Lactic acid bacteria and yeast strains isolated from fermented fish (Budu) identified as candidate ruminant probiotics based on in vitro rumen fermentation characteristics.

Background and Aim: Probiotic supplementation can assist with manipulating the rumen microbial ecosystem. Lactic acid bacteria and yeast from fermented fish (Budu) as the indigenous food from West Sumatra, Indonesia, are potential probiotics for livestock. This study aims to select the best candidate lactic acid bacteria and yeast strains from fermented fish as ruminant probiotics and evaluate the effect of their supplementation on the characteristics of rumen fermentation, feed digestion, and total gas production in vitro. Materials and Methods: This study used nine treatments, performed in triplicate, in a completely randomized design. The substrate ratio comprised of 70% Pennisetum purpureum forage and 30% concentrate. Five lactic acid bacteria and three yeast isolates were used in this study. Treatments were as follows: T0: control (basal diet); T1: T0 + Lactobacillus parabuchneri strain 3347; T2: T0 + Lactobacillus buchneri strain 5296; T3: T0 + Lactobacillus harbinensis JCM 16178; T4: T0 + Schleiferilactobacillus harbinensis strain LH991; T5: T0 + L. parabuchneri strain 6902; T6: T0 + Pichia kudriavzevii strain B-5P; T7: T0 + P. kudriavzevii strain CBS 5147; and T8: T0 + commercial yeast (Saccharomyces cerevisiae). The lactic acid bacteria inoculum contained 1.02 × 1011 colony-forming unit (CFU)/mL, while the yeast inoculum contained 1.5 × 1010 CFU/mL. Results: The results showed that four lactic acid bacteria and three yeast produced a higher total gas yield (104-183.33 mL) compared to the control (103 mL). Supplementation with lactic acid bacteria in the rumen fermentation in vitro showed dry matter digestibility of 63%-70% and organic matter digestibility (OMD) of 64%-71%. We observed that total volatile fatty acid (VFA) production in all treatments was significantly higher (86-121 mM) compared to the control (81 mM). The concentration of NH3 production was higher in all treatments (12.33-16.83 mM) than in the control (12.25 mM). Meanwhile, the probiotic supplementation did not cause a significant change in the rumen pH (6.86-7.12). Supplementation with the lactic acid bacteria S. harbinensis strain LH991 consistently demonstrated the best results from the parameters of dry and OMD (70.29% and 71.16%, respectively), total VFA (121.67 mM), NH3 (16.83 mM), and total gas production (149.17 mL). The best results were observed from the yeast candidate P. kudriavzevii strain B-5P, where the results were dry and OMD (67.64% and 69.55% respectively), total VFA (96.67 mM), NH3 (13.42 mM), and total gas production (183.33 mL). Conclusion: Based on the obtained results, lactic acid bacteria S. harbinensis strain LH991 and yeast P. kudriavzevii strain B-5P are attractive candidates to be utilized as probiotics for ruminants based on their potential to improve rumen fermentation in vitro. This probiotic supplementation can increase the digestibility of feed ingredients, production of total VFA and NH3, and total gas produced.

The Role of Vitamin D Binding Protein and Vitamin D Level in Mortality of Sepsis Patients.

Background: Vitamin D plays crucial roles in immune cell function, including macrophage activation, immune response modulation, and antimicrobial peptide production. Low vitamin D levels can result in reduced immune response, heightened inflammation, and impaired organ function, thereby exacerbating sepsis severity and impacting patient prognosis. This study investigates the influence of vitamin D binding protein expression and vitamin D levels on the mortality of septic patients. Methods: This analytical observational study employs a case-control approach and involves patients at the Critical Care Unit of Dr. M. Djamil General Hospital in Padang, Indonesia. The study comprises 40 patients in the case group and 40 patients in the control group. Vitamin D and vitamin D binding protein levels are assessed using the enzyme-linked immunosorbent assay method. Results: Vitamin D and vitamin D binding protein levels were observed to be lower in the case group compared to the control group. In the case group, the majority of patients had vitamin D binding protein levels below 200 µg/mL. A significant association was found between vitamin D levels and mortality in sepsis patients (P< 0.05). Patients with vitamin D levels below 20 µg/mL faced a 2.54 times higher risk of mortality than those with levels exceeding 20 µg/mL. Conclusions: Diminished levels of vitamin D binding protein and vitamin D contribute to an increased risk of mortality in septic patients.

Vitamin D-Binding Protein and the Role of its Gene Polymorphisms in the Mortality of Sepsis Patients.

OBJECTIVE: This study aimed to determine the role of vitamin D-binding protein (VDBP) gene polymorphisms (especially at locus rs7041), vitamin D-binding protein levels, and vitamin D levels in mortality in sepsis patients. PATIENTS AND METHODS: We performed the analytic observational study with a case-control approach. A total of 80 patients were included in this study, 40 patients were grouped as the case group and 40 patients were grouped as the control group. The patients were diagnosed with sepsis and treated in the Intensive Care Unit (ICU), M. Djamil Hospital, Indonesia. The VDBP rs7041 gene polymorphism was analyzed using the polymerase chain reaction procedure. VDBP and vitamin D levels were examined using the enzyme-linked immunosorbent assay (ELISA) method. RESULTS: The case group showed lower mean vitamin D and VDBP levels than the control group (P<0.05). There were more variations in the rs7041 gene VDBP (mutant) locus in the case group than in the control group, and this difference was considered statistically significant, P<0.05. The results of this study indicate that the occurrence of polymorphism or variations at locus rs7401 (mutant) causes a decrease in VDBP and vitamin D levels. A decrease in vitamin D levels correlates with the incidence of mortality in sepsis patients. CONCLUSION: Polymorphism gene VDBP at locus rs7041 causes a decrease in the production of VDBP, a vitamin D carrier protein.

Metagenomic analysis and biodiversity of bacteria in traditional fermented fish or Budu from West Sumatera, Indonesia.

Objective: This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality. Materials and methods: To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the 16S-rRNA gene in the V3-V4 region from two types of Budu and carried out in duplicate. Results: Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are Lentibacillus kimchi (1.878%-2.21%), Staphylococcus cohnii (0.597%-0.70%), Peptostreptococcus russeli (0.00%-0.002%), Clostridium disporicum (0.073%-0.09%), Clostridium novyi (0.00%-0.01%), Nioella sediminis (0.00%-0.001%), and Shewanella baltica (0.00%-0.003%). Lentibacillus kimchi, S. cohnii, and C. disporicum are found in both Budu. Nioella sediminis and S. baltica are found in Budu Pariaman. Peptostreptococcus russeli and C. novyi were found in Budu Pasaman. Conclusion: Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the Enterococcaceae family, genus Vagococcus, and pathogenic bacteria, such as S. cohnii, P. russeli, C. disporicum, and S. baltica. The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.

Growth Phase Influence the Gene Expression and Metabolite Production Related to Indole-3-Acetic Acid (IAA) Biosynthesis by Serratia plymuthica UBCF_13.

<b>Background and Objective:</b> The optimization of the indole-3-acetic acid (IAA) producing capability of <i>Serratia plymuthica</i> UBCF_13 has been intensively studied. This work tried to reveal the effect of growth phases on IAA production, gene expression and metabolite synthesis related to the IAA biosynthesis pathway. <b>Materials and Methods:</b> The growth curve and IAA production were measured every 3 hrs. The putative IAA biosynthesis pathway was investigated based on the UBCF_13 genome. To identify the possible pathway of IAA biosynthesis in UBCF_13, we applied the Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and High-Performance Liquid Chromatography (HPLC) analysis to measure the transcript levels of each gene and indole metabolite production based on tryptophan treatment at different times of incubation. <b>Results:</b> The optimal IAA production on colorimetric assay was at 9 hrs of incubation (initial stationary phase). The level expression of <i>puuC</i>, <i>DDC</i>, <i>oxdA</i>, <i>amiE</i>, <i>nthA</i> and <i>nthB</i> have been upregulated maximum in 3 hrs of culture time (lag phase), except <i>tyrB</i> and <i>ipdC</i>. The highest transcript level of the genes was found in nitrile hydratase genes (<i>nthA</i> and <i>nthB</i>) and indole-3- acetamide (IAM) has been detected as the only intermediate in the crude extract of UBCF_13 thus the IAM pathway may be used to produce IAA. The maximum IAA production on HPLC analysis was found at 21 hrs of incubation (late stationary phase). <b>Conclusion:</b> This study gives a new insight that the best time to measure gene expression and intermediates related to the IAA biosynthetic pathway in bacteria was found at a specific growth phase.

Physicochemical and Morphological Characteristics of Starch and Flour Obtained from Green Banana cv. Raja (Musa paradisiaca cv. Raja) in West Sumatra, Indonesia.

<b>Background and Objective:</b> Banana cv. <i>Raja</i> is widely cultivated in West Sumatra, Indonesia. The physicochemical properties of starch and flour were investigated to determine their functional food prospects in industrial food. <b>Materials and Methods:</b> Starch and flour of banana cv. <i>Raja</i> was characterized using proximate analysis, Scanning Electron Microscopy (SEM), X-Ray Diffraction (XRD), Fourier-Transform Infrared (FT-IR), X-Ray Fluorescence (XRF) and Rapid Visco-Analyzer (RVA). <b>Results:</b> Banana cv. <i>Raja</i> starch contains 40.73% starch, 17.49% amylose, 55.5% water, 0.66% ash, 0.83% protein and 0.18% fat. The size of the granules is ranging from 20-30 µm in irregular and ellipsoidal-truncated shapes. The structure of crystallinity belongs to the type B while the gelatinization temperature is 74.9°C. Furthermore, the starch composed of 41.06% potassium, 12.85% phosphorus, 12.74% iron, 9.4% calcium and 7.5% magnesium. <b>Conclusion:</b> The morphological and physicochemical starch characteristics of Banana cv. <i>Raja</i> and has similar characteristics with its flour. Meanwhile the swelling power and the solubility value of the flour were higher than the starch. The gelatinization temperatures of starch and flour were 74.9 and 73.4°C, respectively.

Development of Rapid and Less Hazardous Plant DNA Extraction Protocol using Potassium Phosphate Buffer.

<b>Background and Objective:</b> Protocols commonly used in plant DNA extraction were known to be highly time-consuming and harmful due to the application of some hazardous reagents. Therefore, it was not applicable for such laboratories with limited resources as well as for high-throughput analysis. This study was aimed to develop a rapid yet less hazardous DNA extraction protocol for a plant using potassium phosphate buffer. <b>Materials and Methods:</b> Genomic DNA of chili pepper (<i>Capsicum annuum</i>) was extracted using potassium phosphate buffer and its efficacy was compared to three widely known protocols (CTAB-based, mini preparation and commercial kit). The extracted DNA from those four methods was evaluated based on its quality, quantity, practicality and cost per reaction. <b>Results:</b> Genomic DNA resulted from potassium phosphate buffer-based protocol exhibited comparable quality with adequate concentration for further downstream analysis. Results of PCR and sequencing were also emphasized the amplifiable DNA quality from this developed protocol. Compared to those commonly used protocols, potassium phosphate buffer consisted of 5 main working steps only, thus providing a simple yet rapid plant DNA extraction protocol. Since this protocol used ethanol only, it also offered a less hazardous and low-cost protocol that applicable for those resource-limited laboratories. <b>Conclusion:</b> This developed protocol provided a promising alternative of plant DNA extraction that might be applicable for both large scale analysis and any laboratory type. Further investigation was needed to evaluate its efficacy in extracting genomic DNA from various plants with different morphological characteristic.

Association of Gene Polymorphism of Bactericidal Permeability Increasing Protein Rs4358188, Cluster of Differentiation 14 Rs2569190, Interleukin 1ß Rs1143643 and Matrix Metalloproteinase-16 Rs2664349 with Neonatal Sepsis.

BACKGROUND: Neonatal sepsis is a health problem because it causes serious morbidity and mortality in neonate intensive care units. The susceptibility of neonates occurs due to the immaturity of immune system development as well as due to maternal and environmental risk factors that can cause infection. Identification of genetic variation in genes involved in the inflammatory process can help clarify the pathophysiology of sepsis in high-risk patients, useful for the development of new diagnostic tools, and specific management plans for more accurate predictions of patient's prognosis. AIM: This study aims to determine the association between gene polymorphism of BPI rs4358188, CD14 rs2569190, IL1ß rs1143643 or MMP16 rs2664349 and the incidence of neonatal sepsis. METHODS: Cross-sectional observational studies with genomic DNA samples from infants with sepsis and non-sepsis which were stored according to the standard storage of genetic materials in the Biomedical Laboratory of Faculty of Medicine Universitas Andalas Padang City, Indonesia. This study is part of a previous study by Rukmono P. Continued with PCR examination, sequencing and bioinformatics analysis. RESULTS: Only IL1ß rs1143643 G > A gene polymorphism was associated with the incidence of neonatal sepsis and was statistically significant (p = 0.017). No significant association was found between gene polymorphisms of BPI rs4358188 G > T, CD14 rs2569190 A>G or MMP16 rs2664349 G > A and neonatal sepsis (p > 0.05). CONCLUSION: Gene polymorphism of IL1ß rs1143643 G > A is associated with the incidence of neonatal sepsis.

Correlation between Estrogen Levels with Lipid Profile in Menopause Women in West Sumatera.

BACKGROUND: Menopause is a condition where women had not experienced menstruation for 12 consecutive cycles. At menopause period, there is alteration in women reproductive cycle where estrogen decreased and lipid status altered. AIM: This study is aimed to understand the association of estrogen level and lipid status in menopause women. METHODS: This study was an observational study with cross-sectional design underwent in Obstetrics and Gynecology Polyclinic Dr M. Djamil Hospital, Padang to examine estrogen level and lipid level in 107 menopause women aged between 40-60 years old. The study was conducted for 6 months. The relationship between estrogen level and lipid profile was done using correlation test and p-value < 0.05 is significant. RESULTS: There was no significant correlation between estrogen and total cholesterol (p = 0.146), LDL (p = 0.496), HDL (p = 0.172) and triglyceride (p = 0.296) in menopause women. There was negative correlation between estrogen with total cholesterol (r = -0.141; p = 0.146), HDL (r = -0.133; p = 0.172) and triglyceride (r = -0.1; p = 0.296) and a little positive correlation with LDL (r = 0.06; p = 0.496). Estrogen levels are not related to total Cholesterol, LDL, HDL, and triglyceride in menopause women. CONCLUSION: Estrogen levels did not correlate with lipid status in menopause women in West Sumatera.

Molecular identification and phylogenetic analysis of GABA-producing lactic acid bacteria isolated from indigenous dadih of West Sumatera, Indonesia.

Background: Dadih (fermented buffalo milk) is a traditional Indonesian food originating from West Sumatra province. The fermentation process is carried out by lactic acid bacteria (LAB), which are naturally present in buffalo milk.  Lactic acid bacteria have been reported as one of potential producers of γ-aminobutyric acid (GABA). GABA acts as a neurotransmitter inhibitor of the central nervous system. Methods: In this study, molecular identification and phylogenetic analysis of GABA producing LAB isolated from indigenous dadih of West Sumatera were determined. Identification of the GABA-producing LAB DS15 was based on conventional polymerase chain reaction. 16S rRNA gene sequence analysis was used to identify LAB DS15. Results: PCR of the 16S rRNA gene sequence of LAB DS15 gave an approximately 1400 bp amplicon.  Phylogenetic analysis showed that LAB DS15 was Pediococcusacidilactici, with high similarity of 99% at 100% query coverage to Pediococcusacidilactici strain DSM 20284. Conclusions: It can be concluded that GABA producing LAB isolated from indigenous dadih was Pediococcus acidilactici.

Elevation in tropical sky islands as the common driver in structuring genes and communities of freshwater organisms.

Tropical mountains are usually characterized by a vertically-arranged sequence of ecological belts, which, in contrast to temperate habitats, have remained relatively stable in space across the Quaternary. Such long-lasting patterning of habitats makes them ideal to test the role of environmental pressure in driving ecological and evolutionary processes. Using Sumatran freshwater mayfly communities, we test whether elevation, rather than other spatial factors (i.e. volcanoes, watersheds) structures both species within communities and genes within species. Based on the analysis of 31 mayfly (Ephemeroptera) communities and restriction-site-associated-DNA sequencing in the four most ubiquitous species, we found elevation as the major spatial component structuring both species and genes in the landscape. In other words, similar elevations across different mountains or watersheds harbor more similar species and genes than different elevations within the same mountain or watershed. Tropical elevation gradients characterized by environmental conditions that are both steep and relatively stable seasonally and over geological time scales, are thus responsible for both ecological and genetic differentiation. Our results demonstrate how in situ ecological diversification at the micro-evolutionary level might fuel alpha- and beta- components of diversity in tropical sky islands.

Enhancement of a Novel Isolate of Serratia plymuthica as Potential Candidate for an Antianthracnose.

BACKGROUND AND OBJECTIVE: A new rhizobacteria isolate of Serratia plymuthica (strain UBCR_12) exhibited a promising potential as a biocontrol agent for anthracnose causing agent Colletotrichum gloeosporioides. The aim of this study was to characterize its antagonistic activity and explore the factors contributing to a higher inhibition activity. MATERIALS AND METHODS: The antifungal effect of UBCR_12 against C. gloeosporioides was assayed under various pH values and nutritional sources. Culture supernatant obtained from UBCR_12 and C. gloeosporioides co-culture was also tested for its inhibitory activity. In addition, the antagonistic range of this isolate was examined against Sclerotium rolfsii and Fusarium oxysporum. Statistical analysis was done using one way analysis of variance and further processed using Fisher's Least Significant Difference (LSD) test with a p<0.05. RESULTS: The UBCR_12 induced inhibition was shown to be stable over time at pH 7, while peptone addition led to a faster induction (2 days after treatment) and glucose treatment to a higher activity. Of all these modifications, preliminary co-culture experiments with fungal cells resulted in the best antagonistic activity of UBCR_12 culture supernatant of about 30.66%. This isolate also showed a wide range of antagonistic activity due to its high suppression against S. rolfsii and F. oxysporum from soybean. CONCLUSION: Both environmental and biotic manipulations contributed an elevated inhibition rate of UBCR_12 against C. gloeosporioides. A proportional combination of the factors stimulating antagonistic activity of this strain is recommended to be utilized for the development of this strain as an antianthracnose. The enhanced antifungal effects of UBCR_12 resulted under each type of modification were varied indicating the difference of cell responses. It suggests that certain antifungal mechanism could be generated by modifying the environmental factor required for its induction. In addition, the application of cell-free culture supernatant provides an alternative solution in the utilization of biocontrol agents. For large scale application, it could minimize the risk of population outbreaks and harmful effects due to the living cells application.