Displaying publications 21 - 40 of 928 in total

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  1. A novel biological recovery approach for PHA employing selective digestion of bacterial biomass in animals
    Ong SY, Zainab-L I, Pyary S, Sudesh K
    Appl Microbiol Biotechnol, 2018 Mar;102(5):2117-2127.
    PMID: 29404644 DOI: 10.1007/s00253-018-8788-9
    Polyhydroxyalkanoate (PHA) is a family of microbial polyesters that is completely biodegradable and possesses the mechanical and thermal properties of some commonly used petrochemical-based plastics. Therefore, PHA is attractive as a biodegradable thermoplastic. It has always been a challenge to commercialize PHA due to the high cost involved in the biosynthesis of PHA via bacterial fermentation and the subsequent purification of the synthesized PHA from bacterial cells. Innovative enterprise by researchers from various disciplines over several decades successfully reduced the cost of PHA production through the efficient use of cheap and renewable feedstock, precisely controlled fermentation process, and customized bacterial strains. Despite the fact that PHA yields have been improved tremendously, the recovery and purification processes of PHA from bacterial cells remain exhaustive and require large amounts of water and high energy input besides some chemicals. In addition, the residual cell biomass ends up as waste that needs to be treated. We have found that some animals can readily feed on the dried bacterial cells that contain PHA granules. The digestive system of the animals is able to assimilate the bacterial cells but not the PHA granules which are excreted in the form of fecal pellets, thus resulting in partial recovery and purification of PHA. In this mini-review, we will discuss this new concept of biological recovery, the selection of the animal model for biological recovery, and the properties and possible applications of the biologically recovered PHA.
    Matched MeSH terms: Bacteria/genetics; Bacteria/metabolism*
  2. Fulltext A pentaplex PCR assay for the detection and differentiation of Shigella species
    Ojha SC, Yean Yean C, Ismail A, Singh KK
    Biomed Res Int, 2013;2013:412370.
    PMID: 23509722 DOI: 10.1155/2013/412370
    The magnitude of shigellosis in developing countries is largely unknown because an affordable detection method is not available. Current laboratory diagnosis of Shigella spp. is laborious and time consuming and has low sensitivity. Hence, in the present study, a molecular-based diagnostic assay which amplifies simultaneously four specific genes to identify invC for Shigella genus, rfc for S. flexneri, wbgZ for S. sonnei, and rfpB for S. dysenteriae, as well as one internal control (ompA) gene, was developed in a single reaction to detect and differentiate Shigella spp. Validation with 120 Shigella strains and 37 non-Shigella strains yielded 100% specificity. The sensitivity of the PCR was 100 pg of genomic DNA, 5.4 × 10(4) CFU/ml, or approximately 120 CFU per reaction mixture of bacteria. The sensitivity of the pentaplex PCR assay was further improved following preincubation of the stool samples in gram-negative broth. A preliminary study with 30 diarrhoeal specimens resulted in no cross-reaction with other non-Shigella strains tested. We conclude that the developed pentaplex PCR assay is robust and can provide information about the four target genes that are essential for the identification of the Shigella genus and the three Shigella species responsible for the majority of shigellosis cases.
    Matched MeSH terms: Gram-Negative Bacteria/isolation & purification
  3. A polyisoprenylated ketone from Calophyllum enervosum
    Taher M, Idris MS, Ahmad F, Arbain D
    Phytochemistry, 2005 Mar;66(6):723-6.
    PMID: 15771897
    A polyisoprenylated ketone named enervosanone has been isolated from the stem bark of Calophyllum enervosum together with three known compounds, cambogin, osajaxanthone and epicatechin. Their structures were determined by spectroscopic analysis. The antimicrobial evaluations of the isolated compounds were also reported.
    Matched MeSH terms: Anti-Bacterial Agents/isolation & purification; Bacteria/drug effects
  4. Fulltext A rare case of Ralstonia mannitolilytica infection in an end stage renal patient on maintenance dialysis during municipal water contamination
    Lim CTS, Lee SE
    Pak J Med Sci, 2017 10 27;33(4):1047-1049.
    PMID: 29067090 DOI: 10.12669/pjms.334.13112
    Ralstonia mannitolilytica is a gram negative soil bacterium. Ralstonia infection though rare, has become the emerging nosocomial pathogens in hospital settings. Various clinical manifestations had been described as well as the mode of transmission. Despite its low virulence factor, it is able to survive under harsh condition and this may potentially cause significant morbidity and mortality especially in immunocompromised patients. Outbreak of Ralstonia mannitolilytica infections in the hospital are typically associated with contaminated medical supplies or instruments. We described here a case of Ralstonia mannitolilytica infection in a dialysis patient that occurred during the municipal reservoir water contamination crisis. In this report, we will also describe the behaviour of Ralstonia genus and its 4 main species, namely R. pickettii, R. solanacearum, R. insidiosa, and R. mannitolilytica and the choices of antibiotic therapy based on literature review.
    Matched MeSH terms: Gram-Negative Bacteria
  5. A review of bacterial cellulose-based drug delivery systems: their biochemistry, current approaches and future prospects
    Abeer MM, Mohd Amin MC, Martin C
    J Pharm Pharmacol, 2014 Aug;66(8):1047-61.
    PMID: 24628270 DOI: 10.1111/jphp.12234
    The field of pharmaceutical technology is expanding rapidly because of the increasing number of drug delivery options. Successful drug delivery is influenced by multiple factors, one of which is the appropriate identification of materials for research and engineering of new drug delivery systems. Bacterial cellulose (BC) is one such biopolymer that fulfils the criteria for consideration as a drug delivery material.
    Matched MeSH terms: Bacteria/metabolism*
  6. Fulltext A review of recent advances in the decontamination of mycotoxin and inactivation of fungi by ultrasound
    Hashemi Moosavi M, Mousavi Khaneghah A, Javanmardi F, Hadidi M, Hadian Z, Jafarzadeh S, et al.
    Ultrason Sonochem, 2021 Nov;79:105755.
    PMID: 34562735 DOI: 10.1016/j.ultsonch.2021.105755
    Innovative technologies for the pasteurization of food products have increased due to the global demand for higher-quality food products. In this regard, the current article aimed to provide an overview regarding the latest research on US application in the decontamination of fungi in food products and highlight the parameters influencing the effectiveness of this method. Therefore, the related article with inactivation of fungi and mycotoxins by ultrasound among last four years (2018-2021) by using terms such as 'mycotoxin,' 'inactivation,' 'ultrasound,' 'decontamination' among some international databases such as PubMed, Web of Science, Embase and Google Scholar" was retrieved. Ultrasound (US) is considered a non-thermal decontamination method for food products. In US, the release of energy due to the acoustic phenomenon destroys microorganisms. This technology is advantageous as it is inexpensive, eco-friendly, and does not negatively affect food products' food structure and organoleptic properties. The influence of the US on food structure and organoleptic properties dramatically depends on the intensity and energy density applied In addition, it can preserve higher levels of ascorbic acid, lycopene, and chlorophyll in sonicated food products. The treatment conditions, including frequency, intensity, duration, temperature, and processing pressure, influence the effectiveness of decontamination. However, US displays synergistic or antagonistic effects on bacteria, yeasts, molds, and mycotoxins when combined with other types of decontamination methods such as chemical and thermal approaches. Thus, further research is needed to clarify these effects. Overall, the application of US methods in the food industry for decreasing the microbial content of food products during processing has been applied. However, the use of US with other techniques needs to be studied further.
    Matched MeSH terms: Bacteria
  7. A review on microalgal-bacterial co-culture: The multifaceted role of beneficial bacteria towards enhancement of microalgal metabolite production
    Tong CY, Honda K, Derek CJC
    Environ Res, 2023 Jul 01;228:115872.
    PMID: 37054838 DOI: 10.1016/j.envres.2023.115872
    Mass microalgal-bacterial co-cultures have come to the fore of applied physiological research, in particularly for the optimization of high-value metabolite from microalgae. These co-cultures rely on the existence of a phycosphere which harbors unique cross-kingdom associations that are a prerequisite for the cooperative interactions. However, detailed mechanisms underpinning the beneficial bacterial effects onto microalgal growth and metabolic production are rather limited at the moment. Hence, the main purpose of this review is to shed light on how bacteria fuels microalgal metabolism or vice versa during mutualistic interactions, building upon the phycosphere which is a hotspot for chemical exchange. Nutrients exchange and signal transduction between two not only increase the algal productivity, but also facilitate in the degradation of bio-products and elevate the host defense ability. Main chemical mediators such as photosynthetic oxygen, N-acyl-homoserine lactone, siderophore and vitamin B12 were identified to elucidate beneficial cascading effects from the bacteria towards microalgal metabolites. In terms of applications, the enhancement of soluble microalgal metabolites is often associated with bacteria-mediated cell autolysis while bacterial bio-flocculants can aid in microalgal biomass harvesting. In addition, this review goes in depth into the discussion on enzyme-based communication via metabolic engineering such as gene modification, cellular metabolic pathway fine-tuning, over expression of target enzymes, and diversion of flux toward key metabolites. Furthermore, possible challenges and recommendations aimed at stimulating microalgal metabolite production are outlined. As more evidence emerges regarding the multifaceted role of beneficial bacteria, it will be crucial to incorporate these findings into the development of algal biotechnology.
    Matched MeSH terms: Bacteria/metabolism
  8. A review on the potential of polyhydroxyalkanoates production from oil-based substrates
    Chien Bong CP, Alam MNHZ, Samsudin SA, Jamaluddin J, Adrus N, Mohd Yusof AH, et al.
    J Environ Manage, 2021 Nov 15;298:113461.
    PMID: 34435568 DOI: 10.1016/j.jenvman.2021.113461
    Polyhydroxyalkanoate (PHA) is a type of polyesters produced in the form of accumulated intracellular granules by many microorganisms. It is viewed as an environmentally friendly bioproduct due to its biodegradability and biocompatibility. The production of the PHA using oil substrates such as waste oil and plant oil, has gained considerable attention due to the high product yield and lower substrate cost. Nevertheless, the PHA fermentation using oil substrate is complicated due to the heterogenous fatty acid composition, varied bio-accessibility and possible inhibitory effect on the bacterial culture. This review presents the current state-of-the-art of PHA production from oil-based substrates. This paper firstly discusses the technical details, such as the choice of bacteria strain and fermentation conditions, characteristic of the oil substrate as well as the PHA composition and application. Finally, the paper discusses the challenges and prospects for up-scaling towards a cleaner and effective bioprocess. From the literature review, depending on the cell culture and the type of PHA produced, the oil platform can have a PHA yield of 0.2-0.8 g PHA/g oil substrate, with PHA content mostly from 40 to 90% of the cell dry weight. There is an on-going search for more effective oil-utilising PHA producers and lower cost substrate for effective PHA production. The final application of the PHA polymer influences the treatment needed during downstream processing and its economic performance. PHA with different compositions exhibits varied decomposition behaviour under different conditions, requiring further insight towards its management towards a sustainable circular economy.
    Matched MeSH terms: Bacteria
  9. Fulltext A secondary mode of action of polymyxins against Gram-negative bacteria involves the inhibition of NADH-quinone oxidoreductase activity
    Deris ZZ, Akter J, Sivanesan S, Roberts KD, Thompson PE, Nation RL, et al.
    J Antibiot (Tokyo), 2014 Feb;67(2):147-51.
    PMID: 24169795 DOI: 10.1038/ja.2013.111
    Polymyxin B and colistin were examined for their ability to inhibit the type II NADH-quinone oxidoreductases (NDH-2) of three species of Gram-negative bacteria. Polymyxin B and colistin inhibited the NDH-2 activity in preparations from all of the isolates in a concentration-dependent manner. The mechanism of NDH-2 inhibition by polymyxin B was investigated in detail with Escherichia coli inner membrane preparations and conformed to a mixed inhibition model with respect to ubiquinone-1 and a non-competitive inhibition model with respect to NADH. These suggest that the inhibition of vital respiratory enzymes in the bacterial inner membrane represents one of the secondary modes of action for polymyxins.
    Matched MeSH terms: Gram-Negative Bacteria/drug effects*; Gram-Negative Bacteria/enzymology*
  10. A simple method to screen for azo-dye-degrading bacteria
    Syed MA, Sim HK, Khalid A, Shukor MY
    J Environ Biol, 2009 Jan;30(1):89-92.
    PMID: 20112868
    A stab-culture method was adapted to screen for azo dyes-decolorizing bacteria from soil and water samples. Decolorized azo dye in the lower portion of the solid media indicates the presence of anaerobic azo dyes-decolorizing bacteria, while aerobic decolorizing bacteria decolorizes the surface portion of the solid media. Of twenty soil samples tested, one soil sample shows positive results for the decolourisation of two azo dyes; Biebrich scarlet (BS) and Direct blue 71 (DB) under anaerobic conditions. A gram negative and oxidase negative bacterial isolate was found to be the principal azo dyes degrader The isolate was identified by using the Biolog identification system as Serratia marcescens.
    Matched MeSH terms: Bacteria/growth & development; Bacteria/isolation & purification; Bacteria/metabolism*
  11. A study of heavy metals and their fate in the composting of tannery sludge
    Haroun M, Idris A, Syed Omar SR
    Waste Manag, 2007;27(11):1541-50.
    PMID: 17113767
    Tannery waste is categorized as toxic and hazardous in Malaysia due to its high content of Cr (in excess of 500 mg/kg) and other heavy metals. Heavy metals, when in high enough concentrations, have the potential to be both phytotoxic and zootoxic. Heavy metals are found as contaminants in tannery sludge. This investigation aimed to identify the fate of chromium, cadmium, copper, lead, and zinc concentrations in tannery sludge throughout a 50-day composting cycle. The results of this study showed a general increase in the removal of Cr, Cd, Pb, and to a much smaller extent Zn and Cu, manifested by a decrease in their overall concentrations within the solid fraction of the final product (the decreases were likely the result of leaching). Furthermore, in using a sequential extraction method for sludge composting at different phases of treatment, a large proportion of the heavy metals were found to be associated to the residual fraction (70-80%) and fractions more resistant to extraction, X-NaOH, X-EDTA, X-HNO3 (12-29%). Less than 2% of the metals were bound to bioavailable fractions X-(KNO3+H2O).
    Matched MeSH terms: Bacteria/metabolism
  12. A synopsis of the origins and function of dental plaque and pellicle
    Park AW, Yaacob HB
    J Nihon Univ Sch Dent, 1994 Sep;36(3):157-74.
    PMID: 7989958
    Matched MeSH terms: Bacteria, Anaerobic/metabolism
  13. Fulltext Acinetobacter spp. infections in Malaysia: a review of antimicrobial resistance trends, mechanisms and epidemiology
    Mohd Rani F, A Rahman NI, Ismail S, Alattraqchi AG, Cleary DW, Clarke SC, et al.
    Front Microbiol, 2017;8:2479.
    PMID: 29312188 DOI: 10.3389/fmicb.2017.02479
    Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987-2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008-2009 and thereafter, rates have remained fairly constant (e.g., 50-60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that blaOXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.
    Matched MeSH terms: Bacteria; Drug Resistance, Bacterial*
  14. Actinobacteria-a promising natural source of anti-biofilm agents
    Azman AS, Mawang CI, Khairat JE, AbuBakar S
    Int Microbiol, 2019 Dec;22(4):403-409.
    PMID: 30847714 DOI: 10.1007/s10123-019-00066-4
    A biofilm is a community of microorganisms attached to a surface and embedded in a matrix of extracellular polymeric substances. Biofilms confer resistance towards conventional antibiotic treatments; thus, there is an urgent need for newer and more effective antimicrobial agents that can act against these biofilms. Due to this situation, various studies have been done to investigate the anti-biofilm effects of natural products including bioactive compounds extracted from microorganisms such as Actinobacteria. This review provides an insight into the anti-biofilm potential of Actinobacteria against various pathogenic bacteria, which hopefully provides useful information, guidance, and improvements for future antimicrobial studies. Nevertheless, further research on the anti-biofilm mechanisms and compound modifications to produce more potent anti-biofilm effects are required.
    Matched MeSH terms: Anti-Bacterial Agents/metabolism; Anti-Bacterial Agents/pharmacology*; Anti-Bacterial Agents/chemistry; Bacteria/drug effects; Actinobacteria/metabolism; Actinobacteria/chemistry*
  15. Fulltext Actinomycosis of Distal Phalanx Twenty Years after Flap Reconstruction of Index Finger: A Case Report
    Prashant N, Azuhairy A
    Malays Orthop J, 2018 Mar;12(1):48-50.
    PMID: 29725514 MyJurnal DOI: 10.5704/MOJ.1803.011
    Actinomycosis is a chronic granulomatous suppurative infection caused by anaerobic bacteria from genus Actinomyces which are normal flora of mouth, colon and vagina. Actinomycosis of upper extremity is rare. We report a case of actinomycosis of the distal phalanx of finger many years after flap reconstruction. The patient presented with two months' history of chronic discharging sinus from the tip of his right index finger, which had sustained a degloving injury 20 years previously. It had been treated with an anterior chest wall flap which had healed uneventfully but was bulky due to excess tissue from the donor site. Radiograph revealed osetomyelitis changes of distal phalanx. Debulking surgery with curettage of the distal phalanx was done. Wound healing was uneventful. He was treated with six weeks of metronidazole and ciprofloxacin. The discharge from the distal phalanx cultured actinomycosis odontolyticus. Histopathology of the debrided tissue showed chronic inflammation. As far as we are aware, there are no reports of actinomycosis in a flap involving the finger treated previously with a chest wall skin flap. The infection was probably dormant for many years before manifesting as a discharging sinus. Although the finger flap was bulky, it was not problematic until it started to have serous discharge. With a thorough debridement of all infected tissue, six weeks of antibiotic was adequate. Ciprofloxacin was prescribed based on discharge culture sensitivity. Metronidazole was added as actinomycosis is anaerobic. Response was prompt as patient was not immunocompromised. At follow-up six months post-surgery the finger had recovered with good function. If not for the discharging sinus, patient would probably have tolerated his bulky finger for the rest of his life.
    Matched MeSH terms: Bacteria, Anaerobic
  16. Fulltext Acute toxicity evaluation, antibacterial, antioxidant and immunomodulatory effects of Melastoma malabathricum
    Alnajar ZA, Abdulla MA, Ali HM, Alshawsh MA, Hadi AH
    Molecules, 2012;17(3):3547-59.
    PMID: 22433579 DOI: 10.3390/molecules17033547
    Melastoma malabathricum (MM) is a well-known plant in Malaysian traditional medicine, locally known as senduduk. Its ethanol and aqueous extracts have been used in the present investigation to study the immunomodulatory role on human peripheral blood mononuclear cell (PBMC), and the DPPH, ABTS and FRAP free radical scavenging activities were also measured. Total flavonoids and total phenolic contents were assayed and the antibacterial effect was tested against four species of bacteria; two Gram-positive (Staphylococcus aureus and Streptococcus agalactiae) and two Gram-negative (Escherichia coli and Klebsilla pneumonia). The tests were carried out using the disc diffusion, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) methods. Moreover, the acute toxicity was evaluated in vivo on the ethanol extract of MM to establish its safety when administered orally. In our results, both extracts of MM showed abilities to scavenge DPPH and ABTS free radicals, IC(50) values: (11.599 ± 0.84, 10.573 ± 0.58 µmol/L) and (62.657 ± 0.78, 63.939 ± 0.48 µmol/L) for ethanol and aqueous extracts respectively. Indeed the ethanol extract evidenced high phenolic content (384.33 ± 0.005 mg/g), flavonoids contents (85.8 ± 0.009 mg/g) and ferric reducing antioxidant power (33,590 ± 0.038 mmol/g), with high activity against S. aureus and S. agalactiae (11 ± 0.3 and 12 ± 0.6 mm inhibition zones). Likewise, the percentage of peripheral blood mononuclear cells (PBMC) viability was increased in response to MM, IC(50) values (1.781 ± 1.2 and 6.545 ± 0.93 µg/mL) for ethanol and aqueous extracts, respectively. In addition, our results showed that the MM extract is safe even at a high dose of 5,000 mg/kg and has no oral toxicity. These findings suggest the excellent medicinal bioactivity of MM and explain the popularity of this plant in the folk medicine as a remedy for different illnesses.
    Matched MeSH terms: Gram-Negative Bacteria/drug effects; Gram-Positive Bacteria/drug effects
  17. Adaptational properties and applications of cold-active lipases from psychrophilic bacteria
    Maiangwa J, Ali MS, Salleh AB, Rahman RN, Shariff FM, Leow TC
    Extremophiles, 2015 Mar;19(2):235-47.
    PMID: 25472009 DOI: 10.1007/s00792-014-0710-5
    Psychrophilic microorganisms are cold-adapted with distinct properties from other thermal classes thriving in cold conditions in large areas of the earth's cold environment. Maintenance of functional membranes, evolving cold-adapted enzymes and synthesizing a range of structural features are basic adaptive strategies of psychrophiles. Among the cold-evolved enzymes are the cold-active lipases, a group of microbial lipases with inherent stability-activity-flexibility property that have engaged the interest of researchers over the years. Current knowledge regarding these cold-evolved enzymes in psychrophilic bacteria proves a display of high catalytic efficiency with low thermal stability, which is a differentiating feature with that of their mesophilic and thermophilic counterparts. Improvement strategies of their adaptive structural features have significantly benefited the enzyme industry. Based on their homogeneity and purity, molecular characterizations of these enzymes have been successful and their properties make them unique biocatalysts for various industrial and biotechnological applications. Although, strong association of lipopolysaccharides from Antarctic microorganisms with lipid hydrolases pose a challenge in their purification, heterologous expression of the cold-adapted lipases with affinity tags simplifies purification with higher yield. The review discusses these cold-evolved lipases from bacteria and their peculiar properties, in addition to their potential biotechnological and industrial applications.
    Matched MeSH terms: Bacteria/enzymology*
  18. Fulltext Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia
    Ho A, Zuan ATK, Mendes LW, Lee HJ, Zulkeflee Z, van Dijk H, et al.
    Microb Ecol, 2022 Nov;84(4):1154-1165.
    PMID: 34716776 DOI: 10.1007/s00248-021-01908-3
    Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.
    Matched MeSH terms: Bacteria/genetics
  19. Fulltext Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations
    Shashkova T, Popenko A, Tyakht A, Peskov K, Kosinsky Y, Bogolubsky L, et al.
    PLoS One, 2016;11(2):e0148386.
    PMID: 26894828 DOI: 10.1371/journal.pone.0148386
    BACKGROUND: Intestinal microbiota plays an important role in the human health. It is involved in the digestion and protects the host against external pathogens. Examination of the intestinal microbiome interactions is required for understanding of the community influence on host health. Studies of the microbiome can provide insight on methods of improving health, including specific clinical procedures for individual microbial community composition modification and microbiota correction by colonizing with new bacterial species or dietary changes.

    METHODOLOGY/PRINCIPAL FINDINGS: In this work we report an agent-based model of interactions between two bacterial species and between species and the gut. The model is based on reactions describing bacterial fermentation of polysaccharides to acetate and propionate and fermentation of acetate to butyrate. Antibiotic treatment was chosen as disturbance factor and used to investigate stability of the system. System recovery after antibiotic treatment was analyzed as dependence on quantity of feedback interactions inside the community, therapy duration and amount of antibiotics. Bacterial species are known to mutate and acquire resistance to the antibiotics. The ability to mutate was considered to be a stochastic process, under this suggestion ratio of sensitive to resistant bacteria was calculated during antibiotic therapy and recovery.

    CONCLUSION/SIGNIFICANCE: The model confirms a hypothesis of feedbacks mechanisms necessity for providing functionality and stability of the system after disturbance. High fraction of bacterial community was shown to mutate during antibiotic treatment, though sensitive strains could become dominating after recovery. The recovery of sensitive strains is explained by fitness cost of the resistance. The model demonstrates not only quantitative dynamics of bacterial species, but also gives an ability to observe the emergent spatial structure and its alteration, depending on various feedback mechanisms. Visual version of the model shows that spatial structure is a key factor, which helps bacteria to survive and to adapt to changed environmental conditions.

    Matched MeSH terms: Anti-Bacterial Agents/pharmacology; Bacteria/drug effects; Bacteria/genetics; Bacteria/metabolism; Drug Resistance, Bacterial
  20. Fulltext AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp
    See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, et al.
    Sci Rep, 2017 02 22;7:42968.
    PMID: 28225085 DOI: 10.1038/srep42968
    Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.
    Matched MeSH terms: Planococcus Bacteria/enzymology*; Planococcus Bacteria/isolation & purification
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