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.

Lactic acid bacteria in Asian fermented foods and their beneficial roles in human health.

Fermented foods have been a staple in human diets for thousands of years, garnering attention for their health and medicinal benefits. Rich in lactic acid bacteria (LAB) with probiotic properties, these foods play a crucial role in positively impacting the host's gut microbiome composition and overall health. With a long history of safe consumption, fermented foods effectively deliver LAB to humans. Intake of LAB from fermented foods offers three main benefits: (1) enhancing digestive function and managing chronic gastrointestinal conditions, (2) modulating the immune system and offering anti-inflammatory effects to prevent immune-related diseases, and (3) synthesizing vitamins and various bioactive compounds to improve human health. In this review, we highlighted the diverse LAB present in Asian fermented foods and emphasized LAB-rich fermented foods as a natural and effective solution for health enhancement and disease prevention.

Investigation of the impact of multi-strain probiotics containing Saccharomyces cerevisiae on porcine production.

A balanced intestinal microbiome controls intestinal bacterial diseases, helps regulate immunity, and digests and utilizes nutrients, ultimately having a positive effect on the productivity of industrial animals. Yeasts help in the digestion process by breaking down indigestible fibers and producing organic acids, vitamins, and minerals. In particular, polysaccharides such as beta-glucan and mannan-oligosaccharides, which are present in the cell wall of yeast, inhibit the adhesion of pathogens to the surface of the gastrointestinal tract and increase resistance to disease to help maintain and improve intestinal health. Among the yeast additives used in animal feed, Saccharomyces cerevisiae is one of the most commonly used probiotics. However, it does not naturally reside in the intestine, so if it is supplied in combination with other species of probiotics that can compensate for it, many benefits and synergies can be expected for pigs in terms of maintaining intestinal health such as supplementing the immune system and improving digestion. A number of previous studies have demonstrated that dietary complex probiotic supplementation has growth-promoting effects in pigs, suggesting that multiple strains of probiotics may be more effective than single strain probiotics due to their additive and synergistic effects. In practice, however, the effects of complex probiotics are not always consistent, and can be influenced by a variety of factors. Therefore, this review comprehensively examines and discusses the literature related to the effects of complex probiotics using Saccharomyces cerevisiae in pig production.

Antibiotic resistance in livestock, environment and humans: One Health perspective.

Antibiotic resistance (AR) is a complex, multifaceted global health issue that poses a serious threat to livestock, humans, and the surrounding environment. It entails several elements and numerous potential transmission routes and vehicles that contribute to its development and spread, making it a challenging issue to address. AR is regarded as an One Health issue, as it has been found that livestock, human, and environmental components, all three domains are interconnected, opening up channels for transmission of antibiotic resistant bacteria (ARB). AR has turned out to be a critical problem mainly because of the overuse and misuse of antibiotics, with the anticipation of 10 million annual AR-associated deaths by 2050. The fact that infectious diseases induced by ARB are no longer treatable with antibiotics foreshadows an uncertain future in the context of health care. Hence, the One Health approach should be emphasized to reduce the impact of AR on livestock, humans, and the environment, ensuring the longevity of the efficacy of both current and prospective antibiotics.

Complete genome sequence of Enterococcus faecium strain AK_C_05 with potential characteristics applicable in livestock industry.

The Enterococcus faecium (E. faecium) strain AK_C_05 was isolated from cheonggukjang, the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes. It possesses genes, which encodes enzymes such as alpha-galactosidase (EC 3.2.1.22), beta-glucosidase (EC 3.2.1.21) and alpha-L-arabinofuranosidase (EC 3.2.1.55) enabling efficient utilization of carbohydrates. Based on Clusters of Orthologous Groups analysis, E. faecium strain AK_C_05 showed specialization in carbohydrate transport and metabolism indicating the ability to generate energy using a variety of carbohydrates.

Characteristics of Lactococcus petauri GB97 lysate isolated from porcine feces and its in vitro and in vivo effects on inflammation, intestinal barrier function, and gut microbiota composition in mice.

IMPORTANCE: Weaning is a crucial step in piglet management to improve pork production. During the weaning phase, disruption of epithelial barrier function and intestinal inflammation can lead to decreased absorption of nutrients and diarrhea. Therefore, maintaining a healthy intestine, epithelial barrier function, and gut microbiota composition in this crucial phase is strategic for optimal weaning in pigs. We isolated a lysate of Lactococcus petauri GB97 (LPL97) from healthy porcine feces and evaluated its anti-inflammatory activities, barrier integrity, and gut microbial changes in LPS-induced murine macrophages and DSS-induced colitis mice. We found that LPL97 regulated the immune response by downregulating the TLR4/NF-κB/MAPK signaling pathway both in vitro and in vivo. Furthermore, LPL97 alleviated the disruption of intestinal epithelial integrity and gut microbiota dysbiosis in colitis mice. This study indicates that LPL97 has the potential to be developed as an alternative feed additive to antibiotics for the swine industry.

Exploring the multifaceted factors affecting pork meat quality.

The significance of pork meat quality extends far beyond mere consumer satisfaction, encompassing crucial aspects such as health and nutrition, economic impact, reputation and branding, food safety, and sustainability within the global food system. Influenced by a multitude of factors, each playing a pivotal role in shaping its sensory attributes and consumer appeal, pork meat quality stands as a cornerstone of the meat industry. Thus, understanding these factors are imperative for ensuring consistent high-quality pork production, aligning with consumer preferences, and elevating overall satisfaction levels. In this review, we provide a comprehensive overview of the diverse factors affecting pork meat quality, including genetic characteristics, rearing systems, feed composition, gender differences, pre-slaughter handling, and meat aging processes.

Swine gut microbiome associated with non-digestible carbohydrate utilization.

Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.

Cutting-edge knowledge on the roles of phytobiotics and their proposed modes of action in swine.

With the ban on antibiotics in the swine industry, the exploration of alternative options has highlighted phytobiotics as a promising substitute for antibiotic growth promoters, aiming to foster a more sustainable swine industry. Phytobiotics are non-nutritive natural bioactive components derived from plants that offer numerous health benefits. They exhibit antioxidative, antimicrobial, and anti-inflammatory effects. Phytobiotics can be utilized in various forms, including solid, dried, ground, or as extracts, either in crude or concentrated form. They are characterized by low residual levels, a lack of resistance development, and minimal adverse effects. These qualities make phytobiotics an attractive choice for enhancing health and productivity in swine, presenting them as a viable alternative to antibiotics. While there is a general understanding of the effects of phytobiotics, there is still a need for detailed information regarding their effectiveness and mechanisms of action in practical settings. Therefore, the purpose of this mini review was to summarize the current knowledge supporting the roles of phytobiotics and their proposed modes of action, with a specific focus on swine.

Analysis of antibiotic resistance genes in pig feces during the weaning transition using whole metagenome shotgun sequencing.

Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.

Development of the standard mouse model for human bacterial vaginosis induced by Gardnerella vaginalis.

Bacterial vaginosis (BV) is a polymicrobial syndrome characterized by a diminished number of protective bacteria in the vaginal flora. Instead, it is accompanied by a significant increase in facultative and strict anaerobes, including Gardnerella vaginalis (G. vaginalis). BV is one of the most common gynecological problems experienced by reproductive age-women. Because an ideal and standard animal model for human BV induced by G. vaginalis is still underdeveloped, the main objective of this study was to develop a mouse model for human BV induced by G. vaginalis to demonstrate the clinical attributes observed in BV patients. A total of 80 female ICR mice were randomly assigned to 4 groups and intravaginally inoculated with different doses of G. vaginalis: NC (uninfected negative control), PC1 (inoculated with 1 × 105 CFU of G. vaginalis), PC2 (inoculated with 1 × 106 CFU of G. vaginalis) and PC3 (inoculated with 1 × 107 CFU of G. vaginalis). The myeloperoxidase (MPO) activity and serum concentrations of cytokines (IL-1ß, IL-10) in mice administered with G. vaginalis were significantly higher than those of the control group. Gross lesion and histopathological analysis of reproductive tract of mice inoculated with G. vaginalis showed inflammation and higher epithelial cell exfoliation compared to the control group. In addition, vaginal swabs from the mice inoculated with G. vaginalis showed the presence of clue cells, which are a characteristic feature of human BV. Altogether, our results suggested that G. vaginalis is sufficient to generate comparable clinical attributes seen in patients with BV.

Comparative analysis of the pig gut microbiome associated with the pig growth performance.

There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.

Effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs.

Introduction: This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs. Methods: A total of 300 crossbred pigs [(Landrace × Yorkshire] × Duroc; 8.87 ± 0.34 kg of average initial body weight [BW]; 4 weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block = BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 × 107 CFU/mL) and S. cerevisiae (1 × 107 CFU/mL) at 3 mL/pig/day for 4 weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis. Results and Discussion: The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p < 0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.

Complete genome sequence of Lactococcus taiwanensis strain K_LL004, encoding hydrolytic enzymes of plant polysaccharides isolated from grasshopper (Oxya chinensis sinuosa).

The Lactococcus taiwanensis strain K_LL004 was isolated from the gut of a grasshopper (Oxya chinensis sinuosa) collected from local farm in Korea. L. taiwanensis strain K_LL004 is the functional probiotic candidate with an ability to hydrolyse plant polysaccharides. The complete genome of the L. taiwanensis strain K_LL004 contains one circular chromosome (1,995,099 bp) with a guanine + cytosine (GC) content of 38.8%. Moreover, 1,929 Protein-coding sequence, 19 rRNA genes, and 62 tRNA genes were identified based on results of annotation. L. taiwanensis strain K_LL004 has a gene, which encodes hydrolytic enzymes such as beta-glucosidase and beta-xylosidase, that hydrolyzes plant polysaccharides.

Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.

Gut microbial shifts by synbiotic combination of Pediococcus acidilactici and lactulose in weaned piglets challenged with Shiga toxin-producing Escherichia coli.

Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.

Rice as an alternative feed ingredient in swine diets.

It has become important to explore alternative feed ingredients to reduce feed costs, which are burdensome for livestock production. In addition, it is desirable to find efficient and functional alternative ingredients for traditional feed ingredients in pig diets, considering the stress and sensitivity of disease of pig. Rice is produced around the world like corn that is the typical energy source in pig diets. Although the nutritional quality varies depending on the degree of milling, rice, except whole grains (paddy rice), contains more starch than corn and its structure and granule size are easier to digest than corn. In addition, the fact that rice has fewer non-starch polysaccharides (NSP) and anti-nutritional factors (ANFs) is also effective in improving digestibility and various polyphenols in rice can help modulation of immune responses, which can be beneficial to the gastrointestinal environment and health of pig. Many studies have been conducted on rice focusing on things such as degree of milling, substitution rates of corn, granule size, and processing methods. Most results have shown that rice can be partially or completely used to replace corn in pig diets without negatively affecting pig growth and production. While further research should focus on the precise biological mechanisms at play, it was confirmed that the use of rice could reduce the use of antibiotics and pig removal and protect pigs from gastrointestinal diseases including diarrhea. From this point of view, rice can be evaluated as a valuable feed ingredient for swine diets.

Evaluation of brown rice to replace corn in weanling pig diet.

This study was conducted to evaluate the effects of brown rice (Japonica) on growth performance, nutrient digestibility, and blood parameters of weanling pigs. A total of 60 weanling pigs (28-day-old, 30 barrows and 30 gilts, 6.73 ± 0.77 kg body weight [BW]) were randomly allotted to 2 dietary treatments (6 pigs per pen; 5 replicates per treatment) in a randomized complete block design with the initial BW and sex as blocks. The dietary treatments were a typical nursery diet based on corn and soybean meal (CON) and the CON replaced 50% of corn with brown rice (BR). Pigs were fed respective dietary treatments for 5 weeks. For the last week of experiment period, pigs were fed respective dietary treatments containing 0.2% chromic oxide as an indigestible marker. Fecal samples were collected from randomly selected 1 pig in each pen daily for the last 3 d after the 4-d adjustment period. Blood was collected from randomly selected 1 pig in each pen on d 0, 3, 7, and 14 after weaning. Compared with pig fed CON diet, pigs fed the BR diet were found to have higher (p < 0.05) final BW, overall average daily gain, and apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of dry matter and energy. However, there were no significant differences between the groups with respect to average daily feed intake, gain to feed ratio, frequency of diarrhea, and the AID and ATTD of crude protein during overall experimental period. Similarly, there were no significant differences on blood parameters between the groups. Thus, the findings of this study indicate that brown rice (Japonica) can be used to replace 50% of corn in the diet of pigs during the nursery period without negatively affecting growth performance, nutrient digestibility, or blood parameters.

Effects of Substitution of Corn with Ground Brown Rice on Growth Performance, Nutrient Digestibility, and Gut Microbiota of Growing-Finishing Pigs.

The present study was conducted to evaluate the effects of replacing corn with brown rice on growth performance, nutrient digestibility, carcass characteristics, and gut microbiota of growing and finishing pigs. A total of 100 growing pigs (23.80 ± 2.96 kg BW; 10 weeks of age) were randomly allotted to 4 dietary treatments (5 pigs/pen; 5 replicates/treatment) in a randomized complete block design (block = BW) as follows: corn-soybean meal basal diet (CON) and replacing corn with 50% (GBR50), 75% (GBR75), and 100% (GBR100) of ground brown rice. Each trial phase was for 6 weeks. During the growing period, there were no differences on growth performance and nutrient digestibility among dietary treatments. Similarly, no differences were found on growth performance, nutrient digestibility, and carcass characteristics of pigs during the finishing period among dietary treatments. As a result of the beta diversity analysis, microbial populations were not clustered between CON and GBR100 during the growing phase, but clustered into two distinct groups of CON and GBR100 during the finishing phase. In conclusion, brown rice can be added to the diets of growing-finishing pigs by replacing corn up to 100% without negatively affecting growth performance of the pigs; additionally, this may have an effect on changes in pig intestinal microbiota if continued for a long time.

Complete genome sequence of Salmonella enterica strain K_SA184, multidrug resistance bacterium isolated from lamb (Ovis aries).

Salmonella enterica is a representative foodborne pathogen in the world. The S. enterica strain K_SA184 was isolated from the lamb (Ovis aries), which was collected from a local traditional market in South Korea. In this study, the S. enterica strain K_SA184 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The final complete genome of the S. enterica strain K_SA184 consist of one circular chromosome (4,725,087 bp) with 52.3% of guanine + cytosine (G + C) content, 4,363 of coding sequence (CDS), 85 of tRNA, and 22 of rRNA genes. The S. enterica strain K_SA184 genome includes encoding virulence genes, such as Type III secretion systems and multidrug resistance related genes.