Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data.

The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated that ion's polarizability and mass-to-charge ratio (m/z) have the most significant predictive power for traveling-wave IM CCS values in relation to other physicochemical properties of ions. Constructed solely based on these two physicochemical properties, our CCS prediction approach demonstrated high accuracy (mean relative error of <3.0%) even when trained with limited data (15 CCS values). Given its ability to excel with limited data, our approach harbors immense potential for constructing a precisely predicted CCS database tailored to each distinct experimental setup. A Python script for CCS prediction using our approach is freely available at https://github.com/MSBSiriraj/SVR_CCSPrediction under the GNU General Public License (GPL) version 3.

Functional genome analysis and anti-Helicobacter pylori activity of a novel bacteriocinogenic Lactococcus sp. NH2-7C from Thai fermented pork (Nham).

Helicobacter pylori, linked to gastric diseases, is targeted for probiotic treatment through bacteriocin production. Bacteriocins have gained recognition for their non-toxic effects on host cells and their ability to combat a wide range of pathogens. This study aimed to taxonomically characterize and evaluate the safety and probiotic properties of the novel species of Lactococcus sp. NH2-7C isolated from fermented pork, as well as its bacteriocin NH2-7C, both in vitro and in silico. Comparative genotypic analysis revealed an average nucleotide identity of 94.96%, an average amino acid identity of 94.29%, and a digital DNA-DNA hybridization value of 63.80% when compared to Lactococcus lactis subsp. lactis JCM 5805T. These findings suggest that strain NH2-7C represents a novel species within the genus Lactococcus. In silico assessments confirmed the non-pathogenic nature of strain NH2-7C and the absence of genes associated with virulence and biogenic amine formation. Whole-genome analysis revealed the presence of the nisA gene responsible for nisin A production, indicating its potential as a beneficial compound with anti-Helicobacter pylori activity and non-toxic characteristics. Probiotic assessments indicated bile salt hydrolase and cholesterol assimilation activities, along with the modulation of interleukin-6 and tumour necrosis factor-α secretion. Strain NH2-7C demonstrated gastrointestinal tolerance and the ability to adhere to Caco-2 cells, affirming its safety and probiotic potential. Additionally, its ability to produce bacteriocins supports its suitability as a functional probiotic strain with therapeutic potential. However, further in vitro and in vivo investigations are crucial to ensure its safety and explore potential applications for Lactococcus sp. NH2-7C as a probiotic agent.

Production of Lactobacillus plantarum ghosts by conditional expression of a prophage-encoded holin.

Bacterial ghosts (BGs) are nonviable empty bacterial cell envelopes with intact cellular morphology and native surface structure. BGs made from pathogenic bacteria are used for biomedical and pharmaceutical applications. However, incomplete pathogenic cell inactivation during BG preparation raises safety concerns that could limit the intended use. Therefore, safer bacterial cell types are needed for BG production. Here, we produced BGs from the food-grade Gram-positive bacterium Lactobacillus plantarum TBRC 2-4 by conditional expression of a prophage-encoded holin (LpHo). LpHo expression was regulated using the pheromone-inducible pSIP system and LpHo was localized to the cell membrane. Upon LpHo induction, a significant growth retardation and a drastic decrease in cell viability were observed. LpHo-induced cells also showed membrane pores by scanning electron microscopy, membrane depolarization by flow cytometry, and release of nucleic acid contents in the cell culture supernatant, consistent with the role of LpHo as a pore-forming protein and L. plantarum ghost formation. The holin-induced L. plantarum BG platform could be developed as a safer alternative vehicle for the delivery of biomolecules.

Development of a Novel D-Lactic Acid Production Platform Based on Lactobacillus saerimneri TBRC 5746.

D-Lactic acid is a chiral, three-carbon organic acid, that bolsters the thermostability of polylactic acid. In this study, we developed a microbial production platform for the high-titer production of D-lactic acid. We screened 600 isolates of lactic acid bacteria (LAB) and identified twelve strains that exclusively produced D-lactic acid in high titers. Of these strains, Lactobacillus saerimneri TBRC 5746 was selected for further development because of its homofermentative metabolism. We investigated the effects of high temperature and the use of cheap, renewable carbon sources on lactic acid production and observed a titer of 99.4 g/L and a yield of 0.90 g/g glucose (90% of the theoretical yield). However, we also observed L-lactic acid production, which reduced the product's optical purity. We then used CRISPR/dCas9-assisted transcriptional repression to repress the two Lldh genes in the genome of L. saerimneri TBRC 5746, resulting in a 38% increase in D-lactic acid production and an improvement in optical purity. This is the first demonstration of CRISPR/dCas9-assisted transcriptional repression in this microbial host and represents progress toward efficient microbial production of D-lactic acid.

Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae.

BACKGROUND: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. RESULTS: The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. CONCLUSIONS: In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

Whole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3, a gamma-aminobutyric acid (GABA)-producing strain isolated from Thai pickled weed.

Lactiplantibacillus pentosus 9D3, a prominent gamma-aminobutyric acid (GABA)-producing bacteria isolated from Thai pickled weed was characterized for its safety and probiotic properties via whole-genome analysis and in vitro testing. The whole-genome sequence of L. pentosus 9D3 was determined using a hybrid-sequencing approach, combining PacBio and Illumina technologies. A 3.81-Mbp genome of L. pentosus 9D3 consisting of one 3.65-Mbp chromosome and six plasmids (1.9-71.9 Kbp) was identified with an estimated GC content of 46.09% and 3,456 predicted genes. The strain was confirmed to be Lactiplantibacillus pentosus according to the high average nucleotide identity value of >95% and digital DNA-DNA hybridization scores of >70% to the L. pentosus type strain. Comparative genome analysis with other L. pentosus strains showed that the GABA-producing capability was specific to the strain 9D3. Genes related to GABA biosynthesis and transport were identified on a plasmid, pLPE-70K, indicating the acquired nature of this property. The safety of L. pentosus 9D3 was demonstrated through the lack of genes related to the production of toxins, biogenic amines, and antimicrobial drugs. Although the strain exhibited resistance to ampicillin and chloramphenicol, none of the antimicrobial resistance (AMR) genes were associated with mobile elements, i.e., plasmids and prophages. Therefore, the strain is considered to have low risk of transferring the AMR genes to other, potentially pathogenic bacteria. In addition, L. pentosus 9D3 showed good survivability in the gastrointestinal tract environment and was able to adhere to the intestinal cell in vitro. Therefore, L. pentosus 9D3 is concluded to be safe, with the potential to be used as a probiotic, exerting its health benefit through GABA production in the food system. The GABA-producing capability of the strain in vivo is the subject of further investigation.

Chitooligosaccharide Conjugates Prepared Using Several Phenolic Compounds via Ascorbic Acid/H2O2 Free Radical Grafting: Characteristics, Antioxidant, Antidiabetic, and Antimicrobial Activities.

Chitooligosaccharide (COS)-polyphenol (PPN) conjugates prepared using different PPNs, including gallic, caffeic, and ferulic acids, epigallocatechin gallate, and catechin, at various concentrations were characterized via UV-visible, FTIR, and 1H-NMR spectra and tested for antioxidant, antidiabetic, and antimicrobial activities. Grafting of PPNs with COS was achieved. The highest conjugation efficiency was noticed for COS-catechin (COS-CAT), which was identified to have the highest total phenolic content (TPC) out of all the conjugates (p < 0.05). For antioxidant activities, DPPH and ABTS radical scavenging activities (DPPH-RSA and ABTS-RSA, respectively), oxygen radical absorbance capacity (ORAC), ferric reducing antioxidant power (FRAP), and metal chelating activity (MCA) of all the samples were positively correlated with the TPC incorporated. COS-CAT had higher DPPH-RSA, ABTS-RSA, ORAC, and FRAP than COS and all other COS-PPN conjugates (p < 0.05). In addition, COS-CAT also showed the highest antidiabetic activity of the conjugates, as determined by inhibitory activity toward α-amylase, α-glucosidase, and pancreatic lipase (p < 0.05). COS-CAT also had the highest antimicrobial activity against all tested Gram-negative and Gram-positive bacteria (p < 0.05). Overall, grafting of PPNs, especially CAT on COS, significantly enhanced bioactivities, including antioxidant and antimicrobial, which could be used to retard spoilage and enhance shelf-life of various food systems. Moreover, the ability of COS-CAT to inhibit digestive enzymes reflects its preventive effect on diabetes mellitus and its complications.

The functional starter and its genomic insight for histamine degradation in fish sauce.

Histamine is a biogenic amine significantly formed in fish sauce leading to a major concern in consumers. This study aimed to identify a halophilic bacterium for histamine degradation in fish sauce, and understand its genomic insight to enhance histamine degradation activity. We discovered the novel halophilic bacterium, Bacillus piscicola FBU1786, degrading histamine and other biogenic amines. Its histamine breakdown was growth-associated in a wide range of NaCl concentrations, pH, and temperature from 4% to 18%, 6.0 to 9.0, and 30 to 45 °C, respectively. Genome sequencing revealed the presence of Cu2+-binding oxidase-encoding genes and their heterologous expression with Cu2+ supplementation triggered histamine degradation in E. coli. The degree of histamine breakdown in B. piscicola FBU1786 could be enhanced by Cu2+ addition. Histamine degradation of the culture was evaluated in raw fish sauce mixtures to partially mimic the condition during fish sauce fermentation. Histamine degradation was suppressed to the extent of raw fish sauce, but could be restored by Cu2+ supplementation. Together, this study disclosed B. piscicola FBU1786 with the potent histamine degradation activity, identified Cu2+-binding oxidases responsible for histamine breakdown, and enhanced histamine degradation of the culture using Cu2+ supplementation.

Synergistic enzyme cocktail between levansucrase and inulosucrase for superb levan-type fructooligosaccharide synthesis.

Inulosucrase (ISC) and levansucrase (LSC) utilise sucrose and produce inulin- and levan-type fructans, respectively. This study aims to propose a new strategy to improve levan-type fructooligosaccharide (L-FOS) production. The effect of ISC/ LSC -mixed reaction was elucidated on L-FOS production. The presence of ISC in the LSC reaction significantly leads to the higher production of L-FOSs as the main products. Furthermore, the different ratios between ISC and LSC affected the distribution of L-FOSs. A greater amount of ISC compared to LSC promoted the synthesis of short-chain L-FOSs. Conversely, when LSC was increased, the synthesis of longer-chain L-FOSs was enhanced. The addition of trisaccharide mixtures obtained from either a single ISC or LSC reaction could enhance L-FOSs synthesis in the LSC reaction. Analysis of these trisaccharides revealed that most species of the oligosaccharides were similar, with 1-kestose being the major one. The supplement of only 1-kestose in the LSC reaction showed similar results to those of the reaction in the presence of trisaccharide mixtures. Moreover, the results were supported by molecular dynamics simulations. This work not only provides an improvement in L-FOS production but also revealed and supported some insights into the mechanism of fructansucrases.

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand.

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2-19.3 % and 69.84-84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30-40 °C, at pH 7.0 and with 10-15 % (w/v) NaCl. It contained l-Orn-d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA-DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus Halobacillus, for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

Predicting lupus membranous nephritis using reduced picolinic acid to tryptophan ratio as a urinary biomarker.

The current gold standard for classifying lupus nephritis (LN) progression is a renal biopsy, which is an invasive procedure. Undergoing a series of biopsies for monitoring disease progression and treatments is unlikely suitable for patients with LN. Thus, there is an urgent need for non-invasive alternative biomarkers that can facilitate LN class diagnosis. Such biomarkers will be very useful in guiding intervention strategies to mitigate or treat patients with LN. Urine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Metabolomics was performed to identify potential metabolites, which could be specific for the classification of membranous LN. The ratio of picolinic acid (Pic) to tryptophan (Trp) ([Pic/Trp] ratio) was found to be a promising candidate for LN diagnostic and membranous classification. It has high potential as an alternative biomarker for the non-invasive diagnosis of LN.

Study of the Lipolysis Effect of Nanoliposome-Encapsulated Ganoderma lucidum Protein Hydrolysates on Adipocyte Cells Using Proteomics Approach.

Excessive lipid accumulation is a serious condition. Therefore, we aimed at developing safe strategies using natural hypolipidemic products. Lingzhi is an edible fungus and potential lipid suppression stimulant. To use Lingzhi as a functional hyperlipidemic ingredient, response surface methodology (RSM) was conducted to optimize the time (X1) and enzyme usage (X2) for the hydrolysate preparation with the highest degree of hydrolysis (DH) and % yield. We encapsulated the hydrolysates using nanoscale liposomes and used proteomics to study how these nano-liposomal hydrolysates could affect lipid accumulation in adipocyte cells. RSM analysis revealed X1 at 8.63 h and X2 at 0.93% provided the highest values of DH and % yields were 33.99% and 5.70%. The hydrolysates were loaded into liposome particles that were monodispersed. The loaded nano-liposomal particles did not significantly affect cell survival rates. The triglyceride (TG) breakdown in adipocytes showed a higher TG increase compared to the control. Lipid staining level upon the liposome treatment was lower than that of the control. Proteomics revealed 3425 proteins affected by the liposome treatment, the main proteins being TSSK5, SMU1, GRM7, and KLC4, associated with various biological functions besides lipolysis. The nano-liposomal Linzghi hydrolysate might serve as novel functional ingredients in the treatment and prevention of obesity.

High-Resolution QTOF-MRM for Highly Accurate Identification and Quantification of Trace Levels of Triterpenoids in Ganoderma lucidum Mycelium.

The accurate quantification of triterpenoids in Ganoderma lucidum mushroom in the mycelium stage is challenging due to their low concentrations, interference from other possible isomers, and the complex matrix. Here, a high-resolution quadrupole-time-of-flight mass spectrometry "multiple reaction monitoring" with target enhancement (HR-QTOF-MRM) method was developed to quantify seven target triterpenoids in G. lucidum. The performance of this method was compared against an optimized QQQ-MRM method. The HR-QTOF-MRM was shown to be capable of distinguishing target triterpenoids from interferent peaks in the presence of matrices. The HR-QTOF-MRM LOD and LLOQ values were found to be one to two times lower than those derived from the QQQ-MRM method. Intraday and interday variabilities of the HR-QTOF-MRM demonstrated better reproducibility than the QQQ-MRM. In addition, excellent recoveries of the analytes ranging from 80 to 117% were achieved. Spiking experiments were carried out to verify and compare the quantitative accuracy of the two methods. The HR-QTOF-MRM method provided better percent accuracy, ranging from 84% to 99% (<3% RSD), compared with the range of 69 to 114% (<4%RSD) given by the QQQ-MRM method. These results demonstrate that the new HR-QTOF-MRM mode is able to improve sensitivity, reproducibility, and accuracy of trace level analysis of triterpenoids in the complex biological samples. The triterpenoid concentrations were in the range of nondetect to 0.06-6.72 mg/g of dried weight in fruiting body and to 0.0009-0.01 mg/g of dried weight in mycelium.

Insights Into Transcriptome Profiles Associated With Wooden Breast Myopathy in Broilers Slaughtered at the Age of 6 or 7 Weeks.

Transcriptomes associated with wooden breast (WB) were characterized in broilers at two different market ages. Breasts (Pectoralis major) were collected, 20-min postmortem, from male Ross 308 broilers slaughtered at 6 and 7 weeks of age. The breasts were classified as "non-WB" or "WB" based on palpation hardness scoring (non-WB = no abnormal hardness, WB = consistently hardened). Total RNA was isolated from 16 samples (n = 3 for 6 week non-WB, n = 3 for 6 week WB; n = 5 for 7 week non-WB, n = 5 for 7 week WB). Transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique, and compared between non-WB and WB samples of the same age. Among 6 week broilers, 910 transcripts were differentially expressed (DE) (false discovery rate, FDR < 0.05). Pathway analysis underlined metabolisms of glucose and lipids along with gap junctions, tight junction, and focal adhesion (FA) signaling as the top enriched pathways. For the 7 week broilers, 1,195 transcripts were identified (FDR < 0.05) with regulation of actin cytoskeleton, mitogen-activated protein kinase (MAPK) signaling, protein processing in endoplasmic reticulum and FA signaling highlighted as the enriched affected pathways. Absolute transcript levels of eight genes (actinin-1 - ACTN1, integrin-linked kinase - ILK, integrin subunit alpha 8 - ITGA8, integrin subunit beta 5 - ITGB5, protein tyrosine kinase 2 - PTK2, paxillin - PXN, talin 1 - TLN1, and vinculin - VCL) of FA signaling pathway were further elucidated using a droplet digital polymerase chain reaction. The results indicated that, in 6 week broilers, ITGA8 abundance in WB was greater than that of non-WB samples (p < 0.05). Concerning 7 week broilers, greater absolute levels of ACTN1, ILK, ITGA8, and TLN1, accompanied with a reduced ITGB5 were found in WB compared with non-WB (p < 0.05). Transcriptional modification of FA signaling underlined the potential of disrupted cell-cell communication that may incite aberrant molecular events in association with development of WB myopathy.

In Vitro Mechanism Assessment of Zearalenone Removal by Plant-Derived Lactobacillus plantarum BCC 47723.

Zearalenone (ZEA) is a harmful secondary fungal metabolite, produced primarily by plant pathogenic fungi mostly belonging to the genus Fusarium. It is involved in reproductive disorders in animals since its structure is similar to the estrogen hormone. This induces precocious pubertal changes, fertility problems, and hyper estrogenic disorders. The main objectives of this study were to evaluate the ZEA removal capacity of plant-derived lactic acid bacteria (LAB) and to investigate the possible components and mechanisms involved in the removal of ZEA by physically and chemically treated plant-derived LAB. The bacterial cells were characterized using scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), and the analysis of zeta potential, and hydrophobic index. Results revealed that 17 out of 33 plant-derived LAB exhibited ZEA removal from liquid medium. The percentage of removal ranged from 0.5-23% and Lactobacillus plantarum BCC 47723, isolated from wild spider flower pickle (Pag-sian-dorng), exhibited the highest removal. The alteration of proteins on L. plantarum BCC 47723 structure by Sodium dodecyl sulphate (SDS) treatment was positively affected on ZEA removal, whereas that of lipids on ZEA removal was negatively observed. Heat treatment influenced the higher ZEA adsorption. SEM images showed that the morphologies of modified bacterial cells were distinctly deformed and damaged when compared with untreated control. FTIR analysis indicated that the original functional groups, which included amide (C=O, C-N), carboxyl (C=O, C-O, O-H), methylene (C=C), and alcohol (O-H) groups, were not changed after ZEA adsorption. The zeta potential indicated that electrostatic interaction was not involved in the ZEA removal, while hydrophobicity was the main force to interact with ZEA. These findings can conclude that adsorption by hydrophobicity is the main mechanism for ZEA removal of plant-derived L. plantarum BCC 47723. The alteration of bacterial cell structure by heat treatment enhanced the efficiency of L. plantarum BCC 47723 for ZEA reduction. Its activity can be protected by the freeze-drying technique. Hence, plant-derived L. plantarum BCC 47723 can be considered as an organic adsorbent for ZEA reduction in food and feedstuff.

Influence of non-phosphate and low-sodium salt marination in combination with tumbling process on properties of chicken breast meat affected by white striping abnormality.

This study investigated the effects of non-phosphate and low-sodium (NPLS) marination on properties of white striping chicken breasts (WSCB). Chicken breasts were collected from slaughterhouse and classified as normal (NCB, n = 24) and severe WS (WSCB, n = 120). Sixty WSCB samples were vacuum-tumbled (30 min, 2 °C) with NPLS solution, containing 2.8% (w/v) potassium bicarbonate, 2.9% (w/v) potassium chloride, and 1.5% (w/v) sorbitol at the ratio of meat-to-marinade of 4 to 1 (w/w). The other 60 WSCB received no marination were assigned as nonmarinated WSCB. Properties of marinated (n = 12) and nonmarinated (n = 12) WSCB samples were determined at 0, 3, 7, 10, and 14 days of the storage at 4 °C. Properties of the NCB were also determined on day 0. Concerning day 0, the marinated WSCB exhibited higher (p < 0.05) pH, moisture content, total cooked yield, protein solubility, hardness, cohesiveness, and chewiness along with lower (p < 0.05) cooked loss, expressible water, and shear force than those of nonmarinated WSCB and NCB. Based on nuclear magnetic resonance spectroscopy, bound, intra-myofibrillar, and extra-myofibrillar water of cooked marinated WSCB were greater (p < 0.05) than those of cooked nonmarinated WSCB. The greater (p < 0.05) weight loss, moisture content, and total cooking yield were observed in marinated samples compared to those of nonmarinated WSCB throughout the storage period. Although microbial stability was reduced (p < 0.05), no difference (p ≥ 0.05) in lipid oxidation was detected between the treatments. The findings suggest the NPLS marination as a promising process for improving water holding capacity of the WSCB. PRACTICAL APPLICATION: This study presents the promising application of non-phosphate, low-sodium (NPLS) marination combined with vacuum-tumbling in improving water holding capacity of chicken breast meat affected with white striping condition. Although microbial stability of the marinated breast was negatively affected, no adverse impacts on lipid oxidation was observed during storage up to 14 days.

Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand.

Streptococcus suis, a zoonotic bacterial pathogen, has negative economic impacts on both intensive swine production and human health worldwide. Whole-genome sequencing and comparative genomic analysis have been widely used for comprehensive classification and investigation of the genetic basis of several S. suis strains obtained from distinct hosts in different geographic areas, revealing great genetic diversity of this zoonotic pathogen. In this study, whole-genome sequences of antibiotic-resistant S. suis strains isolated from human patients (2 strains), diseased pigs (4 strains), and asymptomatic pigs (3 strains) in Thailand were compared with known genomes of 1186 S. suis strains. Single-nucleotide polymorphism-based phylogenetic analysis indicated that the Thai-isolated S. suis strains have close genetic relatedness to S. suis strains isolated from Canada, China, Denmark, Netherlands, United Kingdom, and United States of America. The genome analysis revealed genes conferring antibiotic resistance (aad(6), ant(6)-Ia, ermB, tet(O), patB, and sat4) and gene clusters (aph(3')-IIIa and aac(6')-Ie-aph(2″)-Ia) associated with aminoglycoside, macrolide, and fluoroquinolone resistance in S. suis in Thailand. This work provides additional resources for future genomic epidemiology investigation of S. suis.

Nutritional Properties and Oxidative Indices of Broiler Breast Meat Affected by Wooden Breast Abnormality.

Wooden breast (WB) abnormality adversely impacts the quality of chicken meat and has been linked with oxidative stress. In this study, breast samples were taken from carcasses of 7-week-old Ross 308 broilers 20-min and 24-h postmortem. Five WB and seven non-WB control samples were assigned based on palpatory hardness (non-WB = no unusual characteristics and WB = focal or diffused hardness). WB exhibited lower contents of protein and the amino acids, i.e., isoleucine, leucine and valine, lighter surface color, lower shear force, greater drip loss and altered mineral profiles (p ≤ 0.05). Despite no difference in lipid oxidation, a greater degree of protein oxidation was found in the WB meat (p ≤ 0.05). Absolute transcript abundances of superoxide dismutase, hypoxia inducible factor 1 alpha and pyruvate dehydrogenase kinase 1 were greater in WB (p ≤ 0.05), whereas lactate dehydrogenase A expression was lower in WB (p ≤ 0.05). The findings support an association between oxidative stress and the altered nutritional and technological properties of chicken meat in WB.

An efficient ABC transporter signal peptide directs heterologous protein secretion in food-grade hosts.

An efficient expression-secretion system for heterologous protein production in food-grade hosts, Lactobacillus plantarum and Bacillus subtilis, is still required to broaden their applications. The optimal signal peptide compatible with both the desired protein and the target host is important for the system. Here, we constructed new expression-secretion vectors to be used in both bacteria. A natural plasmid originating from food-grade L. plantarum BCC9546 was used as a core vector combined with a strong constitutive promoter, L-ldh promoter, and various signal peptides from several types of L. plantarum proteins: ABC transporter, cell wall-associated and extracellular proteins. A gene encoding 88-kDa amylase isolated from starch-related L. plantarum TBRC470 was used as a gene model to evaluate the systems. By comparing the amounts of secreted amylase from the recombinant strains to that of wild type, all signal peptides gave higher yields of secreted amylase in recombinant B. subtilis. Interestingly, two ABC transporter signal peptides from glutamine and mannose ABC transporters provided noticeably high levels of secreted amylase in recombinant L. plantarum. Moreover, these signal peptides also gave high yields of secreted amylase in recombinant B. subtilis. From the results, the signal peptide of glutamine ABC transporter, which functions in essential amino acid transportation that is a precursor for synthesis of nitrogen-containing compounds and nitrogen homeostasis, has a potential use in development of an efficient expression-secretion system for heterologous protein production in both food-grade hosts.

Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp.

Biofloc systems generate and accumulate microbial aggregates known as bioflocs. The presence of bioflocs has been shown to change gut bacterial diversity and stimulate innate immunity in shrimp. The microbial niche of bioflocs may therefore have the potential to drive shifts in the shrimp gut microbiota associated with stimulation of innate immunity. We performed shotgun metagenomic analysis and 16S rRNA-based amplicon sequencing to characterize complex bacterial members in bioflocs and the shrimp digestive tract, respectively. Moreover, we determined whether biofloc-grown shrimp with discrete gut microbiomes had an elevation in local immune-related gene expression and systemic immune activities. Our findings demonstrated that the bacterial community in bioflocs changed dynamically during Pacific white shrimp cultivation. Metagenomic analysis revealed that Vibrio comprised 90% of the biofloc population, while Pseualteromonas, Photobacterium, Shewanella, Alteromonas, Bacillus, Lactobacillus, Acinetobacter, Clostridium, Marinifilum, and Pseudomonas were also detected. In the digestive tract, biofloc-grown shrimp maintained the presence of commensal bacteria including Vibrio, Photobacterium, Shewanella, Granulosicoccus, and Ruegeria similar to control shrimp. However, Vibrio and Photobacterium were significantly enriched and declined, respectively, in biofloc-grown shrimp. The presence of bioflocs upregulated immune-related genes encoding serine proteinase and prophenoloxidase in digestive organs which are routinely exposed to gut microbiota. Biofloc-grown shrimp also demonstrated a significant increase in systemic immune status. As a result, the survival rate of biofloc-grown shrimp was substantially higher than that of the control shrimp. Our findings suggested that the high relative abundance of vibrios in bioflocs enriched the number of vibrios in the digestive tract of biofloc-grown shrimp. This shift in gut microbiota composition may be partially responsible for local upregulation of immune-related gene expression in digestive organs and systemic promotion of immune status in circulating hemolymph.