The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.
The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
In the last three decades, Clostridium difficile infection (CDI) has increased in incidence and severity in many countries worldwide. The increase in CDI incidence has been particularly apparent among surgical patients. Therefore, prevention of CDI and optimization of management in the surgical patient are paramount. An international multidisciplinary panel of experts from the World Society of Emergency Surgery (WSES) updated its guidelines for management of CDI in surgical patients according to the most recent available literature. The update includes recent changes introduced in the management of this infection.
Temperature is known to influence the operational efficiency of enhanced biological phosphorus removal (EBPR) systems. This study investigated the impact of thermal stress above 30°C on the properties of an EBPR community established with tropical inoculum. The results confirmed the stability of the 30°C EBPR system with high P-removal efficiency over 210 days. Accumulibacter was abundant in the community. When the EBPR sludge was subjected to a sudden temperature increase to 35°C under multiple cycles of anaerobic-aerobic phases, each lasting 4 h, high P-removal was maintained over 2 days, before gradually failing when the Competibacter appeared to outcompete Accumulibacter. These data suggested that the EBPR capacity is robust when subjected to occasional thermal stress. However, it could not be maintained even for a short time under temperature stress at 40°C. Thus, the threshold temperature for tropical EBPR failure is between 35°C and 40°C. PRACTITIONER POINTS: EBPR was stably maintained at 30°C with Accumulibacter being dominant. Good EBPR activities persisted for a short period at 35°C. EBPR was deteriorated at 40°C. The threshold temperature for tropical EBPR failure is between 35°C and 40°C.
In this study, a two-stage domesticated shear-loop anaerobic contact stabilization (SLACS) system is introduced as a new reactor design to enhance methane productivity with significant reduction in hydrogen sulphide (H2S) synthesis. Due to the rich sulfate content in industrial wastewaters, the initial fermentation phase of anaerobic digestion is highly acidifying and often leads to severe performance losses, digester's instability, and even culture crash. The SLACS system functions as a dissimilatory sulfate reduction - methanogenic reactor consisting of two compartments, a shear-loop anaerobic bed (SLAB) unit and an anaerobic plug flow (APF) unit. The functional role of the SLAB unit is not limited to acidogenesis but also sulfidogenic processes, which curtails H2S generation in the APF unit (methanogenic stage). Experimental observations indicated that pH serves a critical role in the cohabitation of acidogenic and sulfidogenic microbes in the SLAB unit. Although acidogenesis was not influenced by pH within the range of 4.5-6.0, it is vital to stabilize the pH of this unit at 5.4 to establish a steady sulfate reduction of above 75%. The highest desulfurization achieved in this compartment was 88% under a hydraulic retention time (HRT) of 4 h. With an average methane productivity of 256 mL g-1 VS, the methanogenic performance of the two-stage domesticated SLACS system shows a 32% methanogenic proficiency higher than that of the one-stage digestion system. Microbial community structure within the system carried out via Next Generation Sequencing (NGS) provided qualitative data on the sludge's sulfidogenic and methanogenic performance.
The availability of paddy husk from rice processing plants remains high owing to increase in the worldwide rice consumption. Increasing demand for chicken products leads to poultry wastes production. Co-composting of the aforementioned wastes could solve the indiscriminate disposal of these wastes. Thus, co-composting of paddy husk and chicken slurry with clinoptilolite zeolite and urea as additive was carried out. Clinoptilolite zeolite was used to enhance ammonium and nitrate retention in the compost. Temperature of the compost was monitored three times daily for 55 days. Cation exchange capacity, organic matter, ash, humic acids, pH, total C, N, C/N ratio; total P, exchangeable Ca, Mg, K, NH4+, NO3-, and heavy metals contents were determined using standard procedures. pH, total N, humic acids, ash, NH4+, NO3-, P, Ca, Mg, and K contents increased but the salinity, heavy metals contents, and microbial population were low after the co-composting process. Zea mays L. (test crop) seed germination rate in distilled water and the compost were not significantly different. Growth of Spinach oleracea (test crop) on a peat-based growing medium and the compost was also not significantly different. These findings were possible because the clinoptilolite zeolite used in co-composting reduced accumulation of heavy metals that may have damage effects on the test crops. Mature compost with good agronomic properties can be produced by co-composting chicken slurry and paddy husk using clinoptilolite zeolite and urea as additives.
The purpose of this study was to investigate the composition of throat microbiota in pulmonary tuberculosis patients (PTB) in comparison to healthy tuberculin skin test positive (TSTp) and negative (TSTn) individuals. Throat swabs samples were collected, and the microbiota was characterized. Richer operational taxonomic units (OTUs) were present in PTB group, compared to TSTp and TSTn. Regarding alpha diversity analysis there was a higher community diversity in TSTn compared to TSTp. Beta diversity analysis showed different species composition in TSTp compared to TSTn and PTB. There was higher presence of Firmicutes in PTB and TSTn compared to TSTp group at phylum level. At the genus level, Leuconostoc and Enterococcus were higher in TSTn compared to TSTp and Pediococcus, Chryseobacterium, Bifidobacterium, Butyrivibrio, and Bulleidia were higher in PTB compared to TSTn. Streptococcus was higher in TSTn compared to PTB and Lactobacillus in PTB compared to TSTp. At species level, Streptococcus sobrinus and Bulleidia moorei were higher in PTB compared to TSTn individuals, while Lactobacillus salivarius was higher in PTB compared to TSTp. The differences in the microbiome composition could influence the resistance/susceptibility to Mtb infection.
Mycorrhiza, a mutualistic association between fungi and higher plants, has been documented extensively, but much less is known about the development of arbuscular mycorrhizal (AM) fungi and their effects on the growth of peanuts (Arachis hypogea L.). Therefore, the mycorrhizal status of Glomus spp. was investigated in the following diverse substrate soil conditions: non-autoclaved soil, autoclaved soil and autoclaved soil plus soil microbiota. The results indicated that both the arbuscular mycorrhizae, Glomus mosseae (Nicol. & Gerd.) Gerd. & Trappe, and Glomus fasciculatum (Thaxter) Gerd. & Trappe emend. Walker & Koske were infective to peanut, but displayed a differential impact on peanut growth depending on the microbial biomass content of the substrate soils. G. mosseae proved to be the most effective at improving peanut growth.
Malaysia is one of the countries that are loaded with mega biodiversity which
includes microbial communities. Phages constitute the major component in the microbial
communities and yet the numbers of discovered phages are just a minute fraction of
its population in the biosphere. Taking into account of a huge numbers of waiting to be
discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s
was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile
flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae
family under the order of Caudovirales. Genomic sequence analyses revealed phage
YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content.
Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome,
using bioinformatics annotation software; Rapid Annotation using Subsystem Technology
(RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are
classified as hypothetical proteins and there are two unidentified proteins. Even though
majority of the coded putative proteins have high amino acids similarities to phages from the
genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own
distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the
growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.
This study was carried out to determine from bacterial profiling to the bacterial profiles of head lice among the Orang Asli communities. The head lice were collected from Orang Asli community volunteers. The surface sterilized head lice pools were subjected to genomic DNA extraction while next generation sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform. Six female and three male head lice identified as Pediculus humanus capitis were collected. A total of 111 368 number of NGS sequencing reads were recorded while another 223 bacterial taxa sequences were obtained. Symbiotic bacteria showed the highest number of reads, with Arsenophonus and Rhodococcus sequences being the most abundant genera in the female and male samples, respectively. The female head lice contained a more distinct microbial diversity. Amongst the pathogenic bacterial species sequences noted were the methicillin-resistant Staphylococcus aureus, Streptobacillus moniliformis, Haemophilus influenzae, Bordetella pertussis and Acinetobacter baumannii. The 16S rRNA genome sequencing revealed a number of rare and pathogenic bacterial species within the head lice of the Orang Asli. The socio-economic practices of the community which involved forest foraging and hunting, and their poor living conditions potentially facilitated the transmission of zoonotic bacterial pathogens, including those found within the head lice. Hence, there is the possibility that the head lice could serve as vectors for the transmission of pathogenic bacteria. This study highlighted the diverse microbial community found within the head lice's gut of the Orang Asli, with the detection of multiple rare and pathogenic bacteria capable of causing severe infections.
Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation.
Ticks are hematophagous vectors of arthropod-borne disease agents globally. In Malaysia, despite seroprevalence studies indicating the presence of tick-borne diseases among the indigenous people, the etiological agents of these diseases are still unclear. These indigenous people, also known as the Orang Asli, still live in forested areas with frequent contact with wildlife. Wild boar are ubiquitously found in the forested areas where the Orang Asli communities are located and are commonly hunted as a food supplement. In this study, we aim to determine the tick species parasitizing wild boar from an Orang Asli community, and explore the tick-associated bacterial communities using 16 s rRNA amplicon sequencing on the Ion Torrent PGM™ platform. A total of 72 ticks were collected from three wild boar and were morphologically identified as Haemaphysalis hystricis (n = 32), Dermacentor compactus (n = 15), Amblyomma testudinarium (n = 13), Dermacentor steini (n = 10) and Dermacentor atrosignatus (n = 2). Across all tick samples, 910 bacterial taxa were identified. Although the bacterial communities were not significantly distinct between tick species in beta-diversity analyses, Coxiella, Rickettsia and Francisella were detected at high relative abundance in H. hystricis, D. compactus and D. steini respectively. Many other bacterial genera, including those that have been described in many different tick species, were also identified, including Pseudomonas, Acinetobacter, Staphylococcus and Corynebacterium. Beta-diversity analyses also showed that the bacterial communities were separated based on the animal host from which the ticks were collected from, suggesting that the bacterial communities here may be influenced by the animal skin microflora, host blood or the environment. PCR screening confirmed the presence of Rickettsia sp. related to spotted fever group Rickettsia in some of the ticks. This study provides baseline knowledge of the microbiome of H. hystricis, D. atrosignatus, D. compactus, D. steini and A. testudinarium parasitizing wild boar in this region. The information gained in this study provides the basis to target our efforts in H. hystricis, D. compactus and D. steini for the future investigation of vector competence and the zoonotic potential for the Coxiella, Rickettsia and Francisella detected here, as well as their implications for the risks of tick-borne diseases among the Orang Asli communities.
The association between diabetes mellitus and chronic periodontal disease has long been established. Most of the researches linking these two very common chronic diseases were based on type 2 diabetes mellitus and chronic periodontal disease. However, this study was conducted to investigate the association between type 1 diabetes and chronic periodontal disease in Malaysian subjects. Forty-one Malaysian subjects, of which 20 subjects were type 1 diabetics and with chronic periodontal disease (test group) and 21 subjects with only chronic periodontal disease (control group), were included in the study. Periodontal parameters and plaque samples for microbiological evaluation were done at baseline, 2 and 3 months after nonsurgical periodontal therapy. Blood samples were taken from only the test group and evaluated for HbA1c at baseline and 3 months after periodontal therapy. There were no statistically significant difference in periodontal parameters between groups (P>0.05) and no significant improvement in the level of HbA1c in the test group. Microbiological studies indicated that there were significant reductions in the levels of the tested pathogens in both groups. The results of our study were similar to the findings of several other studies that had been done previously.
Human stomach is the only known natural habitat of Helicobacter pylori (Hp), a major bacterial pathogen that causes different gastroduodenal diseases. Despite this, the impact of Hp on the diversity and the composition of the gastric microbiota has been poorly studied. In this study, we have analyzed the culturable gastric microbiota of 215 Malaysian patients, including 131 Hp positive and 84 Hp negative individuals that were affected by different gastric diseases. Non-Hp bacteria isolated from biopsy samples were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry based biotyping and 16SrRNA sequencing. The presence of Hp did not significantly modify the diversity of the gastric microbiota. However, correlation was observed between the isolation of Streptococci and peptic ulcer disease. In addition, as a first report, Burkholderia pseudomallei was also isolated from the gastric samples of the local population. This study suggested that there may be geographical variations in the diversity of the human gastric microbiome. Geographically linked diversity in the gastric microbiome and possible interactions between Hp and other bacterial species from stomach microbiota in pathogenesis are proposed for further investigations.
Sick building syndrome (SBS) is a collection of nonspecific syndromes linked with the built environment. The occurrence of SBS is associated with humidity, ventilation, moulds and microbial compounds exposure. However, no study has reported the association between indoor microbiome and SBS. In this study, 308 students were surveyed for SBS symptoms from 21 classrooms of 7 junior high schools from Johor Bahru, Malaysia, and vacuum dust from floor, desks and chairs was collected. High throughput amplicon sequencing (16S rRNA gene and ITS region) and quantitative PCR were conducted to characterize the absolute concentration of bacteria and fungi taxa. In total, 326 bacterial and 255 fungal genera were detected in dust with large compositional variation among classrooms. Also, half of these samples showed low compositional similarity to microbiome data deposited in the public database. The number of observed OTUs in Gammaproteobacteria was positively associated with SBS (p = 0.004). Eight microbial genera were associated with SBS (p
Tropical peatlands are globally important ecosystems with high C storage and are endangered by anthropogenic disturbances. Microbes in peatlands play an important role in sustaining the functions of peatlands as a C sink, yet their characteristics in these habitats are poorly understood. This research aimed to elucidate the responses of these complex ecosystems to disturbance by exploring greenhouse gas (GHG) emissions, nutrient contents, soil microbial communities and the functional interactions between these components in a primary and secondary peat swamp forest in Peninsular Malaysia. GHG measurements using closed chambers, and peat sampling were carried out in both wet and dry seasons. Microbial community phenotypes and nutrient content were determined using phospholipid fatty acid (PLFA) and inductively-coupled plasma mass spectrometry (ICP-MS) analyses respectively. CO2 emissions in the secondary peat swamp forest were > 50% higher than in the primary forest. CH4 emission rates were ca. 2 mg m-2 h-1 in the primary forest but the secondary forest was a CH4 sink, showing no seasonal variations in GHG emissions. Almost all the nutrient concentrations were significantly lower in the secondary forest, postulated to be due to nutrient leaching via drainage and higher rates of decomposition. Cu and Mo concentrations were negatively correlated with CO2 and CH4 emissions respectively. Microbial community structure was overwhelmingly dominated by bacteria in both forest types, however it was highly sensitive to land-use change and season. Gram-positive and Gram-negative relative abundance were positively correlated with CO2 and CH4 emissions respectively. Drainage related disturbances increased CO2 emissions, by reducing the nutrient content including some with known antimicrobial properties (Cu & Na) and by favouring Gram-positive bacteria over Gram-negative bacteria. These results suggest that the biogeochemistry of secondary peat swamp forest is fundamentally different from that of primary peat swamp forest, and these differences have significant functional impacts on their respective environments.
Antibiotic residues in swine manure when entered the soil would most likely affect the complex composition and functions of the soil microbiome, which is also responsible for degrading these antibiotics. Three different methods of adding ciprofloxacin (CIP), a common antibiotic used in the swine industry, to the soil were used to investigate the effects of CIP on the soil microbiome and the degradation of CIP. Results of the study showed that the microbiome could promote the degradation of CIP in the soil when CIP was incorporated into the soil together with manure. However, the CIP degradation time was prolonged when adding the manure of swine fed with diet containing CIP in the soil. All treatments did not affect the copy number of the resistance genes, except for aac(6')-Ib-cr, as compared with the initial numbers of each treatment. MiSeq Illumina sequencing and Biolog-ECO microplates results showed that CIP had a significant effect on the abundance, structure, and function of the soil microbiome, but different addition methods resulted in distinct effects. Results of the present study demonstrated that the microbiome and fate of CIP responded differently to the different methods of adding CIP to the soil.
Nanoplastics (NPs) are widely distributed environmental pollutants that can disrupt intestinal immunity of crustaceans. In this study, the effects of NPs on gut immune enzyme activities, cell morphology, apoptosis, and microbiota diversity of Litopenaeus vannamei were investigated. L. vannamei was exposed to five concentrations of NPs (0, 0.1, 1, 5, and 10 mg/L) for 28 days. The results showed that higher concentrations of NPs damaged the intestinal villi, promoted formation of autophagosomes, increased intestinal non-specific immunoenzyme activities, and significantly increased apoptosis at 10 mg/L. In response to exposure to NPs, the expression levels of ATG3, ATG4, ATG12, Caspase-3, p53, and TNF initially increased and then decreased. In addition, the concentration of NPs was negatively correlated to the expression levels of the genes of interest and intestinal enzyme activities, suggesting that exposure to NPs inhibited apoptosis and immune function. The five dominant phyla of the gut microbiota (Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinomycetes) were similar among groups exposed to different concentrations of NPs, but the abundances tended to differ. Notably, exposure to NPs increased the abundance of pathogenic bacteria. These results confirm that exposure to NPs negatively impacted intestinal immune function of L. vannamei. These findings provide useful references for efficient breeding of L. vannamei.
Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.