Did you mean: planococcoceae
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Sub-cellular Biochemistry 2021Thermostability is a key factor in the industrial and clinical application of enzymes, and understanding mechanisms of thermostability is valuable for molecular biology... (Review)
Review
Thermostability is a key factor in the industrial and clinical application of enzymes, and understanding mechanisms of thermostability is valuable for molecular biology and enzyme engineering. In this chapter, we focus on the thermostability of leucine dehydrogenase (LDH, EC 1.4.1.9), an amino acid-metabolizing enzyme that is an NAD-dependent oxidoreductase which catalyzes the deamination of branched-chain l-amino acids (BCAAs). LDH from Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has already been applied to quantify the concentration of BCAAs in biological specimens. However, the molecular mechanism of its thermostability had been unknown because no high-resolution structure was available. Here, we discuss the thermostability of GstLDH on the basis of its structure determined by cryo-electron microscopy. Sequence comparison with other structurally characterized LDHs (from Lysinibacillus sphaericus and Sporosarcina psychrophila) indicated that non-conserved residues in GstLDH, including Ala94, Tyr127, and the C-terminal region, are crucial for oligomeric stability through intermolecular interactions between protomers. Furthermore, NAD binding to GstLDH increased the thermostability of the enzyme as additional intermolecular interactions formed on cofactor binding. This knowledge is important for further applications and development of amino acid metabolizing enzymes in industrial and clinical fields.
Topics: Bacillaceae; Cryoelectron Microscopy; Enzyme Stability; Geobacillus stearothermophilus; Leucine Dehydrogenase; Sporosarcina
PubMed: 33252736
DOI: 10.1007/978-3-030-58971-4_10 -
Frontiers in Microbiology 2019The family / is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable...
The family / is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily , the evolutionary history of this family, containing the potent mosquitocidal species , remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family / and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available / and representative species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family / or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family / based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family /, namely gen. nov., gen. nov., and gen. nov., as well as the transfer of 25 misclassified species from the families / and into these three genera and in , , , and genera. These amendments establish a coherent taxonomy and evolutionary history for the family /, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family within the emended family .
PubMed: 32010063
DOI: 10.3389/fmicb.2019.02821 -
Environmental Microbiology Dec 2021Exposure to a diverse microbial environment during pregnancy and early postnatal period is important in determining predisposition towards allergy. However, the effect...
Exposure to a diverse microbial environment during pregnancy and early postnatal period is important in determining predisposition towards allergy. However, the effect of environmental microbiota exposure during preconception, pregnancy and postnatal life on development of allergy in the child has not been investigated so far. In the S-PRESTO (Singapore PREconception Study of long Term maternal and child Outcomes) cohort, we collected house dust during all three critical window periods and analysed microbial composition using 16S rRNA gene sequencing. At 6 and 18 months, the child was assessed for eczema by clinicians. In the eczema group, household environmental microbiota was characterized by presence of human-associated bacteria Actinomyces, Anaerococcus, Finegoldia, Micrococcus, Prevotella and Propionibacterium at all time points, suggesting their possible contributions to regulating host immunity and increasing the susceptibility to eczema. In the home environment of the control group, putative protective effect of an environmental microbe Planomicrobium (Planococcaceae family) was observed to be significantly higher than that in the eczema group. Network correlation analysis demonstrated inverse relationships between beneficial Planomicrobium and human-associated bacteria (Actinomyces, Anaerococcus, Finegoldia, Micrococcus, Prevotella and Propionibacterium). Exposure to natural environmental microbiota may be beneficial to modulate shed human-associated microbiota in an indoor environment.
Topics: Bacteria; Child; Cohort Studies; Eczema; Female; Humans; Microbiota; Pregnancy; RNA, Ribosomal, 16S
PubMed: 34309161
DOI: 10.1111/1462-2920.15684 -
Journal of Bacteriology Jun 2022The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis,...
The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis, sporulation involves up to 500 genes, many of which do not have orthologs in other bacilli and/or clostridia. Previous studies identified about 60 sporulation genes of B. subtilis that were shared by all spore-forming members of the . These genes are referred to as the sporulation core or signature, although many of these are also found in genomes of nonsporeformers. Using an expanded set of 180 firmicute genomes from 160 genera, including 76 spore-forming species, we investigated the conservation of the sporulation genes, in particular seeking to identify lineages that lack some of the genes from the conserved sporulation core. The results of this analysis confirmed that many small acid-soluble spore proteins (SASPs), spore coat proteins, and germination proteins, which were previously characterized in bacilli, are missing in spore-forming members of and other classes of . A particularly dramatic loss of sporulation genes was observed in the spore-forming members of the families and . Fifteen species from diverse lineages were found to carry (-interrupting) elements of different sizes that all encoded SpoIVCA-like recombinases but did not share any other genes. Phylogenetic trees built from concatenated alignments of sporulation proteins and ribosomal proteins showed similar topology, indicating an early origin and subsequent vertical inheritance of the sporulation genes. Many members of the phylum () are capable of producing endospores, which enhance the survival of important Gram-positive pathogens that cause such diseases as anthrax, botulism, colitis, gas gangrene, and tetanus. We show that the core set of sporulation genes, defined previously through genome comparisons of several bacilli and clostridia, is conserved in a wide variety of sporeformers from several distinct lineages of . We also detected widespread loss of sporulation genes in many organisms, particularly within the families and Members of these families, such as Lysinibacillus sphaericus and Clostridium innocuum, could be excellent model organisms for studying sporulation mechanisms, such as engulfment, formation of the spore coat, and spore germination.
Topics: Bacillus; Bacillus subtilis; Bacterial Proteins; Clostridium; Firmicutes; Humans; Phylogeny; Spores, Bacterial
PubMed: 35638784
DOI: 10.1128/jb.00079-22 -
Applied and Environmental Microbiology Aug 2023Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO production. Biocement is... (Review)
Review
Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on . Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.
Topics: Ammonium Compounds; Calcium Carbonate; Chemical Precipitation; Conservation of Energy Resources; Industrial Microbiology; Sporosarcina; Urea
PubMed: 37439668
DOI: 10.1128/aem.01794-22 -
Archives of Microbiology Jul 20222,4,6-trinitrotoluene (TNT), a nitro-aromatic explosive commonly used for defense and several non-violent applications is contributing to serious environmental pollution...
2,4,6-trinitrotoluene (TNT), a nitro-aromatic explosive commonly used for defense and several non-violent applications is contributing to serious environmental pollution problems including human health. The current study investigated the remediation potential of a native soil isolate, i.e., Indiicoccus explosivorum (strain S5-TSA-19) isolated from collected samples of an explosive manufacturing site, against TNT. The survivability of I. explosivorum against explosives is indirectly justified through its isolation; thus, it is being chosen for further study. At a TNT concentration of 120 mg/L within an optimized environment (i.e., at 30 °C and 120 rpm), the isolate was continually incubated for 30 days in a minimal salt medium (MSM). The proliferation of the isolate and the concentration of TNT, nitrate, nitrite, and ammonium ion were evaluated at a particular time during the experiment. Within 168 h (i.e., 7 days) of incubation, I. explosivorum co-metabolically degraded 100% TNT. The biodegradation procedure succeeded the first-order kinetics mechanism. Formations of additional metabolites like 2,4-dinitrotoluene (DNT), 2,4-diamino-6-nitrotoluene (2-DANT), and 2-amino-4,6-dinitrotoluene (2-ADNT), were also witnessed. TNT seems to be non-toxic for the isolate, as it reproduced admirably in TNT presence. To date, it is the first report of Indiicoccus explosivorum, efficiently bio-remediating TNT, i.e., a nitro-aromatic compound via different degradation pathways, leading to the production of simpler as well as less harmful end products. Further, at the field-scale application, Indiicoccus explosivorum may be explored for the bioremediation of TNT (i.e., a nitro-aromatic compound)-contaminated effluents.
Topics: Humans; Biodegradation, Environmental; Kinetics; Planococcaceae; Trinitrotoluene
PubMed: 35778571
DOI: 10.1007/s00203-022-03057-8 -
Heliyon Oct 2021Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through...
Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites ( sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers ( PLFA, DNA .) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families and in MX-80 Batch 1 incubations; along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (, fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints ( low water activity and high swelling pressure in the confined bentonite) would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.
PubMed: 34703919
DOI: 10.1016/j.heliyon.2021.e08131 -
Frontiers in Medicine 2022To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
OBJECTIVE
To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
METHODS
In total, 29 preliminarily diagnosed ITP patients and 33 healthy volunteers were enrolled. Fecal bacterial were analyzed based on 16S rRNA sequencing. Plasma cytokines and motabolites were analyzed using flow cytometry and liquid chromatography-mass spectrometry (LC-MS), respectively.
RESULTS
, , and were enriched at the genus level in ITP patients, while , , were depleted. At the phylum level, the relative abundance of and increased in ITP patients, while , , and the ratio decreased. Plasma levels of 5-hydroxyeicosatetraenoic acid (5-HETE), 6-trans-12-epi-leukotriene B4 (6t,12e-LTB), and resolvin D2 (RvD) were upregulated, and stachydrine, dowicide A, dodecanoylcarnitine were downregulated in ITP patients. Furthermore, RvD is positively correlated with order , 5-HETE is positively correlated with genus , and 6t,12e-LTB is positively correlated with genus . In addition, stachydrine is positively correlated with family , dowicide A is positively correlated with class , and dodecanoylcarnitine is positively correlated with order . Plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were upregulated in ITP patients.
CONCLUSION
Our study revealed a relationship between microbiota and fatty metabolism in ITP. Gut microbiota may participate in the pathogenesis of ITP through affecting cytokine secretion, interfering with fatty metabolism.
PubMed: 35665326
DOI: 10.3389/fmed.2022.810612 -
Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
European Journal of Clinical... Apr 2021Limited available animal and human data suggest an association between dysbiosis of gut microbiota and PCOS. We aimed to determine whether gut microbiota in lean women...
BACKGROUND
Limited available animal and human data suggest an association between dysbiosis of gut microbiota and PCOS. We aimed to determine whether gut microbiota in lean women with PCOS shows any alterations compared to healthy women.
MATERIALS AND METHODS
Twenty-four lean patients with PCOS phenotype A according to the Rotterdam 2003 diagnostic criteria and 22 BMI-matched healthy women were included in this study. Anthropometric, hormonal and biochemical measurements were carried out in all participants. 16S rRNA gene V3-V4 region amplicon sequencing was performed on stool samples. Preprocessing of the raw data was performed using QIIME, and both QIIME and R packages were used for microbiome analysis.
RESULTS
Bacterial richness and diversity did not show a significant difference between patients and controls. Beta diversity was similar between the groups. However, Erysipelotrichaceae, Proteobacteria, Gammaproteobacteria, Enterobacteriaceae, Planococcaceae, Gemmules and Bacillales were significantly abundant in PCOS group according to LEfSe analysis. Clostridium cluster XVII showed increased abundance in patient group, while Clostridium sensustricto and Roseburia were decreased compared to controls. Random forest prediction analysis revealed Clostridium cluster XIVb as the most discriminative feature of patient group and Roseburia for healthy controls. Testosterone and androstenedione were negatively correlated with alpha and phylogenetic diversity.
CONCLUSIONS
Our results suggest that gut microbiome of lean PCOS patients with full phenotype shows compositional alterations with similar bacterial richness and diversity compared to controls and that hyperandrogenism is associated with dysbiosis.
Topics: Androstenedione; Bacillales; Body Mass Index; Case-Control Studies; Clostridium; Enterobacteriaceae; Female; Firmicutes; Gammaproteobacteria; Gastrointestinal Microbiome; Humans; Planococcaceae; Polycystic Ovary Syndrome; Proteobacteria; RNA, Ribosomal, 16S; Testosterone; Young Adult
PubMed: 32991745
DOI: 10.1111/eci.13417