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The Science of the Total Environment Jun 2024Schwertmannite (Sch) is found in environments abundant in iron and sulfate. Microorganisms that utilize iron or sulfate can induce the phase transition of...
Schwertmannite (Sch) is found in environments abundant in iron and sulfate. Microorganisms that utilize iron or sulfate can induce the phase transition of Schwertmannite, consequently leading to the redistribution of coexisting pollutants. However, the impact of the molar ratio of sulfate to iron (S/Fe) on the microbial-mediated transformation of Schwertmannite and its implications for the fate of cadmium (Cd) have not been elucidated. In this study, we examined how S/Fe influenced mineral transformation and the fate of Cd during microbial reduction of Cd-loaded Schwertmannite by Desulfovibrio vulgaris. Our findings revealed that an increase in the S/Fe ratio facilitated sulfate-reducing bacteria (SRB) in mitigating the toxicity of Cd, thereby expediting the generation of sulfide (S(-II)) and subsequently triggering mineral phase transformation. As the S/Fe ratio increased, the predominant minerals in the system transitioned from prismatic-cluster vivianite to rose-shaped mackinawite. The Cd phase and distribution underwent corresponding alterations. Cd primarily existed in its oxidizable state, with its distribution being directly linked not only to FeS content but also showing a robust correlation with phosphorus. The coexistence of vivianite and FeS minerals proved to be more favorable for Cd immobilization. These findings have significant implications for understanding the biogeochemistry of iron (oxyhydr)oxides and Cd fate in anaerobic environments.
PubMed: 38936727
DOI: 10.1016/j.scitotenv.2024.174275 -
Environmental Pollution (Barking, Essex... Jun 2024The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their...
The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.
PubMed: 38936038
DOI: 10.1016/j.envpol.2024.124453 -
Frontiers in Microbiology 2024Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and...
Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) " Syntrophopropionicum ammoniitolerans", a syntrophic acetate-oxidizing bacterium (SAOB) and a novel hydrogenotrophic methanogen, for which we propose the provisional name " Methanoculleus ammoniitolerans". The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation.
PubMed: 38933034
DOI: 10.3389/fmicb.2024.1389257 -
Frontiers in Microbiology 2024Antibiotics frequently induce abnormal liver function. Omadacycline is a novel aminomethylcycline antibiotic, which shows potent activity against Gram-positive and...
INTRODUCTION
Antibiotics frequently induce abnormal liver function. Omadacycline is a novel aminomethylcycline antibiotic, which shows potent activity against Gram-positive and Gram-negative aerobic, anaerobic, and atypical (including ) bacteria. Of note, omadacycline is tolerable in most patients with liver impairment. However, evidence regarding the application of omadacycline in patients with pneumonia after experiencing liver dysfunction is scarce.
METHODS
The current study reported 6 cases of patients with pneumonia receiving omadacycline as subsequent antibiotics after experiencing liver dysfunction.
RESULTS
These 6 cases were admitted to the hospital for pneumonia and received antibiotic therapy, including piperacillin-tazobactam, imipenem, meropenem, and moxifloxacin. After receiving these antibiotics, increased liver enzymes were noted. Although hepatoprotective therapy (such as magnesium isoglycyrrhizinate and glutathione) was given, the liver function was still abnormal. According to metagenomic next-generation sequencing, these patients were diagnosed with pneumonia. Considering the abnormal liver function, the antibiotic therapy was switched to omadacycline-containing antibiotic therapy. After that, liver function was improved, and the infection was ameliorated. Ultimately, all patients discharged from the hospital, including 2 patients who achieved complete clinical symptomatic improvement and 4 patients who achieved partial clinical symptomatic improvement.
DISCUSSION
This study emphasizes the successful treatment of switching to omadacycline after experiencing abnormal liver function in patients with pneumonia. This study suggests that omadacycline may serve as an optional antibiotic for patients with pneumonia, especially when occurring liver dysfunction. However, more clinical studies are required to validate our findings.
PubMed: 38933033
DOI: 10.3389/fmicb.2024.1408443 -
Microbial Biotechnology Jun 2024In recent years, the production of volatile fatty acids (VFA) through mixed culture fermentation (MCF) has been gaining attention. Most authors have focused on the...
In recent years, the production of volatile fatty acids (VFA) through mixed culture fermentation (MCF) has been gaining attention. Most authors have focused on the fermentation of carbohydrates, while other possible substrates, such as proteins, have not been considered. Moreover, there is little information about how operational parameters affect the microbial communities involved in these processes, even though they are strongly related to reactor performance and VFA selectivity. Hence, this study aims to evaluate how microbial composition changes according to three different parameters (pH, type of protein and micronutrient addition) during anaerobic fermentation of protein-rich side streams. For this, two continuous stirred tank reactors (CSTR) were fed with two different proteins (casein and gelatine) and operated at different conditions: three pH values (5.0, 7.0 and 9.0) with only macronutrients supplementation and two pH values (5.0 and 7.0) with micronutrients' supplementation as well. Firmicutes, Proteobacteria and Bacteroidetes were the dominant phyla in the two reactors at all operational conditions, but their relative abundance varied with the parameters studied. At pH 7.0 and 9.0, the microbial composition was mainly affected by protein type, while at acidic conditions the driving force was the pH. The influence of micronutrients was dependent on the pH and the protein type, with a special effect on Clostridiales and Bacteroidales populations. Overall, this study shows that the acidogenic microbial community is affected by the three parameters studied and the changes in the microbial community can partially explain the macroscopic results, especially the process selectivity.
Topics: Fatty Acids, Volatile; Fermentation; Bioreactors; Hydrogen-Ion Concentration; Bacteria; Anaerobiosis; Proteins; Biota; Microbiota
PubMed: 38932670
DOI: 10.1111/1751-7915.14505 -
Microorganisms Jun 2024Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is...
Bacterial Diversity and Vertical Distribution Patterns in Sandy Sediments: A Study on the Bacterial Community Structure Based on Environmental Factors in Tributaries of the Yangtze River.
Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is known about the relationship between biogeochemistry processes and vertical spatial distribution of bacterial communities in sandy sediments. In this study, we used fluorescence quantitative PCR, high-throughput sequencing technology and statistical analysis to explore the vertical distribution pattern of bacterial community diversity and its influencing factors in sandy sediments of the Yangtze River Basin. The aim is to enrich the understanding of the ecological characteristics and functions of bacteria in river ecosystems. The results showed that both sediment bacterial abundance and diversity showed a gradual decrease from surface to bottom in the vertical distribution. The main environmental factors that influenced the bacterial distribution pattern were pore water dissolved oxygen (DO), total nitrogen (TN) concentration and sediment nitrogen (N) content. The dominant bacterial species, and , are suitable for growth and reproduction in high oxygen and nutrient-richer environments, while prefers low oxygen or anaerobic conditions. The vertical distribution pattern of bacteria and its influencing factors in river sandy sediment found in this study differ from the results in mud sediment, which may be related to the larger granular gap between sandy sediment and the lower content of organic matter. The findings of this study further our understanding of the distribution patterns and ecological preferences of microbial communities in river sediments, providing insights into how these communities may adapt to varying environmental conditions.
PubMed: 38930560
DOI: 10.3390/microorganisms12061178 -
Microorganisms Jun 2024Understanding the microbiological profiles of peri-implant conditions is crucial for developing effective preventive and therapeutic strategies. This narrative review... (Review)
Review
Understanding the microbiological profiles of peri-implant conditions is crucial for developing effective preventive and therapeutic strategies. This narrative review analyzes the microbial profiles associated with healthy peri-implant sites, peri-implant mucositis, and peri-implantitis, along with related microbiological sampling and analyses. Healthy peri-implant sites are predominantly colonized by , , , and species, in addition to Gram-positive cocci and facultatively anaerobic rods, forming a stable community that prevents pathogenic colonization and maintains microbial balance. In contrast, peri-implant mucositis shows increased microbial diversity, including both health-associated and pathogenic bacteria such as red and orange complex bacteria, contributing to early tissue inflammation. Peri-implantitis is characterized by even greater microbial diversity and a complex pathogenic biofilm. Predominant pathogens include , , , , and unique species like and . Additionally, less common species such as and , contributing to disease progression through biofilm formation and increased inflammatory response, along with and human cytomegalovirus with a still not defined role, and contribute to disease progression through biofilm formation, immune modulation, and synergistic inter-kingdom interactions. Future research should standardize diagnostic criteria, employ advanced molecular techniques, integrate microbial data with clinical factors, and highlight inter-kingdom interactions.
PubMed: 38930519
DOI: 10.3390/microorganisms12061137 -
Microorganisms May 2024Two thermophilic spore-forming sulfate-reducing strains, 435 and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both...
Two thermophilic spore-forming sulfate-reducing strains, 435 and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (/) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C, iso-C, C, and C. In sulfate-reducing conditions, the strains utilized H/CO, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as '' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435 was carried out to determine its taxonomic affiliation. The genome size of strain 435 was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435 and members of the genus , 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is 435 (=VKM B-1492 = DSM 23196). A genome analysis of strain 435 revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.
PubMed: 38930497
DOI: 10.3390/microorganisms12061115 -
Microorganisms May 2024() is an anaerobic, spore-forming Gram-positive rod responsible for necrotizing gangrene, bacteremia in patients with cancer or gastrointestinal tract infection....
() is an anaerobic, spore-forming Gram-positive rod responsible for necrotizing gangrene, bacteremia in patients with cancer or gastrointestinal tract infection. virulence is due in large part to toxin production. In 2014, a new enterotoxin, BEC (binary enterotoxin of ) encoded by and genes, distinct from enterotoxin (CPE) encoded by the gene, has been described. BEC-producing strains can be causative agents of acute gastroenteritis in humans. We present herein the case of a 64-year-old man who presented to the emergency department of Toulouse University Hospital with pneumonia and septic shock, without digestive symptoms. Blood cultures showed bacteremia and despite appropriate antibiotic treatment the patient passed away 7 h after admission. The characterization of the strain by whole genome sequencing revealed the presence of typical genes of : gene (alpha-toxin, phospholipase C) and (theta-toxin, perfringolysine). Surprisingly, this strain also harbored and genes encoding the recently described BEC toxin. Interestingly, alpha-toxin typing of our isolate and other published BEC isolates showed that they belonged to different PLC subtypes, confirming the high genetic diversity of these strains. To our knowledge, it is the first clinical case reporting bacteremia due to a BEC-producing isolate.
PubMed: 38930477
DOI: 10.3390/microorganisms12061095 -
Microorganisms May 2024Although root (AMR) has been noted as an ingredient in ruminant feed, the impacts of AMR feeding on rumen fermentation and the microbial community structure within the...
Although root (AMR) has been noted as an ingredient in ruminant feed, the impacts of AMR feeding on rumen fermentation and the microbial community structure within the rumen are yet to be evaluated. This study investigated the effects of AMR supplementation on rumen fermentation characteristics and microbial community structures in goats. In two sets of feeding experiments, four Japanese native goats were fed AMR (10 g/kg DM/day/head) for three weeks per experiment. The rumen fluid samples were analyzed using high-performance liquid chromatography for fermentation products and next-generation sequencing for microbial analysis. The rumen fluid samples in the second experiment were also subject to an in vitro anaerobic fermentation test. The results indicated a significant modification, with a higher volatile fatty acid (VFA) content in the rumen fluid of goats in the feeding period than before feeding ( < 0.01). The microbial analysis revealed a significant increase in community diversity ( < 0.05) following AMR feeding, and the rumen bacterial community increased in two families belonging to the order Oscillospirales in Firmicutes ( < 0.05). The phylum Verrucomicrobiota was observed to be significantly less abundant after AMR feeding than during the control period ( < 0.05). Notably, the linear discriminant analysis revealed that the families with largely unknown functions in the rumen (Oscillospiraceae, Rikenellaceae, Muribaculaceae, and vadinBB97) were the determinants of the community split between control and AMR feeding. Increased fermentation rate by AMR feeding was also supported by an in vitro culture experiment, which resulted in faster VFA production without affecting methane production in total gas production. The study demonstrated that AMR can significantly facilitate change in the bacterial community structure in the goat rumen involving a shift of the favoring fibrolytic bacteria towards VFA production. The long-term effects of AMR supplementation and its applicability across different ruminant species, with potential benefits for animal health and productivity, should be addressed.
PubMed: 38930452
DOI: 10.3390/microorganisms12061067