbiome of sheep undergoes significant alterations with age, as evidenced by comparing the microbiota of younger and older sheep. For instance, (Shabana et al., 2021)reported a rise in microbial diversity in mature sheep. This finding aligns with observations in Tibetan sheep, where similar age-related microbiome changes were noted (Wang et al., 2021).
Examining the breeds uncovers notable distinctions. Among sheep from the Tibetan Plateau, the intestinal microbiome's composition shifts with the breed, while in Italian sheep, the primary variations were linked to care conditions (Chang et al., 2020; Minozzi et al., 2020). This underscores the crucial role of ecological and genetic factors in shaping a microbial community. Notably, Chinese Mongolian sheep exhibited an exceptionally high microbiota diversity, suggesting significant adaptive flexibility of the microbiome (Zeng et al., 2017). Research on other breeds, like Qinghai sheep, reveals considerable heterogeneity in microbiome composition across different sections of the gastrointestinal tract (Wang et al., 2021).
The rumen microbiome is crucial for achieving high feeding efficiency, largely due to the variety and abundance of presented microorganisms (Zhang et al., 2021). For instance, in sheep that produce low levels of methane, the microbiome is rich in lactate-producing microorganisms like Sharpea spp., which help decrease methanogenesis (Kamke et al., 2016).
Tanca et al. (2017) carried out a comprehensive investigation of the sheep's large intestine microbiota using a multiomic approach, which included 16S rRNA sequencing, shotgun metagenomics, and shotgun metaproteomics. The research aimed to explore the taxonomic composition and functional capabilities of the microbial community, along with analyzing active metabolic pathways. The primary bacteria found in the microbiota were from the Firmicutes and Bacteroidetes phyla, making up over 80% of the total. Specific metabolic functions were identified, such as methanogenesis in Euryarchaeota archaea and acetogenesis in Firmicutes bacteria. Overall, the researchers identified 2,097 gene families and 441 protein families. Focus is given to catabolic processes, including the transport and decomposition of carbohydrates, which is important for the effective digestion of plant foods. In addition, the study revealed proteins associated with the eukaryotic part of the microbiota, including fungi and protozoa. These results highlight the complexity of sheep microbiota and its important role in metabolism, immune function, and physiological homeostasis. This study lays the foundation for further work aimed at studying the effects of diet and housing conditions on the composition of the microbiota, which can significantly affect the improvement of sheep health and productivity.
In addition to the gastrointestinal tract, the microbiota of other organs, such as the genital tract, are also important. In the vaginal microbiome, for example, the genera Pasteurella and Actinobacillus are associated with eubiosis, while Hemophilus and Ureaplasma indicate dysbiosis, which affects the results of artificial insemination (Pyles et al., 2021; Serrano et al., 2020).
The microbiota of the skin plays a role in the development and treatment of contagious dermatitis of sheep hooves (CODD). The disease is associated with a change in the composition of the microbiota, where the Porphyromonadaceae and Fusobacteriaceae families predominate, while antibiotic therapy helps restore a healthy microbiome (Duncan et al., 2021). In a study by Usié et al. (2023). For the first time, genome-wide metagenomic sequencing (WMGS) was used to analyze the microbiome in sheep hoof rot, which revealed differences in bacterial composition at different stages of the disease and identified key species associated with disease progression (Usié et al., 2023).
The main findings of sheep microbiome studies, including dominant taxa, functional insights, and environmental influences, are comparatively illustrated in Figure 2.
2.2. Horses (Equus caballus Linnaeus, 1758) microbiome
Horses play an important role in a variety of human activities, including sports, agricultural use, work tasks, and livestock. The hindgut microbiome of horses is essential for energy production and protection against intestinal disorders, with its composition differing between digestive compartments and individuals (Julliand and Grimm, 2016).
Diet has a significant impact on the composition of the microbiome. Diets high in fiber maintain microbial balance, while feeds high in starch can cause dysbiosis associated with diseases such as colitis and colic (Chaucheyras-Durand et al., 2022). Feed additives such as prebiotics and probiotics help increase beneficial bacteria and stabilize the microbiome under stress (Ganda et al., 2023).
In horses, the microbiota of intestine develops immediately in postnatal period, with early colonization by mare`s fecal and vaginal microbiota, and becomes similar to adult horses within the first week (Husso et al., 2020).
Research also highlights human generated activities, such as captivity and domestication, notably modify the composition of horse`s gut microbiome (Metcalf et al., 2017).
Additionally, the intestinal microbiome of horses is characterized by a high diversity of bacteriophages, suggesting unique environmental parameters that affect the structure and function of microbial communities (Babenko et al., 2020).
A comprehensive metagenomic study of the equine fecal microbiome revealed wide taxonomic diversity, including numerous new genera and species of bacteria. As part of this study, 123 metagenomically assembled genomes (MAGs) of high or medium quality belonging to bacteria and archaea were collected, and almost 200 bacteriophage genomes were identified, highlighting the complexity of the equine intestinal microbiome (Gilroy et al., 2022). This diversity is important for understanding the role of microbiomes in converting a fiber-rich diet into body weight and physical endurance.
The fecal microbiome of Exmoor ponies varied significantly depending on the level of human exposure, including differences in diet, medication use, and exercise. These changes were accompanied by shifts in the composition of microbial taxa and functional characteristics, such as increased metabolism of amino acids and lipids in ponies with a high level of management (Bull et al., 2024). Similarly, the addition of probiotics to the diet of horses had an effect on the composition of the intestinal microbiome, while analysis continues to determine changes in specific groups of bacteria (Konen et al., 2019).
Advances in sequencing technologies, such as target site enrichment by hybridization capture (TEHC), have improved the characterization of the equine fecal microbiome. TEHC provides a more complete and accurate understanding of microbial communities compared to traditional amplicon sequencing of the 16S rRNA gene, allowing a deeper study of the structure and functions of the microbiome (Álvarez Narváez et al., 2024). The integration of metagenomic data with physiological indicators lays the foundations for a deeper understanding of the role of equine microbiome in health and disease. The development of tools such as the microbiome coefficient (Myscore) makes it possible to quantify the similarity of the horse microbiome with typical or atypical profiles, which can potentially help in diet management and correction (Jacobs et al., 2024). As research progresses, the possibilities of microbiome diagnostics and therapeutic approaches in the field of equine health continue to expand (Kauter et al., 2019).
The main findings of horse microbiome studies, including dominant taxa, functional insights, and environmental influences, are comparatively illustrated in Figure 3.
2.3. Cattle (Bos taurus Linnaeus, 1758) microbiome
The microbiome of cattle plays an important role in animal health, productivity, and environmental impact. It affects the efficiency of feed assimilation, milk and meat production, methane emissions, and immunity (Wang and Guan, 2022). The gastrointestinal tract contains a complex microbiome that controls the digestion and fermentation of feed (Kim et al., 2017). Microbiome dysbiosis is associated with various diseases, including respiratory, skin, and metabolic disorders (Khalil et al., 2021). The microbiome of the reproductive tract, which is formed in the early stages of life, is of key importance for reproductive health and fertility (Adnane and Chapwanya, 2022). Recently, advanced methods such as metagenomics have been used in research to characterize the microbiome and its relationship to host nutrition and health (Kim et al., 2017). Understanding and managing the bovine microbiome opens up prospects for improving production efficiency, improving animal health, and ensuring environmental sustainability in animal husbandry (Khalil et al., 2021; Wang and Guan, 2022).
Recent metagenomic studies have expanded our understanding of diverse and complex microbial communities in different parts of the gastrointestinal tract (Mao et al., 2016). The composition of the bovine microbiome varies significantly within the gastrointestinal tract, with Firmicutes, Bacteroidetes, and Proteobacteria being the predominant type (Mao et al., 2016). Factors such as feed absorption efficiency, methane emissions, and meat quality depend on the gut microbiome, underscoring its importance for sustainable beef production (Mizoguchi and Guan, 2024). In addition, methanogenic archaea such as Methanobrevibacter play a role in methane production, affecting greenhouse gas emissions (Mizoguchi and Guan, 2024). Approaches to microbiome engineering, including feed additives such as tannins and essential oils, are being explored to reduce methane emissions while maintaining rumen function (Mizoguchi and Guan, 2024).Stress before slaughter can affect the gastrointestinal microbiome, potentially affecting food safety (Costello et al., 2025). Understanding the intestinal microbiome of cattle and its interactions with the host organism is crucial for developing strategies aimed at increasing the sustainability of beef production, improving animal health and meat quality (Kim et al., 2017; Mizoguchi and Guan, 2024).
Metagenomics based on the so-called new generation sequencing (NGS) was first used to detect glycoside hydrolases in the rumen of dairy cows (Brulc et al., 2009), as well as to evaluate the diversity of bacteria in the rumen and feces of beef cattle (Callaway et al., 2010). Nowadays, hundreds of metagenomic studies have been published on various aspects of the rumen microbiome, such as the effect of feed additives or diets on the rumen microbiome, the early stages of its colonization in young animals, and a variety of enzymes, especially glycoside hydrolases (Kim et al., 2017).
Diet plays an important role in the formation of the microbiome. Diets high in fiber favor cellulolytic bacteria, while diets high in starch shift the microbial balance toward lactate-producing bacteria, which may increase the risk of acidosis (Mao et al., 2016). Antibiotics destroy microbial communities, reducing diversity and potentially leading to antimicrobial resistance. Alternative methods such as probiotics and probiotic treatments are being explored to maintain intestinal health and reduce dependence on antibiotics (Wang and Guan, 2022). Microbial colonization begins at birth and develops over time. The microbiome at an early age is influenced by the mother's microbiota and colostrum intake, which affects long-term health and productivity (Adnane and Chapwanya, 2022). Housing conditions, stresses, and geographical differences also shape the microbiome of cattle. Research shows that pasture-based systems promote a more diverse microbiota compared to limited feeding (Khalil et al., 2021).
Genome-centered analysis revealed 523 uncultivated bacteria and 15 predominantly uncultivated archaea in the rumen, which highlights the diversity of microbial life involved in the decomposition of lignocellulose and the production of volatile fatty acids (Gharechahi et al., 2021). In Japan, 146 metagenomically assembled genomes (MAGs) were reconstructed, revealing 54 new strains with enzymes associated with the decomposition of plant biomass (Sato et al., 2022). A large-scale study in Scotland collected 913 microbial genomes, discovering new species and genes involved in carbohydrate metabolism, which significantly expanded the coverage of the genomes of scar microorganisms in public databases (Stewart et al., 2018). Comparative studies using 16S rRNA gene sequencing and metagenomic shotgun sequencing revealed differences in the structures of microbial communities and the abundance of functional genes between different breeds of cattle, such as Japanese black cattle and crossbred bulls (Sato et al., 2021).
Metagenomic approaches are used to identify food pathogens in the beef production chain, which provides insight into the ecology of pathogens and changes in their populations during processing (Yang et al., 2016). Multiomic research is being integrated to improve cattle production and health by studying the active functional dynamics of the microbiome and its interaction with the host (Wang and Guan, 2022).
The main findings of cattle microbiome studies, including dominant taxa, functional insights, and environmental influences, are comparatively illustrated in Figure 4.
2.4. Camels (Camelus dromedarius Linnaeus, 1758) microbiome
Recent advances in molecular genetics have significantly expanded our understanding of camel genomics. The dromedary camel genome, approximately 2.38 GB in size and containing more than 20,000 genes, has been sequenced and organized at the chromosomal level (Piro, 2021). Genetic studies have revealed various population structures of camels from different regions (Piro, 2021). Various molecular methods, including microsatellites, mitochondrial DNA analysis, and single nucleotide polymorphisms (SNPs), have been used to study genetic diversity, domestication processes, and phenotypic traits in camels (Piro, 2021; Ramadan and Inoue-Murayama, 2017).The unique genetic makeup of camels contributes to their ability to survive in harsh environments and has potential medical applications (Ali et al., 2019). While interest in improving the productive qualities of camels is growing, researchers emphasize the importance of balancing genetic improvement with conservation efforts, especially for the endangered wild double-humped camel (Burger et al., 2019). Double-humped camels serve as an important vehicle in the cold desert regions of China and Mongolia. Wang's 2012 study examined the 2.01 GB genome sequences of both wild and domestic double-humped camels. The camel genome was estimated at 2.38 GB, containing 20,821 protein-coding genes. Phylogenetic analysis shows that camels shared common ancestors with other artiodactyls approximately 55-60 million years ago. The rapidly evolving genes in the camel lineage are significantly enriched in metabolic pathways, and these changes may underlie the insulin resistance commonly seen in these animals. The indicators of heterozygosity throughout the genome in both wild and domestic camels were also estimated as 1.0 × 10-3. However, the domestic camel has genomic regions with significantly lower heterozygosity, and olfactory receptors are enriched in these regions (Jirimutu et al., 2012).
Recent studies have revealed the extensive diversity of the camel microbiome, with deep metagenomic sequencing revealing new microbial species and strong correlations between microbiome composition and camel characteristics (Mubaraki, 2025). The microbiome of camel rumen is structurally similar, but differs in composition from other ruminants, with significant enrichment by cellulolytic bacteria (Ming et al., 2017). Metagenomic analysis has identified key microbes responsible for the degradation and fermentation of lignocellulose, with Bacteroidetes, Firmicutes, and Fibrobacteres playing a crucial role (Gharechahi et al., 2015). A comparative analysis of fecal microbial communities in cattle and double-humped camels has shown that Firmicutes and Verrucomicrobia are the predominant types in camels with species-specific differences at the genus level (Gharechahi and Salekdeh, 2018). The complex gut microbiota plays a key role in the metabolism and health of the host. However, the main microbial communities in bactrian camels of different ages remain completely unclear. We used high-throughput sequencing of the 16S rRNA gene to study the temporal variability of the fecal microbiota in bactrian camels. At the age of 2 months, the fecal microbiota consisted of Firmicutes, Proteobacteria, and Actinobacteria. At the ages of 1 and 3 years, the fecal microbiota was dominated by Firmicutes, Bacteroidetes, and Verrucomicrobia. At the level of the genus, Blautia, Fusobacterium, and Bifidobacterium were more numerous at the age of 2 months, as well as Escherichia-Shigella. Ruminococcaceae_CG005, Akkermansia and Christensenellaceae_R7_group were the most numerous at the ages of 1 and 3 years. The diversity and stability of the gut microbiota increased with age. At the age of 2 months, the enrichment of genes associated with diseases of the immune system was observed. This study is the first to examine the distribution of the gut microbiota in double-humped camels of different ages and creates an environment for future research on camel microbiology (He et al., 2019).
The diverse microbiome present in the rumen of ruminants facilitates the digestion of plant fiber. In this study, a fractional metagenomic analysis of microbes adhering to plant fiber in camel rumen was performed to identify key species contributing to the degradation of lignocellulose and fermentation of short-chain volatile fatty acids (VFA). The density of genes in the metagenome encoding glycoside hydrolases was estimated at 25 per Mb of collected DNA, which is significantly higher than reported in other metagenomes, including cow rumen. There was also a significant representation of sequences encoding scaffoldins, doctrines, and cohesins, indicating the potential for cellulosome-mediated degradation of lignocellulose. Binning of the collected metagenome allowed us to identify 65 high-quality bins of the genome, which showed a high diversity of enzymes that degrade lignocellulose. The species associated with Bacteroidetes showed a high proportion of genes for enzymes for the branching and degradation of oligosaccharides, while the species belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases, and thus these lines were probably key to ensuring the degradation of lignocellulose. The presence of many “polysaccharide utilization loci” (PUL) in Bacteroidetes genomes indicates their broad substrate specificity and high potential for carbohydrate degradation. Analysis of the pathways of VFA biosynthesis showed that the genes necessary for acetate synthesis were present in several species, except Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively through the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes, and Fibrobacteres. Butyrate was obtained through the butyryl-CoA: acetate-CoA transferase pathway by Bacteroidetes and Lentisphaerae species, but in general through the butyrate kinase pathway by Firmicutes species. The analysis confirmed that the microbiome of camel rumen is a dense and at the same time largely untapped source of enzymes with the potential for use in several biotechnological processes, including biofuels, fine chemicals, and the food industry (Gharechahi and Salekdeh, 2018).
The main findings of camel microbiome studies, including dominant taxa, functional insights, and environmental influences, are comparatively illustrated in Figure 5.
2.5. Chickens (Gallus gallus domesticus Linnaeus, 1758) microbiome
The intestinal microbiota of chickens is a complex ecosystem that has a significant impact on the health, digestion and productivity of poultry. The interaction between the host and microorganisms promotes the absorption of nutrients, the production of vitamins (for example, vitamin K and B vitamins), and stimulates the development of the immune system and prevents colonization of the intestine by pathogens such as Salmonella and Campylobacter (Kumar et al., 2018). The intestinal microflora also plays an important role in the metabolism of short-chain fatty acids (SCFA), which not only serve as an energy source for intestinal cells but also create unfavorable conditions for the growth of harmful bacteria by lowering the pH in the intestine (Ricke, 2003).
The composition of the microbiota is influenced by many factors, including the age of the bird, the location in the gastrointestinal tract, the type of feeding, and the use of probiotics and prebiotics (Pan and Yu, 2014; Mancabelli et al., 2016). Studies show that the microbiota of the cecum is the richest and most diverse, while Lactobacillus, Enterococcus, and Clostridium dominate in the small intestine (Oakley et al., 2014; Rehman et al., 2007). Feeding methods also have a significant impact: for example, the use of probiotics such as fructooligosaccharides (FOS) and galactooligosaccharides (GOS) increases the number of beneficial bacteria, especially Bifidobacterium and Lactobacillus, while inhibiting the growth of Escherichia coli and Clostridium perfringens (Danzeisen et al., 2011; Apajalahti et al., 2004).
High-throughput sequencing makes it possible to analyze a huge number of bacterial sequences, which makes it possible to detect changes in the microbiota under the influence of various factors, including diet, age, and antibiotic use (Wei et al., 2013; Teirlynck et al., 2011).
A study conducted to compare the intestinal microbiota of commercially raised broiler chickens (BC) and free-range chickens (FRC) confirmed that the composition of the microbiota varies significantly depending on the conditions of detention. It has been established that Firmicutes are the dominant type in the BC microbiota, while Bacteroidetes and Proteobacteria predominate in FRC, which is probably due to differences in diet and the intensive use of antibiotics in industrial poultry farming. In addition, analysis of the cecal resistome revealed a higher content of antibiotic-resistant bacteria in BC. Functional analysis of the FRC microbiome showed increased expression of genes associated with the breakdown of complex carbohydrates (Mancabelli et al., 2016).
The main findings of chicken microbiome studies, including dominant taxa, functional insights, and environmental influences, are comparatively illustrated in Figure 6.
2.6. Microbiome and livestock adaptation in Kazakhstan
Analyses of ethological and productive traits across livestock species highlight that their adaptation to specific environmental conditions is closely intertwined with microbiome restructuring. In Kazakh mares, pasture-based management results in milk with low fat and elevated protein and lactose levels, which not only supports organic kumis production but also plays a critical role in shaping the gut microbiome of foals (Toishimanov et al., 2025; Sharapatov et al., 2025). In beef cattle, the strength of maternal instinct directly influences early calf development and the establishment of the intestinal microbiome, with Canadian lines showing faster adaptation compared to European ones. Likewise, the adaptation of Simmental cattle to hot and mountainous climates is accompanied by shifts in both milk and meat productivity, reflecting genotype-environment interactions that include restructuring of the rumen microbiome (Kazhgaliyev et al., 2023; Shakirov et al., 2023). In goats, seasonal changes in grazing, resting, and watering patterns determine feed efficiency and meat productivity, with corresponding shifts in the rumen microbiota that enhance resilience under extreme steppe conditions (Assanbayev et al., 2025). Collectively, these findings illustrate a unifying principle behavioral and physiological adaptations in livestock are consistently mirrored by structural and functional changes in their microbiomes, underpinning productivity and resilience across diverse ecological niches.
3. Discussion
Animal microbiome is a complex and diverse community of microorganisms that significantly affect the health, immunity, behavior, and productivity of animals. Its research creates chances for the creation of innovative methods and more sustainable methods of animal husbandry to maintain and improve animal welfare, health and productivity.
A study of publications shows that interest in studying the microbiome of farm animals has increased significantly since 2016, with a peak in 2017 and 2021. The geographical scope of the research, which includes the USA, Europe and Asia, indicates the global nature of this topic. The stable level of publications in recent years confirms its continued relevance to the science and practice of animal husbandry.
In all the considered types of farm animals (sheep, horses, cattle, camels) and chickens, the intestinal microbiome and the microbiota of other organs (skin, reproductive tract) has a major impact on key aspects of animal life: digestion, immunity, productivity, behavior, and reproductive health. Commonly, the diet, age, and conditions of the host have a complex effect on the composition and functionality of the microbial community.
Sheep show high microbiome variability depending on breed, age, and diet. This makes them a convenient model for ruminant research; at the same time, the variability of traits (for example, the level of methanogenesis) can significantly affect productivity.
Horses have a particularly complex gut, responsible for the fermentation of fiber. In some cases, domestication and captivity lead to a decrease in the diversity of microbiome, increasing the probability of dysbiosis.
Cattle have the most extensive research base due to their economic importance. Considerable attention is paid to rumen microbiome, which determines feed efficiency and methane emissions.
Camels are distinguished by the unique composition of the rumen microbiota, which can efficiently process hard-to-reach plant fiber.
Chickens exhibit a complex intestinal microbiota that reacts to both dietary factors (probiotics, antibiotics) and housing conditions (industrial and free-range). At the same time, changes in the composition of microbiota affect the productivity and quality of meat.
Overall, cross-species comparisons reveal that ruminants (cattle, sheep, camels) share a predominance of Firmicutes and Bacteroidetes, while monogastric species (horses, chickens) show higher representation of Proteobacteria and Actinobacteria. However, dominant taxa vary by organ system and feeding strategy, highlighting species-specific adaptations.
Majority of studies do not consider age-related changes and the influence of the early stages of microbiota formation (especially important for young animals when the main microbial communities are formed). There is a need for larger samples that consider genetic characteristics and heterogeneous conditions (climate, region, maintenance system, seasonality) in order to increase the reproducibility and practical applicability of the data obtained.
This review highlights the crucial role of the microbiome in shaping the health, productivity, and adaptation of livestock of various species. Comparative analysis among sheep, horses, cattle, camels, and chickens revealed both common and species-specific microbial communities that support digestive efficiency, immunity, and behavior. The integration of metagenomic tools and regional research, including those conducted in Kazakhstan, expands the global understanding of the animal husbandry microbiota. Future research should focus on linking microbial markers with productive traits to develop microbiome-based breeding and feeding strategies for sustainable livestock production.
Acknowledgments
Funding for this research was provided by the Ministry of Science and Higher Education of the Republic of Kazakhstan (2024-2026) under grant BR24992940: “Creation highly productive sheep population in north-eastern region Kazakhstan based on development effective selection techniques and introduction resource-saving technologies”
Data Availability Statement
No new data were created or analyzed in this study. Data sharing is not applicable to this article.
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Editor:
Takako Matsumura Tundisi
