Ruminal Phages - A Review

A review of bacteriophage and their application in domestic animals in a post-antibiotic era

Bacteriophages (phages for short) are the most abundant biological entities on Earth and are natural enemies of bacteria. Genomics and molecular biology have identified subtle and complex relationships among phages, bacteria and their animal hosts. This review covers composition, diversity and factors affecting gut phage, their lifecycle in the body, and interactions with bacteria and hosts. In addition, research regarding phage in poultry, aquaculture and livestock are summarized, and application of phages in antibiotic substitution, phage therapy and food safety are reviewed.

Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.

Biotechnological lactic acid production from low-cost renewable sources via anaerobic microbial processes

Lactic acid (LA) production from microbial fermentation using low-cost renewable sources has emerged as an attractive alternative to the use of petroleum-based products. This approach not only offers sustainable solutions for waste management but also enables the production of value-added products in an eco-friendly manner. However, to make this approach economically viable, optimizing the production process for high yield, productivity, and purity while minimizing costs is crucial. To address these challenges, various approaches have been proposed, including the use of neutralizing agents, high cell density cultures, co-cultures, fed-batch fermentation, and product removal strategies. Overall, this review underscores the potential of microbial fermentation for LA production as a sustainable and cost-effective solution to meet the growing demand for eco-friendly products. Further optimization of fermentation processes and the development of new microbial strains and fermentation techniques are key to advancing this approach. The production of LA through microbial fermentation presents a sustainable and eco-friendly solution to the increasing demand for eco-friendly products. With continued innovation, we can expect to see a significant reduction in the environmental impact of industrial processes, coupled with a more cost-effective and high-purity source of lactic acid for various industries.

Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle

Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.

Rumen protozoa and viruses: The predators within and their functions-A mini-review

The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.

Understanding the Diversity and Roles of the Ruminal Microbiome

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

Isolation and characterization of strictly anaerobic cellulolytic rumen bacterial species from Sahiwal cattle

Objective

To isolate and characterize cellulolytic rumen bacteria from the rumen of Sahiwal cattle using rumen bacterial inoculum to increase the nutritional value of rice bran used as broiler feed.

Materials and Methods

The ruminal liquid was kept at an optimal pH of 6.9 and a redox potential of less than -300 mV while being incubated anaerobically at 39°C in a medium containing rumen fluid glucose cellobiose agar. By using the Hungate technique, the organisms were detected based on their morphological, physiological, biochemical, and molecular testing.

Results

The findings revealed that the isolated Ruminococcus albus, and Ruminococcus flavifaciens were obligate anaerobic, generally Gram-positive, nonmotile cocci or rod, single or pair, occasionally short chain, producing yellow pigment when grown on cellulose, and having a clear zone around the colonies. Both isolate fermented sugars such as cellobiose, glucose, and lactose, as well as decomposed xylan. The results also showed that the isolates recognized as Ruminococcus spp., a cellulolytic rumen bacterium, were catalase-negative, indole-negative, and gelatin liquefaction-positive.

Conclusion

Isolation and characterization of Ruminococcus spp. may be helpful for Bangladesh in reducing the cost of producing poultry feed and circumventing restrictions on rice bran use. We can also develop more efficient and long-lasting plans to enhance poultry performance and feed efficiency, as well as increase the nutritional value of rice bran used as broiler feed, by understanding how various Ruminococcus spp. function in this process.

Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.

A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals

Viruses have a potential to modify the ruminal digestion via infection and cell lysis of prokaryotes, suggesting that viruses are related to animal performance and methane production. This study aimed to elucidate the genome-based diversity of rumen viral communities and the differences in virus structure between individuals and cattle breeds and to understand how viruses influence on the rumen. To these ends, a metagenomic sequencing of virus-like particles in the rumen of 22 Japanese cattle, including Japanese Black (JB, n = 8), Japanese Shorthorn (n = 2), and Japanese Black sires × Holstein dams crossbred steers (F1, n = 12) was conducted. Additionally, the rumen viromes of six JB and six F1 that were fed identical diets and kept in a single barn were compared. A total of 8,232 non-redundant viral genomes (≥5-kb length and ≥50% completeness), including 982 complete genomes, were constructed, and rumen virome exhibited lysogenic signatures. Furthermore, putative hosts of 1,223 viral genomes were predicted using tRNA and clustered regularly interspaced short palindromic repeat (CRISPR)-spacer matching. The genomes included 1 and 10 putative novel complete genomes associated with Fibrobacter and Ruminococcus, respectively, which are the main rumen cellulose-degrading bacteria. Additionally, the hosts of 22 viral genomes, including 2 complete genomes, were predicted as methanogens, such as Methanobrevibacter and Methanomethylophilus. Most rumen viruses were highly rumen and individual specific and related to rumen-specific prokaryotes. Furthermore, the rumen viral community structure was significantly different between JB and F1 steers, indicating that cattle breed is one of the factors influencing the rumen virome composition.IMPORTANCEHere, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure. More importantly, we revealed differences of viral communities between JB and F1 cattle, indicating that cattle breed is a factor that influences the establishment of rumen virome. These results suggest the possibility of rumen virus transmission from mother to offspring and its potential to influence beef production traits. These rumen viral genomes and findings provide new insights into the characterizations of the rumen viruses.

Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil

Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.