Alterations in the Gut Microbiome Composition of People Living with HIV in the Asia-Pacific Region: A Systematic Review.

Human immunodeficiency virus (HIV) infection continues to present a global health issue. Recent studies have explored the potential role of the gut microbiome in HIV infection for novel therapeutic approaches. We investigated the gut microbiome composition of people living with HIV (PLHIV) in the Asia-Pacific region. This review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. An electronic search was conducted in the PubMed/MEDLINE, Scopus, and ScienceDirect databases using keywords such as "HIV", "PLHIV", "AIDS", "gut microbiome", "gut dysbiosis", and "metagenomics". Only peer-reviewed and full-text studies published in English were included. A total of 15 studies from the Asia-Pacific region were included for analysis. Compared to healthy controls, PLHIV showed an increased abundance of Proteobacteria and its genera, which may be considered pathobionts, and decreased abundances of Bacteroidetes and several genera under Firmicutes with known short-chain fatty acid and immunoregulatory activities. Predominant taxa such as Ruminococcaceae and Prevotellaceae were also associated with clinical factors such as CD4 count, the CD4/CD8 ratio, and inflammatory cytokines. This review highlights gut microbiome changes among PLHIV in the Asia-Pacific region, indicating potential bacterial signatures for prognostication. The partial restoration of the microbiome toward beneficial taxa may ensure the long-term success of treatment, promoting immune recovery while maintaining viral load suppression.

Virgin Coconut Oil as Adjunctive Therapy for Hospitalized COVID-19 Patients in a Tertiary Referral Hospital: A Randomized Controlled Trial.

Background: Virgin coconut oil (VCO) has anti-viral and anti-inflammatory properties, making it a potential therapeutic candidate against COVID-19 infection. Objective: To determine the efficacy and safety of VCO as adjunctive therapy for hospitalized patients with COVID-19. Methods: We conducted a randomized, open-label controlled trial involving laboratory-confirmed COVID-19 patients admitted at the Philippine General Hospital. The study participants were randomized to the intervention group who received virgin coconut oil with local standard of care, or to the control group who received local standard of care alone. Results: We enrolled 39 participants into the VCO group and 38 participants into the control group. Significantly fewer participants in the VCO group had abnormal CRP levels at the end of treatment compared to control. (relative risk [RR] 0.75, 95% confidence interval [CI] 0.58 to 0.95; p=0.02) No significant difference was found in the duration of hospital stay (mean 9.33 days for VCO vs. 10.29 days for control; p=0.45) and time to symptom resolution (mean 6.8 days for VCO, vs. 6.74 days for control; p=0.91). Although the proportion of patients who developed the secondary outcomes of mortality, need for ICU admission, need for invasive ventilation, and negative viral conversion was lower in the VCO group, results did not reach statistical significance. The VCO group had larger reduction in the inflammatory markers ferritin, lactate dehydrogenase, TNF-alpha, IP-10 and IL-6, but results did not reach statistical significance. Adverse events were significantly higher in the VCO group (RR 4.87, 95% CI 1.14 to 20.79; p=0.03). Conclusion: This clinical trial on hospitalized patients showed significant benefit in CRP levels of participants given VCO compared to control. There was no significant benefit in the use of VCO as adjunctive therapy in reducing duration of hospital stay. Larger studies are needed to conclusively demonstrate the effect of VCO on other clinical outcomes and inflammatory markers.

Draft genome sequence of Pediococcus acidilactici 3G3 isolated from Philippine fermented pork.

Pediococcus acidilactici is a well-studied fermentative bacterium reported to have potential probiotic properties. Here, we report the draft genome of P. acidilactici 3G3 previously isolated from burong babi, a Philippine fermented pork dish. The 3G3 draft genome has 1,886,498 bp, a GC content of 42.27%, and a completeness of 99.38%.

Culture and Maintenance of Immune Cells to Model Innate Immune Status at the Feto-maternal Interface.

The inflammatory process leading to human labor is mostly facilitated by immune cells, which can be studied by isolating and characterizing primary immune cells from the feto-maternal interface. However, difficulty and inconsistency in sampling approaches of immune cells and short lifespan in vitro prevent their usage in mechanistic studies to understand the maternal-fetal immunobiology. To address these limitations, existing cell line models can be differentiated into immune-like cells for use in reproductive biology experiments. In this chapter, we discussed cell culture methods of maintaining and differentiating HL-60, THP-1, and NK-92 cells to obtain neutrophil-like, macrophage-like, and decidual natural killer-like cells, respectively, which can then be used together with intrauterine cells to elucidate and investigate immune mechanisms that contribute to parturition.

Autophagy Determines Distinct Cell Fates in Human Amnion and Chorion Cells.

Human fetal membranes (amniochorion) that line the intrauterine cavity consist of two distinct cell layers; single-layer amnion epithelial cells (AEC) and multilayer chorion trophoblast cells (CTC). These layers are connected through a collagen-rich extracellular matrix. Cellular remodeling helps support membrane growth and integrity during gestation and helps to maintain pregnancy. Preterm prelabor rupture of the human amniochorionic (fetal) membrane (pPROM) is antecedent to 40% of all spontaneous preterm birth. Oxidative stress (OS) induced activation of the p38 MAPK due to various maternal risk exposures and the amniochorion cells' senescence are reported pathological features of pPROM. Our transcriptomics analysis implicated dysregulated autophagy and epithelial-mesenchymal transition (EMT) in fetal membranes from pPROM. The molecular interplay between OS-induced p38 MAPK activation, autophagy, and EMT was investigated in AECs and CTCs to better understand the involvement of autophagy and EMT. We report the differential impact of OS on the autophagic machinery in AECs and CTCs, resulting in distinct cell fates. In AECs, OS-induced p38 MAPK activation causes autophagosome accumulation and reduced autophagic flux mediated by decreased ULK1 activity and kinase activity, leading to senescence. In CTCs, induction of autophagy has a limited effect; however, inhibition of autophagy led to SQSTM1-mediated EMT of trophoblast cells. Autophagy, EMT, and senescence were associated with proinflammatory changes. Thus, AECs and CTCs respond differently to OS via differential autophagy response, partly mediated via p38 MAPK. Besides senescence, OS-induced autophagy dysregulation in amniochorion cells may play a mechanistic role in pPROM pathophysiology.

Safety assessment of five candidate probiotic lactobacilli using comparative genome analysis.

Micro-organisms belonging to the Lactobacillus genus complex are often used for oral consumption and are generally considered safe but can exhibit pathogenicity in rare and specific cases. Therefore, screening and understanding genetic factors that may contribute to pathogenicity can yield valuable insights regarding probiotic safety. Limosilactobacillus mucosae LM1, Lactiplantibacillus plantarum SK151, Lactiplantibacillus plantarum BS25, Limosilactobacillus fermentum SK152 and Lactobacillus johnsonii PF01 are current probiotics of interest; however, their safety profiles have not been explored. The genome sequences of LM1, SK151, SK152 and PF01 were downloaded from the NCBI GenBank, while that of L. plantarum BS25 was newly sequenced. These genomes were then annotated using the Rapid Annotation using Subsystem Technology tool kit pipeline. Subsequently, a command line blast was performed against the Virulence Factor Database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD) to identify potential virulence factors and antibiotic resistance (AR) genes. Furthermore, ResFinder was used to detect acquired AR genes. The query against the VFDB identified genes that have a role in bacterial survivability, platelet aggregation, surface adhesion, biofilm formation and immunoregulation; and no acquired AR genes were detected using CARD and ResFinder. The study shows that the query strains exhibit genes identical to those present in pathogenic bacteria with the genes matched primarily having roles related to survival and surface adherence. Our results contribute to the overall strategies that can be employed in pre-clinical safety assessments of potential probiotics. Gene mining using whole-genome data, coupled with experimental validation, can be implemented in future probiotic safety assessment strategies.

Targeting the Filipino gut microbiota in the management of hypertension.

BACKGROUND: Hypertension is a major health problem in the Philippines, being the second leading disease and the second leading factor driving the most death and disability in the country. Despite efforts made toward increasing awareness, improving availability of medications, and strengthening patient adherence, more than 7 in every 10 hypertensive Filipinos still have uncontrolled hypertension. MAIN BODY: In the recent years, the role of gut microbiota in hypertension has been highlighted, with studies showing alterations in the gut microbiota of hypertensive individuals and its positive effect on the pharmacokinetics of some antihypertensive drugs. CONCLUSIONS: These findings show how gut microbiota can be an important but possibly overlooked consideration in the management of hypertension in the Philippines. Clinicians might benefit from maximizing the relationship between gut microbiota and hypertension to achieve good BP control and ultimately address the burden of uncontrolled hypertension in the country.

Draft genome sequence of Lactiplantibacillus plantarum BS25 isolated from a local fermented rice-shrimp mixture from the Philippines.

The draft genome sequence of Lactiplantibacillus plantarum BS25, previously isolated from a fermented rice-shrimp mixture (balao-balao) in the Philippines, was analyzed. The genome contains 3,264,139 bp (44.62% GC%), and a total of 3,069 predicted coding sequences, 2 rRNAs, and 52 tRNAs.

The Circulating miRNA Profile of Chronic Hepatitis D and B Patients Is Comparable but Differs from That of Individuals with HBeAg-Negative HBV Infection.

miRNAs circulating in whole serum and HBsAg-particles are differentially expressed in chronic hepatitis B (CHB) and HBeAg-negative-HBV infection (ENI); their profiles are unknown in chronic hepatitis D (CHD). Serum- and HBsAg-associated miRNAs were analyzed in 75 subjects of 3 well-characterized groups (CHB 25, CHD 25, ENI 25) using next-generation sequencing (NGS). Overall miRNA profiles were consonant in serum and HBsAg-particles but significantly different according to the presence of hepatitis independently of Hepatitis D Virus (HDV)-co-infection. Stringent (Bonferroni Correction < 0.001) differential expression analysis showed 39 miRNAs upregulated in CHB vs. ENI and 31 of them also in CHD vs. ENI. miRNA profiles were coincident in CHB and CHD with only miR-200a-3p upregulated in CHB. Three miRNAs (miR-625-3p, miR-142-5p, and miR-223-3p) involved in immune response were upregulated in ENI. All 3 hepatocellular miRNAs of MiR-B-Index (miR-122-5p, miR-99a-5p, miR-192-5p) were overexpressed in both CHB and CHD patients. In conclusion, CHD and CHB patients showed highly similar serum miRNA profiling that was significantly different from that of individuals with HBeAg-negative infection and without liver disease.

Trends in ELISA-Based Flavivirus IgG Serosurveys: A Systematic Review.

Flaviviruses include virus species that are major public health threats worldwide. To determine the immunity landscape of these viruses, seroprevalence studies are often performed using IgG ELISA, which is a simple and rapid alternative to the virus neutralization test. In this review, we aim to describe the trends in flavivirus IgG ELISA-based serosurveys. A systematic literature review using six databases was performed to collate cohort and cross-sectional studies performed on the general population. A total of 204 studies were included in this review. The results show that most studies were performed on dengue virus (DENV), whereas Japanese Encephalitis Virus (JEV) was the least studied. For geographic distribution, serosurveys followed known disease prevalence. Temporally, the number of serosurveys increased after outbreaks and epidemics except for JEV, for which studies were performed to demonstrate the effectiveness of vaccination campaigns. Commercial kits were more commonly used than in-house assays for DENV, West Nile Virus (WNV), and Zika virus (ZIKV). Overall, most studies employed an indirect ELISA format, and the choice of antigens varied per virus. This review shows that flavivirus epidemiology is related to the regional and temporal distribution of serosurveys. It also highlights that endemicity, cross-reactivities, and kit availabilities affect assay choice in serosurveys.

Saliva as alternative to naso-oropharyngeal swab for SARS-CoV-2 detection by RT-qPCR: a multicenter cross-sectional diagnostic validation study.

Saliva has been demonstrated as feasible alternative to naso-oropharyngeal swab (NOS) for SARS-CoV-2 detection through reverse transcription quantitative/real-time polymerase chain reaction (RT-qPCR). This study compared the diagnostic agreement of conventional NOS, saliva with RNA extraction (SE) and saliva without RNA extraction (SalivaDirect) processing for RT-qPCR in identifying SARS-CoV-2. All techniques were also compared, as separate index tests, to a composite reference standard (CRS) where positive and negative results were defined as SARS-CoV-2 detection in either one or no sample, respectively. Of 517 paired samples, SARS-CoV-2 was detected in 150 (29.01%) NOS and 151 (29.21%) saliva specimens. The saliva-based tests were noted to have a sensitivity, specificity and accuracy (95% confidence interval) of 92.67% (87.26%, 96.28%), 97.55% (95.40%, 98.87%) and 96.13% (94.09%, 97.62%), respectively, for SE RT-qPCR and 91.33% (85.64%, 95.30%), 98.91% (97.23%, 99.70%) and 96.71% (94.79%, 98.07%), respectively, for SalivaDirect RT-qPCR compared to NOS RT-qPCR. Compared to CRS, all platforms demonstrated statistically similar diagnostic performance. These findings suggest that both conventional and streamlined saliva RT-qPCR are at least non-inferior to conventional NOS RT-qPCR in detecting SARS-CoV-2.

Gut microbiome status of urban and rural Filipino adults in relation to diet and metabolic disorders.

Here, we aim to understand the condition of the gut microbiome of Filipino adults in relation to their diet and metabolic status. Compared to rural Albay (n = 67), the gut microbiome of subjects living in urban Manila (n = 25) was more colonized by the order Clostridiales, which was negatively correlated with host carbohydrate consumption. Principal component analysis using the genus composition of the 92 total subjects indicated four microbiome types: one type driven by Prevotella, which was associated with high rice consumption and mainly consisted of healthy Albay subjects, one Clostridiales-driven group containing a number of type 2 diabetes mellitus (T2D) subjects from both Manila and Albay who showed lower butyrate levels in association with a decrease in Mediterraneibacter faecis, and the other two types showing dysbiosis-like microbiomes with Lactobacillus and Bifidobacterium overgrowth, with a high ratio of T2D and obese subjects. Multivariate logistic regression analysis suggested high dietary energy intake, and two Veillonellaeae genera, Dialister and Megasphaera, as T2D risk factors, while Prevotella and M. faecis as anti-T2D factors. In conclusion, low-carbohydrate diets restructured the Prevotella-driven gut microbiome, which may predispose Filipino people with high energy diet to T2D.

Immunomodulatory potential of four candidate probiotic Lactobacillus strains from plant and animal origin using comparative genomic analysis.

Probiotic strains from different origins have shown promise in recent decades for their health benefits, for example in promoting and regulating the immune system. The immunomodulatory potential of four Lactobacillus strains from animal and plant origins was evaluated in this paper based on their genomic information. Comparative genomic analysis was performed through genome alignment, average nucleotide identity (ANI) analysis and gene mining for putative immunomodulatory genes. The genomes of the four Lactobacillus strains show relative similarities in multiple regions, as observed in the genome alignment. However, ANI analysis showed that L. mucosae LM1 and L. fermentum SK152 are the most similar when considering their nucleotide sequences alone. Gene mining of putative immunomodulatory genes studied from L. plantarum WCFS1 yielded multiple results in the four potential probiotic strains, with L. plantarum SK151 showing the largest number of genes at around 74 hits, followed by L. johnsonii PF01 at 41 genes when adjusted for matches with at least 30 % identity. Looking at the immunomodulatory genes in each strain, L. plantarum SK151 and L. johnsonii PF01 may have wider activity, covering both immune activation and immune suppression, as compared to L. mucosae LM1 and L. fermentum SK152, which could be more effective in activating immune cells and the pro-inflammatory cascade rather than suppressing it. The similarities and differences between the four Lactobacillus species showed that there is no definitive trend based on the origin of isolation alone. Moreover, higher percentage identities between genomes do not directly correlate with higher similarities in potential activity, such as in immunomodulation. The immunomodulatory function of each of the four Lactobacillus strains should be observed and verified experimentally in the future, since some the activity of some genes may be strain-specific, which would not be identified through comparative genomics alone.

A synthetic peptide analog of in silico-predicted immunogenic epitope unique to dengue virus serotype 2 NS1 antigen specifically binds immunoglobulin G antibodies raised in rabbits.

Development of a serotyping-capable dengue detection test is hampered by the absence of an identified unique marker that can detect specific dengue virus (DENV) serotype. In the current commercially available antibody-capture diagnostic methods, immobilized nonstructural 1 (NS1) antigen indiscriminately binds and detects immunoglobulin M or immunoglobulin G against any serotype, thus limiting its capability to distinguish existing serotypes of dengue. Identification of dengue serotype is important because certain serotypes are associated with severe forms of dengue as well as dengue hemorrhagic fever. In this study, we aimed to identify an immunogenic epitope unique to DENV2 NS1 antigen and determine the binding specificity of its synthetic peptide mimotope to antibodies raised in animal models. Selection of a putative B-cell epitope from the reported DENV2 NS1 antigen was done using Kolaskar and Tongaonkar Antigenicity prediction, Emini surface accessibility prediction, and Parker hydrophilicity prediction available at the immune epitope database and analysis resource. Uniqueness of the B-cell epitope to DENV2 was analyzed by BLASTp. Immunogenicity of the synthetic peptide analog of the predicted immunogenic epitope was tested in rabbits. The binding specificity of the antibodies raised in animals and the synthetic peptide mimotope was tested by indirect ELISA. A synthetic peptide analog comprising the unique epitope of DENV2 located at the 170th-183rd position of DENV2 NS1 was found to be immunogenic in animal models. The antipeptide antibody produced in rabbits showed specific binding to the synthetic peptide mimotope of the predicted unique DENV2 NS1 immunogenic epitope.

Plasma amino acid and urine organic acid profiles of Filipino patients with maple syrup urine disease (MSUD) and correlation with their neurologic features.

BACKGROUND: Maple syrup urine disease (MSUD) is the most common inborn error of metabolism in the country. The cause of the neuropathology is still not well established although accumulation of branched chain amino acids (BCAA) and alteration in large neutral amino acids (LNAA) as well as energy deprivation are suggested. It is therefore the aim of this study to determine the plasma amino acid and urine organic acid profiles of patients with MSUD and correlate the findings with their neurologic features. METHODOLOGY: Twenty six Filipino patients with MSUD were studied in terms of their plasma amino acid and urine organic acid profiles. Their results were compared with 26 age and sex matched controls. The neurologic features were correlated with the results of the plasma amino acids and urine organic acids. RESULTS: Majority of the patients with MSUD had developmental delay/intellectual disability (88%), speech delay (69%), and seizures (65%). Their amino acid profiles revealed low glutamine and alanine with high levels of leucine, isoleucine, phenylalanine, threonine and alloisoleucine compared to controls (p < 0.05). The urine organic acids showed significantly elevated excretion of the branched chain ketoacids and succinate (p < 0.05). However there were no biochemical markers that correlated significantly with the neurologic features. CONCLUSION: The findings suggest that there could still be altered LNAA metabolism among patients with MSUD when the BCAAs are elevated. Although the biochemical findings were not significantly correlated with the neurologic features, the study showed that prevention and avoidance of neurologic disturbances may still rely primarily on early diagnosis and prompt institution of treatment, along with strict compliance with the dietary regimen and maintenance of good metabolic control over time.