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Postmortem skin microbiome signatures associated with human cadavers within the first 12 h at the morgue

Iancu L, Muslim A, Aazmi S, Jitaru V

Front Microbiol, 2023;14:1234254.
PMID: 37564294 DOI: 10.3389/fmicb.2023.1234254

INTRODUCTION: Forensic microbiome studies expanded during the last decade, aiming to identify putative bacterial biomarkers to be used for the postmortem interval (PMI) estimation. Bacterial diversity and dynamics during decomposition are influenced by each individual's micro and macroenvironment, ante and postmortem conditions, varying across body sites and time. The skin, the largest organ of the human body, hosts a diverse microbial diversity, representing the first line of defense of a living individual. Targeting the investigation of the postmortem skin microbiome could help understanding the role of microbes during decomposition, and association with the ante and postmortem conditions.
METHODS: The current study aimed to identify the postmortem skin microbiome signatures associated with eight human bodies, received at the Institute of Legal Medicine Iasi, Romania, during April and May 2021. A total of 162 samples (including triplicate) representing face and hands skin microbiome were investigated via Illumina MiSeq, upon arrival at the morgue (T0) and after 12 hours (T1).
RESULTS: The taxonomic characteristics of the skin microbiota varied across different body sites. However, there were no significant differences in taxonomic profiles between collection time, T0 and T1, except for some dynamic changes in the abundance of dominant bacteria. Moreover, different microbial signatures have been associated with a specific cause of death, such as cardiovascular disease, while an elevated blood alcohol level could be associated with a decrease in bacterial richness and diversity.
DISCUSSION: The places where the bodies were discovered seemed to play an important role in explaining the bacterial diversity composition. This study shows promising results towards finding common postmortem bacterial signatures associated with human cadavers within the first 12h at the morgue.
Fulltext Ascaris lumbricoides harbors a distinct gut microbiota profile from its human host: Preliminary insights

Muslim A, Aazmi S, Er YX, Shahrizal S, Lim YAL

Food Waterborne Parasitol, 2024 Mar;34:e00223.
PMID: 38323096 DOI: 10.1016/j.fawpar.2024.e00223

In indigenous populations where soil-transmitted helminths (STH) infections are endemic, STH parasites (i.e., Ascaris lumbricoides, Trichuris trichiura, hookworms) often co-exist and co-evolve with the gut microbiota of their human hosts. The association between STH infections and the gut microbiota of the colonized human hosts has been established, but few studies explored the gut microbiota of the parasites. This preliminary study aimed to characterize the microbiota of the STH parasite for further understanding the STH parasite-host relationship. The gut microbial genomic DNA from four adult A. lumbricoides worms recovered from a six-year-old indigenous Negrito boy living in an STH-endemic village in Perak, Peninsular Malaysia was extracted and sequenced for the V3-V4 region of the 16S rRNA. The microbiota profiles of these worms were characterized and compared with the gut microbiota of their human host, including the profiles from four STH-positive and three STH-negative individuals from the same tribe and village. The gut microbial structure of A. lumbricoides was found to be differed significantly from their human host. The worms contained lower gut bacterial abundance and diversity than human. This difference was evident in the beta diversity analysis which showed a clear separation between the two sample types. While both Firmicutes (52.3%) and Bacteroidetes (36.6%) are the predominant phyla followed by Proteobacteria (7.2%) in the human gut, the microbiota of Ascaris gut is highly dominated by Firmicutes, constituting 84.2% relative abundance (mainly from the genus Clostridium), followed by Proteobacteria (11.1%), Tenericutes (1.8%) and Bacteroidetes (1.5%). The parasites were also found to alter the microbial structure of the human gut following infection based on the relatively higher bacterial abundance in STH-positive versus STH-negative participants. Further studies with a greater number of Ascaris adults and human hosts are needed to confirm the gut microbiota profiles.
Fulltext In Vitro Cytopathogenic Activities of Acanthamoeba T3 and T4 Genotypes on HeLa Cell Monolayer

Mohd Hussain RH, Abdul Ghani MK, Khan NA, Siddiqui R, Aazmi S, Halim H, et al.

Pathogens, 2022 Dec 05;11(12).
PMID: 36558808 DOI: 10.3390/pathogens11121474

Amoebic keratitis and encephalitis are mainly caused by free-living amoebae of the genus Acanthamoeba, which consists of both pathogenic and nonpathogenic species. The global distribution, amphizoic properties and the severity of the disease caused by Acanthamoeba species have inspired the scientific community to put more effort into the isolation of Acanthamoeba, besides exploring the direct and indirect parameters that could signify a pathogenic potential. Therefore, this study was performed to characterize the pathogenic potential of Acanthamoeba isolated from contact lens paraphernalia and water sources in Malaysia. Various methodologies were utilized to analyze the thermotolerance and osmotolerance, the secretion level of proteases and the cytopathic effect of trophozoites on the cell monolayer. In addition, the in vitro cytopathogenicity of these isolates was assessed using the LDH-release assay. A total of 14 Acanthamoeba isolates were classified as thermo- and osmotolerant and had presence of serine proteases with a molecular weight of 45-230 kDa. Four T4 genotypes isolated from contact lens paraphernalia recorded the presence of serine-type proteases of 107 kDa and 133 kDa. In contrast, all T3 genotypes isolated from environmental samples showed the presence of a 56 kDa proteolytic enzyme. Remarkably, eight T4 and a single T3 genotype isolates demonstrated a high adhesion percentage of greater than 90%. Moreover, the use of the HeLa cell monolayer showed that four T4 isolates and one T3 isolate achieved a cytopathic effect in the range of 44.9-59.4%, indicating an intermediate-to-high cytotoxicity level. Apart from that, the LDH-release assay revealed that three T4 isolates (CL5, CL54 and CL149) and one T3 isolate (SKA5-SK35) measured an exceptional toxicity level of higher than 40% compared to other isolates. In short, the presence of Acanthamoeba T3 and T4 genotypes with significant pathogenic potential in this study reiterates the essential need to reassess the functionality of other genotypes that were previously classified as nonpathogenic isolates in past research.
Molecular characterisation and potential pathogenicity analysis of Acanthamoeba isolated from recreational lakes in Peninsular Malaysia

Abdul Halim R, Mohd Hussain RH, Aazmi S, Halim H, Ahmed Khan N, Siddiqui R, et al.

J Water Health, 2023 Sep;21(9):1342-1356.
PMID: 37756200 DOI: 10.2166/wh.2023.186

The present study aims to identify the Acanthamoeba genotypes and their pathogenic potential in three recreational lakes in Malaysia. Thirty water samples were collected by purposive sampling between June and July 2022. Physical parameters of water quality were measured in situ while chemical and microbiological analyses were performed in the laboratory. The samples were vacuum filtered through nitrate filter, cultured onto non-nutrient agar and observed microscopically for amoebic growth. DNAs from positive samples were extracted and made to react with polymerase chain reaction using specific primers. Physiological tolerance tests were performed for all Acanthamoeba-positive samples. The presence of Acanthamoeba was found in 26 of 30 water samples by PCR. The highest rate in lake waters contaminated with amoeba was in Biru Lake (100%), followed by Titiwangsa Lake (80%) and Shah Alam Lake (80%). ORP, water temperature, pH and DO were found to be significantly correlated with the presence of Acanthamoeba. The most common genotype was T4. Temperature- and osmo-tolerance tests showed that 8 (30.8%) of the genotypes T4, T9 and T11 were highly pathogenic. The presence of genotype T4 in habitats related to human activities supports the relevance of this amoeba as a potential public health concern.
Food-grade algae modified Schiff base-chitosan benzaldehyde composite for cationic methyl violet 2B dye removal: RSM statistical parametric optimization

Agha HM, Abdulhameed AS, Jawad AH, Sidik NJ, Aazmi S, Wilson LD, et al.

Int J Phytoremediation, 2024;26(4):459-471.
PMID: 37583281 DOI: 10.1080/15226514.2023.2246596

This work aims to apply the use of food-grade algae (FGA) composited with chitosan-benzaldehyde Schiff base biopolymer (CHA-BD) as a new adsorbent (CHA-BA/FGA) for methyl violet 2B (MV 2B) dye removal from aqueous solutions. The effect of three processing variables, including CHA-BA/FGA dosage (0.02-0.1 g/100 mL), pH solution (4-10), and contact duration (10-120 min) on the removal of MV 2B was investigated using the Box-Behnken design (BBD) model. Kinetic and equilibrium dye adsorption profiles reveal that the uptake of MV 2B dye by CHA-BA/FGA is described by the pseudo-second kinetics and the Langmuir models. The thermodynamics of the adsorption process (ΔG°, ΔH°, and ΔS°) reveal spontaneous and favorable adsorption parameters of MV 2B dye onto the CHA-BA/FGA biocomposite at ambient conditions. The CHA-BA/FGA exhibited the maximum ability to absorb MV 2B of 126.51 mg/g (operating conditions: CHA-BA/FGA dose = 0.09 g/100 mL, solution pH = 8.68, and temperature = 25 °C). Various interactions, including H-bonding, electrostatic forces, π-π stacking, and n-π stacking provide an account of the hypothesized mechanism of MV 2B adsorption onto the surface of CHA-BA/FGA. This research reveals that CHA-BA/FGA with its unique biocomposite structure and favorable adsorption properties can be used to remove harmful cationic dyes from wastewater.
Fulltext Gut Microbiota Composition in the First and Third Trimester of Pregnancy among Malay Women is Associated with Body Mass Index: A Pilot Study

Abdullah B, Idorus MY, Daud S, Aazmi S, Pillai TK, Zain ZM

Malays J Med Sci, 2023 Feb;30(1):116-128.
PMID: 36875193 DOI: 10.21315/mjms2023.30.1.10

BACKGROUND: This study has analysed the pattern of gut microbiota during the first and third trimesters among pregnant Malay women.
METHODS: This was a pilot prospective observational study involving 12 pregnant Malay women without any endocrine disorders and on neither antibiotics nor probiotics. Demographic details and anthropometric measurements were obtained, and the faecal 16S ribosomal ribonucleic acid (rRNA) metagenome microbiota of the first and third trimesters (T1 and T3) were analysed. Univariate and multivariate statistics, partial least squares discriminant analysis (PLSDA) and Kendall rank correlation testing were used to identify key genera and associations with pregnancy trimester and body mass index (BMI).
RESULTS: The most abundant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, with significant differences in composition at the genus level demonstrated between T1 and T3. Sequencing showed a statistically significant difference in beta diversity between normal and abnormal BMI at all taxonomic ranks (R 2 = 0.60; Q 2 = 0.23) and genus levels (R 2 = 0.57; Q 2 = 0.37). The relative abundances of Akkermansia (P < 0.05; false discovery rate [FDR] < 0.05), Olsenella (P < 0.05; FDR < 0.05) and Oscillospira (P < 0.05; FDR < 0.05) were found to be significantly higher in normal BMI cases by 2.4, 3.4 and 3.1 times, respectively.
CONCLUSION: Three genera (Akkermansia, Olsenella and Oscillospira) were correlated with normal BMI during pregnancy. All three could be promising biotherapeutic targets in body weight regulation during pregnancy, subsequently reducing complications associated with higher BMI.
Physicochemical fabrication of chitosan and algae with crosslinking glyoxal for cationic dye removal: Insight into optimization, kinetics, isotherms, and adsorption mechanism

Agha HM, Abdulhameed AS, Jawad AH, Sidik NJ, Aazmi S, ALOthman ZA, et al.

Int J Biol Macromol, 2023 Dec 31;253(Pt 5):127112.
PMID: 37774818 DOI: 10.1016/j.ijbiomac.2023.127112

Herein, a highly efficient and sustainable adsorbent of cross-linked chitosan-glyoxal/algae biocomposite (CHT-GLX/ALG) adsorbent was developed through an innovative hydrothermal cross-linking method. The CHT-GLX/ALG biocomposite was characterized using several complementary analytical methods that include CHN-O, XRD, FTIR, SEM-EDX, and pHpzc. This new adsorbent, named CHT-GLX/ALG, was utilized for the adsorption of a cationic dye (methyl violet 2B; MV 2B), from synthetic wastewater. The optimization of the dye adsorption process involved key parameters is listed: CHT-GLX/ALG dosage (from 0.02 to 0.1 g/100 mL), pH (from 4 to 10), and contact time (from 20 to 180 min) that was conducted using the Box-Behnken design (BBD). The optimal adsorption conditions for the highest decolorization efficiency of MV 2B (97.02 %) were estimated using the statistical model of the Box-Behnken design. These conditions include a fixed adsorbent dosage of 0.099 g/100 mL, pH 9.9, and a 179.9 min contact time. The empirical data of MV 2B adsorption by CHT-GLX/ALG exhibited favorable agreement with the Freundlich isotherm model. The kinetic adsorption profile of MV 2B by CHT-GLX/ALG revealed a good fit with the pseudo-second-order model. The maximum adsorption capacity (qmax) for MV 2B by CHT-GLX/ALG was estimated at 110.8 mg/g. The adsorption of MV 2B onto the adsorbent can be attributed to several factors, including electrostatic interactions between the negatively charged surface of CHT-GLX/ALG and the MV 2B cation, as well as n-π and H-bonding. These interactions play a crucial role in facilitating the effective adsorption of MV 2B onto the biocomposite adsorbent. Generally, this study highlights the potential of CHT-GLX/ALG as an efficient and sustainable adsorbent for the effective removal of organic dyes.
Enhancing cationic dye removal via biocomposite formation between chitosan and food grade algae: Optimization of algae loading and adsorption parameters

Agha HM, Abdulhameed AS, Jawad AH, Aazmi S, Sidik NJ, De Luna Y, et al.

Int J Biol Macromol, 2024 Feb;258(Pt 1):128792.
PMID: 38110162 DOI: 10.1016/j.ijbiomac.2023.128792

Herein, a natural material including chitosan (CTS) and algae (food-grade algae, FGA) was exploited to attain a bio-adsorbent (CTS/FGA) for enhanced methyl violet 2B dye removal. A study of the FGA loading into CTS matrix showed that the best mixing ratio between CTS and FGA to be used for the MV 2B removal was 50 %:50 % (CTS/FGA; 50:50 w/w). The present study employed the Box-Behnken design (RSM-BBD) to investigate the impact of three processing factors, namely CTS/FGA-(50:50) dose (0.02-0.1 g/100 mL), pH of solution (4-10), and contact time (5-15 min) on the decolorization rate of MV 2B dye. The results obtained from the equilibrium and kinetic experiments indicate that the adsorption of MV 2B dye on CTS/FGA-(50:50) follows the Langmuir and pseudo-second-order models, respectively. The CTS/FGA exhibits an adsorption capacity of 179.8 mg/g. The characterization of CTS/FGA-(50:50) involves the proposed mechanism of MV 2B adsorption, which primarily encompasses various interactions such as electrostatic forces, n-π stacking, and H-bonding. The present study demonstrates that CTS/FGA-(50:50) synthesized material exhibits a distinctive structure and excellent adsorption properties, thereby providing a viable option for the elimination of toxic cationic dyes from polluted water.
Fulltext Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore

Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, et al.

Singapore Med J, 2019 Oct;60(10):512-521.
PMID: 30488079 DOI: 10.11622/smedj.2018152

INTRODUCTION: The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome. PPIs are commonly used for the treatment of acid-related disorders. We hypothesised that PPI therapy might perturb microbial communities and alter the gut microbiome.
METHODS: Healthy subjects of Chinese (n = 12), Malay (n = 12) and Indian (n = 10) ancestry, aged 21-37 years, were enrolled. They provided a baseline stool sample (Day 1) and were then given a course of omeprazole at therapeutic dose (20 mg daily) for seven days. Stool samples were collected again on Day 7 and 14 (one week after stopping omeprazole). Microbial DNA was extracted from the stool samples, followed by polymerase chain reaction, library construction, 16S rRNA sequencing using Illumina MiSeq, and statistical and bioinformatics analyses.
RESULTS: The findings showed an increase in species richness (p = 0.018) after omeprazole consumption on Day 7, which reverted to baseline on Day 14. There were significant increases in the relative abundance of Streptococcus vestibularis (p = 0.0001) and Veillonella dispar (p = 0.0001) on Day 7, which diminished on Day 14. Faecalibacterium prausnitzii, Sutterella stercoricanis and Bacteroides denticanum were characteristic of Chinese, Malays and Indians, respectively. Lactobacillaceae and Bacteroides xylanisolvens were the signature taxa of male and female subjects, respectively.
CONCLUSION: The study demonstrated alterations in the gut microbiome following omeprazole treatment. This may explain the underlying pathology of increased risk of Clostridium difficile infections associated with omeprazole therapy.