Search Results (86)

Background. The establishment and diversity of the gut microbiota during early childhood are fundamental for immune regulation and metabolic processes, with factors such as prematurity, delivery method, antibiotic treatment, and breastfeeding significantly impacting microbiome development and potential health outcomes. Objectives/Methods. This comparative study examined the gut microbiota composition in children aged 6–8 and 9–12 months, born via spontaneous labor at ≥38 weeks’ gestation, who either did not receive antibacterial therapy or required beta-lactam antibiotics. The composition of the colonic microbiota was analyzed in these fecal samples using a quantitative real-time PCR (qRT-PCR). Results. Significant differences in microbiota composition were observed between groups. Children treated with antibiotics exhibited a statistically significant reduction in alpha diversity indices (Shannon and Simpson), along with decreased colonization of key functionally important microorganisms, including obligate anaerobic bacteria such as Faecalibacterium prausnitzii, Clostridium leptum, Bacteroides spp., and metabolically active Bifidobacteria (B. bifidum, B. breve, B. longum). Conclusions. These microbiota alterations may adversely affect child health by diminishing microbial balance and functional potential, especially during this critical period of immune and metabolic development. The decline in anti-inflammatory, short-chain fatty acid-producing bacteria elevates the risk for allergic, atopic, dysbiotic, and metabolic conditions. Recognizing these impacts underscores the importance of strategies to supports microbiota restoration after antibiotic use, such as probiotics, prebiotics, and dietary interventions. Further research should focus on microbiota recovery dynamics to facilitate early intervention and optimize pediatric health outcomes. Overall, understanding antibiotic effects on gut microbiota can guide more judicious treatment approaches, reducing long-term health risks. Full article

Saline and highly alkaline soda lakes are often characterized by a persistent nitrogen loss and high sulfide levels. Cyanobacteria are key aerobic diazotrophs in soda lakes, where light-dependent nitrogen fixation (NF) is crucial for sustaining ecosystem functioning. While sulfide is a well-known inhibitor of oxygenic photosynthesis, some cyanobacteria may tolerate it and utilize it via anoxygenic photosynthesis. In this study, we investigated the NF and anoxygenic photosynthesis in the genus Sodalinema, including non-heterocystous cyanobacteria widely distributed in soda and saline environments around the world and possessing an anaerobe-like nitrogenase. Our data suggest that their nif-operon could have been more likely acquired in soda or saline–alkaline lakes from natronophilic sulfate-reducing bacteria of the family Desulfonatronovibrionaceae than in the marine environment. It was shown that Sodalinema sp. P-1104, isolated from a southwestern Siberian soda lake, is capable of NF only in a light/dark switching mode, both in oxic and anoxic conditions. Sulfide did not suppress photosynthesis and stimulated NF up to threefold in oxygenic conditions. Anaerobic NF was obligately sulfide-dependent and supported by anoxygenic photosynthesis. However, removal of photosynthetic oxygen due to the high reducing potential of sulfide stimulated NF to a greater extent than does the use of sulfide through anoxygenic photosynthesis. Full article

Bifidobacteria, a genus of obligate anaerobes, comprise a major component of the intestinal microbiota. Importantly, bifidobacteria participate in immune reactions. These bacteria carry a species-specific operon in which the fn3 gene encodes a multifunctional protein FN3 that mediates bacterial adhesion to the intestinal epithelium and is capable of binding individual cytokines. Bioinformatics and biochemical approaches were used to study the possible interaction of recombinant ∆FN3 fragments of B. longum and B. bifidum strains with cytokines TNF-α, IL-6, IL-8, and IL-10. De novo molecular modeling generated, for the first time, the structural models of species-derived ∆FN3 proteins and revealed new tentative regions for differential cytokine binding. Combined treatment with ∆FN3 and TNF-α induced TNF-α mRNA abundance in the human monocytic cell line. Altogether, these findings provide structural evidence for the regulation of immune reactions by microbiota-derived proteins. Full article

Aerobic anoxygenic phototrophs (AAPs) are intrinsically paradoxical; these species use a pathway commonly found in oxygen-deprived environments called anoxygenic photosynthesis, as a supplementary energy source to their obligately aerobic respiration. At the surface, such a combination seems odd, but AAPs thrive in a plethora of environments and are phylogenetically broad, suggesting that this feature is advantageous and ecologically valuable. The range of habitats and taxonomy have been reviewed, yet the main element which unites the group, their anoxygenic photosynthesis, which is diverse in its components, has not received the deserved attention. The intricate light-capturing photosynthetic complex forms the site of photon-induced energy transfer and therefore, the core basis of the process. It has two parts: the reaction center and light harvesting complex(es). The variability in composition and overall usage of the apparatus is also reflected in the genome, specifically the photosynthetic gene cluster. In this review, what is known about the differences in structure, light wavelength absorption range, activity, and related genomic content and the insights into potential AAP evolution from anaerobic anoxygenic phototrophs will be discussed. The work provides an elegant summation of knowledge accumulated about the photosynthetic apparatus and prospects that can fill yet remaining gaps. Full article

Clostridioides difficile is an obligate anaerobe and is primarily transmitted via the fecal–oral route. Data characterizing the microbiome changes accompanying transitions from non-colonized to C. difficile colonized subjects are currently lacking. In this retrospective cohort study, we examined 16S rRNA gene sequencing data in a total of 481 fecal samples belonging to 107 patients. Based on C. difficile status over time, patients were categorized as Negative-to-Positive, Negative Control, and Positive Control. A linear mixed effects model was fitted to investigate the changes in the Shannon α-diversity index over time. Zero-inflated negative binomial/Poisson mixed effects models or generalized linear mixed models with negative binomial/Poisson distribution were used to investigate the changes in taxon counts over time among different groups. A total of 107 patients were eligible for the study. The median number of stool samples per patient was 3 (IQR 2–4). A total of 42 patients transitioned from C. difficile negative to positive (Negative-to-Positive), 47 patients remained negative throughout their tests (Negative Control) and 18 were always C. difficile positive (Positive Control). A significant difference in microbiome composition between the last negative samples and the first positive samples were shown in Negative-to-Positive patients, ANOSIM p = 0.022. In Negative-to-Positive patients, the phylum Pseudomonadota and family Enterobacteriaceae increased significantly in the first positive samples compared to the last negative samples, p = 0.0075 and p = 0.0094, respectively. Within the first 21 days, Actinomycetota decreased significantly over time in the Positive Control group compared to the other two groups (p < 0.001) while Bacillota decreased in both the Negative-to-Positive group and Positive Control. These results demonstrate that the transition from C. difficile negative to C. difficile positive is associated with alterations in gut microbial communities and their compositional patterns over time. Moreover, these changes play an important role in both the emergence and intensification of the gut microbiome dysbiosis in patients who transitioned from C. difficile negative to positive and those who always tested positive. Full article

Background/Objectives: Veillonella species are Gram-negative, non-motile, non-fermentative, obligate anaerobic cocci. They are typically considered commensals of the oral cavity, respiratory tract, genitourinary tract, and gastrointestinal tract. It may be a rare cause of dental infections and discitis/spondylodiscitis. Methods: We report the case of an 80-year-old patient diagnosed with discitis caused by Veillonella parvula, isolated from blood. In addition, we performed a comprehensive literature review summarizing all reported cases of discitis or spondylodiscitis caused by Veillonella species. Results: In our case, antimicrobial susceptibility testing was performed using the Kirby–Bauer disc diffusion method. Based on the results, the patient was treated with amoxicillin/clavulanate, which led to a favourable clinical outcome. A review of the literature revealed that, to date, only 14 cases of spondylodiscitis or discitis caused by Veillonella spp. have been reported. Potential risk factors for Veillonella spp. bacteremia were identified in only 9 cases. The most commonly affected site was the lumbar or lumbosacral spine. Magnetic resonance imaging was consistently regarded as the diagnostic gold standard. Most patients presented with localized pain. The overall therapeutic approach generally consisted of an initial course of intravenous antibiotics, typically ceftriaxone administered either as monotherapy or in combination with metronidazole, followed by an oral regimen with amoxicillin/clavulanate, given alone or alongside metronidazole. Conclusions: Spondylodiscitis due to V. parvula remains extremely rare. Although antimicrobial susceptibility patterns remain heterogeneous, beta-lactams, particularly amoxicillin/clavulanate, appear effective in most cases, and treatment regimens typically involve an initial intravenous phase followed by oral therapy. Full article

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