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.

The HIF-1α/PLOD2 axis integrates extracellular matrix organization and cell metabolism leading to aberrant musculoskeletal repair.

While hypoxic signaling has been shown to play a role in many cellular processes, its role in metabolism-linked extracellular matrix (ECM) organization and downstream processes of cell fate after musculoskeletal injury remains to be determined. Heterotopic ossification (HO) is a debilitating condition where abnormal bone formation occurs within extra-skeletal tissues. Hypoxia and hypoxia-inducible factor 1α (HIF-1α) activation have been shown to promote HO. However, the underlying molecular mechanisms by which the HIF-1α pathway in mesenchymal progenitor cells (MPCs) contributes to pathologic bone formation remain to be elucidated. Here, we used a proven mouse injury-induced HO model to investigate the role of HIF-1α on aberrant cell fate. Using single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics analyses of the HO site, we found that collagen ECM organization is the most highly up-regulated biological process in MPCs. Zeugopod mesenchymal cell-specific deletion of Hif1α (Hoxa11-CreERT2; Hif1afl/fl) significantly mitigated HO in vivo. ScRNA-seq analysis of these Hoxa11-CreERT2; Hif1afl/fl mice identified the PLOD2/LOX pathway for collagen cross-linking as downstream of the HIF-1α regulation of HO. Importantly, our scRNA-seq data and mechanistic studies further uncovered that glucose metabolism in MPCs is most highly impacted by HIF-1α deletion. From a translational aspect, a pan-LOX inhibitor significantly decreased HO. A newly screened compound revealed that the inhibition of PLOD2 activity in MPCs significantly decreased osteogenic differentiation and glycolytic metabolism. This suggests that the HIF-1α/PLOD2/LOX axis linked to metabolism regulates HO-forming MPC fate. These results suggest that the HIF-1α/PLOD2/LOX pathway represents a promising strategy to mitigate HO formation.

Hybrid nutraceutical of 2-ketoglutaric acid in improving inflammatory bowel disease: Role of prebiotics and TAK1 inhibitor.

The main cause of inflammatory bowel disease (IBD) is abnormal intestinal permeability due to the disruption of the tight junction of the intestinal barrier through a pathogen-mediated inflammatory mechanism and an imbalance of the gut microbiota. This study aimed to evaluate whether 2-ketoglutaric acid alleviated permeability dysfunction with tight junction localization, activated the transforming growth factor beta-activated kinase 1 (TAK1) inflammation pathway, and regulated the homeostasis of the intestinal microbiome in vitro and in vivo IBD model. Our findings revealed that 2-ketoglutaric acid significantly suppressed abnormal intestinal permeability, delocalization of tight junction proteins from the intestinal cell, expression of inflammatory cytokines, such as TNF-α, both in vitro and in vivo. 2-Ketoglutaric acid was found to directly bind to TAK1 and inhibit the TNF receptor-associated factor 6 (TRAF6)-TAK1 interaction, which is related to the activation of nuclear factor kappa B (NF-κB) pathways, thereby regulating the expression of mitogen-activated protein kinase. Dietary 2-ketoglutaric acid also alleviated gut microbiota dysbiosis and IBD symptoms, as demonstrated by improvements in the intestine length and the abundance of Ligilactobacillus, Coriobacteriaceae_UCG_002, and Ruminococcaceae_unclassified in mice with colitis. This study indicated that 2-ketoglutaric acid binds to TAK1 for activity inhibition which is related to the NF-κB pathway and alleviates abnormal permeability by regulating tight junction localization and gut microbiome homeostasis. Therefore, 2-ketoglutaric acid is an effective nutraceutical agent and prebiotic for the treatment of IBD.

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.

Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors.

Lysyl hydroxylase 2 (LH2) catalyzes the formation of highly stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs), thus promoting lung cancer metastasis through its capacity to modulate specific types of collagen cross-links within the tumor stroma. Using 1 and 2 from our previous high-throughput screening (HTS) as lead probes, we prepared a series of 1,3-diketone analogues, 1-18, and identified 12 and 13 that inhibit LH2 with IC50's of approximately 300 and 500 nM, respectively. Compounds 12 and 13 demonstrate selectivity for LH2 over LH1 and LH3. Quantum mechanics/molecular mechanics (QM/MM) modeling indicates that the selectivity of 12 and 13 may stem from noncovalent interactions like hydrogen bonding between the morpholine/piperazine rings with the LH2-specific Arg661. Treatment of 344SQ WT cells with 13 resulted in a dose-dependent reduction in their migration potential, whereas the compound did not impede the migration of the same cell line with an LH2 knockout (LH2KO).

Development and Characterization of Inula britannica Extract-Loaded Liposomes: Potential as Anti-Inflammatory Functional Food Ingredients.

We investigated the potential of Inula britannica extract encapsulated in liposomes as a functional food ingredient with enhanced bioavailability and stability. Inula britannica, known for its anti-inflammatory properties and various health benefits, was encapsulated using a liposome mass production manufacturing method, and the physical properties of liposomes were evaluated. The liposomes exhibited improved anti-inflammatory effects in lipopolysaccharide-activated RAW 264.7 macrophages, suppressing the production of pro-inflammatory mediators such as nitric oxide and prostaglandin E2 and downregulating the expression of iNOS and COX-2 transcription factors. Additionally, we observed reduced production of pro-inflammatory cytokines TNF-α, IL-6, and IL-1ß, and modulation of the NF-κB and mitogen-activated protein kinase signaling pathways. These findings suggest that Inula britannica extract encapsulated in liposomes could serve as a valuable functional food ingredient for managing and preventing inflammation-related disorders, making it a promising candidate for incorporation into various functional food products. The enhanced absorption and stability provided by liposomal encapsulation can enable better utilization of the extract's beneficial properties, promoting overall health and well-being.

Novel next generation sequencing panel method for the multiple detection and identification of foodborne pathogens in agricultural wastewater.

Detecting and identifying the origins of foodborne pathogen outbreaks is a challenging. The Next-Generation Sequencing (NGS) panel method offers a potential solution by enabling efficient screening and identification of various bacteria in one reaction. In this study, new NGS panel primer sets that target 18 specific virulence factor genes from six target pathogens (Bacillus cereus, Yersinia enterocolitica, Staphylococcus aureus, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus) were developed and optimized. The primer sets were validated for specificity and selectivity through singleplex PCR, confirming the expected amplicon size. Crosscheck and multiplex PCR showed no interference in the primer set or pathogenic DNA mixture. The NGS panel analysis of spiked water samples detected all 18 target genes in a single reaction, with pathogen concentrations ranging from 108 to 105 colony-forming units (CFUs) per target pathogen. Notably, the total sequence read counts from the virulence factor genes showed a positive association with the CFUs per target pathogen. However, the method exhibited relatively low sensitivity and occasional false positive results at low pathogen concentrations of 105 CFUs. To validate the detection and identification results, two sets of quantitative real-time PCR (qPCR) analyses were independently performed on the same spiked water samples, yielding almost the same efficiency and specificity compared to the NGS panel analysis. Comparative statistical analysis and Spearman correlation analysis further supported the similarity of the results by showing a negative association between the NGS panel sequence read counts and qPCR cycle threshold (Ct) values. To enhance NGS panel analysis for better detection, optimization of primer sets and real-time NGS sequencing technology are essential. Nonetheless, this study provides valuable insights into applying NGS panel analysis for multiple foodborne pathogen detection, emphasizing its potential in ensuring food safety.

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.

Improvement of crAssphage detection/quantification method and its extensive application for food safety.

Water-borne diseases are usually caused by the fecal-oral transmission of human fecal pathogens. Traditionally, coliforms and enterococci are widely used as indicator bacteria, but they do not allow to differentiate between human and animal fecal contamination. Owing to its presence only in the human gut environment, crAssphage has been suggested as an alternative indicator of human fecal contamination to overcome the above challenges. In this study, 139 human and 89 animal fecal samples (e.g., chicken, cow, dog, pig, pigeon, and mouse) were collected. For the rapid detection of human crAssphage in fecal samples, quantitative real-time PCR (qPCR) was performed using five different oligonucleotide primer/probe combinations. These included three previously reported oligonucleotide primer/probe combinations (RQ, CPQ056, and CrAssBP) and two newly developed combinations (ORF00018-targeting CrAssPFL1 and ORF00044-targeting CrAssPFL2). The detection rate (crAssphage-positive rate) in human fecal samples were 23.0, 30.2, 28.8, 20.1, and 30.9%, respectively, suggesting CrAssPFL2 showed the highest detection rate. Furthermore, the lowest copy numbers (436.16 copy numbers) could be detected using the CrAssPFL2 combination. Interestingly, no difference in crAssphage detection rates was found between healthy people and intestinal inflammatory patients. As expected, no crAssphage was detected in any animal fecal samples, indicating its human specificity. Furthermore, qPCR analysis of sewage samples collected from five different sewage treatment plants revealed that they were all contaminated with 105.71 copy numbers/mL of crAssphage on average. The simulation test of crAssphage-contaminated food samples also confirmed that the detection limit was from 107.55 copy numbers of crAssphage in foods. Therefore, the newly developed and optimized qPCR would be useful for the sensitive detection of crAssphage while identifying the source of human fecal contamination.

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.

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).

Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition.

The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.

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.

Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods.

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 108-105 CFU of target strains. However, a few false-positive results were shown at 106-105 CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.

Discovery and characterization of a new genotype of Salmonella enterica serovar Bareilly isolated from diarrhea patients of food-borne outbreaks.

Since the first food-borne outbreak of Salmonella enterica serovar Bareilly in the UK (2010), it has been recognized as a new type of food-borne pathogen in S. enterica. To detect and characterize this new serovar pathogen in South Korea, a total of 175 Salmonella strains was isolated and 31 isolates were identified as S. Bareilly from various food-borne outbreaks between 2014 and 2018. While pulsed-field gel electrophoresis (PFGE) analysis using XbaI revealed two major groups (A and B) each with two subgroups (A1, A2/B1, B2), average nucleotide identity (ANI), single nucleotide polymorphism (SNP), and in silico multilocus sequence typing (MLST) analyses confirmed only two major groups. Interestingly, extended SNP analysis with 67 S. Bareilly strains from outbreaks in other countries revealed that A group strains between 2014 and 2016 shared a close evolutionary relationship with the strains from outside of South Korea; however, the B group strains in 2018 were located in a separate SNP tree branch. These findings suggest that the A group may share common ancestor with the strains of previous outbreaks in the UK or other countries, while the B group is a new genotype. Comparative virulence factor (VF) analysis between the A and B group strains showed that S. Bareilly in the B group has more various than that of the A group. A comparative biofilm formation assay supports for this, which B group strain GG-21 has higher biofilm formation activity than A group strain GG-07. Antibiotic susceptibility test of 31 S. Bareilly strains revealed high susceptibility to 17 tested antibiotics, suggesting that S. Bareilly can be easily treated by antibiotics.

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.

Independent Component Analysis Identifies the Modulons Expanding the Transcriptional Regulatory Networks of Enterohemorrhagic Escherichia coli.

The elucidation of the transcriptional regulatory networks (TRNs) of enterohemorrhagic Escherichia coli (EHEC) is critical to understand its pathogenesis and survival in the host. However, the analyses of current TRNs are still limited to comprehensively understand their target genes generally co-regulated under various conditions regardless of the genetic backgrounds. In this study, independent component analysis (ICA), a machine learning-based decomposition method, was used to decompose the large-scale transcriptome data of EHEC into the modulons, which contain the target genes of several TRNs. The locus of enterocyte effacement (LEE) and the Shiga toxin (Stx) modulons mainly consisted of the Ler regulon and the Stx prophage genes, respectively, confirming that ICA properly grouped the co-regulated major virulence genes of EHEC. Further investigation revealed that the LEE modulon contained the hypothetical Z0395 gene as a novel member of the Ler regulon, and the Stx modulon contained the thi and cus locus genes in addition to the Stx prophage genes. Correspondingly, the Stx prophage genes were also regulated by thiamine and copper ions known to control the thi and cus locus genes, respectively. The modulons effectively clustered the genes co-regulated regardless of the growth conditions and the genetic backgrounds of EHEC. The changed activities of the individual modulons successfully explained the differential expressions of the virulence and survival genes during the course of infection in bovines. Altogether, these results suggested that ICA of the large-scale transcriptome data can expand and enhance the current understanding of the TRNs of EHEC.