Search Results (79)

Most large-scale crude oil spills occur in marine environments. We screened easily propagable/maintainable halophiles to develop agents for the bioremediation of marine spills. A bacterial strain isolated from a polluted region of the Great Salt Lake was characterized and tested for its ability to degrade crude oil. The strain (Salinivibrio costicola) is motile, catalase- and lipase-positive, a facultative anaerobe, and an obligate halophile. Its growth optimum and tolerance ranges are: NaCl (5%, 1.25–10%), pH (8, 6–10), and temperature (22 °C, 4–45 °C). Its genome (3,166,267 bp) consists of two circular chromosomes and a plasmid, containing 3197 genes, including some genes potentially relevant to hydrocarbon metabolism. The strain forms a biofilm but is considered nonpathogenic and is sensitive to some common antibiotics. Lytic bacteriophages infecting the strain are rare in the water samples we tested. The strain survived on desiccated agar media at room temperature for a year, grew optimally in complex media containing 0.1–1% crude oil, but failed to reduce total recoverable petroleum hydrocarbons from crude oil. Thus, a recalcitrant halophile may endure crude oil without mineralizing. Due to some of their advantageous attributes, such strains can be considered for genetic manipulation to develop improved agents for bioremediation. Full article

Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray–Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia–Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat’s gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host’s energy balance and health under seasonal contexts. Full article

Bacteroides pyogenes is a Gram-negative obligate anaerobe rod. It is naturally found in the oral microbiome of cats and dogs, which represents a primary source of disease for humans. The present review provides an update on the role of B. pyogenes as a pathogen responsible for infections in humans. Indeed, an increasing number of B. pyogenes infections have been reported in recent years, including skin and soft tissue infections as well as severe diseases like osteomyelitis, Lemierre’s syndrome, and bloodstream infection. Pre-analytical and analytical phases are crucial to guarantee the isolation of anaerobic bacteria, including B. pyogenes. Moreover, the introduction of MALDI-TOF mass spectrometry and 16S rRNA sequencing in clinical microbiology laboratories may be partially responsible for the increasing number of reports of B. pyogenes infections. However, the mechanisms underlying the pathogenicity of B. pyogenes remain poorly understood and require further investigations. Indeed, despite common antimicrobial susceptibilities, infections frequently persist and require multiple courses of antibiotics. In addition, based on literature data, this review indicates that treatment of skin and soft tissue infections often necessitates surgical procedures and hospitalization. Full article

Background/Objectives: Continuous monitoring blood culture systems (CMBCSs) are revolutionary automated instruments that facilitate the rapid identification of pathogens in blood samples from patients with sepsis. However, with only a few CMBCSs being widely used as references, user dependency on these limited options has grown. In response, a new CMBCS was developed and compared with existing systems to evaluate microbial growth. Methods: HubCentra84 was compared to BacT/Alert^® 3D and BACTEC™ FX. Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Bacteroides fragilis, and Candida albicans were selected as representative clinically infectious microorganisms. Colonies from pure cultures were diluted with 0.9% saline to create simulated sepsis specimens (SSSs). The SSSs were injected into dedicated culture bottles for each instrument. Thirty paired tests were performed for each strain. Results: Colony-forming units of the added SSSs were consistent according to bacteria, and all strains demonstrated robust growth in three CMBCSs. Time-to-positivity was uniformly observed according to the instruments used. The novel CMBCS detected the growth of the clinically significant bacteria S. aureus, S. pneumoniae, E. coli, and P. aeruginosa approximately 2 h faster than the other two systems. However, it was approximately 200 min slower for C. albicans and 3000 min for B. fragilis. Conclusions: The novel CMBCS demonstrates advantages in detecting the growth of common clinical bacteria. Although slow growth was detected for certain microorganisms, it successfully captured the growth of all tested microorganisms. Full article

Background/Objectives: Several independent studies have associated prostate cancer (PCa) with specific groups of bacteria, most of them reporting the presence of anaerobic or microaerophilic species such as Cutibacterium acnes (C. acnes). Such findings suggest a prostate cancer-related bacterial dysbiosis, in a manner similar to the association between Helicobacter pylori infection and gastric cancer. In an earlier exploratory study looking for such dysbiosis events, using a culturomics approach, we discovered that the presence of obligate anaerobes (OAs) along with C. acnes was associated with increased prostate-specific antigen (PSA) levels in 39 participants. Methods: Building on this, in this study, we analyzed 89 post-rectal examination urine samples, from men with prostate cancer attending the PROVENT trial, using 16S rDNA sequencing. Our investigation focused on the impact of six previously identified OA genera (Finegoldia, Fusobacterium, Prevotella, Peptoniphilus_A, Peptostreptococcus, and Veillonella_A) on PSA levels. However, an additional data-driven approach was followed to uncover more taxa linked to increased PSA. Results: Our analysis revealed a statistically significant association between Peptostreptococcus and elevated PSA levels. Additionally, there were potential interactions between Prevotella and Fusobacterium. Interestingly, we also found that an aerobe, Ochrobactrum_A,was significantly linked to higher PSA levels. Conclusions: These findings suggest that OA-related dysbiosis may contribute to elevated PSA levels through prostate cell damage even before prostate cancer develops, possibly playing a role in chronic inflammation and the hypervascular changes seen in precancerous lesions. Future clinical trials with larger cohorts are needed to further evaluate the role of OA in prostate cancer development and progression. Full article

A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during the anaerobic cultivation with excessive production of extracellular NH₄⁺ despite of presence of other fixed N nutrients. The BNF of strain OS1-26 was distinguished from the other well-known Clostridium diazotrophs, such as C. pasteurianum and C. acetobutylicum. The altruistic N-fixing ability of the strain may play a pivotal role in providing N nutrients to the microbial community and plants in the soil ecosystem. The microorganism grew at 25–35 °C (optimum 30–35 °C) and pH 5.0–8.0 (optimum 6.0–8.0) but was not able to grow in the presence of >0.5% NaCl. The major cellular fatty acids of strain OS1-26 were C_16:0, C_14:0, and the summed feature consisted of C_16:1 ω7c and C_16:1 ω6c (35.63%, 25.29%, and 18.84%, respectively). The 16S rRNA phylogeny indicated that strain OS1-26 is a member of the genus Clostridium, and the closest species are C. aciditolerans, C. nitrophenolicum, and C. thailandense, with 16S rRNA sequence similarities such as 99.71%, 98.52%, and 98.45%, respectively. In spite of the high 16S rRNA sequence similarity, strain OS1-26 showed overall genomic relatedness, such as the average nucleotide identity (ANI), and phenotypical features distinctly different from Clostridium aciditolerans. Although the species taxonomy of strain OS1-26 is undetermined within the genus Clostridium based on overall genomic and phenotypic properties, further studies on the soil bacterial strain would enhance our understanding of its taxonomic identity, ecological roles for the terrestrial soil N cycle, and the potential to be developed as a biological N fertilizer. Full article

Obligate anaerobic beer spoilage bacteria have been a menace to the brewing industry for several decades. Technological advances in the brewing process aimed at suppressing aerobic spoilers gave rise to problems with obligate anaerobes. In previous studies, the metabolic spectrum of Pectinatus and Megasphaera species has been described, but their metabolism in the beer environment remains largely unknown. We used high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS-SPME-GCMS) to further characterize beer spoiled by 30 different strains from six beer-spoiling species of Pectinatus and Megasphaera (P. cerevisiiphilus, P. frisingensis, P. haikarae, M. cerevisiae, M. paucivorans, and M. sueciensis). We detected differences in carbohydrate utilization and the volatile organic compounds (volatilome) produced during beer spoilage by all six species. We were able to show that glycerol, one of the basic components of beer, is the common carbon source used by all strains. It appears that this carbon source allows for anaerobic beer spoilage by Pectinatus and Megasphaera despite the spoilage-preventing intrinsic barriers of beer (iso-α-acids, ethanol, low pH, scarce nutrients); thus, extrinsic countermeasures are key for prevention. Full article

YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity and disrupted biofilm formation. Ap4A thus plays a central role in bacterial physiology and metabolism, and its hydrolysis by YqeK is intimately linked to the ability of these microbes to cope with stress. Although YqeK is reported to hydrolyze Ap4A under aerobic conditions, all four existing crystal structures reveal an active site that consists of a diiron center, portraying a cryptic chemical nature for the active metallocofactor. This study examines two YqeK proteins from two ecologically diverse parent organisms: the obligate anaerobe Clostridium acetobutylicum and the facultative aerobe Bacillus halodurans. Both enzymes utilize Fe-based cofactors for catalysis, while under ambient or oxidative conditions, Bh YqeK hydrolyzes Ap4A more efficiently compared to Ca YqeK. This redox-dependent activity difference stems from the following two molecular mechanisms: the incorporation of mixed-metal, Fe-based bimetallic cofactors, in which the second metal is redox inert (i.e., Fe–Zn) and the upshift of the Fe–Fe cofactor reduction potentials. In addition, three strictly conserved, positively charged residues vicinal to the active site are critical for tuning Ap4A hydrolysis. In conclusion, YqeK is an Fe-dependent phosphohydrolase that appears to have evolved to permit Ap4A hydrolysis under different environmental niches (aerobic vs. anaerobic) by expanding its cofactor configuration and O₂ tolerance. Full article

This study evaluates the dynamic shift in the microbiota at the peri-implant site of titanium (Ti) and zirconia (Zr) implants subjected to experimental peri-implantitis (PI) and, for the first time, of implants made of ceria-stabilized alumina-reinforced zirconia (Ce-TZP/Al), a revolutionary zirconia that is set to play a key role in modern implant dentistry. One- and two-piece (TP) implants, including Ce-TZP/AL TP/G3 glass, were placed bilaterally (six implants/side) in five beagle dogs to mimic a natural vs. ligature-induced PI following a split-mouth design. The experiment spanned 30 weeks from tooth extraction. Both PI models promoted plaque deposition at peri-implant sites. Comparatively, the PI induced by ligatures favored the deposition of anaerobes (p = 0.047 vs. natural). Regardless of the model, the plaque deposition pattern was entirely dependent on the implanted material. Ligated Ti and Zr implant sites accumulated up to 2.14 log CFU/mL unit anaerobic load (p ≤ 0.033 vs. non-ligated implant sites), predominantly comprising obligate anaerobes. Naturally occurring PI induced the deposition of co-occurring networks of obligate anaerobes and less oxygen-dependent bacteria. PI induction favored the enrichment of Ti and Zr sites with bacterial taxa belonging to the orange and red complexes (up to 28% increase naturally and up to 71% in the ligated hemiarch). Anaerobic deposition was significantly lower in ligated Ce-TZP/Al implant sites (p ≤ 0.014 vs. TI and Zr) and independent of the induction model (0.63–1 log units of increase). Facultative bacteria prevailed at Ce-TZP/AL sites. The abundance was lower in the Ce-TZP/AL TP implant. Unlike Ti and Zr sites, taxa from the orange and red complexes were negligible. Biofilms configured at the Ti and Zr sites after ligation-induced PI resemble those found in severe IP. We hypothesize that, although surface properties (surface energy and surface roughness) and physicochemical properties of the substrate play an important role in bacterial adhesion and subsequent plaque formation, Ce-TZP/Al modulates several biological activities that preserve the integrity of the gingival seal by limiting PI progression. In conclusion, biofilm progression differs in peri-implant sites according to the specific properties of the material. Ce-TZP/A, unlike titanium or zirconia, prevents dysbiosis in sites subjected to experimental PI and preserves the microbial signature of emergent obligate anaerobes related to PI development. Full article

The relative abundances of Bacteroidetes and Fusobacteria phyla have been reported to be decreased in dogs with chronic enteropathies. In colitis, obligate anaerobes (e.g., Bacteroides and Fusobacterium) are likely to vanish in response to the heightened oxidative stress in the colon’s inflammatory environment. The ability to adhere to the colonic mucosa is viewed as an essential step for obligate anaerobic bacteria to colonize and subsequently interact with the host’s epithelium and immune system. The reintroduction of a balanced community of obligate anaerobic bacteria using probiotics can restore the microbial function in the intestine. We found no studies on dogs regarding the adhesion properties of Bacteriodes vulgatus and Fusobacterium varium on paraffin-embedded canine colonic mucosa. Thus, the objective of this study is to investigate the adhesion capacities of these two bacterial species to paraffin-embedded colonic mucosa from healthy dogs. Additionally, we investigated their hydrophobicity properties to determine whether differences in adhesion capability can be explained by this factor. The results of our study showed that B. vulgatus adhered significantly lower than F. varium to the canine colonic mucosa (p = 0.002); however, B. vulgatus showed higher hydrophobicity (46.1%) than F. varium (12.6%). In conclusion, both bacteria have potential as probiotics, but further studies will be required to determine the efficacy and safety of the strains to be used, which strains to use, and the reasons other than hydrophobicity for attachment. Full article

The incidence of human Campylobacter jejuni infections is increasing worldwide. It is highly desirable to prevent campylobacteriosis in individuals at risk for severe disease with antibiotics-independent non-toxic compounds. Activated charcoal (AC) has long been used as an anti-diarrheal remedy. Here, we tested the disease-mitigating effects of oral AC versus placebo in human gut microbiota-associated (hma) IL-10^−/− mice starting a week prior to C. jejuni infection. On day 6 post-infection, the gastrointestinal C. jejuni loads were comparable in both infected cohorts, whereas campylobacteriosis symptoms such as wasting and bloody diarrhea were mitigated upon AC prophylaxis. Furthermore, AC application resulted in less pronounced C. jejuni-induced colonic epithelial cell apoptosis and in dampened innate and adaptive immune cell responses in the colon that were accompanied by basal concentrations of pro-inflammatory mediators including IL-6, TNF-α, IFN-γ, and nitric oxide measured in colonic explants from AC treated mice on day 6 post-infection. Furthermore, C. jejuni infection resulted in distinct fecal microbiota shift towards higher enterobacterial numbers and lower loads of obligate anaerobic species in hma mice that were AC-independent. In conclusion, our pre-clinical placebo-controlled intervention study provides evidence that prophylactic oral AC application mitigates acute murine campylobacteriosis. Full article

Food resources are essential for the survival and growth of the population. Soil phytopathogenic nematodes cause great damage to agricultural crops, endangering food supplies and resources in general. Different methods have been used to control them. However, this issue still requires a more effective solution. Caenorhabditis elegans (CGC strain wild-type N2) was applied as a model with an Escherichia coli OP50 feeding substrate for nematodes. Our approach was based on the thermodynamically substantiated creation of growth conditions that are unfavorable for nematodes to suppress them irreversibly. The thermodynamic calculations showed that obligate anaerobic conditions, namely the absence of oxygen and a low redox potential (−100 mV and below), were potentially unacceptable for nematodes. Anaerobic conditions were created using both abiogenic (physicochemical) and biological methods. Abiogenic anaerobic conditions were achieved by preventing oxygen access and adding low-potential sodium sulfide (Eh = −250...−200 mV) to the cultivation medium. By applying biological methods, Pleurotus ostreatus Po4 and E. coli O₂ was completely removed and the redox potential was decreased from +100…+200 mV to −100...−200 mV (in particular, due to the synthesis of H₂S). Even the short-term exposure (1–2 days) of nematodes under anaerobic conditions led to their suppression and death. Thus, the short-term creation of anaerobic conditions in the soil may be an effective method to control, e.g., phytopathogenic aerobic nematodes. This research contributes to the development of foundations to preserve agricultural plants and increase crop yield as well as the development of an approach for the environmentally friendly control of phytopathogens. Full article

Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum Firmicutes and Bacteroidota were the most abundant in both the winter and summer pig rectum. However, Proteobacteria became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0–8Dvs. WPG 16–40D, p < 0.0001; WPS 0–16Dvs. WPS 24–40D, p = 0.003; SPG 0D vs. SPG 8–40D, p = 0.0005; and SPS 0D vs. SPS 8–40D, p = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus Vagococcus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI. Full article

Understanding the energy metabolism and its regulation is one of the clues to metabolic engineering of stress-resistant lignocellulose-converting microbial strains, also including the promising ethanologen Zymomonas mobilis. Z. mobilis is an obligately fermentative, facultatively anaerobic bacterium, carrying an active respiratory chain with low energy-coupling efficiency. Its respiration does not supply energy to aerobically growing cultures on sugary media, yet oxidative phosphorylation has been demonstrated in non-growing cells with ethanol. Here, we show, for the first time, that in respiring, non-growing Z. mobilis cells receiving regular small amounts of ethanol, oxidative phosphorylation significantly contributes to the maintenance of their viability. No improvement of viability is seen in the NADH dehydrogenase (ndh)-deficient respiratory mutant, which is unable to oxidize ethanol. The ethanol effect is also hampered by the protonophoric uncoupler CCCP, or the inhibitor of ATP synthase, DCCD. At higher concentrations (6% v/v), ethanol causes stress that slows down culture growth. By monitoring the activity of several respiratory gene promoters under ethanol stress with the green fluorescent protein reporter system, we demonstrate downregulation of these promoters, in particular the ndh promoter. We speculate that the decrease in respiratory chain activity in response to stress conditions mitigates the production of reactive oxygen species. Full article

Bacterial vaginosis (BV) is a most common microbiological syndrome. Multiplex next-generation sequencing (NGS) or molecular tests allow a complete and accurate vaginal microbiota profiling in order to determine the primary causative agent. Due to the high costs and limited availability of NGS, the multiplex real-time PCR draws more attention. The present study aimed to evaluate the microbial composition and dominant lactobacilli species in non-pregnant women with bacterial vaginosis using a multiplex RT-PCR test and determine its diagnostic significance. In total, 331 women complaining of vaginal discharge were included. BV was confirmed upon clinical examination and Nugent criteria. A real-time PCR test was carried out with a new Femoflor test, which identifies opportunistic bacteria, STD pathogens, and some viruses. According to the results, the rate of lactobacilli is significantly reduced in BV-affected patients when compared to healthy women. Moreover, the rate of L. crispatus significantly decreases, while the rate of L. iners remains high. Among obligate anaerobic bacteria, Gardnerella vaginalis was the most prevalent in women with BV. The Femoflor test demonstrated high sensitivity and specificity for diagnosing BV. Moreover, the test allows the identification of infection in women with intermediate vaginal microbiota, as well as STD pathogens, and viruses. Thus, the application of real-time PCR tests can be effectively used in vaginal microbiota evaluation in women with BV, intermediate vaginal microbiota, and healthy women. In addition, this test may be used as an alternative to the Amsel criteria and Nugent scoring method in diagnosing BV. Full article