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.

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.

Change in the Gut Microbiota of Lactating Sows and Their Piglets by Inclusion of Dietary Spray-Dried Plasma in Sow Diets.

This study aimed to investigate the effects of dietary spray-dried plasma (SDP) on the gut microbiota of lactating sows and their piglets. A total of 12 sows were randomly assigned to one of two dietary treatment groups in a completely randomized design. The treatments were a sow diet based on corn and soybean meal (CON), and a CON diet with an added 1% SDP. The sows were fed the dietary treatments from d 30 before farrowing to weaning (d 28). The fecal samples of three sows from each treatment and two of their randomly selected piglets were collected to verify their fecal microbiota. There were no differences in the alpha diversity and distinct clustering of the microbial communities in the sows and their piglets when SDP was added to the sow diets from late gestation to weaning. The fecal microbiota of the lactating sows and their piglets showed a higher relative abundance of the phylum Bacteroidota and genus Lactobacillus and Ruminococcus and showed a lower relative abundance of the phylum Bacillota and genus Bacteroides, Escherichia/Shigella, and Clostridium in the sows fed the SDP diet than those fed the CON diet. Overall, these results show that the addition of SDP to the sow diet during lactation altered the gut environment with positive microbial composition changes. These results were similar in the nursing piglets, suggesting that the control of the sow diets during lactation may contribute to the intestinal health and growth in piglets after weaning.

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.

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.

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.

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.

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.

Effects of different stocking density and various phytogenic feed additives dosage levels on growing-finishing pigs.

This study was to investigate the effects of different phytogenic feed additives (PFA) dosage levels in growing- finishing pigs stressed by high stocking density. A total of 72 mix sexed 12 weeks growing pigs ([Landrace × Yorkshire] × Duroc) with initial body weight (BW) of 49.28 ± 4.58 kg were used for 8 weeks. There were 3 replicate pens in each treatment group, with 3 pigs per pen. The dietary treatment groups consisted of basal diets in animal welfare density (negative control [NC]), basal diet in high stocking density (positive control [PC]), PC + 0.04% essential oil (ES1), PC + 0.08% essential oil (ES2), PC + 0.10% bitter citrus extract & essential oil (CES1), PC + 0.20% bitter citrus extract & essential oil (CES2), PC + 0.05% grape pomace extract (GP1), PC + 0.10% grape pomace extract (GP2). The reduction of space allowance decreased (p < 0.05) average daily gain, feed efficiency, and digestibility of dry matter, crude protein, and gross energy. Also, the fecal score of PC groups increased (p < 0.05) compared with other groups. Basic behaviors (feed intake, standing, lying) were inactive (p < 0.05) and singularity behavior (biting) was increased (p < 0.10) under high stocking density. There was no difference in blood profile. However, the supplementation of PFA alleviated the negative effects such as reduced growth performance, nutrient digestibility, and some increasing stress indicators in th blood (cortisol) and animal behavior (biting). In conclusion, the negative effect of high stocking density was most effectively mitigated by the normal dosage of the mixture of bitter citrus extract and essential oil additive (CES1).

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.

Collinsella urealyticum sp. nov., a urease-positive bacterial strain isolated from swine faeces.

A novel actinobacterial strain, designated AGMB00827T, was isolated from swine faeces. Strain AGMB00827T was obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped bacterium. Comparative analyses based on the 16S rRNA gene and whole genome sequence revealed that strain AGMB00827T was affiliated to the genus Collinsella, and was most closely related to Collinsella vaginalis Marseille-P2666T (= KCTC 25056T). Biochemical analysis showed strain AGMB00827T was negative for catalase and oxidase. Interestingly, strain AGMB00827T possessed urease activity, which was determined by traditional methods (API test and Christensen's urea medium), unlike related strains. Furthermore, the major cellular fatty acids (> 10%) of the isolate were C18:1 ω9c, C16:0, C16:0 DMA and C18:2 ω9,12c DMA. Based on the whole genome sequence analysis, the DNA G + C content of strain AGMB00827T was 52.3%, and the genome size and numbers of rRNA and tRNA genes were 1,945,251 bp, 3 and 46, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain AGMB00827T and C. vaginalis KCTC 25056 T were 71.0 and 23.2%, respectively. Additionally, the genome analysis revealed that strain AGMB00827T possesses urease gene cluster including ureABC and ureDEFG while the related strains do not have those genes, which is consistent with the urease activity. On the basis of polyphasic taxonomic approach, strain AGMB00827T represents a novel species within the genus Collinsella, for which the name Collinsella urealyticum sp. nov. is proposed. The type strain is AGMB00827T (= KCTC 25287T = GDMCC 1.2724T).

Dietary yeast cell wall enhanced intestinal health of broiler chickens by modulating intestinal integrity, immune responses, and microbiota.

This study was conducted to determine the effects of dietary yeast cell wall (YCW) on growth performance, intestinal health, and immune responses of broiler chickens. In a randomized completely block design (block: initial body weight), a total of 800 broilers (Ross 308; 45.18 ± 3.13 g of initial body weight) were assigned to 2 dietary treatments (40 birds/pen; 10 replicates/treatment) and fed for 5 wk: 1) a basal broiler diet based on corn-soybean meal (CON) and 2) CON + 0.05% dietary YCW. Growth performance was measured at intervals in 3 phase feed program. On the final day of the study, one bird per pen was randomly selected and euthanized for sample collection. Broilers fed YCW had decreased (P < 0.05) feed conversion ratio during the grower phase compared with those fed CON. The YCW increased (P < 0.05) villus height to crypt depth ratio in the duodenum, jejunum, and ileum compared with the CON. In addition, the YCW tended to higher (P < 0.10) number of goblet cells in the duodenum than in the CON. Broilers fed YCW had increased (P < 0.05) serum TGF- ß1, ileal gene expression of the claudin family, and relative abundance of Lactobacillus, Prevotella, and Enterococcus compared with the CON, but decreased serum TNF-α (P < 0.05), IL-1ß (P < 0.05), and IL-6 (P < 0.10), ileal gene expression of IL-6 (P < 0.05), and relative abundance of Clostridium (P < 0.05). The present study demonstrated that the addition of dietary YCW in broiler diets enhanced the intestinal health of broiler chickens and may be associated with modulated intestinal morphology and integrity by upregulating tight junction-related protein gene expression and modifying the ileal microbiota. In addition, dietary YCW modulated immune responses and inflammatory cytokine gene expression in the ileum.

Effects of supplemental different clay minerals in broiler chickens under cyclic heat stress.

The objective of this study was to investigate the effect of supplementing clay minerals and organic chromium in feed on broiler chicken under heat stress (HS). A total of 90 one-day-old broiler chicken (Arbor Acres) with an initial body weight of 45.0 ± 0.2 g were assigned to five treatment groups (six replications, three birds each cage): 1) NC group, basal diet under room temperature environment; 2) PC group, basal diet under high temperature (HT) environment; 3) ILT group, basal diet + 1% illite + HT; 4) ZLT group, basal diet + 1% zeolite + HT; 5) OC group, basal diet + 400 ppb/kg organic chromium + HT. The ILT and ZLT groups had significantly higher body weight than the PC group in 4 weeks. Apparent total tract digestibility of gross energy was increased in the ILT, ZLT, and OC groups compared to the PC group. The NC group had lower foot-pad dermatitis score than other groups. Escherichia coli population in the cecum and feces was decreased in the ZLT group than in the PC group. Lactobacillus in cecum and feces was significantly increased in the ZLT group than in the PC group. Regarding blood profiles, blood cortisol was decreased in the NC and ILT groups compared to the PC group. Water holding capacity and pH were increased in the ZLT group than the PC group. In conclusion, according to the results of growth performance, nutrients digestibility, bacteria counts, and meat characteristics, supplementation of the ZLT in broiler diet can alleviate HS.

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.

Parabacteroides faecalis sp. nov. Isolated from Swine Faeces.

A Gram-negative, obligate anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated AGMB00274T was isolated from swine faeces. An 16S rRNA gene analysis indicated that strain AGMB00274T belonged to the genus Parabacteroides, with the highest similarity to Parabacteroides johnsonii (P. johnsonii) DSM 18315T (sequence similarity of 94.9%). The genome size of strain AGMB00274T was 4,308,683 bp, with a DNA G+C content of 42.5 mol%. The biochemical analysis of strain AGMB00274T showed that it was positive for gelatin hydrolysis and α-fucosidase, but negative for the acid production from D-glucose, D-mannitol, D-maltose, salicin, glycerol, D-cellobiose, D-mannose, D-melezitose, D-sorbitol, D-trehalose, and negative for α-arabinosidase, glutamic acid decarboxylase, and pyroglutamic acid arylamidase. The dominant cellular fatty acids (> 10%) of the isolate were anteiso-C15: 0 (23.2%), iso-C15: 0 (16.6%), C18: 1 ω9c (16.4%), summed feature 11 (iso-C17: 0 3-OH and/or C18: 2 DMA) (12.5%), and C16: 0 (11.3%). The major respiratory quinones of strain AGMB00274T were MK-9 (55.4%) and MK-10 (44.6%). The major polar lipid was phosphatidylethanolamine. Based on phylogenetic, genetic, physiological, and chemotaxonomic analyses, as a novel species of the genus Parabacteroides, strain AGMB00274T was proposed with the name Parabacteroides faecalis sp. nov. The type strain used was AGMB00274T (= KCTC 25286T = GDMCC 1.2742T).

Caproiciproducens faecalis sp. nov., Isolated from Cow Faeces.

The bacterial strain AGMB10547T was isolated from cow faeces deposited by the National Institute of Animal Science in Cheonan, Republic of Korea. The strain AGMB10547T possessed the phenotypic, biochemical and chemotaxonomic characteristics of the bacteria of the family Oscillospiraceae. The isolate was obligately anaerobic, non-motile, Gram-positive and rod-shaped bacteria. The growth of strain AGMB10547T occurred within 35-40 °C (optimum at 37 °C), at pH 6-7 (optimum of 7) and in the presence of 0.5-2.0% (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain AGMB10547T belonged to the genus Caproiciproducens and was most closely related to Caproiciproducens galactitolivorans BS-1T (96.9%). The DNA G+C content was 49.0 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0, C14:0 DMA, C16:1 ω9c and C16:0. The average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH) values between strain AGMB10547T and C. galactitolivorans BS-1T were 75.5% and 19.2%. Based on the phenotypic, genotypic, biochemical and chemotaxonomic analyses, strain AGMB10547T represents a novel species of the genus Caproiciproducens, for which the name Caproiciproducens faecalis sp. nov. is proposed. The type strain AGMB10547T (=KCTC 25200T=NBRC 115006T=GDMCC 1.2575T).

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.

Mouse feeding study and microbiome analysis of sourdough bread for evaluation of its health effects.

Sourdough bread fermented with yeast and lactic acid bacteria (LAB) is thought to have various beneficial health effects. However, its beneficial effects were not fully evaluated with in vivo mouse model. To evaluate these effects in vivo, a mouse feeding study and microbiome analysis of white bread containing 40% sourdough (WBS) and yeast-leavened white bread (WB) were performed. Although feed consumption and body weight increased with WBS, the glycemic index was reduced, suggesting a diabetes-lowering effect, probably due to the presence of dietary fiber and short-chain fatty acids (SCFA). In addition, a mineral absorption test showed that WBS increased magnesium absorption owing to phytate degradation during fermentation. Interestingly, WBS decreased total cholesterol and triglycerides, probably due to the dietary fiber and SCFA in LAB. In addition, the ratio of low- and high-density lipoprotein was decreased in WBS, implying potential risk reduction for cardiovascular disease. An immunomodulatory assay of WBS revealed that pro-inflammatory cytokines TNF-α and IL-6 were decreased, suggesting anti-inflammatory activity. Gluten degradation by fermentation and antioxidation activity of menaquinol/ubiquinol by gut microbiota also supported the anti-inflammatory activity of sourdough bread. Furthermore, some beneficial gut bacteria, including Akkermansia, Bifidobacterium, and Lactobacillus, were increased in WBS. In particular, Akkermansia has been associated with anti-inflammatory properties. Consequently, WBS has beneficial effects on health, including decreased glycemic index and cholesterol, increased mineral availability and absorption, anti-inflammatory properties, and establishment of healthy gut microbiota.