-
Respirology Case Reports Jun 2024Odontogenic infections can spread to the respiratory tract. Despite the known role of as the primary pathogen in periodontitis, the association between infection and...
Odontogenic infections can spread to the respiratory tract. Despite the known role of as the primary pathogen in periodontitis, the association between infection and risk of pneumonia or lung abscess remains unknown. In this report, we present a case of lung abscess caused by infection. The pathogen was detected by metagenomic next-generation sequencing (mNGS) in the bronchoalveolar lavage fluid of the patient. The clinical characteristics and possible mechanisms of the infection are discussed. is a conditional pathogen that can cause lung abscess in the presence of helper bacteria and reduced host immune status. The course of treatment should be personalized and might be longer than 3 months.
PubMed: 38831800
DOI: 10.1002/rcr2.1391 -
Microbial Ecology Jun 2024Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen...
Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (NO) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.
Topics: Nitrogen; Aquaculture; Denitrification; Bacteria; Ponds; Microbiota; Animals; Penaeidae; Nitrous Oxide; Geologic Sediments; Oxidation-Reduction; Ammonium Compounds
PubMed: 38831142
DOI: 10.1007/s00248-024-02378-z -
Radiology Case Reports Aug 2024Mycetoma, commonly known as Madura foot, is a chronic and progressively destructive granulomatous disease caused by a fungus or anaerobic filamentous bacteria that...
Mycetoma, commonly known as Madura foot, is a chronic and progressively destructive granulomatous disease caused by a fungus or anaerobic filamentous bacteria that affects the skin, subcutaneous tissue, and bones primarily in tropical and subtropical regions, with males between the ages of 20-40 having occupational exposure to outdoor environments, such as farming, predominantly affected. It is one of the World Health Organization's 17 "neglected tropical diseases," characterized by a clinical trial of localized mass-like soft tissue injury with draining sinuses that discharge grains of infectious material. Here, we present a case report of a 40-year-old male with type 2 diabetes mellitus and a history of fieldwork, who exhibited early manifestations of mycetoma. Unlike the typical diffuse presentation seen in advanced cases, this patient's early presentation prompted diagnostic challenges due to its atypical nature. We highlight the importance of recognizing the early signs of mycetoma, particularly in individuals with predisposing factors such as diabetes and occupational exposure. Diagnostic dilemmas may arise, leading to potential misdiagnosis. Additionally, we emphasize the crucial role of biopsy in confirming the diagnosis, alongside imaging techniques, to facilitate timely intervention and management, thereby significantly impacting patient outcomes.
PubMed: 38827041
DOI: 10.1016/j.radcr.2024.05.007 -
The Journal of Biological Chemistry May 2024Antibiotic-resistant Enterobacterales pose a major threat to healthcare systems worldwide, necessitating the development of novel strategies to fight such hard-to-kill...
Antibiotic-resistant Enterobacterales pose a major threat to healthcare systems worldwide, necessitating the development of novel strategies to fight such hard-to-kill bacteria. One potential approach is to develop molecules that force bacteria to hyper-activate prodrug antibiotics, thus rendering them more effective. In the present work, we aimed to obtain proof-of-concept data to support that small molecules targeting transcriptional regulators can potentiate the antibiotic activity of the prodrug metronidazole (MTZ) against Escherichia coli under aerobic conditions. By screening a chemical library of small molecules, a series of structurally related molecules were identified that had little inherent antibiotic activity but showed substantial activity in combination with ineffective concentrations of MTZ. Transcriptome analyses, functional genetics, thermal shift assays, and electrophoretic mobility shift assays were then used to demonstrate that these MTZ boosters target the transcriptional repressor MarR, resulting in the upregulation of the marRAB operon and its downstream MarA regulon. The associated upregulation of the flavin-containing nitroreductase, NfsA, was then shown to be critical for the booster-mediated potentiation of MTZ antibiotic activity. Transcriptomic studies, biochemical assays, and electron paramagnetic resonance measurements were then used to show that under aerobic conditions, NfsA catalyzed 1-electron reduction of MTZ to the MTZ radical anion which in turn induced lethal DNA damage in E. coli. This work reports the first example of prodrug boosting in Enterobacterales by transcriptional modulators and highlights that MTZ antibiotic activity can be chemically induced under anaerobic growth conditions.
PubMed: 38825006
DOI: 10.1016/j.jbc.2024.107431 -
FEMS Microbiology Ecology May 2024Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between...
Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.
Topics: Animals; Rumen; Sheep; Methane; Gastrointestinal Microbiome; Sheep Diseases; Bacteria; Archaea; Haemonchus; Trichostrongylus; Microbiota; Nematode Infections
PubMed: 38821514
DOI: 10.1093/femsec/fiae083 -
FEMS Microbiology Reviews Jun 2024Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of... (Review)
Review
Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.
Topics: Fermentation; Bacteria; Carbohydrate Metabolism; Metabolic Networks and Pathways
PubMed: 38821505
DOI: 10.1093/femsre/fuae016 -
Chemosphere Aug 2024Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries... (Review)
Review
Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.
Topics: Biodegradation, Environmental; Anaerobiosis; Benzene Derivatives; Benzene; Toluene; Xylenes; Environmental Pollutants; Hydrocarbons, Aromatic
PubMed: 38821131
DOI: 10.1016/j.chemosphere.2024.142490 -
Frontiers in Microbiology 2024Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this...
Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this approach remain unclear, in part because pathogen reduction appears to be both strain and ecology dependent. Here we tested the ability of five probiotic strains, including some from common probiotic genera and , to reduce binding of sv. Typhimurium to epithelial cells subsp. emerged as a promising strain; however, Typhimurium infection outcome in epithelial cells was dependent on inoculation order, with unable to rescue host cells from preceding or concurrent infection. We further investigated the complex mechanisms underlying this interaction between , Typhimurium, and epithelial cells using a multi-omics approach that included gene expression and altered metabolism via metabolomics. Incubation with repressed apoptotic pathways and induced anti-inflammatory cascades in epithelial cells. In contrast, co-incubation with increased in Typhimurium the expression of virulence factors, induced anaerobic metabolism, and repressed components of arginine metabolism as well as altering the metabolic profile. Concurrent application of the probiotic and pathogen notably generated metabolic profiles more similar to that of the probiotic alone than to the pathogen, indicating a central role for metabolism in modulating probiotic-pathogen-host interactions. Together these data imply crosstalk via small molecules between the epithelial cells, pathogen and probiotic that consistently demonstrated unique molecular mechanisms specific probiotic/pathogen the individual associations.
PubMed: 38812689
DOI: 10.3389/fmicb.2024.1387498 -
Frontiers in Microbiology 2024Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil...
Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, we employed a "time and space parallel" method. Four restoration stages, namely corn field (Corn), short-term restoration wetland (2 years, ST), long-term restoration wetland (8 years, LT) and natural wetland (>25 years, NW), were selected to represent the restoration time and geographical location in Naolihe Nature Wetland. We investigated the composition and diversity of soil microbial communities in different restoration wetland (from corn fields to natural wetlands) by using 16S rRNA and ITS rRNA gene sequencing. We also performed chemical experiments to measure soil enzyme activity and physicochemical properties at each sampling site. The results showed that soil physicochemical properties and enzyme activities significantly differed with the extension of wetland restoration years ( < 0.05). Proteobacteria, Acidobacteria, and Actinobacteria are the most dominant phyla in bacterial. The alpha diversity of soil bacteria was the highest in the corn field (Corn), and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. There are two most dominant phyla (Ascomycota and Mucoromycota) in fungal. However, the alpha diversity of soil fungi was the lowest in the Corn and LT stage, and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. The research findings indicated that the changes in soil physicochemical properties with the extension of wetland restoration years play a significant role in shaping the structure and diversity changes of soil microbial communities. Through the analyses of bacterial and fungal functions using the FUNGuild and FAPROTAX databases, the results showed that the abundance of aerobic bacteria in the soil increased more than that of anaerobic bacteria as the wetland restoration years prolonged, while the abundance of saprotrophic, symbiotic, and pathogenic fungi in the soil significantly decreased with the prolonged wetland restoration years. This study will help us better understand the process of restoration after farmland abandonment, providing valuable reference information for the implementation of a series of wetland ecological restoration projects in the future.
PubMed: 38808276
DOI: 10.3389/fmicb.2024.1403849 -
Frontiers in Cellular and Infection... 2024This study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing... (Comparative Study)
Comparative Study
Comparative characterization of supragingival plaque microbiomes in malocclusion adult female patients undergoing orthodontic treatment with removable aligners or fixed appliances: a descriptive cross-sectional study.
OBJECTIVES
This study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing orthodontic treatment.
METHODS
Supragingival plaque samples from 48 female individuals underwent microbiome analysis (16S rRNA gene sequencing) using PacBio Sequel sequencing. The study included 13 adults without orthodontic treatment needs as the control group (Group C), and 35 patients with comparable initial orthodontic conditions who received treatment at a university clinic in Beijing, China. The treatment involved either traditional fixed brackets (Group B, n = 17) or Invisalign aligners (Group AT, n = 18). Bioinformatics methods were used for data analysis.
RESULTS
From the 48 plaque samples, a total of 334,961 valid reads were obtained, averaging 6,978 sequences per sample. The 16S rDNA sequences were classified into 25,727 amplicon sequence variants (ASVs). Significant variances in alpha and beta diversity among the groups were noted. Group B microbiome exhibited an increased presence of Gram-negative bacteria. At the phylum level, was significantly more prevalent in Group C samples, while was enriched in Group B samples. Family-level relative abundance analysis showed a notable increase in (formerly TM7) and in Group B. Genus-level analysis revealed a significant rise in in Group AT. Fixed orthodontic appliances were linked to oral microbiome changes, notably an enhanced relative abundance of anaerobes, including periodontal pathogens.
CONCLUSION
The observation points to the impact of orthodontic appliance on the oral microbial community, highlighting the difference between traditional braces (Group B) and clear aligners (Group AT)in terms of the predominance of anaerobic and gram negative bacteria. This emphasizes the importance of considering the microbiological effects when choosing orthodontic appliance and underscores the need for tailored oral hygiene practices for individuals undergoing these treatments. This research might provide insights that could assist in the development of innovative cleaning techniques and antibacterial materials.
Topics: Humans; Female; Microbiota; Cross-Sectional Studies; Adult; Dental Plaque; RNA, Ribosomal, 16S; Orthodontic Appliances, Fixed; Young Adult; Malocclusion; Bacteria; DNA, Bacterial; China; Orthodontic Appliances, Removable
PubMed: 38803569
DOI: 10.3389/fcimb.2024.1350181