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Nature Aug 2022Stimulator of interferon genes (STING) is an antiviral signalling protein that is broadly conserved in both innate immunity in animals and phage defence in prokaryotes....
Stimulator of interferon genes (STING) is an antiviral signalling protein that is broadly conserved in both innate immunity in animals and phage defence in prokaryotes. Activation of STING requires its assembly into an oligomeric filament structure through binding of a cyclic dinucleotide, but the molecular basis of STING filament assembly and extension remains unknown. Here we use cryogenic electron microscopy to determine the structure of the active Toll/interleukin-1 receptor (TIR)-STING filament complex from a Sphingobacterium faecium cyclic-oligonucleotide-based antiphage signalling system (CBASS) defence operon. Bacterial TIR-STING filament formation is driven by STING interfaces that become exposed on high-affinity recognition of the cognate cyclic dinucleotide signal c-di-GMP. Repeating dimeric STING units stack laterally head-to-head through surface interfaces, which are also essential for human STING tetramer formation and downstream immune signalling in mammals. The active bacterial TIR-STING structure reveals further cross-filament contacts that brace the assembly and coordinate packing of the associated TIR NADase effector domains at the base of the filament to drive NAD hydrolysis. STING interface and cross-filament contacts are essential for cell growth arrest in vivo and reveal a stepwise mechanism of activation whereby STING filament assembly is required for subsequent effector activation. Our results define the structural basis of STING filament formation in prokaryotic antiviral signalling.
Topics: Animals; Antiviral Agents; Bacterial Proteins; Bacteriophages; Cryoelectron Microscopy; Dinucleoside Phosphates; Humans; Immunity, Innate; Membrane Proteins; Operon; Receptors, Interleukin-1; Sphingobacterium; Toll-Like Receptors
PubMed: 35859168
DOI: 10.1038/s41586-022-04999-1 -
Frontiers in Microbiology 2022Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate...
Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate precipitation (MICP) to form crystalline secondary cave deposits known as speleothems. The urease family is a group of enzymes involved in MICP that catalyze the breakdown of urea, which is a source of energy, into ammonia and carbonate. Carbonate anions are effluxed to the extracellular surface of the bacterium where it then binds to environmental calcium to form calcium carbonate which then continues to grow in crystal form. Here, we studied bacterial communities from speleothems collected from the Iron Curtain Cave (ICC) in Chilliwack, B.C., Canada, to characterize these organisms and determine whether urease-positive (U+) bacteria were present in the cave and their potential impact on speleothem formation. The ICC is a carbonate cave located on the northside of Chipmunk Ridge, presenting a unique environment with high iron content sediment and limestone structures throughout. With six pools of water throughout the cave, the environment is highly humid, with temperatures ranging between 4 and 12°C depending on the time of year. Ninety-nine bacterial strains were isolated from popcorn (PCS) and soda straw (SSS) speleothems. These isolates were screened for urease enzymatic activity, with 11 candidates found to be urease-positive. After incubation, species-specific crystal morphologies were observed. Popcorn speleothem provided more bacterial diversity overall when compared to soda straw speleothem when examined under a culture-based method. Nearly twice as many U+ isolates were isolated from popcorn speleothems compared to soda straw speleothems. The U+ candidates were identified to the genus level by 16S rRNA analysis, and two isolates underwent whole-genome sequencing. Two novel species were identified as sp. PCS056 and sp. SSS035. Both isolates demonstrated the most crystal production as well as the most morphologically dissimilar crystal shapes in broth culture and were found to produce crystals as previously observed in both agar and broth media. The results from this study are consistent with the involvement of urease-positive bacteria isolated from the ICC in the formation of cave speleothems. 16S rRNA sequencing revealed a diverse set of microbes inhabiting the speleothems that have urease activity. Whole-genome sequencing of the two chosen isolates confirmed the presence of urease pathways, while revealing differences in urease pathway structure and number. This research contributes to understanding microbial-associated cave formation and degradation, with applications to cave conservation, microbiota composition, and their role in shaping the cave environment.
PubMed: 35847116
DOI: 10.3389/fmicb.2022.933388 -
Indian Journal of Critical Care... Jun 2022is a rare cause of human infections worldwide. After reviewing the literature, we could find only eight case reports to date. The majority of cases were of cellulitis...
UNLABELLED
is a rare cause of human infections worldwide. After reviewing the literature, we could find only eight case reports to date. The majority of cases were of cellulitis and septicemia. Most of these patients were immunocompromised and the recovery rate was lesser. We present a case of a young female diagnosed with scrub typhus complicated by acute respiratory distress syndrome who developed septicemia and septic shock due to . She was managed with sensitive antibiotic levofloxacin, clinically improved, and discharged in satisfactory condition.
HOW TO CITE THIS ARTICLE
Bansal S, Varshney S. Scrub Typhus Complicated by Rare Human Pathogen Indian J Crit Care Med 2022;26(6):742-744.
PubMed: 35836642
DOI: 10.5005/jp-journals-10071-24254 -
PloS One 2022This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different...
This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different degradation periods was analyzed using MiSeq high-throughput sequencing. The results showed that 14 days after inoculation, the filter paper enzyme and endoglucanase activities increased to 2.55 U·mL-1 and 2.34 U·mL-1. The xylanase, laccase, and lignin peroxidase activities rose to 9.86 U·mL-1, 132.16 U·L-1, and 85.43 U·L-1 after 28 d, which was consistent with changes in the straw degradation rate. The degradation rates of straw, lignin, cellulose, and hemicellulose were 31.43%, 13.67%, 25.04%, and 21.69%, respectively, after 28 d of fermentation at 15°C. Proteobacteria, Firmicutes, and Bacteroidetes were the main bacterial species in samples at different degradation stages. The dominant genera included Pseudomonas, Delftia, and Paenibacillus during the initial stage (1 d, 7 d) and the mid-term stage (14 d). The key functional microbes during the late stage (21 d, 28 d) were Rhizobium, Chryseobacterium, Sphingobacterium, Brevundimonas, and Devosia. Changes in the bacterial consortium structure and straw degradation characteristics during different degradation periods were clarified to provide a theoretical basis for the rational utilization of microbial decomposer M44.
Topics: Bacteria; Cellulose; Fermentation; Lignin; Microbial Consortia; Temperature
PubMed: 35802565
DOI: 10.1371/journal.pone.0270162 -
Scientific Reports May 2022Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal...
Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the "Microbial Redox Index (MRI)," an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation-reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
Topics: Gastric Mucosa; Gastritis; Helicobacter Infections; Helicobacter pylori; Humans; Microbiota; Oxidation-Reduction; Peptic Ulcer; RNA, Ribosomal, 16S
PubMed: 35589904
DOI: 10.1038/s41598-022-12431-x -
Animal Bioscience Dec 2022The observation that temperate C3 and tropical C4 forage silages easily produce large amounts of ethanol or acetic acid has puzzled researchers for many years. Hence,...
OBJECTIVE
The observation that temperate C3 and tropical C4 forage silages easily produce large amounts of ethanol or acetic acid has puzzled researchers for many years. Hence, this study aimed to assess the effects of epiphytic microbiota from C3 forages (Italian ryegrass and oat) on fermentative products and bacterial community structure in C4 forage (sorghum) silage.
METHODS
Through microbiota transplantation and γ-ray irradiation sterilization, the irradiated sorghum was treated: i) sterile distilled water (STSG); ii) epiphytic microbiota from sorghum (SGSG); iii) epiphytic microbiota from Italian ryegrass (SGIR); iv) epiphytic microbiota from oat (SGOT).
RESULTS
After 60 days, all the treated groups had high lactic acid (>63.0 g/kg dry matter [DM]) contents and low pH values (<3.70), acetic acid (<14.0 g/kg DM) and ammonia nitrogen (<80.0 g/kg total nitrogen) contents. Notably, SGIR (59.8 g/kg DM) and SGOT (77.6 g/kg DM) had significantly (p<0.05) higher ethanol concentrations than SGSG (14.2 g/kg DM) on day 60. After 60 days, Lactobacillus were predominant genus in three treated groups. Higher proportions of Chishuiella (12.9%) and Chryseobacterium (7.33%) were first found in silages. The ethanol contents had a positive correlation (p<0.05) with the abundances of Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium.
CONCLUSION
The epiphytic bacteria on raw materials played important roles in influencing the silage fermentation products between temperate C3 and tropical C4 forages. The quantity and activity of hetero-fermentative Lactobacillus, Chishuiella, Acinetobacter, Stenotrophomonas, Chryseobacterium, and Sphingobacterium may be the key factors for the higher ethanol contents and DM loss in silages.
PubMed: 35507862
DOI: 10.5713/ab.21.0543 -
Bioinorganic Chemistry and Applications 2022This research raises the potential use of coordination polymers as new useful materials in two essential research fields, allowing the obtaining of a new multiartificial...
This research raises the potential use of coordination polymers as new useful materials in two essential research fields, allowing the obtaining of a new multiartificial enzyme with the capacity to inhibit the growth of bacteria resistance. The fine selection of the ligands allows the design of a new 2D coordination polymer (CP), with the formula [Cu(IBA)(OH)]·6nHO, by the combination of Cu (II) as the metal center with a pseudoamino acid (HIBA = isophthaloyl bis -alanine). Quantitative total X-ray fluorescence (TXRF) analyses show that the obtained CP can gradually release Cu (II) ions. Additionally, this CP can be nanoprocessed and transformed into a metal-organic gel (MOG) by using different Cu (II) salt concentrations and the application of ultrasounds. Considering its nanometric dimensions, the slow Cu (II) release and its simple processability, its performance as an artificial enzyme, and its antibacterial ability were explored. The results obtained show the first nanocoordination polymer acting as an artificial multienzyme (peroxidase, catalase, and superoxodismutase) exhibiting antibacterial activity in the presence of hydrogen peroxide, with selective behavior for three bacterium strains (). Indeed, this CP shows a more robust inhibition capacity for . Going beyond that, as there are no comfortable and practically clinical tests capable of detecting the presence of , the compound can be easily embedded to form moldable gelatin that will facilitate the handling and low-cost commercial kits.
PubMed: 35449715
DOI: 10.1155/2022/8788221 -
Microbiome Mar 2022The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure...
BACKGROUND
The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.
METHODS
Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.
RESULTS
Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.
CONCLUSIONS
Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.
Topics: Animals; Anura; Chytridiomycota; Microbiota; Mycoses; RNA, Ribosomal, 16S
PubMed: 35272699
DOI: 10.1186/s40168-021-01215-6 -
Microorganisms Jan 2022Larvae of the black soldier fly (BSF) are polyphagous feeders and show tremendous bioconversion capabilities of organic matter into high-quality insect biomass....
Larvae of the black soldier fly (BSF) are polyphagous feeders and show tremendous bioconversion capabilities of organic matter into high-quality insect biomass. However, the digestion of lignocellulose-rich palm oil side streams such as palm kernel meal (PKM) is a particular challenge, as these compounds are exceptionally stable and are mainly degraded by microbes. This study aimed to investigate the suitability of BSF larvae as bioconversion agents of PKM. Since the intestinal microbiota is considered to play a key role in dietary breakdown and in increasing digestibility, the bacterial and fungal communities of BSF larvae were characterized in a culture-dependent approach and screened for their putative entomopathogenicity. The lethality of six putative candidates was investigated using intracoelomal injection. In total, 93 isolates were obtained with a bacterial share of 74% that were assigned to the four phyla , , , and . Members of the genera , and are part of the core microbiome, as they were frequently described in the gut of larvae regardless of diet, nutritional composition, or rearing conditions. With 75%, a majority of the fungal isolates belonged to the phylum . We identified several taxa already published to be able to degrade lignocelluloses, including , , yeasts, or filamentous species. The injection assays revealed pronounced differences in pathogenicity against the larvae. While caused no, weak (23.3%), moderate (53.3%), and and high (≥80%) lethality, injection resulted in 100% lethality.
PubMed: 35208774
DOI: 10.3390/microorganisms10020319 -
Biotechnology For Biofuels Dec 2021Pleurotus ostreatus is an edible mushroom popularly cultivated worldwide. Distilled grain waste (DGW) is a potential substrate for P. ostreatus cultivation. However,...
BACKGROUND
Pleurotus ostreatus is an edible mushroom popularly cultivated worldwide. Distilled grain waste (DGW) is a potential substrate for P. ostreatus cultivation. However, components in DGW restrict P. ostreatus mycelial growth. Therefore, a cost-effective approach to facilitate rapid P. ostreatus colonization on DGW substrate will benefit P. ostreatus cultivation and DGW recycling.
RESULTS
Five dominant indigenous bacteria, Sphingobacterium sp. X1, Ureibacillus sp. X2, Pseudoxanthomonas sp. X3, Geobacillus sp. X4, and Aeribacillus sp. X5, were isolated from DGW and selected to develop a consortium-based microbial agent to compost DGW for P. ostreatus cultivation. Microbial agent inoculation led to faster carbohydrate metabolism, a higher temperature (73.2 vs. 71.2 °C), a longer thermophilic phase (5 vs. 3 days), and significant dynamic changes in microbial community composition and diversity in composts than those of the controls. Metagenomic analysis showed the enhanced microbial metabolisms, such as xenobiotic biodegradation and metabolism and terpenoid and polyketide metabolism, during the mesophilic phase after microbial agent inoculation, which may facilitate the fungal colonization on the substrate. In accordance with the bioinformatic analysis, a faster colonization of P. ostreatus was observed in the composts with microbial inoculation than in control after composting for 48 h, as indicated from substantially higher fungal ergosterol content, faster lignocellulose degradation, and higher lignocellulase activities in the former than in the latter. The final mushroom yield shared no significant difference between composts with microbial inoculation and control, with 0.67 ± 0.05 and 0.60 ± 0.04 kg fresh mushroom/kg DGW, respectively (p > 0.05).
CONCLUSION
The consortium-based microbial agent comprised indigenous microorganisms showing application potential in composting DGW for providing substrate for P. ostreatus cultivation and will provide an alternative to facilitate DGW recycling.
PubMed: 34920748
DOI: 10.1186/s13068-021-02089-4